Table of Contents

Biology: The Science of Our Lives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3Science and the Scientific Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3Theories Contributing to Modern Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Development of the Theory of Evolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5 The Modern View of the Age of the Earth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5Development of the Modern View of Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Darwinian Evolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7The Diversity of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8Characteristics of Living things . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Levels of Organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Structure of Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14Organic Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26Origin of the Earth and Life. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Is There Life on Mars, Venus, Anywhere Else?? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 29Terms Applied to Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Components of Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31The Origins of Multicellularity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Microscopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Cell Size and Shape. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35The Cell Membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36The Nucleus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Ribosomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Endoplasmic Reticulum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Golgi Apparatus and Dictyosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38Mitochondria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Cell Movement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Water and Solute Movement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43Cells and Diffusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Active and Passive Transport. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Carrier-assisted Transport. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Types of transport molecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Vesicle-mediated transport. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48The Cell Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Prokaryotic Cell Division. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Eukaryotic Cell Division. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Mitosis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53Life Cycles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Phases of Meiosis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Comparison of Mitosis and Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57Laws of Thermodynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Potential vs. Kinetic energy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

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Table of Contents ContinuedEndergonic and exergonic. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Oxidation/Reduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Enzymes: Organic Catalysts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61The Nature of ATP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64Glycolysis, the Universal Process. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66Anaerobic Pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66Aerobic Respiration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67What is Photosynthesis? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69Leaves and Leaf Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69The Nature of Light. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70Chlorophyll and Accessory Pigments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70Stages of Photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72C-4 Pathway. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .74The Carbon Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75Review Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76Heredity, historical perspectives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79The Monk and his peas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79Principle of segregation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80Dihybrid Crosses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82Mutations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85Genetic Terms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85The modern view of the gene. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87Interactions among genes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88Polygenic inheritance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89Genes and chromosomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90Chromosome abnormalities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 The physical carrier of inheritance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92The structure of DNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94DNA Replication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96Protein Synthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99The structure of hemoglobin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .101Transcription: making an RNA copy of a DNA sequence. . . . . . . . . . . . . . . . . . . . . . . . . 103 Ecology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109Population Growth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109Mutualism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113Parasitism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

Commensalism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113

Altering Population Growth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115Range and Density. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116Ecology Definitions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117Community Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117Classification of Communities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117Change in Communities Over Time. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126Ecosystems and Communities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127Biogeochemical Cycles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

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INTRODUCTION: THE NATURE OF SCIENCE AND BIOLOGY

Biology: The Science of Our Lives

Biology literally means "the study of life". Biology is such a broad field, covering the minute workings of chemical machines inside our cells, to broad scale concepts of ecosystems and global climate change. Biologists study intimate details of the human brain, the composition of our genes, and even the functioning of our reproductive system. Biologists recently all but completed the deciphering of the human genome, the sequence of deoxyribonucleic acid (DNA) bases that may determine much of our innate capabilities and predispositions to certain forms of behavior and illnesses. DNA sequences have played major roles in criminal cases (O.J. Simpson, as well as the reversal of death penalties for many wrongfully convicted individuals), as well as the impeachment of President Clinton. We are bombarded with headlines about possible health risks from favorite foods (Chinese, Mexican, hamburgers, etc.) as well as the potential benefits of eating other foods such as cooked tomatoes. Infomercials tout the benefits of metabolism-adjusting drugs for weight loss. Many Americans are turning to herbal remedies to ease arthritis pain, improve memory, as well as improve our moods.

Can a biology book give you the answers to these questions? No, but it will enable you learn how to sift through the biases of investigators, the press, and others in a quest to critically evaluate the question. To be honest, five years after you are through with this class it is doubtful you would remember all the details of metabolism. However, you will know where to look and maybe a little about the process of science that will allow you to make an informed decision. Will you be a scientist? Yes, in a way. You may not be formally trained as a science major, but you can think critically, solve problems, and have some idea about what science can and cannot do. I hope you will be able to tell the shoe from the shinola.

Science and the Scientific Method

Science is an objective, logical, and repeatable attempt to understand the principles and forces operating in the natural universe. Science is from the Latin word, scientia, to know. Good science is not dogmatic, but should be viewed as an ongoing process of testing and evaluation. One of the hoped-for benefits of students taking a biology course is that they will become more familiar with the process of science.

Humans seem innately interested in the world we live in. Young children drive their parents batty with constant "why" questions. Science is a means to get some of those whys answered. When we shop for groceries, we are conducting a kind of scientific experiment. If you like Brand X of soup, and Brand Y is on sale, perhaps you try Brand Y. If you like it you may buy it again, even when it is not on sale. If you did not like Brand Y, then no sale will get you to try it again.

In order to conduct science, one must know the rules of the game (imagine playing Monopoly and having to discover the rules as you play! Which is precisely what one does with some computer or videogames (before buying the cheat book). The scientific method is to be used as a guide that can be modified. In some sciences, such as taxonomy and certain types of geology, laboratory experiments are not necessarily performed. Instead, after formulating a hypothesis, additional observations and/or collections are made from different localities.

Steps in the scientific method commonly include:

1. Observation: defining the problem you wish to explain. 2. Hypothesis: one or more falsifiable explanations for the observation. 3. Experimentation: Controlled attempts to test one or more hypotheses. 4. Conclusion: was the hypothesis supported or not? After this step the hypothesis is either modified or rejected,

which causes a repeat of the steps above.

After a hypothesis has been repeatedly tested, a hierarchy of scientific thought develops. Hypothesis is the most common, with the lowest level of certainty. A theory is a hypothesis that has been repeatedly tested with little modification, e.g. The Theory of Evolution. A Law is one of the fundamental underlying principles of how the Universe is organized, e.g. The Laws of Thermodynamics, Newton's Law of Gravity. Science uses the word theory differently than it is used in the

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general population. Theory to most people, in general nonscientific use, is an untested idea. Scientists call this a hypothesis.

Scientific experiments are also concerned with isolating the variables. A good science experiment does not simultaneously test several variables, but rather a single variable that can be measured against a control. Scientific controlled experiments are situations where all factors are the same between two test subjects, except for the single experimental variable.

Consider a commonly conducted science fair experiment. Sandy wants to test the effect of gangsta rap music on pea plant growth. She plays loud rap music 24 hours a day to a series of pea plants grown under light, and watered every day. At the end of her experiment she concludes gangsta rap is conducive to plant growth. Her teacher grades her project very low, citing the lack of a control group for the experiment. Sandy returns to her experiment, but this time she has a separate group of plants under the same conditions as the rapping plants, but with soothing Led Zeppelin songs playing. She comes to the same conclusion as before, but now has a basis for comparison. Her teacher gives her project a better grade.

Theories Contributing to Modern Biology

Modern biology is based on several great ideas, or theories:

1. The Cell Theory 2. The Theory of Evolution by Natural Selection 3. Gene Theory 4. Homeostasis

Robert Hooke (1635-1703), one of the first scientists to use a microscope to examine pond water, cork and other things, referred to the cavities he saw in cork as "cells", Latin for chambers. Mattias Schleiden (in 1838) concluded all plant tissues consisted of cells. In 1839, Theodore Schwann came to a similar conclusion for animal tissues. Rudolf Virchow, in 1858, combined the two ideas and added that all cells come from pre-existing cells, formulating the Cell Theory. Thus there is a chain-of-existence extending from your cells back to the earliest cells, over 3.5 billion years ago. The cell theory states that all organisms are composed of one or more cells, and that those cells have arisen from pre-existing cells.

James Watson (L) and Francis Crick (R), and the model they built of the structure of deoxyribonucleic acid, DNA. While a model may seem a small thing, their development of the DNA model fostered increased understanding of how genes work. Image from the Internet.

In 1953, American scientist James Watson and British scientist Francis Crick developed the model for deoxyribonucleic acid (DNA), a chemical that had (then) recently been deduced to be the physical carrier of inheritance. Crick hypothesized the mechanism for DNA replication and further linked DNA to proteins, an idea since referred to as the central dogma. Information from DNA "language" is converted into RNA (ribonucleic acid) "language" and then to the "language" of proteins. The central dogma explains the influence of heredity (DNA) on the organism (proteins).

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Homeostasis is the maintenance of a dynamic range of conditions within which the organism can function. Temperature, pH, and energy are major components of this concept. Thermodynamics is a field of study that covers the laws governing energy transfers, and thus the basis for life on earth. Two major laws are known: the conservation of matter and energy, and entropy. These will be discussed in more detail in a later chapter. The universe is composed of two things: matter (atoms, etc.) and energy.

These first three theories are very accepted by scientists and the general public. The theory of evolution is well accepted by scientists and most of the general public. However, it remains a lightening rod for school boards, politicians, and television preachers. Much of this confusion results from what the theory says and what it does not say.

Development of the Theory of Evolution

Modern biology is based on several unifying themes, such as the cell theory, genetics and inheritance, Francis Crick's central dogma of information flow, and Darwin and Wallace's theory of evolution by natural selection. In this first unit we will examine these themes and the nature of science.

The Ancient Greek philosopher Anaxiamander (611-547 B.C.) and the Roman philosopher Lucretius (99-55 B.C.) coined the concept that all living things were related and that they had changed over time. The classical science of their time was observational rather than experimental. Another ancient Greek philosopher, Aristotle developed his Scala Naturae, or Ladder of Life, to explain his concept of the advancement of living things from inanimate matter to plants, then animals and finally man. This concept of man as the "crown of creation" still plagues modern evolutionary biologists.

Post-Aristotlean "scientists" were constrained by the prevailing thought patterns of the Middle Ages -- the inerrancy of the biblical book of Genesis and the special creation of the world in a literal six days of the 24-hour variety. Archbishop James Ussher of Ireland, in the late 1600's calculated the age of the earth based on the genealogies from Adam and Eve listed in the biblical book of Genesis. According to Ussher's calculations, the earth was formed on October 22, 4004 B.C. These calculations were part of Ussher's book, History of the World. The chronology he developed was taken as factual, and was even printed in the front pages of bibles. Ussher's ideas were readily accepted, in part because they posed no threat to the social order of the times; comfortable ideas that would not upset the linked apple carts of church and state.

Often new ideas must "come out of left field", appearing as wild notions, but in many cases prompting investigation which may later reveal the "truth". Ussher's ideas were comfortable, the Bible was viewed as correct, therefore the earth must be only 5000 years old.

Geologists had for some time doubted the "truth" of a 5,000 year old earth. Leonardo da Vinci (painter of the Last Supper, and the Mona Lisa, architect and engineer) calculated the sedimentation rates in the Po River of Italy. Da Vinci concluded it took 200,000 years to form some nearby rock deposits. Galileo, convicted heretic for his contention that the Earth was not the center of the Universe, studied fossils (evidence of past life) and concluded that they were real and not inanimate artifacts. James Hutton, regarded as the Father of modern geology, developed the Theory of Uniformitarian’s, the basis of modern geology and paleontology. According to Hutton's work, certain geological processes operated in the past in much the same fashion as they do today, with minor exceptions of rates, etc. Thus many geological structures and processes cannot be explained if the earth was only a mere 5000 years old.

The Modern View of the Age of the Earth

Radiometric age assignments based on the rates of decay of radioactive isotopes, not discovered until the late 19th century, suggest the earth is over 4.5 billion years old. The Earth is thought older than 4.5 billion years, with the oldest known rocks being 3.96 billion years old. Geologic time divides into eons, eras, and smaller units.

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The geologic time scale, highlighting some of the firsts in the evolution of life. One way to represent geological time. Note the break during the Precambrian. If the vertical scale was truly to scale the Precambrian would account for 7/8 of the graphic.

Development of the modern view of Evolution

Erasmus Darwin (1731-1802; grandfather of Charles Darwin) a British physician and poet in the late 1700's, proposed that life had changed over time, although he did not present a mechanism. Georges-Louis Leclerc, Comte de Buffon (pronounced Bu-fone; 1707-1788) in the middle to late 1700's proposed that species could change. This was a major break from earlier concepts that species were created by a perfect creator and therefore could not change because they were perfect, etc.

Swedish botanist Carl Linne (more popularly known as Linneus, after the common practice of the day which was to Latinize names of learned men), attempted to pigeon-hole all known species of his time (1753) into immutable categories. Many of these categories are still used in biology, although the underlying thought concept is now evolution and not immutability of species. Linnean hierarchical classification was based on the premise that the species was the smallest unit, and that each species (or taxon) belonged to a higher category.

Linnean Hierarchical for Classification of Species

Kingdom AnimaliaPhylum (Division is used for plants) Chordata Class Mammalia Order Primates

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Family Hominidae Genus Homo Species sapiens

Pneumonic: King Phillip Crossed Over For Ginger Snaps

Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly. For example Man in English is Hombre in Spanish, Mensch in German, and Homo in Latin. Linneus settled on Latin, which was the language of learned men at that time. If a scientist refers to Homo, all scientists know what he or she means.

William "Strata" Smith (1769-1839), employed by the English coal mining industry, developed the first accurate geologic map of England. He also, from his extensive travels, developed the Principle of Biological Succession. This idea states that each period of Earth history has its own unique assemblages of fossils. In essence Smith fathered the science of stratigraphy, the correlation of rock layers based on (among other things) their fossil contents. He also developed

an idea that life had changed over time, but did not overtly state that.

Abraham Gottlob Werner and Baron Georges Cuvier (1769-1832) were among the foremost proponents of catastrophism, the theory that the earth and geological events had formed suddenly, as a result of some great catastrophe (such as Noah's flood). This view was a comfortable one for the times and thus was widely accepted. Cuvier eventually proposed that there had been several creations that occurred after catastrophes. Louis Agassiz (1807-1873) proposed 50-80 catastrophes and creations.

Jean Baptiste de Lamarck (1744-1829) developed one of the first theories on how species changed. He proposed the inheritance of acquired characteristics to explain, among other things, the length of the giraffe neck. The Lamarckian view is that modern giraffe's have long necks because their ancestors progressively gained longer necks due to stretching to reach food higher and higher in trees. According to the 19th century concept of use and disuse the stretching of necks resulted in their development, which was somehow passed on to their progeny. Today we realize that only bacteria are able to incorporate non-genetic (nonheritable) traits. Lamarck's work was a theory that plainly stated that life had changed over time and provided (albeit an erroneous) mechanism of change.

Darwinian evolution

Charles Darwin, former divinity student and former medical student, secured (through the intercession of his geology professor) an unpaid position as ship's naturalist on the British exploratory vessel H.M.S. Beagle. The voyage would provide Darwin a unique opportunity to study adaptation and gather a great deal of proof he would later incorporate into his theory of evolution. On his return to England in 1836, Darwin began (with the assistance of numerous specialists) to catalog his collections and ponder the seeming "fit" of organisms to their mode of existence. He eventually settled on four main points of a radical new hypothesis:

1. Adaptation: all organisms adapt to their environments. 2. Variation: all organisms are variable in their traits. 3. Over-reproduction: all organisms tend to reproduce beyond their environment's capacity to support them (this is

based on the work of Thomas Malthus, who studied how populations of organisms tended to grow geometrically until they encountered a limit on their population size).

4. Since not all organisms are equally well adapted to their environment, some will survive and reproduce better than others -- this is known as natural selection. Sometimes this is also referred to as "survival of the fittest". In reality this merely deals with the reproductive success of the organisms, not solely their relative strength or speed.

Unlike the upper-class Darwin, Alfred Russel Wallace (1823-1913) came from a different social class. Wallace spent many years in South America, publishing salvaged notes in Travels on the Amazon and Rio Negro in 1853. In 1854,

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Wallace left England to study the natural history of Indonesia, where he contracted malaria. During a fever Wallace managed to write down his ideas on natural selection.

In 1858, Darwin received a letter from Wallace, in which Darwin's as-yet-unpublished theory of evolution and adaptation was precisely detailed. Darwin arranged for Wallace's letter to be read at a scientific meeting, along with a synopsis of his own ideas. To be correct, we need to mention that both Darwin and Wallace developed the theory, although Darwin's major work was not published until 1859 (the book On the Origin of Species by Means of Natural Selection, considered by many as one of the most influential books written). While there have been some changes to the theory since 1859, most notably the incorporation of genetics and DNA into what is termed the "Modern Synthesis" during the 1940's, most scientists today acknowledge evolution as the guiding theory for modern biology.

Recent revisions of biology curricula stressed the need for underlying themes. Evolution serves as such a universal theme. An excellent site devoted to Darwin's thoughts and work is available by clicking here. At that same site is a timeline showing many of the events mentioned above in their historical contexts.

The Diversity of Life

Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things. We also utilize Linneus' hierarchical classification system, adopting (generally) five kingdoms of living organisms. Viruses, as discussed later, are not considered living.. Recent studies suggest that there might be a sixth Kingdom, the Archaea.

A simple phylogenetic representation of three domains of life" Archaea, Bacteria (Eubacteria), and Eukaryota (all eukaryotic groups: Protista, Plantae, Fungi, and Animalia).

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The Five Kingdoms.

KingdomMethods of Nutrition

Organization Environmental Significance Examples

Monera

(in the broadest sense, including organisms usually placed in the Domain Archaea).

Photosynthesis, chemosynthesis, decomposer, parasitic.

Single-celled, filament, or colony of cells; all prokaryotic.

Monerans play various roles in almost all food chains, including producer,consumer, and decomposer.

Cyanobacteria are important oxygen producers.

Many Monerans also produce nitrogen, vitamins, antibiotics, and are important compoents in human and animal intestines.

Bacteria (E. coli), cyanobacteria (Oscillatoria), methanogens, and thermacidophiles.

Protista

Photosynthesis, absorb food from environment, or trap/engulf smaller organisms.

Single-celled, filamentous, colonial, and multicelled; all eukaryotic.

Important producers in ocean/pond food chain.

Source of food in some human cultures.

Phytoplankton component that is one of the major producers of oxygen

Plankton (both phytoplankton and zooplankton), algae (kelp, diatoms, dinoflagellates),and Protozoa (Amoeba, Paramecium).

Fungi

Absorb food from a host or from their environment.

All heterotrophic.

Single-celled, filamentous, to multicelled; all eukaryotic.

Decomposer, parasite, and consumer.

Produce antibiotics,help make bread and alcohol.

Crop parasites (Dutch Elm Disease, Karnal Bunt, Corn Smut, etc.).

 Mushrooms (Agaricus campestris, the commercial mushroom), molds, mildews, rusts and smuts (plant parasites), yeasts (Saccharomyces cerevisae, the brewer's yeast).

Plantae

Almost all photosynthetic, although a few parasitic plants are known.

All multicelled, photosynthetic, autotrophs..

Food source, medicines and drugs, dyes, building material, fuel.

Producer in most food chains.

Angiosperms (oaks, tulips, cacti),gymnosperms (pines, spuce, fir), mosses, ferns,liverworts, horsetails (Equisetum, the scouring rush)

Animalia

All heterotrophic. Multicelled heterotrophs capable of movement at some stage during their life history (even couch potatoes).

Consumer level in most food chains (herbivores,carnivores,omnivores).

Food source, beasts of burden and transportation, recreation, and companionship.

Sponges, worms,molluscs, insects, starfish,mammals, amphibians,fish, birds, reptiles, and dinosaurs, and people.

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Monera, the most primitive kingdom, contain living organisms remarkably similar to ancient fossils. Organisms in this group lack membrane-bound organelles associated with higher forms of life. Such organisms are known as prokaryotes. Bacteria (technically the Eubacteria) and blue-green bacteria (sometimes called blue-green algae, or cyanobacteria) are the major forms of life in this kingdom. The most primitive group, the archaebacteria, are today restricted to marginal habitats such as hot springs or areas of low oxygen concentration.

Protista were the first of the eukaryotic kingdoms, these organisms and all others have membrane-bound organelles, which allow for compartmentalization and dedication of specific areas for specific functions. The chief importance of Protista is their role as a stem group for the remaining Kingdoms: Plants, Animals, and Fungi. Major groups within the Protista include the algae, euglenoids, ciliates, protozoa, and flagellates.

Scanning electron micrographs of diatoms (Protista).There are two basic types of diatoms: bilaterally symmetrical (left) and radially symmetrical (right).

Light micrographs of some protistans.

Fungi are almost entirely multicellular (with yeast, Saccharomyces cerviseae, being a prominent unicellular fungus), heterotrophic (deriving their energy from another organism, whether alive or dead), and usually having some cells with two nuclei (multinucleate, as opposed to the more common one, or uninucleate) per cell. Ecologically this kingdom is important (along with certain bacteria) as decomposers and recyclers of nutrients. Economically, the Fungi provide us with food (mushrooms; Bleu cheese/Roquefort cheese; baking and brewing), antibiotics (the first of the wonder drugs, penicillin, was isolated from a fungus Penicillium), and crop parasites (doing several billion dollars per year of damage).

Plantae include multicelled organisms that are all autotrophic (capable of making their own food by the process of photosynthesis, the conversion of sunlight energy into chemical energy). Ecologically, this kingdom is generally (along with photosynthetic organisms in Monera and Protista) termed the producers, and rest at the base of all food webs. A food

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web is an ecological concept to trace energy flow through an ecosystem. Economically, this kingdom is unparalleled, with agriculture providing billions of dollars to the economy (as well as the foundation of "civilization"). Food, building materials, paper, drugs (both legal and illegal), and roses, are plants or plant-derived products.

Animalia consists entirely of multicellular heterotrophs that are all capable (at some point during their life history) of mobility. Ecologically, this kingdom occupies the level of consumers, which can be subdivided into herbivore (eaters of plants) and carnivores (eaters of other animals). Humans, along with some other organisms, are omnivores (capable of functioning as herbivores or carnivores). Economically, animals provide meat, hides, beasts of burden, pleasure (pets), transportation, and scents (as used in some perfumes).

Characteristics of living things

Living things have a variety of common characteristics.

Organization. Living things exhibit a high level of organization, with multicellular organisms being subdivided into cells, and cells into organelles, and organelles into molecules, etc.

Homeostasis. Homeostasis is the maintenance of a constant (yet also dynamic) internal environment in terms of temperature, pH, water concentrations, etc. Much of our own metabolic energy goes toward keeping within our own homeostatic limits. If you run a high fever for long enough, the increased temperature will damage certain organs and impair your proper functioning. Swallowing of common household chemicals, many of which are outside the pH (acid/base) levels we can tolerate, will likewise negatively impact the human body's homeostatic regime. Muscular activity generates heat as a waste product. This heat is removed from our bodies by sweating. Some of this heat is used by warm-blooded animals, mammals and birds, to maintain their internal temperatures.

Adaptation. Living things are suited to their mode of existence. Charles Darwin began the recognition of the marvelous adaptations all life has that allow those organisms to exist in their environment.

Reproduction and heredity. Since all cells come from existing cells, they must have some way of reproducing, whether that involves asexual (no recombination of genetic material) or sexual (recombination of genetic material). Most living things use the chemical DNA (deoxyribonucleic acid) as the physical carrier of inheritance and the genetic information. Some organisms, such as retroviruses (of which HIV is a member), use RNA (ribonucleic acid) as the carrier. The variation that Darwin and Wallace recognized as the wellspring of evolution and adaptation, is greatly increased by sexual reproduction.

Growth and development. Even single-celled organisms grow. When first formed by cell division, they are small, and must grow and develop into mature cells. Multicellular organisms pass through a more complicated process of differentiation and organogenesis (because they have so many more cells to develop).

Energy acquisition and release. One view of life is that it is a struggle to acquire energy (from sunlight, inorganic chemicals, or another organism), and release it in the process of forming ATP (adenosine triphosphate).

Detection and response to stimuli (both internal and external). Interactions. Living things interact with their environment as well as each other. Organisms obtain raw materials

and energy from the environment or another organism. The various types of symbioses (organismal interactions with each other) are examples of this.

Levels of Organization

Biosphere: The sum of all living things taken in conjunction with their environment. In essence, where life occurs, from the upper reaches of the atmosphere to the top few meters of soil, to the bottoms of the oceans. We divide the earth into atmosphere (air), lithosphere (earth), hydrosphere (water), and biosphere (life).

Ecosystem: The relationships of a smaller groups of organisms with each other and their environment. Scientists often speak of the interrelatedness of living things. Since, according to Darwin's theory, organisms adapt to their environment, they must also adapt to other organisms in that environment. We can discuss the flow of energy through an ecosystem from photosynthetic autotrophs to herbivores to carnivores.

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Community: The relationships between groups of different species. For example, the desert communities consist of rabbits, coyotes, snakes, birds, mice and such plants as sahuaro cactus (Carnegia gigantea), Ocotillo, creosote bush, etc. Community structure can be disturbed by such things as fire, human activity, and over-population.

Species: Groups of similar individuals who tend to mate and produce viable, fertile offspring. We often find species described not by their reproduction (a biological species) but rather by their form (anatomical or form species).

Populations: Groups of similar individuals who tend to mate with each other in a limited geographic area. This can be as simple as a field of flowers, which is separated from another field by a hill or other area where none of these flowers occur.

Individuals: One or more cells characterized by a unique arrangement of DNA "information". These can be unicellular or multicellular. The multicellular individual exhibits specialization of cell types and division of labor into tissues, organs, and organ systems.

Organ System: (in multicellular organisms). A group of cells, tissues, and organs that perform a specific major function. For example: the cardiovascular system functions in circulation of blood.

Organ: (in multicellular organisms). A group of cells or tissues performing an overall function. For example: the heart is an organ that pumps blood within the cardiovascular system.

Tissue: (in multicellular organisms). A group of cells performing a specific function. For example heart muscle tissue is found in the heart and its unique contraction properties aid the heart's functioning as a pump. .

Cell: The fundamental unit of living things. Each cell has some sort of hereditary material (either DNA or more rarely RNA), energy acquiring chemicals, structures, etc. Living things, by definition, must have the metabolic chemicals plus a nucleic acid hereditary information molecule.

Organelle: A subunit of a cell, an organelle is involved in a specific subcellular function, for example the ribosome (the site of protein synthesis) or mitochondrion (the site of ATP generation in eukaryotes).

Molecules, atoms, and subatomic particles: The fundamental functional levels of biochemistry.

It is thus possible to study biology at many levels, from collections of organisms (communities), to the inner workings of a cell (organelle).

Learning Objectives

Name the special molecule that sets living things apart from the nonliving world and be able to explain why this molecule is important.

The cell is considered to be the basic living unit. Be able to distinguish between single-celled organisms and multicelled organisms.

Be able to arrange in order, from smallest to largest, the levels of organization that occur in nature and to write a brief description of each.

What does the term metabolism mean to the cell and the organism. Organisms use a molecule known as ATP to transfer chemical energy from one molecule to another. Why is this essential for

living things to exist. Homeostasis is defined as a state in which the conditions of an organism's internal environment are maintained within

tolerable limits. What mechanisms in your body are involved with homeostasis?

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Reproduction is the means by which each new organism arises. Why is this an essential characteristic of life? How are DNA and cellular reproduction linked in the process of inheritance? A trait that assists an organism in survival and reproduction in a certain environment is said to be adaptive. What sorts of

adaptive traits do you have? How do they aid your survival? List the five kingdoms of life that are currently recognized by most scientists; tell generally what kinds of organisms are

classified in each kingdom, and discuss the new ideas about Domains and how they may alter the five kingdom approach. Arrange in order, from the fewer to the greater numbers of organisms included, the following categories of classification:

class, family, genus, kingdom, order, phylum, and species. Explain what the term biological diversity means to you, and speculate about what caused the great diversity of life on Earth. Define natural selection and briefly describe what is occurring when a population is said to evolve. Outline a set of steps that might be used in the scientific method of investigating a problem. Explain why a control group is used in an experiment. Define what is meant by a theory; cite an actual example that is significant to biology.

Review Questions

1. Which of these scientific terms has the greatest degree of certainty? a) hypothesis; b) theory; c) law; d) guess. 2. The purpose of a control in a scientific experiment is to ___. a) provide a basis of comparison between

experimental and nonexperimental; b) indicate the dependent variable; c) indicate the independent variable; d) provide a baseline from which to graph the data.

3. Which of these theories is not a basis for modern biology? a) evolution; b) creationism; c) cell theory; d) gene theory.

4. The molecule that is the physical carrier of inheritance is known as ___. a) ATP; b) RNA; c) DNA; d) NADH 5. Bacteria belong to the taxonomic kingdom ____. a) Plantae; b) Protista; c) Animalia; d) Fungi; e) Monera 6. Mushrooms belong to which of these taxonomic kingdoms? a) Plantae; b) Protista; c) Animalia; d) Fungi; e)

Monera 7. Papaver somniferum, the opium poppy, belongs to which of these taxonomic kingdoms? a) Plantae; b) Protista; c)

Animalia; d) Fungi; e) Monera 8. The sum of all energy transfers within a cell is known as _____. a) photosynthesis; b) cellular respiration; c)

metabolism; d) replication; e) conjugation. 9. The molecule that is the energy coin of the cell is ___. a) ATP; b) RNA; c) DNA; d) NADH 10. Which of these is NOT a living organism? a) cactus; b) cat; c) algae; d) virus; e) yeast 11. Which of the following is the least inclusive (smallest) unit of classification? a) kingdom; b) species; c) genus; d)

class; e) phylum 12. The scientist(s) credited with developing the theory of evolution by natural selection were ____. a) James Watson

and Francis Crick; b) Aristotle and Lucretius; c) Charles Darwin and Alfred Wallace; d) Robert Hooke and Rudolph Virchow; e) James Watson and Charles Darwin

13. When an organism consists of a single cell, the organism is referred to as ___. a) uninucleate; b) uniport; c) unisexual; d) unicellular

14. According to science, the Earth is ___ years old. a) 4.5 billion; b) 4.5 million; c) 10 billion; d) 10,000; e) 450 million

15. Which of these is not an economic use of bacteria? a) food; b) biotechnology; c) mushrooms; d) food spoilage

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WATER AND ORGANIC MOLECULES

Structure of Water

It can be quite correctly argued that life exists on Earth because of the abundant liquid water. Other planets have water, but they either have it as a gas (Venus) or ice (Mars). Recent studies of Mars reveal the presence sometime in the past of running fluid, possibly water. The chemical nature of water is thus one we must examine as it permeates living systems: water is a universal solvent, and can be too much of a good thing for some cells to deal with.

Water is polar covalently bonded within the molecule. This unequal sharing of the electrons results in a slightly positive and a slightly negative side of the molecule. Other molecules, such as Ethane, are nonpolar, having neither a positive nor a negative side.

The difference between a polar (water) and nonpolar (ethane) molecule is due to the unequal sharing of electrons within the polar molecule. Nonpolar molecules have electrons equally shared within their covalent bonds.

These link up by the hydrogen bond discussed earlier. Consequently, water has a great interconnectivity of individual molecules, which is caused by the individually weak hydrogen bonds, that can be quite strong when taken by the billions.

Water has been referred to as the universal solvent. Living things are composed of atoms and molecules within aqueous solutions (solutions that have materials dissolved in water). Solutions are uniform mixtures of the molecules of two or more substances. The solvent is usually the substance present in the greatest amount (and is usually also a liquid). The substances of lesser amounts are the solutes.

The solubility of many molecules is determined by their molecular structure. You are familiar with the phrase "mixing like oil and water." The biochemical basis for this phrase is that the organic macromolecules known as

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lipids (of which fats are an important, although often troublesome, group) have areas that lack polar covalent bonds. The polar covalently bonded water molecules act to exclude nonpolar molecules, causing the fats to clump together. The structure of many molecules can greatly influence their solubility. Sugars, such as glucose, have many hydroxyl (OH) groups, which tend to increase the solubility of the molecule.

Water tends to disassociate into H+ and OH- ions. In this disassociation, the oxygen retains the electrons and only one of the hydrogens, becoming a negatively charged ion known as hydroxide. Pure water has the same number (or concentration) of H+ as OH- ions. Acidic solutions have more H+ ions than OH- ions. Basic solutions have the opposite. An acid causes an increase in the numbers of H+ ions and a base causes an increase in the numbers of OH- ions.

The pH scale is a logarithmic scale representing the concentration of H+ ions in a solution. Remember that as the H+ concentration increases the OH- concentration decreases and vice versa . If we have a solution with one in every ten molecules being H+, we refer to the concentration of H+ ions as 1/10. Remember from algebra that we can write a fraction as a negative exponent, thus 1/10 becomes 10-1. Conversely 1/100 becomes 10-2 , 1/1000 becomes 10-3, etc. Logarithms are exponents to which a number (usually 10) has been raised. For example log 10 (pronounced "the log of 10") = 1 (since 10 may be written as 101). The log 1/10 (or 10-1) = -1. pH, a measure of the concentration of H+ ions, is the negative log of the H+ ion concentration. If the pH of water is 7, then the concentration of H+ ions is 10-7, or 1/10,000,000. In the case of strong acids, such as hydrochloric acid (HCl), an acid secreted by the lining of your stomach, [H+] (the concentration of H+ ions, written in a chemical shorthand) is 10-1; therefore the pH is 1.

Organic molecules

Organic molecules are those that: 1) formed by the actions of living things; and/or 2) have a carbon backbone. Methane (CH4) is an example of this. If we remove the H from one of the methane units below, and begin

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linking them up, while removing other H units, we begin to form an organic molecule. (NOTE: Not all methane is organically derived, methane is a major component of the atmosphere of Jupiter, which we think is devoid of life). When two methanes are combined, the resultant molecule is Ethane, which has a chemical formula C2H6. Molecules made up of H and C are known as hydrocarbons.

Scientists eventually realized that specific chemical properties were a result of the presence of particular functional groups. Functional groups are clusters of atoms with characteristic structure and functions. Polar

molecules (with +/- charges) are attracted to water molecules and are hydrophilic. Nonpolar molecules are repelled by water and do not dissolve in water; are hydrophobic. Hydrocarbon is hydrophobic except when it has an attached ionized functional group such as carboxyl (acid) (COOH), then molecule is hydrophilic. Since cells are 70-90% water, the degree to which organic molecules interact with water affects their function. One of the most common groups is the -OH (hydroxyl) group. Its presence will enable a molecule to be water soluble.

Isomers are molecules with identical molecular formulas but differ in arrangement of their atoms (e.g., glyceraldehyde and dihydroxyacetone)..

Functional groups in organic molecules.

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Carbon has four electrons in outer shell, and can bond with up to four other atoms (usually H, O, N, or another C). Since carbon can make covalent bonds with another carbon atom, carbon chains and rings that serve as the backbones of organic molecules are possible.

Chemical bonds store energy. The C-C covalent bond has 83.1 Kcal (kilocalories) per mole, while the C=C double covalent bond has 147 Kcal/mole. Energy is in two forms: kinetic, or energy in use/motion; and potential, or energy at rest or in storage. Chemical bonds are potential energy, until they are converted into another form of energy, kinetic energy (according to the two laws of thermodynamics).

Each organic molecule group has small molecules (monomers) that are linked to form a larger organic molecule (macromolecule). Monomers can be joined together to form polymers that are the large macromolecules made of three to millions of monomer subunits.

Macromolecules are constructed by covalently bonding monomers by condensation reactions where water is removed from functional groups on the monomers. Cellular enzymes carry out condensation (and the reversal of the reaction, hydrolysis of polymers). Condensation involves a dehydration synthesis because a water is removed (dehydration) and a bond is made (synthesis). When two monomers join, a hydroxyl (OH) group is removed from one monomer and a hydrogen (H) is removed from the other. This produces the water given off during a condensation reaction. Hydrolysis (hydration) reactions break down polymers in reverse of condensation; a hydroxyl (OH) group from water attaches to one monomer and hydrogen (H) attaches to the other.

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There are four classes of macromolecules (polysaccharides, triglycerides, polypeptides, nucleic acids). These classes perform a variety of functions in cells.

1. Carbohydrates have the general formula [CH2O]n where n is a number between 3 and 6.. Carbohydrates function in short-term energy storage (such as sugar); as intermediate-term energy storage (starch for plants and glycogen for animals); and as structural components in cells (cellulose in the cell walls of plants and many protists), and chitin in the exoskeleton of insects and other arthropods.

Sugars are structurally the simplest carbohydrates. They are the structural unit which makes up the other types of carbohydrates. Monosaccharides are single (mono=one) sugars. Important monosaccharides include ribose (C5H10O5), glucose (C6H12O6), and fructose (same formula but different structure than glucose).

We classify monosaccharides by the number of carbon atoms and the types of functional groups present in the sugar. For example, glucose and fructose, have the same chemical formula (C6H12O6), but a different structure: glucose having an aldehyde (internal hydroxyl shown as: -OH) and fructose having a keto group (internal double-bond O, shown as: =O). This functional group difference, as small as it seems, accounts for the greater sweetness of fructose as compared to glucose.

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In an aqueous solution, glucose tends to have two structures, (alpha) and beta, with an intermediate straight-chain form. The form and form differ in the location of one -OH group. Glucose is a common hexose, six carbon sugar, in plants. The products of photosynthesis are assembled to form glucose. Energy from sunlight is converted into and stored as C-C covalent bond energy. This energy is released in living organisms in such a way that not enough heat is generated at once to incinerate the organisms. One mole of glucose yields 673 Kcal of energy. (A calorie is the amount of heat needed to raise one gram of water one degree C. A Kcal has 1000 times as much energy as a cal.). Glucose is also the form of sugar measured in the human bloodstream.

Monosaccarides: Glucose, Fructose, Galactose, Ribose, and Deoxyribose

Disaccharides are formed when two monosaccharides are chemically bonded together. Sucrose, a common plant disaccharide is composed of the monosaccharides glucose and fructose. Lactose, milk sugar, is a

disaccharide composed of glucose and the monosaccharide galactose. The maltose that flavors a malted milkshake (and other items) is also a disaccharide made of two glucose molecules bonded together as shown in.

Polysaccharides are large molecules composed of individual monosaccharide units. A common plant polysaccharide is starch which is made up of many glucoses (in a polypeptide these are referred to as glucans). Two forms of polysaccharide, amylose and amylopectin makeup what we commonly call starch. The formation of the ester bond by condensation (the removal of water from a molecule) allows the linking of monosaccharides into disaccharides and polysaccharides. Glycogen is an animal storage product that accumulates in the vertebrate liver.

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Cellulose, is a polysaccharide found in plant cell walls. Cellulose forms the fibrous part of the plant cell wall. In terms of human diets, cellulose is indigestible, and thus forms an important, easily obtained part of dietary fiber.

As compared to starch and glycogen, which are each made up of mixtures of and glucoses, cellulose (and the animal structural polysaccharide chitin) are made up of only glucoses. The three-dimensional structure of these polysaccharides is thus constrained into straight microfibrils by the uniform nature of the glucoses, which

resist the actions of enzymes (such as amylase) that breakdown storage polysaccharides (such a starch).

2. Lipids are involved mainly with long-term energy storage. They are generally insoluble in polar substances such as water. Secondary functions of lipids include structural components (as in the case of phospholipids that are the major building block in cell membranes) and "messengers" (hormones) that play roles in communications within and between cells. Lipids are composed of three fatty acids (usually) covalently bonded to a 3-carbon glycerol. The fatty acids are composed of CH2 units, and are hydrophobic/not water soluble.

Fatty acids can be saturated (meaning they have as many hydrogens bonded to their carbons as possible) or unsaturated (with one or more double bonds connecting their carbons, hence fewer hydrogens). A fat is solid at room temperature, while an oil is a liquid under the same conditions. The fatty acids in oils are mostly unsaturated, while those in fats are mostly saturated.

Saturated (palmitic and stearic) and unsaturated (next page Oleic) fatty acids. The term saturated refers to the "saturation" of the molecule by hydrogen atoms. The presence of a double C=C covalent bond reduces the number of hydrogens that can bond to the carbon chain, hence the application of therm "unsaturated".

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Fats and oils function in long-term energy storage. Animals convert excess sugars (beyond their glycogen storage capacities) into fats. Most plants store excess sugars as starch, although some seeds and fruits have energy stored as oils (e.g. corn oil, peanut oil, palm oil, canola oil, and sunflower oil). Fats yield 9.3 Kcal/gm, while carbohydrates yield 3.79 Kcal/gm. Fats thus store six times as much energy as glycogen.

Diets are attempts to reduce the amount of fats present in specialized cells known as adipose cells that accumulate in certain areas of the human body. By restricting the intakes of carbohydrates and fats, the body is forced to draw on its own stores to makeup the energy debt. The body responds to this by lowering its metabolic rate, often resulting in a drop of "energy level." Successful diets usually involve three things: decreasing the amounts of carbohydrates and fats; exercise; and behavior modification.

Another use of fats is as insulators and cushions. The human body naturally accumulates some fats in the "posterior" area. Subdermal ("under the skin") fat plays a role in insulation.

Phospholipids and glycolipids are important structural components of cell membranes. Phospholipids, are modified so that a phosphate group (PO4

-) is added to one of the fatty acids. The addition of this group makes a polar "head" and two nonpolar "tails". Waxes are an important structural component for many organisms, such as the cuticle, a waxy layer covering the leaves and stems of many land plants; and protective coverings on skin and fur of animals.

Cholesterol and steroids: Most mention of these two types of lipids in the news is usually negative. Cholesterol, has many biological uses, it occurs in cell membranes, and its forms the sheath of some types of nerve cells. However, excess cholesterol in the blood has been linked to atherosclerosis, hardening of the arteries. Recent studies suggest a link between arterial plaque deposits of cholesterol, antibodies to the pneumonia-causing form of Chlamydia, and heart attacks. The plaque increases blood pressure, much the way blockages in plumbing cause burst pipes in old houses.

Structure of four steroids..

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3. Proteins are very important in biological systems as control and structural elements. Control functions of proteins are carried out by enzymes and proteinaceous hormones. Enzymes are chemicals that act as organic catalysts (a catalyst is a chemical that promotes but is not changed by a chemical reaction). Structural proteins function in the cell membrane, muscle tissue, etc.

The building block of any protein is the amino acid, which has an amino end (NH2) and a carboxyl end (COOH). The R indicates the variable component (R-group) of each amino acid. Alanine and Valine, for example, are both nonpolar amino acids, but they differ, as do all amino acids, by the composition of their R-groups. All living things (and even viruses) use various combinations of the same twenty amino acids. A very powerful bit of evidence for the phylogenetic connection of all living things.

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Amino acids are linked together by joining the amino end of one molecule to the carboxyl end of another. Removal of water allows formation of a type of covalent bond known as a peptide bond.

Formation of a peptide bond between two amino acids by the condensation (dehydration) of the amino end of one amino acid and the acid end of the other amino acid.

Amino acids are linked together into a polypeptide, the primary structure in the organization of proteins. The primary structure of a protein is the sequence of amino acids, which is directly related to the sequence of information in the RNA molecule, which in turn is a copy of the information in the DNA molecule. Changes in the primary structure can alter the proper functioning of the protein. Protein function is usually tied to their three-dimensional structure. The primary structure is the sequence of amino acids in a polypeptide..

The secondary structure is the tendency of the polypeptide to coil or pleat due to H-bonding between R-groups. The tertiary structure is controlled by bonding (or in some cases repulsion) between R-groups.. Many proteins, such as hemoglobin, are formed from one or more polypeptides. Such structure is termed quaternary structure. Structural proteins, such as collagen, have regular repeated primary structures. Like the structural carbohydrates, the components determine the final shape and ultimately function. Collagens have a variety of functions in living things, such as the tendons, hide, and corneas of a cow. Keratin is another structural protein. It is found in fingernails, feathers, hair, and rhinoceros horns. Microtubules, important in cell division and structures of flagella and cilia (among other things), are composed of globular structural proteins.

4. Nucleic acids are polymers composed of monomer units known as nucleotides. There are a very few different types of nucleotides. The main functions of nucleotides are information storage (DNA), protein synthesis (RNA), and energy transfers (ATP and NAD). Nucleotides, consist of a sugar, a nitrogenous base, and a phosphate. The sugars are either ribose or deoxyribose. They differ by the lack of one oxygen in deoxyribose. Both are pentoses usually in a ring form. There are five nitrogenous bases. Purines (Adenine and Guanine) are double-ring structures, while pyrimidines (Cytosine, Thymine and Uracil) are single-ringed.

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Deoxyribonucleic acid (better known as DNA) is the physical carrier of inheritance for 99% of living organisms. The bases in DNA are C, G, A and T.

Structure of a segment of a DNA double helix.

DNA functions in information storage. The English alphabet has 26 letters that can be variously combined to form over 50,000 words. DNA has four letters (C, G, A, and T, the nitrogenous bases) that code for twenty words (the twenty amino acids found in all living things) that can make an infinite variety of sentences (polypeptides). Changes in the sequences of these bases information can alter the meaning of a sentence.

For example take the sentence: I saw Elvis. This implies certain knowledge (that I've been out in the sun too long without a hat, etc.).

If we alter the sentence by inverting the middle word, we get: I was Elvis (thank you, thank you very much). Now we have greatly altered the information.

A third alteration will change the meaning: I was Levis. Clearly the original sentence's meaning is now greatly changed.

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Changes in DNA information will be translated into changes in the primary structure of a polypeptide, and from there to the secondary and tertiary structures. A mutation is any change in the DNA base sequence. Most mutations are harmful, few are neutral, and a very few are beneficial and contribute the organism's reproductive success. Mutations are the wellspring of variation, variation is central to Darwin and Wallace's theory of evolution by natural selection.

Ribonucleic acid (RNA), was discovered after DNA. DNA, with exceptions in chloroplasts and mitochondria, is restricted to the nucleus (in eukaryotes, the nucleoid region in prokaryotes). RNA occurs in the nucleus as well as in the cytoplasm (also remember that it occurs as part of the ribosomes that line the rough endoplasmic reticulum). There are three types of RNA:

Messenger RNA (mRNA) is the blueprint for construction of a protein.

Ribosomal RNA (rRNA) is the construction site where the protein is made.

Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time.

Adenosine triphosphate, better known as ATP the energy currency or coin of the cell, transfers energy from chemical bonds to endergonic (energy absorbing) reactions within the cell. Structurally, ATP consists of the adenine nucleotide (ribose sugar, adenine base, and phosphate group, PO4

-2) plus two other phosphate groups.

Energy is stored in the covalent bonds between phosphates, with the greatest amount of energy (approximately 7 kcal/mole) in the bond between the second and third phosphate groups. This covalent bond is known as a pyrophosphate bond.

 

Learning Objectives

Dissolved substances are called solutes; a fluid in which one or more substances can dissolve is called a solvent. Describe several solutions that you use everyday in terms of what is the solvent and what is the solute.

Define acid and base and be able to cite an example of each. The concentration of free hydrogen ions in solutions is measured by the pH scale.. Nearly all large biological molecules have theory organization influenced by interactions with water.

Describe this interaction as it exists with carbohydrate molecules. Be able to list the three most abundant elements in living things. Each carbon atom can form as many as four covalent bonds with other carbon atoms as well as with

other elements. Be able to explain why this is so. Be able to list the four main groups of organic molecules and their functions in living things. Enzymes are a special class of proteins that speed up chemical reactions in cells. What about the

structure of proteins allows for the reaction specificity that occurs with most enzymes. Condensation reactions result in the formation of covalent bonds between small molecules to form larger

organic molecules. Be able to describe a condensation reaction in words. Be able to describe what occurs during a hydrolysis reaction. Be able to define carbohydrates and list their functions. The simplest carbohydrates are sugar monomers, the monosaccharides. Be able to give examples and

their functions.

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A polysaccharide is a straight or branched chain of hundreds or thousands of sugar monomers, of the same or different kinds. Be able to give common examples and their functions.

Be able to define lipids and to list their functions. Distinguish between a saturated fat and an unsaturated fat. Why is such a distinction a life and death

matter for many people? A phospholipid has two fatty acid tails attached to a glycerol backbone. What is the importance of these

molecules. Define steroids and describe their chemical structure. Be able to discuss the importance of the steroids

known as cholesterol and hormones. Be able to describe proteins and cite their general functions. Be prepared to make a sketch and name the three parts of every amino acid. Describe the complex structure of a protein through its primary, secondary, tertiary, and quaternary

structure. How does this relate to the three-dimensional structure of proteins? Describe the three parts of every nucleotide.. Be able to give the general functions of DNA and RNA molecules.

Review Questions

1. The chemical reaction where water is removed during the formation of a covalent bond linking two monomers is known as ___. a) dehydration; b) hydrolysis; c) photosynthesis; d) protein synthesis

2. The monomer that makes up polysaccharides is ____. a) amino acids; b) glucose; c) fatty acids; d) nucleotides; e) glycerol

3. Proteins are composed of which of these monomers? a) amino acids; b) glucose; c) fatty acids; d) nucleotides; e) glycerol

4. Which of these is not a function of lipids? a) long term energy storage; b) structures in cells; c) hormones; d) enzymes; e) sex hormones

5. All living things use the same ___ amino acids. a) 4; b) 20; c) 100; d) 64 6. The sequence of ___ bases determines the ___ structure of a protein. a) RNA, secondary; b) DNA,

quaternary; c) DNA, primary; d) RNA, primary 7. Which of these is not a nucleotide base found in DNA? a) uracil; b) adenine; c) guanine; d) thymine; e)

cytosine 8. Which of these carbohydrates constitutes the bulk of dietary fiber? a) starch; b) cellulose; c) glucose; d)

fructose; e) chitin 9. A diet high in _____ is considered unhealthy, since this type of material is largely found in animal

tissues. a) saturated fats; b) testosterone; c) unsaturated fats; d) plant oils 10. The form of RNA that delivers information from DNA to be used in making a protein is ____. a)

messenger RNA; b) ribosomal RNA; c) transfer RNA; d) heterogeneous nuclear RNA 11. The energy locked inside an organic molecule is most readily accessible in a ___ molecule. a) fat; b)

DNA; c) glucose; d) chitin; e) enzyme 12. Phospholipids are important components in ____. a) cell walls; b) cytoplasm; c) DNA; d) cell

membranes; e) cholesterol

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CELLS: ORIGINS

Origin of the Earth and Life

Scientific estimates place the origin of the Universe at between 10 and 20 billion years ago. The theory currently with the most acceptance is the Big Bang Theory, the idea that all matter in the Universe existed in a cosmic egg (smaller than the size of a modern hydrogen atom) that exploded, forming the Universe. Recent discoveries from the Space Telescope and other devices suggest this theory may need some modification. Evidence for the Big Bang includes:

1) The Red Shift: when stars/galaxies are moving away from us the energy they emit is shifted to the red side of the visible-light spectrum. Those moving towards us are shifted to the violet side. This shift is an example of the Doppler effect. Similar effects are observed when listening to a train whistle-- it will sound higher (shorter wavelengths) approaching and lower (longer wavelengths) as it moves away. Likewise red wavelengths are longer than violet ones. Most galaxies appear to be moving away from ours.

2) Background radiation: two Bell Labs scientists discovered that in interstellar space there is a slight background radiation, thought to be the residual after blast remnant of the Big Bang.

Soon after the Big Bang the major forces (such as gravity, weak nuclear force, strong nuclear force, etc.) differentiated. While in the cosmic egg, scientists think that matter and energy as we understand them did not exist, but rather they formed soon after the bang. After 10 million to 1 billion years the universe became clumpy, with matter beginning to accumulate into solar systems. One of those solar systems, ours, began to form approximately 5 billion years ago, with a large "protostar" (that became our sun) in the center. The planets were in orbits some distance from the star, their increasing gravitational fields sweeping stray debris into larger and larger planetesimals that eventually formed planets.

The processes of radioactive decay and heat generated by the impact of planetesimals heated the Earth, which then began to differentiate into a "cooled" outer cooled crust (of silicon, oxygen and other relatively light elements) and increasingly hotter inner areas (composed of the heavier and denser elements such as iron and nickel). Impact (asteroid, comet, planetismals) and the beginnings of volcanism released water vapor, carbon dioxide, methane, ammonia and other gases into a developing atmosphere. Sometime "soon" after this, life on Earth began.

Where did life originate and how?

Extra-terrestrial: In 1969, a meteorite (left-over bits from the origin of the solar system) landed near Allende, Mexico. The Allende Meteorite (and others of its sort) have been analyzed and found to contain amino acids, the building blocks of proteins, one of the four organic molecule groups basic to all life. The idea of panspermia hypothesized that life originated out in space and came to Earth inside a meteorite. Recently, this idea has been revived as Cosmic Ancestry. The amino acids recovered from meteorites are in a group known as exotics: they do not occur in the chemical systems of living things. The ET theory is now not considered by most scientists to be correct, although the August 1996 discovery of the Martian meteorite and its possible fossils have revived thought of life elsewhere in the Solar System.

Supernatural: Since science is an attempt to measure and study the natural world, this theory is outside science (at least our current understanding of science). Science classes deal with science, and this idea is in the category of not-science.

Organic Chemical Evolution: Until the mid-1800's scientists thought organic chemicals (those with a C-C skeleton) could only form by the actions of living things. A French scientist heated crystals of a mineral (a mineral is by definition inorganic), and discovered that they formed urea (an organic chemical) when they cooled. Russian scientist and academician A.I. Oparin, in 1922, hypothesized that cellular life was preceded by a period of chemical evolution. These chemicals, he argued, must have arisen spontaneously under conditions existing billions of years ago (and quite unlike current conditions).

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In 1950, then-graduate student Stanley Miller designed an experimental test for Oparin's hypothesis. Oparin's original hypothesis called for : 1) little or no free oxygen (oxygen not bonded to other elements); and 2) C H O and N in abundance. Studies of modern volcanic eruptions support inference of the existence of such an atmosphere. Miller discharged an electric spark into a mixture thought to resemble the primordial composition of the atmosphere. From the water receptacle, designed to model an ancient ocean, Miller recovered amino acids. Subsequent modifications of the atmosphere have produced representatives or precursors of all four organic macromolecular classes..

The primordial Earth was a very different place than today, with greater amounts of energy, stronger storms, etc. The oceans were a "soup" of organic compounds that formed by inorganic processes (although this soup would not taste umm ummm good). Miller's (and subsequent) experiments have not proven life originated in this way, only that conditions thought to have existed over 3 billion years ago were such that the spontaneous (inorganic) formation of organic macromolecules could have taken place..

The interactions of these molecules would have increased as their concentrations increased. Reactions would have led to the building of larger, more complex molecules. A pre-cellular life would have began with the formation of nucleic acids. Chemicals made by these nucleic acids would have remained in proximity to the nucleic acids. Eventually the pre-cells would have been enclosed in a lipid-protein membrane, which would have resulted in the first cells.

Biochemically, living systems are separated from other chemical systems by three things.

1. The capacity for replication from one generation to another. Most organisms today use DNA as the hereditary material, although recent evidence (ribosome) suggests that RNA may have been the first nucleic acid system to have formed. Nobel laureate Walter Gilbert refers to this as the RNA world. Recent studies suggest a molecular

2. The presence of enzymes and other complex molecules essential to the processes needed by living systems. Miller's experiment showed how these could possibly form.

3. A membrane that separates the internal chemicals from the external chemical environment. This also delimits the cell from not-cell areas. The work of Sidney W. Fox has produced proteinoid spheres, which while not cells, suggest a possible route from chemical to cellular life.

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Fossil evidence supports the origins of life on Earth earlier than 3.5 billion years ago. The North Pole microfossils from Australia, are complex enough that more primitive cells must have existed earlier. From rocks of the Ishua Super Group in Greenland come possibly the earliest cells, as much as 3.8 billion years old. The oldest known rocks on Earth are 3.96 billion years old and are from Arctic Canada. Thus, life appears to have begun soon after the cooling of the Earth and formation of the atmosphere and oceans.

Microfossils from the Apex Chert, North Pole, Australia. These organisms are Archean in age, approximately 3.465 billion years old, and resemble filamentous cyanobacteria.

These ancient fossils occur in marine rocks, such as limestones and sandstones, that formed in ancient oceans. The organisms living today that are most similar to ancient life forms are the archaebacteria. This group is today restricted to marginal environments. Recent discoveries of bacteria at mid-ocean ridges add yet another possible origin for life: at these mid-ocean ridges where heat and molten rock rise to the Earth's surface.

Archaea and Eubacteria are similar in size and shape. When we do recover "bacteria" as fossils those are the two features we will usually see: size and shape. How can we distinguish between the two groups: the use of molecular fossils that will point to either (but not both) groups. Such a chemical fossil has been found and its presence in the Ishua rocks of Greenland (3.8 billion years old) suggests that the archeans were present at that time.

Is there life on Mars, Venus, anywhere else??

The proximity of the Earth to the sun, the make-up of the Earth's crust (silicate mixtures, presence of water, etc.) and the size of the Earth suggest we may be unique in our own solar system, at least. Mars is smaller, farther from the sun, has a lower gravitational field (which would keep the atmosphere from escaping into space) and does show evidence of running water sometime in its past. If life did start on Mars, however, there appears to be no life (as we know it) today. Venus, the second planet, is closer to the sun, and appears similar to Earth in many respects. Carbon dioxide build-up has resulted in a "greenhouse planet" with strong storms and strongly acidic rain. Of all planets in the solar system, Venus is most likely to have some form of carbon-based life. The outer planets are as yet too poorly understood, although it seems unlikely that

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Jupiter or Saturn harbor life as we know it. Like Goldilocks would say "Venus is too hot, Mars is too cold, the Earth is just right!"

Mars: In August 1996, evidence of life on Mars (or at least the chemistry of life), was announced.. The results of years of study are inconclusive at best. The purported bacteria are much smaller than any known bacteria on Earth, were not hollow, and most could possibly have been mineral in origin. However, many scientists consider that the chemistry of life appears to have been established on Mars. Search for martian life (or its remains) continues.

Terms applied to cells

Heterotroph (other-feeder): an organism that obtains its energy from another organism. Animals, fungi, bacteria, and mant protistans are heterotrophs.

Autotroph (self-feeder): an organism that makes its own food, it converts energy from an inorganic source in one of two ways. Photosynthesis is the conversion of sunlight energy into C-C covalent bonds of a carbohydrate, the process by which the vast majority of autotrophs obtain their energy. Chemosynthesis is the capture of energy released by certain inorganic chemical reactions. This is common in certain groups of likely that chemosynthesis predates photosynthesis. At mid-ocean ridges, scientists have discovered black smokers, vents that release chemicals into the water. These chemical reactions could have powered early ecosystems prior to the development of an ozone layer that would have permitted life to occupy the shallower parts of the ocean. Evidence of the antiquity of photosynthesis includes: a) biochemical precursors to photosynthesis chemicals have been synthesized in experiments; and b) when placed in light, these chemicals undergo chemical reactions similar to some that occur in primitive photosynthetic bacteria.

Prokaryotes are among the most primitive forms of life on Earth. Remember that primitive does not necessarily equate to outdated and unworkable in an evolutionary sense, since primitive bacteria seem little changed, and thus may be viewed as well adapted, for over 3.5 Ga. Prokaryote (pro=before, karyo=nucleus): these organisms lack membrane-bound organelles. Some internal membrane organization is observable in a few prokaryotic autotrophs, such as the photosynthetic membranes associated with the photosynthetic chemicals in the photosynthetic bacterium Prochloron..

The Cell Theory is one of the foundations of modern biology. Its major tenets are:

All living things are composed of one or more cells; The chemical reactions of living cells take place within cells; All cells originate from pre-existing cells; and Cells contain hereditary information, which is passed from one generation to another.

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Components of Cells

Cell Membrane (also known as plasma membrane or plasmalemma) is surrounds all cells. It: 1) separates the inner parts of the cell from the outer environment; and 2) acts as a selectively permeable barrier to allow certain chemicals, namely water, to pass and others to not pass. In multicellular organisms certain chemicals on the membrane surface act in the recognition of self. Antigens are substances located on the outside of cells, viruses and in some cases other chemicals. Antibodies are chemicals (Y-shaped) produced by an animal in response to a specific antigen. This is the basis of immunity and vaccination.

Hereditary material (both DNA and RNA) is needed for a cell to be able to replicate and/or reproduce. Most organisms use DNA. Viruses and viroids sometimes employ RNA as their hereditary material. Retroviruses include HIV (Human Immunodefficiency Virus, the causative agent of AIDS) and Feline Leukemia Virus (the only retrovirus for which a successful vaccine has been developed). Viroids are naked pieces of RNA that lack cytoplasm, membranes, etc. They are parasites of some plants and also as possible glimpses of the functioning of pre-cellular life forms. Prokaryotic DNA is organized as a circular chromosome contained in an area known as a nucleoid. Eukaryotic DNA is organized in linear structures, the eukaryotic chromosomes, which are associations of DNA and histone proteins contained within a double membrane nuclear envelope, an area known as the cell nucleus.

Organelles are formed bodies within the cytoplasm that perform certain functions. Some organelles are surrounded by membranes, we call these membrane-bound organelles.

Ribosomes are the tiny structures where proteins synthesis occurs. They are not membrane-bound and occur in all cells, although there are differences between the size of subunits in eukaryotic and prokaryotic ribosomes.

The Cell Wall is a structure surrounding the plasma membrane. Prokaryote and eukaryote (if they have one) cell walls differ in their structure and chemical composition. Plant cells have cellulose in their cell walls, other organisms have different materials comprising their walls. Animals are distinct as a group in their lack of a cell wall.

Membrane-bound organelles occur only in eukaryotic cells. They will be discussed in detail later. Eukaryotic cells are generally larger than prokaryotic cells. Internal complexity is usually greater in eukaryotes, with their compartmentalized membrane-bound organelles, than in prokaryotes. Some prokaryotes, such as Anabaena azollae, and Prochloron, have internal membranes associated with photosynthetic pigments.

The Origins of Multicellularity

The oldest accepted prokaryote fossils date to 3.5 billion years; Eukaryotic fossils to between 750 million years and possibly as old as 1.2-1.5 billion years. Multicellular fossils, purportedly of animals, have been recovered from 750Ma rocks in various parts of the world. The first eukaryotes were undoubtedly Protistans, a group that is thought to have given rise to the other eukaryotic kingdoms. Multicellularity allows specialization of function, for example muscle fibers are specialized for contraction, neuron cells for transmission of nerve messages.

Microscopes

Microscopes are important tools for studying cellular structures. In this class we will use light microscopes for our laboratory observations. Your text will also show light photomicrographs (pictures taken with a light microscope) and electron micrographs (pictures taken with an electron microscope). There are many terms and concepts which will help you in maximizing your study of microscopy.

There are many different types of microscopes used in studying biology. These include the light microscopes (dissecting, compound brightfield, and compound phase-contrast), electron microscopes (transmission and scanning), and atomic force microscope.

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The microscope is an important tool used by biologists to magnify small objects. There are several concepts fundamental to microscopy.

Magnification is the ratio of enlargement (or eduction) between the specimen and its image (either printed photograph or the virtual image seen through the eyepiece). To calculate magnification we multiply the power of each lens through which the light from the specimen passes, indicating that product as GGGX, where GGG is the product. For example: if the light passes through two,lenses (an objective lens and an ocular lens) we multiply the 10X ocular value by the value of the objective lens (say it is 4X): 10 X 4=40, or 40X magnification.

Resolution is the ability to distinguish between two objects (or points). The closer the two objects are, the easier it is to distinguish recognize the distance between them. What microscopes do is to bring small objects "closer" to the observer by increasing the magnification of the sample. Since the sample is the same distance from the viewer, a "virtual image" is formed as the light (or electron beam) passes through the magnifying lenses. Objects such as a human hair appear smooth (and feel smooth) when viewed with the unaided or naked) eye. However, put a hair under a microscope and it takes on a VERY different look!

Working distance is the distance between the specimen and the magnifying lens.

Depth of field is a measure of the amount of a specimen that can be in focus.

Magnification and resolution are terms used frequently in the study of cell biology, often without an accurate definition of their meanings. Magnification is a ratio of the enlargement (or reduction) of an image (drawing or photomicrograph), usually expressed as X1, X1/2, X430, X1000, etc. Resolution is the ability to distinguish between two points. Generally resolution increases with magnification, although there does come a point of diminishing returns where you increase magnification beyond added resolution gain.

Scientists employ the metric system to measure the size and volume of specimens. The basic unit of length is the meter (slightly over 1 yard). Prefixes are added to the "meter" to indicate multiple meters (kilometer) or fractional meters (millimeter). Below are the values of some of the prefixes used in the metric system.

kilo = one thousand of the basic unitmeter = basic unit of length

centi = one hundreth (1/100) of the basic unitmilli = one thousandth (1/1000) of the basic unit

micro = one millionth (1/1,000,000) of the basic unitnano = one billionth (1/1,000,000,000) of the basic unit

The basic unit of length is the meter (m), and of volume it is the liter (l). The gram (g). Prefixes listed above can be applied to all of these basic units, abbreviated as km, kg, ml, mg, nm....etc. The Greek letter micron (µ) is applied to small measurements (thousandths of a millimeter), producing the micrometer (symbolized as µm). Measurements in microscopy are usually expressed in the metric system. General units you will encounter in your continuing biology careers include micrometer (µm, 10-6m), nanometer (nm, 10-9m), and angstrom (Å, 10-10m).

Light microscopes were the first to be developed, and still the most commonly used ones. The best resolution of light microscopes (LM) is 0.2 µm. Magnification of LMs is generally limited by the properties of the glass used to make microscope lenses and the physical properties of their light sources. The generally accepted maximum magnifications in biological uses are between 1000X and 1250X. Calculation of LM magnification is done by multiplying objective value by eyepiece value.

The compound light microscope, uses two ground glass lenses to form the image. The lenses in this microscope, however, are aligned with the light source and specimen so that the light passes through the specimen, rather than reflects off the surface. The compound microscope provides greater magnification (and resolution), but only thin specimens (or thin slices of a specimen) can be viewed with this type of microscope.

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Parts of a Nikon compound microscope. Image courtesy of Nikon Co.

Electron microscopes, are more rarely encountered by beginning biology students. However, the images gathered from these microscopes reveal a greater structure of the cell, so some familiarity with the strengths and weaknesses of each type is useful. Instead of using light as an imaging source, a high energy beam of electrons (between five thousand and one billion electron volts) is focused through electromagnetic lenses (instead of glass lenses used in the light microscope). The increased resolution results from the shorter wavelength of the electron beam, increasing resolution in the transmission electron microscope (TEM) to a theoretical limit of 0.2 nm. The magnifications reached by TEMs are commonly over 100,000X, depending on the nature of the sample and the operating condition of the TEM. The other type of electron microscope is the scanning electron microscope (SEM). It uses a different method of electron capture and displays images on high resolution television monitors. The resolution and magnification of the SEM are less than that of the TEM although still orders of magnitude above the LM.

Learning Objectives

Describe the major scientific ideas on the origin of life and the evidence supporting each one. List the basic physical and biological requirements for life. What planet(s) would these be available on? Be able to cite the main components of the Cell Theory. What did Miller's experiment prove? What did it NOT prove? How does this experiment fit with each of the

hypotheses of the origin of life discussed here? Describe these basic cellular features and their functions: plasma membrane, cytoplasm, and nucleus (nucleoid in

prokaryotes). A micrometer is one-millionth of a meter long. A nanometer is one-billionth of a meter long. Describe the basic structure of prokaryotic cells and cite an example of these cells. Describe the types of microscopes and the types of information scientists can obtain using each one.

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Review Questions

1. Which of these is not a type of cell? a) bacterium; b) amoeba; c) sperm; d) virus 2. The Earth's early atmosphere apparently lacked ___. a) oxygen; b) carbon dioxide; c) water vapor; d) ammonia 3. The oldest fossil forms of life are most similar to _____. a) animals; b) modern bacteria; c) archaebacteria; d)

fungi 4. A prokaryotic cell would not have which of these structures? a) ribosome; b) nucleus; c) cell membrane; d) cell

wall 5. Heterotrophic organisms obtain their food ____. a) from another creature; b) by photosynthesis; c) by chemical

synthesis; d) by ATP synthesis. 6. Ribosomes are cellular structures involved in ____. a) photosynthesis; b) chemosynthesis; c) protein synthesis; d)

carbohydrate synthesis 7. The earliest microscopes used _____ to image the specimens. a) high energy electron beams; b) interatomic

forces; c) low energy electron beams; d) light

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CELLS II: CELLULAR ORGANIZATION

Life exhibits varying degrees of organization. Atoms are organized into molecules, molecules into organelles, and organelles into cells, and so on. According to the Cell Theory, all living things are composed of one or more cells, and the functions of a multicellular organism are a consequence of the types of cells it has. Cells fall into two broad groups: prokaryotes and eukaryotes. Prokaryotic cells are smaller (as a general rule) and lack much of the internal compartmentalization and complexity of eukaryotic cells. No matter which type of cell we are considering, all cells have certain features in common, such as a cell membrane, DNA and RNA, cytoplasm, and ribosomes. Eukaryotic cells have a great variety of organelles and structures.

Cell Size and Shape

The shapes of cells are quite varied with some, such as neurons, being longer than they are wide and others, such as parenchyma (a common type of plant cell) and erythrocytes (red blood cells) being equidimensional. Some cells are encased in a rigid wall, which constrains their shape, while others have a flexible cell membrane (and no rigid cell wall).

The size of cells is also related to their functions. Eggs (or to use the latin word, ova) are very large, often being the largest cells an organism produces. The large size of many eggs is related to the process of development that occurs after the egg is fertilized, when the contents of the egg (now termed a zygote) are used in a rapid series of cellular divisions, each requiring tremendous amounts of energy that is available in the zygote cells. Later in life the energy must be acquired, but at first a sort of inheritance/trust fund of energy is used.

Cells range in size from small bacteria to large, unfertilized eggs laid by birds and dinosaurs. In science we use the metric system for measuring. Here are some measurements and conversions that will aid your understanding of biology.

1 meter = 100 cm = 1,000 mm = 1,000,000 µm = 1,000,000,000 nm

1 centimeter (cm) = 1/100 meter = 10 mm

1 millimeter (mm) = 1/1000 meter = 1/10 cm

1 micrometer (µm) = 1/1,000,000 meter = 1/10,000 cm

1 nanometer (nm) = 1/1,000,000,000 meter = 1/10,000,000 cm

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The Cell Membrane

The cell membrane functions as a semi-permeable barrier, allowing a very few molecules across it while fencing the majority of organically produced chemicals inside the cell. Electron microscopic examinations of cell membranes have led to the development of the lipid bilayer model (also referred to as the fluid-mosaic model). The most common molecule in the model is the phospholipid, which has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails. These phospholipids are aligned tail to tail so the nonpolar areas form a hydrophobic region between the hydrophilic heads on the inner and outer surfaces of the membrane. This layering is termed a bilayer since an electron microscopic technique known as freeze-fracturing is able to split the bilayer.

Cholesterol is another important component of cell membranes embedded in the hydrophobic areas of the inner (tail-tail) region. Most bacterial cell membranes do not contain cholesterol. Cholesterol aids in the flexibility of a cell membrane.

Proteins, are suspended in the inner layer, although the more hydrophilic areas of these proteins "stick out" into the cells interior as well as outside the cell. These proteins function as gateways that will allow certain molecules to cross into and out of the cell by moving through open areas of the protein channel. These integral proteins are sometimes known as gateway proteins. The outer surface of the membrane will tend to be rich in glycolipids, which have their hydrophobic tails embedded in the hydrophobic region of the membrane and their heads exposed outside the cell. These, along with carbohydrates attached to the integral proteins, are thought to function in the recognition of self, a sort of cellular identification system.

The contents (both chemical and organelles) of the cell are termed protoplasm, and are further subdivided into cytoplasm (all of the protoplasm except the contents of the nucleus) and nucleoplasm (all of the material, plasma and DNA etc., within the nucleus).

The Cell Wall

Not all living things have cell walls, most notably animals and many of the more animal-like protistans. Bacteria have cell walls containing the chemical peptidoglycan. Plant cells, have a variety of chemicals incorporated in their cell walls. Cellulose, a nondigestible (to humans anyway) polysaccharide is the most common chemical in the plant primary cell wall. Some plant cells also have lignin and other chemicals embedded in their secondary walls.

The cell wall is located outside the plasma membrane. Plasmodesmata are connections through which cells communicate chemically with each other through their thick walls. Fungi and many protists have cell walls although they do not contain cellulose, rather a variety of chemicals (chitin for fungi).

The nucleus

The nucleus, occurs only in eukaryotic cells. It is the location for most of the nucleic acids a cell makes, such as DNA and RNA. Danish biologist Joachim Hammerling carried out an important experiment in 1943. His work showed the role of the nucleus in controlling the shape and features of the cell. Deoxyribonucleic acid, DNA, is the physical carrier of inheritance and with the exception of plastid DNA (cpDNA and mDNA, found in the chloroplast and mitochondrion respectively) all DNA is restricted to the nucleus. Ribonucleic acid, RNA, is formed in the nucleus using the DNA base sequence as a template. RNA moves out into the cytoplasm where it functions in the assembly of proteins. The nucleolus is an area of the nucleus (usually two nucleoli per nucleus) where ribosomes are constructed.

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Structure of the nucleus. Note the chromatin, uncoiled DNA that occupies the space within the nuclear envelope.

The nuclear envelope, is a double-membrane structure. Numerous pores occur in the envelope, allowing RNA and other chemicals to pass, but the DNA not to pass.

Structure of the nuclear envelope and nuclear pores.

Cytoplasm

The cytoplasm was defined earlier as the material between the plasma membrane (cell membrane) and the nuclear envelope. Fibrous proteins that occur in the cytoplasm, referred to as the cytoskeleton maintain the shape of the cell as well as anchoring organelles, moving the cell and controlling internal movement of structures. Microtubules function in cell division and serve as a "temporary scaffolding" for other organelles. Actin filaments are thin threads that function in cell division and cell motility. Intermediate filaments are between the size of the microtubules and the actin filaments.

Vacuoles and vesicles

Vacuoles are single-membrane organelles that are essentially part of the outside that is located within the cell. The single membrane is known in plant cells as a tonoplast. Many organisms will use vacuoles as storage areas. Vesicles are much smaller than vacuoles and function in transporting materials both within and to the outside of the cell.

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Ribosomes

Ribosomes are the sites of protein synthesis. They are not membrane-bound and thus occur in both prokaryotes and eukaryotes. Eukaryotic ribosomes are slightly larger than prokaryotic ones. Structurally, the ribosome consists of a small and larger subunit. Biochemically, the ribosome consists of ribosomal RNA (rRNA) and some 50 structural proteins. Often ribosomes cluster on the endoplasmic reticulum, in which case they resemble a series of factories adjoining a railroad line.

Endoplasmic reticulum

Endoplasmic reticulum, is a mesh of interconnected membranes that serve a function involving protein synthesis and transport. Rough endoplasmic reticulum (Rough ER) is so-named because of its rough appearance due to the numerous ribosomes that occur along the ER. Rough ER connects to the nuclear envelope through which the messenger RNA (mRNA) that is the blueprint for proteins travels to the ribosomes. Smooth ER; lacks the ribosomes characteristic of Rough ER and is thought to be involved in transport and a variety of other functions.

Golgi Apparatus and Dictyosomes

Golgi Complexes, are flattened stacks of membrane-bound sacs. Italian biologist Camillo Golgi discovered these structures in the late 1890s, although their precise role in the cell was not deciphered until the mid-1900s . Golgi function as a packaging plant, modifying vesicles produced by the rough endoplasmic reticulum. New membrane material is assembled in various cisternae (layers) of the golgi.

Lysosomes

Lysosomes, are relatively large vesicles formed by the Golgi. They contain hydrolytic enzymes that could destroy the cell. Lysosome contents function in the extracellular breakdown of materials. They are commonly known in the cell as the suicide sac.

Mitochondria

Mitochondria contain their own DNA (termed mDNA) and are thought to represent bacteria-like organisms incorporated into eukaryotic cells over 700 million years ago (perhaps even as far back as 1.5 billion years ago). They function as the sites of energy release (following glycolysis in the cytoplasm) and ATP formation (by chemiosmosis). The mitochondrion has been termed the powerhouse of

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the cell. Mitochondria are bounded by two membranes. The inner membrane folds into a series of cristae, which are the surfaces on which adenosine triphosphate (ATP) is generated. The matrix is the area of the mitochondrion surrounded by the inner mitochondrial membrane. Ribosomes and mitochondrial DNA are found in the matrix. The significance of these features will be discussed below..

Mitochondria and endosymbiosis

During the 1980s, Lynn Margulis proposed the theory of endosymbiosis to explain the origin of mitochondria and chloroplasts from permanent resident prokaryotes. According to this idea, a larger prokaryote (or perhaps early eukaryote) engulfed or surrounded a smaller prokaryote some 1.5 billion to 700 million years ago..

Instead of digesting the smaller organisms the large one and the smaller one entered into a type of symbiosis known as mutualism, wherein both organisms benefit and neither is harmed. The larger organism gained excess ATP provided by the "protomitochondrion" and excess sugar provided by the "protochloroplast", while providing a stable environment and the raw materials the endosymbionts required. This is so strong that now eukaryotic cells cannot survive without mitochondria (likewise photosynthetic eukaryotes cannot survive without chloroplasts), and the endosymbionts can not survive outside their hosts. Nearly all eukaryotes have mitochondria. Mitochondrial division is remarkably similar to the prokaryotic methods that will be studied later in this course.

Plastids

Plastids are also membrane-bound organelles that only occur in plants and photosynthetic eukaryotes. Leucoplasts, also known as amyloplasts store starch, as well as sometimes protein or oils. Chromoplasts store pigments associated with the bright colors of flowers and/or fruits.

Chloroplasts, are the sites of photosynthesis in eukaryotes. They contain chlorophyll, the green pigment necessary for photosynthesis to occur, and associated accessory pigments (carotenes and xanthophylls) in photosystems embedded in membranous sacs, thylakoids (collectively a stack of thylakoids are a granum [plural = grana) floating in a fluid termed the stroma. Chloroplasts contain many different types of accessory pigments, depending on the taxonomic group of the organism being observed.

Chloroplasts and endosymbiosis

Like mitochondria, chloroplasts have their own DNA, termed cpDNA. Chloroplasts of Green Algae (Protista) and Plants (descendants of some of the Green Algae) are thought to have originated by endosymbiosis of a prokaryotic alga similar to living Prochloron (the sole genus present in the Prochlorobacteria,). Chloroplasts of Red Algae (Protista) are very similar biochemically to cyanobacteria (also known as blue-green bacteria [algae to chronologically enhanced folks like myself :)]). Endosymbiosis is also invoked for this similarity, perhaps indicating more than one endosymbiotic event occurred.

Cell Movement

Cell movement; is both internal, referred to as cytoplasmic streaming, and external, referred to as motility. Internal movements of organelles are governed by actin filaments and other components of the cytoskeleton. These filaments make an area in which organelles such as chloroplasts can move. Internal movement is known as cytoplasmic streaming. External movement of cells is determined by special organelles for locomotion.

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The cytoskeleton is a network of connected filaments and tubules. It extends from the nucleus to the plasma membrane. Electron microscopic studies showed the presence of an organized cytoplasm. Immunofluorescence microscopy identifies protein fibers as a major part of this cellular feature. The cytoskeleton components maintain cell shape and allow the cell and its organelles to move.

Actin filaments, are long, thin fibers approximately seven nm in diameter. These filaments occur in bundles or meshlike networks. These filaments are polar, meaning there are differences between the ends of the strand. An actin filament consists of two chains of globular actin monomers twisted to form a helix. Actin filaments play a structural role, forming a dense complex web just under the plasma membrane. Actin filaments in microvilli of intestinal cells act to shorten the cell and thus to pull it out of the intestinal lumen. Likewise, the filaments can extend the cell into intestine when food is to be absorbed. In plant cells, actin filaments form tracts along which chloroplasts circulate.

Actin filaments move by interacting with myosin, The myosin combines with and splits ATP, thus binding to actin and changing the configuration to pull the actin filament forward. Similar action accounts for pinching off cells during cell division and for amoeboid movement.

Intermediate filaments are between eight and eleven nm in diameter. They are between actin filaments and microtubules in size. The intermediate fibers are rope-like assemblies of fibrous polypeptides. Some of them support the nuclear envelope, while others support the plasma membrane, form cell-to-cell junctions.

Microtubules are small hollow cylinders (25 nm in diameter and from 200 nm-25 µm in length). These microtubules are composed of a globular protein tubulin. Assembly brings the two types of tubulin (alpha and beta) together as dimers, which arrange themselves in rows.

In animal cells and most protists, a structure known as a centrosome occurs. The centrosome contains two centrioles lying at right angles to each other. Centrioles are short cylinders with a 9 + 0 pattern of microtubule triplets. Centrioles serve as basal bodies for cilia and flagella. Plant and fungal cells have a structure equivalent to a centrosome, although it does not contain centrioles.

Cilia are short, usually numerous, hairlike projections that can move in an undulating fashion (e.g., the protzoan Paramecium, the cells lining the human upper respiratory tract). Flagella are longer, usually fewer in number, projections that move in whip-like fashion (e.g., sperm cells). Cilia and flagella are similar except for length, cilia being much shorter. They both have the characteristic 9 + 2 arrangement of microtubules.

Cilia from an epithelial cell in cross section (TEM x199,500). Note the 9 + 2 arrangement of cilia.

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Cilia and flagella move when the microtubules slide past one another. Both of these locomotion structures have a basal body at base with thesame arrangement of microtubule triples as centrioles. Cilia and flagella grow by the addition of tubulin dimers to their tips.

Flagella work as whips pulling (as in Chlamydomonas or Halosphaera) or pushing (dinoflagellates, a group of single-celled Protista) the organism through the water. Cilia work like oars on a viking longship (Paramecium has 17,000 such oars covering its outer surface).

Not all cells use cilia or flagella for movement. Some, such as Amoeba, Chaos (Pelomyxa) and human leukocytes (white blood cells), employ pseudopodia to move the cell. Unlike cilia and flagella, pseudopodia are not structures, but rather are associated with actin near the moving edge of the cell..

Learning Objectives

Give the function and cellular location of the following basic eukaryotic organelles and structures: cell membrane, nucleus, endoplasmic reticulum, Golgi bodies, lysosomes, mitochondria, ribosomes, chloroplasts, vacuoles, and cell walls.

A micrometer is one-millionth of a meter long. A nanometer is one-billionth of a meter long. How many micrometers tall are you?

Describe the function of the nuclear envelope and nucleolus. Describe the details of the structure of the chloroplast, the site of photosynthesis. Mature, living plant cells often have a large, fluid-filled central vacuole that can store amino acids, sugars, ions,

and toxic wastes. Animal cells generally lack large vacuoles. How do animal cells perform these functions? Microtubules, microfilaments, and intermediate filaments are all main components of the cytoskeleton.

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Flagella and cilia propel eukaryotic cells through their environment; the microtubule organization in these organelles is a 9+2 array.

Review Questions

1. There are ____ micrometers (µm) in one millimeter (mm). a) 1; b) 10; c) 100; d) 1000; e) 1/1000 2. Human cells have a size range between ___ and ___ micrometers (µm). a) 10-100; b) 1-10; c) 100-1000; d) 1/10-

1/1000 3. Chloroplasts and bacteria are ___ in size. a) similar; b) at different ends of the size range; c) exactly the same; d)

none of these. 4. The plasma membrane does all of these except ______. a) contains the hereditary material; b) acts as a boundary

or border for the cytoplasm; c) regulates passage of material in and out of the cell; d) functions in the recognition of self

5. Which of these materials is not a major component of the plasma membrane? a) phospholipids; b) glycoproteins; c) proteins; d) DNA

6. Cells walls are found in members of these kingdoms, except for ___, which all lack cell walls. a) plants; b) animals; c) bacteria; d) fungi

7. The polysaccharide ___ is a major component of plan cell walls. a) chitin; b) peptidoglycan; c) cellulose; d) mannitol; e) cholesterol

8. Plant cells have ___ and ___, which are not present in animal cells. a) mitochondria, chloroplasts; b) cell membranes, cell walls; c) chloroplasts, nucleus; d) chloroplasts, cell wall

9. The ___ is the membrane enclosed structure in eukaryotic cells that contains the DNA of the cell. a) mitochondrion; b) chloroplast; c) nucleolus; d) nucleus

10. Ribosomes are constructed in the ___. a) endoplasmic reticulum; b) nucleoid; c) nucleolus; d) nuclear pore 11. Rough endoplasmic reticulum is the area in a cell where ___ are synthesized. a) polysaccharides; b) proteins; c)

lipids; d) DNA 12. The smooth endoplasmic reticulum is the area in a cell where ___ are synthesized. a) polysaccharides; b) proteins;

c) lipids; d) DNA 13. The mitochondrion functions in ____. a) lipid storage; b) protein synthesis; c) photosynthesis; d) DNA

replication; e) ATP synthesis 14. The thin extensions of the inner mitochondrial membrane are known as _____. a) cristae; b) matrix; c) thylakoids;

d) stroma 15. The chloroplast functions in ____. a) lipid storage; b) protein synthesis; c) photosynthesis; d) DNA replication; e)

ATP synthesis 16. Which of these cellular organelles have their own DNA? a) chloroplast; b) nucleus; c) mitochondrion; d) all of

these 17. The theory of ___ was proposed to explain the possible origin of chloroplasts and mitochondria. a) evolution; b)

endosymbiosis; c) endocytosis; d) cells 18. Long, whiplike microfibrils that facilitate movement by cells are known as ___. a) cilia; b) flagella; c) leather; d)

pseudopodia

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TRANSPORT IN AND OUT OF CELLS

Water and Solute Movement

Cell membranes act as barriers to most, but not all, molecules. Development of a cell membrane that could allow some materials to pass while constraining the movement of other molecules was a major step in the evolution of the cell. Cell membranes are differentially (or semi-) permeable barriers separating the inner cellular environment from the outer cellular (or external) environment.

Water potential is the tendency of water to move from an area of higher concentration to one of lower concentration. Energy exists in two forms: potential and kinetic. Water molecules move according to differences in potential energy between where they are and where they are going. Gravity and pressure are two enabling forces for this movement. These forces also operate in the hydrologic (water) cycle. Remember in the hydrologic cycle that water runs downhill (likewise it falls from the sky, to get into the sky it must be acted on by the sun and evaporated, thus needing energy input to power the cycle).

Diffusion is the net movement of a substance (liquid or gas) from an area of higher concentration to one of lower concentration. You are on a large (10 ft x 10 ft x10 ft) elevator. An obnoxious individual with a lit cigar gets on at the third floor with the cigar still burning. You are also unfortunate enough to be in a very tall building and the person says "Hey we're both going to the 62nd floor!" Disliking smoke you move to the farthest corner you can. Eventually you are unable to escape the smoke! An example of diffusion in action. Nearer the source the concentration of a given substance increases. You probably experience this in class when someone arrives freshly doused in perfume or cologne, especially the cheap stuff.

Since the molecules of any substance (solid, liquid, or gas) are in motion when that substance is above absolute zero (0 degrees Kelvin or -273 degrees C), energy is available for movement of the molecules from a higher potential state to a lower potential state, just as in the case of the water discussed above. The majority of the molecules move from higher to lower concentration, although there will be some that move from low to high. The overall (or net) movement is thus from high to low concentration. Eventually, if no energy is input into the system the molecules will reach a state of equilibrium where they will be distributed equally throughout the system.

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The Cell Membrane

The cell membrane functions as a semi-permeable barrier, allowing a very few molecules across it while fencing the majority of organically produced chemicals inside the cell. Electron microscopic examinations of cell membranes have led to the development of the lipid bilayer model (also referred to as the fluid-mosaic model). The most common molecule in the model is the phospholipid, which has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails. These phospholipids are aligned tail to tail so the nonpolar areas form a hydrophobic region between the hydrophilic heads on the inner and outer surfaces of the membrane. This layering is termed a bilayer since an electron microscopic technique known as freeze-fracturing is able to split the bilayer.

Phospholipids and glycolipids are important structural components of cell membranes. Phospholipids are modified so that a phosphate group (PO4

-) replaces one of the three fatty acids normally found on a lipid. The addition of this group makes a polar "head" and two nonpolar "tails".

Structure of a phospholipid, space-filling model (left) and chain model (right).

Diagram of a cell membrane.

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Cell Membranes from Opposing Neurons (TEM x436,740).

Cholesterol is another important component of cell membranes embedded in the hydrophobic areas of the inner (tail-tail) region. Most bacterial cell membranes do not contain cholesterol.

Proteins are suspended in the inner layer, although the more hydrophilic areas of these proteins "stick out" into the cells interior as well as the outside of the cell. These integral proteins are sometimes known as gateway proteins. Proteins also function in cellular recognition, as binding sites for substances to be brought into the cell, through channels that will allow materials into the cell via a passive transport mechanism, and as gates that open and close to facilitate active transport of large molecules.

The outer surface of the membrane will tend to be rich in glycolipids, which have their hydrophobic tails embedded in the hydrophobic region of the membrane and their heads exposed outside the cell. These, along with carbohydrates attached to the integral proteins, are thought to function in the recognition of self. Multicellular organisms may have some mechanism to allow recognition of those cells that belong to the organism and those that are foreign. Many, but not all, animals have an immune system that serves this sentry function. When a cell does not display the chemical markers that say "Made in Mike", an immune system response may be triggered. This is the basis for immunity, allergies, and autoimmune diseases. Organ transplant recipients must have this response suppressed so the new organ will not be attacked by the immune system, which would cause rejection of the new organ. Allergies are in a sense an over reaction by the immune system. Autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythmatosis, happen when for an as yet unknown reason, the immune system begins to attack certain cells and tissues in the body.

Cells and Diffusion

Water, carbon dioxide, and oxygen are among the few simple molecules that can cross the cell membrane by diffusion (or a type of diffusion known as osmosis ). Diffusion is one principle method of movement of substances within cells, as well as the method for essential small molecules to cross the cell membrane. Gas exchange in gills and lungs operates by this process. Carbon dioxide is produced by all cells as a result of cellular metabolic processes. Since the source is inside the cell, the concentration gradient is constantly being replenished/re-elevated, thus the net flow of CO2 is out of the cell.

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Metabolic processes in animals and plants usually require oxygen, which is in lower concentration inside the cell, thus the net flow of oxygen is into the cell.

Osmosis is the diffusion of water across a semi-permeable (or differentially permeable or selectively permeable) membrane. The cell membrane, along with such things as dialysis tubing and cellulose acetate sausage casing, is such a membrane. The presence of a solute decreases the water potential of a substance. Thus there is more water per unit of volume in a glass of fresh-water than there is in an equivalent volume of sea-water. In a cell, which has so many organelles and other large molecules, the water flow is generally into the cell.

Hypertonic solutions are those in which more solute (and hence lower water potential) is present. Hypotonic solutions are those with less solute (again read as higher water potential). Isotonic solutions have equal (iso-) concentrations of substances. Water potentials are thus equal, although there will still be equal amounts of water movement in and out of the cell, the net flow is zero.

Water relations and cell shape in blood cells.

One of the major functions of blood in animals is the maintain an isotonic internal environment. This eliminates the problems associated with water loss or excess water gain in or out of cells. Again we return to homeostasis. Paramecium and other single-celled freshwater organisms have difficulty since they are usually hypertonic relative to their outside environment. Thus water will tend to flow across the cell membrane, swelling the cell and eventually bursting it. Not good for any cell! The contractile vacuole is the Paramecium's response to this problem. The pumping of water out of the cell by this method requires energy since the water is moving against the concentration gradient. Since ciliates (and many freshwater protozoans) are hypotonic, removal of water crossing the cell membrane by osmosis is a significant problem. One commonly employed mechanism is a contractile vacuole. Water is collected into the central ring of the vacuole and actively transported from the cell.

Active and Passive Transport

Passive transport requires no energy from the cell. Examples include the diffusion of oxygen and carbon dioxide, osmosis of water, and facilitated diffusion.

Active transport requires the cell to spend energy, usually in the form of ATP. Examples include transport of large molecules (non-lipid soluble)

and the sodium-potassium pump.

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Carrier-assisted Transport

The transport proteins integrated into the cell membrane are often highly selective about the chemicals they allow to cross. Some of these proteins can move materials across the membrane only when assisted by the concentration gradient, a type of carrier-assisted transport known as facilitated diffusion. Both diffusion and facilitated diffusion are driven by the potential energy differences of a concentration gradient. Glucose enters most cells by facilitated diffusion. There seem to be a limiting number of glucose-transporting proteins. The rapid breakdown of glucose in the cell (a process known as glycolysis) maintains the concentration gradient. When the external concentration of glucose increases, however, the glucose transport does not exceed a certain rate, suggesting the limitation on transport.

In the case of active transport, the proteins are having to move against the concentration gradient. For example the sodium-potassium pump in nerve cells. Na+ is maintained at low concentrations inside the cell and K+ is at higher concentrations. The reverse is the case on the outside of the cell. When a nerve message is propagated, the ions pass across the membrane, thus sending the message. After the message has passed, the ions must be actively transported back to their "starting positions" across the membrane. This is analogous to setting up 100 dominoes and then tipping over the first one. To reset them you must pick each one up, again at an energy cost. Up to one-third of the ATP used by a resting animal is used to reset the Na-K pump.

Types of transport molecules |

Uniport transports one solute at a time. Symport transports the solute and a cotransported solute at the same time in the same direction. Antiport transports the solute in (or out) and the co-transported solute the opposite direction. One goes in the other goes out or vice-versa.

Vesicle-mediated transport

Vesicles and vacuoles that fuse with the cell membrane may be utilized to release or transport chemicals out of the cell or to allow them to enter a cell. Exocytosis is the term applied when transport is out of the cell.

Endocytosis is the case when a molecule causes the cell membrane to bulge inward, forming a vesicle. Phagocytosis is the type of endocytosis where an entire cell is engulfed. Pinocytosis is when the external fluid is engulfed. Receptor-mediated endocytosis occurs when the material to be transported binds to certain specific molecules in the membrane. Examples include the transport of insulin and cholesterol into animal cells.

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Learning Objectives

Materials are exchanged between the cytoplasm and external cell environment across the plasma membrane by several different processes, some require energy, some do not..

Describe the general structure of a phospholipid molecule and what makes it suitable as a major component of cell membranes.

Explain the behavior of a great number of phospholipid molecules in water. Describe the most recent version of the fluid mosaic model of membrane structure. Molecules moving to regions where they are less concentrated are moving down their concentration gradient. Random movement of like molecules or ions down a concentration gradient is called simple diffusion. When salt is dissolved in water, which is the solute and which is the solvent? Explain osmosis in terms of a differentially permeable membrane. Define tonicity and be able to use the terms isotonic, hypertonic, and hypotonic. When water moves into a plant cell by osmosis, the internal turgor pressure developed pushes on the wall. What

does this do to your understanding of a neglected houseplant?

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CELL DIVISION: BINARY FISSION AND MITOSIS

The Cell Cycle

Despite differences between prokaryotes and eukaryotes, there are several common features in their cell division processes. Replication of the DNA must occur. Segregation of the "original" and its "replica" follow. Cytokinesis ends the cell division process. Whether the cell was eukaryotic or prokaryotic, these basic events must occur.

Cytokinesis is the process where one cell splits off from its sister cell. It usually occurs after cell division. The Cell Cycle is the sequence of growth, DNA replication, growth and cell division that all cells go through. Beginning after cytokinesis, the daughter cells are quite small and low on ATP. They acquire ATP and increase in size during the G1 phase of Interphase. Most cells are observed in Interphase, the longest part of the cell cycle. After acquiring sufficient size and ATP, the cells then undergo DNA Synthesis (replication of the original DNA molecules, making identical copies, one "new molecule" eventually destined for each new cell) which occurs during the S phase. Since the formation of new DNA is an energy draining process, the cell undergoes a second growth and energy acquisition stage, the G2 phase. The energy acquired during G2 is used in cell division (in this case mitosis).

The cell cycle.

Regulation of the cell cycle is accomplished in several ways. Some cells divide rapidly (beans, for example take 19 hours for the complete cycle; red blood cells must divide at a rate of 2.5 million per second). Others, such as nerve cells, lose their capability to divide once they reach maturity. Some cells, such as liver cells, retain but do not normally utilize their capacity for division. Liver cells will divide if part of the liver is removed. The division continues until the liver reaches its former size.

Cancer cells are those which undergo a series of rapid divisions such that the daughter cells divide before they have reached "functional maturity". Environmental factors such as changes in temperature and pH, and declining nutrient levels lead to declining cell division rates. When cells stop dividing, they stop usually at a point late in the G1 phase, the R point (for restriction).

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Prokaryotic Cell Division

Prokaryotes are much simpler in their organization than are eukaryotes. There are a great many more organelles in eukaryotes, also more chromosomes. The usual method of prokaryote cell division is termed binary fission. The prokaryotic chromosome is a single DNA molecule that first replicates, then attaches each copy to a different part of the cell membrane. When the cell begins to pull apart, the replicate and original chromosomes are separated. Following cell splitting (cytokinesis), there are then two cells of identical genetic composition (except for the rare chance of a spontaneous mutation).

The prokaryote chromosome is much easier to manipulate than the eukaryotic one. We thus know much more about the location of genes and their control in prokaryotes.

One consequence of this asexual method of reproduction is that all organisms in a colony are genetic equals. When treating a bacterial disease, a drug that kills one bacteria (of a specific type) will also kill all other members of that clone (colony) it comes in contact with.

Eukaryotic Cell Division

Due to their increased numbers of chromosomes, organelles and complexity, eukaryote cell division is more complicated, although the same processes of replication, segregation, and cytokinesis still occur.

Mitosis

Mitosis is the process of forming (generally) identical daughter cells by replicating and dividing the original chromosomes, in effect making a cellular xerox. Commonly the two processes of cell division are confused. Mitosis deals only with the segregation of the chromosomes and organelles into daughter cells.

Eukaryotic chromosomes occur in the cell in greater numbers than prokaryotic chromosomes. The condensed replicated chromosomes have several points of interest. The kinetochore is the point where microtubules of the spindle apparatus attach. Replicated chromosomes consist of two molecules of DNA (along with their associated histone proteins) known as chromatids. The area where both chromatids are in contact with each other is known as the centromere the kinetochores are on the outer sides of the centromere. Remember that chromosomes are condensed chromatin (DNA plus histone proteins).

During mitosis replicated chromosomes are positioned near the middle of the cytoplasm and then segregated so that each daughter cell receives a copy of the original DNA (if you start with 46 in the parent cell, you should end up with 46 chromosomes in each

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daughter cell). To do this cells utilize microtubules (referred to as the spindle apparatus) to "pull" chromosomes into each "cell". The microtubules have the 9+2 arrangement discussed earlier. Animal cells (except for a group of worms known as nematodes) have a centriole. Plants and most other eukaryotic organisms lack centrioles. Prokaryotes, of course, lack spindles and centrioles; the cell membrane assumes this function when it pulls the by-then replicated chromosomes apart during binary fission. Cells that contain centrioles also have a series of smaller microtubules, the aster, that extend from the centrioles to the cell membrane. The aster is thought to serve as a brace for the functioning of the spindle fibers.

The phases of mitosis are sometimes difficult to separate. Remember that the process is a dynamic one, not the static process displayed of necessity in a textbook.

Prophase

Prophase is the first stage of mitosis proper. Chromatin condenses (remember that chromatin/DNA replicate during Interphase), the nuclear envelope dissolves, centrioles (if present) divide and migrate, kinetochores and kinetochore fibers form, and the spindle forms.

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Metaphase

Metaphase follows Prophase. The chromosomes (which at this point consist of chromatids held together by a centromere) migrate to the equator of the spindle, where the spindles attach to the kinetochore fibers.

Anaphase

Anaphase begins with the separation of the centromeres, and the pulling of chromosomes (we call them chromosomes after the centromeres are separated) to opposite poles of the spindle.

Telophase

Telophase is when the chromosomes reach the poles of their respective spindles, the nuclear envelope reforms, chromosomes uncoil into chromatin form, and the nucleolus (which had disappeared during Prophase) reform. Where there was one cell there are now two smaller cells each with exactly the same genetic information. These cells may then develop into different adult forms via the processes of development.

Cytokinesis

Cytokinesis is the process of splitting the daughter cells apart. Whereas mitosis is the division of the nucleus, cytokinesis is the splitting of the cytoplasm and allocation of the golgi, plastids and cytoplasm into each new cell.

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CELL DIVISION: MEIOSIS AND SEXUAL REPRODUCTION

Meiosis

Sexual reproduction occurs only in eukaryotes. During the formation of gametes, the number of chromosomes is reduced by half, and returned to the full amount when the two gametes fuse during fertilization.

Ploidy

Haploid and diploid are terms referring to the number of sets of chromosomes in a cell. Gregor Mendel determined his peas had two sets of alleles, one from each parent. Diploid organisms are those with two (di) sets. Human beings (except for their gametes), most animals and many plants are diploid. We abbreviate diploid as 2n. Ploidy is a term referring to the number of sets of chromosomes. Haploid organisms/cells have only one set of chromosomes, abbreviated as n. Organisms with more than two sets of chromosomes are termed polyploid. Chromosomes that carry the same genes are termed homologous chromosomes. The alleles on homologous chromosomes may differ, as in the case of heterozygous individuals. Organisms (normally) receive one set of homologous chromosomes from each parent.

Meiosis is a special type of nuclear division which segregates one copy of each homologous chromosome into each new "gamete". Mitosis maintains the cell's original ploidy level (for example, one diploid 2n cell producing two diploid 2n cells; one haploid n cell producing two haploid n cells; etc.). Meiosis, on the other hand, reduces the number of sets of chromosomes by half, so that when gametic recombination (fertilization) occurs the ploidy of the parents will be reestablished.

Most cells in the human body are produced by mitosis. These are the somatic (or vegetative) line cells. Cells that become gametes are referred to as germ line cells. The vast majority of cell divisions in the human body are mitotic, with meiosis being restricted to the gonads.

Life Cycles

Life cycles are a diagrammatic representation of the events in the organism's development and reproduction. When interpreting life cycles, pay close attention to the ploidy level of particular parts of the cycle and where in the life cycle meiosis occurs. For example, animal life cycles have a dominant diploid phase, with the gametic (haploid) phase being a relative few cells. Most of the cells in your body are diploid, germ line diploid cells will undergo meiosis to produce gametes, with fertilization closely following meiosis.

Plant life cycles have two sequential phases that are termed alternation of generations. The sporophyte phase is "diploid", and is that part of the life cycle in which meiosis occurs. However, many plant species are thought to arise by polyploidy, and the use of "diploid" in the last sentence was meant to indicate that the greater number of chromosome sets occur in this phase. The gametophyte phase is "haploid", and is the part of the life cycle in which gametes are produced (by mitosis of haploid cells). In flowering plants (angiosperms) the multicelled visible plant (leaf, stem, etc.) is sporophyte, while pollen and ovaries contain the male and female gametophytes, respectively. Plant life cycles differ from animal ones by adding a phase (the haploid gametophyte) after meiosis and before the production of gametes.

Many protists and fungi have a haploid dominated life cycle. The dominant phase is haploid, while the diploid phase is only a few cells (often only the single celled zygote, as in Chlamydomonas ). Many protists reproduce by mitosis until their environment deteriorates, then they undergo sexual reproduction to produce a resting zygotic cyst.

Phases of Meiosis

Two successive nuclear divisions occur, Meiosis I (Reduction) and Meiosis II (Division). Meiosis produces 4 haploid cells. Mitosis produces 2 diploid cells. The old name for meiosis was reduction/ division. Meiosis I reduces the ploidy

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level from 2n to n (reduction) while Meiosis II divides the remaining set of chromosomes in a mitosis-like process (division). Most of the differences between the processes occur during Meiosis I.

Prophase I

Prophase I has a unique event -- the pairing (by an as yet undiscovered mechanism) of homologous chromosomes. Synapsis is the process of linking of the replicated homologous chromosomes. The resulting chromosome is termed a tetrad, being composed of two chromatids from each chromosome, forming a thick (4-strand) structure. Crossing-over may occur at this point. During crossing-over chromatids break and may be reattached to a different homologous chromosome.

The alleles on this tetrad:

A B C D E F G

A B C D E F G

a b c d e f g

a b c d e f g

will produce the following chromosomes if there is a crossing-over event between the 2nd and 3rd chromosomes from the top:

A B C D E F G

A B c d e f g

a b C D E F G

a b c d e f g

Thus, instead of producing only two types of chromosome (all capital or all lower case), four different chromosomes are produced. This doubles the variability of gamete genotypes. The occurrence of a crossing-over is indicated by a special structure, a chiasma (plural chiasmata) since the recombined inner alleles will align more with others of the same type (e.g. a with a, B with B). Near the end of Prophase I, the homologous chromosomes begin to separate slightly, although they remain attached at chiasmata.

Events of Prophase I (save for synapsis and crossing over) are similar to those in Prophase of mitosis: chromatin condenses into chromosomes, the nucleolus dissolves, nuclear membrane is disassembled, and the spindle apparatus forms.

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Metaphase I

Metaphase I is when tetrads line-up along the equator of the spindle. Spindle fibers attach to the centromere region of each homologous chromosome pair. Other metaphase events as in mitosis.

Anaphase I

Anaphase I is when the tetrads separate, and are drawn to opposite poles by the spindle fibers. The centromeres in Anaphase I remain intact.

Telophase I

Telophase I is similar to Telophase of mitosis, except that only one set of (replicated) chromosomes is in each "cell". Depending on species, new nuclear envelopes may or may not form. Some animal cells may have division of the centrioles during this phase.

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Prophase II

During Prophase II, nuclear envelopes (if they formed during Telophase I) dissolve, and spindle fibers reform. All else is as in Prophase of mitosis. Indeed Meiosis II is very similar to mitosis.

Metaphase II

Metaphase II is similar to mitosis, with spindles moving chromosomes into equatorial area and attaching to the opposite sides of the centromeres in the kinetochore region.

Anaphase II

During Anaphase II, the centromeres split and the former chromatids (now chromosomes) are segregated into opposite sides of the cell.

Telophase II

Telophase II is identical to Telophase of mitosis. Cytokinesis separates the cells.

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Comparison of Mitosis and Meiosis

Mitosis maintains ploidy level, while meiosis reduces it. Meiosis may be considered a reduction phase followed by a slightly altered mitosis. Meiosis occurs in a relative few cells of a multicellular organism, while mitosis is more common.

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Gametogenesis

Gametogenesis is the process of forming gametes (by definition haploid, n) from diploid cells of the germ line. Spermatogenesis is the process of forming sperm cells by meiosis (in animals, by mitosis in plants) in specialized organs known as gonads (in males these are termed testes). After division the cells undergo differentiation to become sperm cells. Oogenesis is the process of forming an ovum (egg) by meiosis (in animals, by mitosis in the gametophyte in plants) in specialized gonads known as ovaries. Whereas in spermatogenesis all 4 meiotic products develop into gametes, oogenesis places most of the cytoplasm into the large egg. The other cells, the polar bodies, do not develop. This all the cytoplasm and organelles go into the egg. Human males produce 200,000,000 sperm per day, while the female produces one egg (usually) each menstrual cycle.

Spermatogenesis

Sperm production begins at puberty at continues throughout life, with several hundred million sperm being produced each day. Once sperm form they move into the epididymis, where they mature and are stored.

Oogenesis

The ovary contains many follicles composed of a developing egg surrounded by an outer layer of follicle cells. Each egg begins oogenesis as a primary oocyte. At birth each female carries a lifetime supply of developing oocytes, each of which is in Prophase I. A developing egg (secondary oocyte) is released each month from puberty until menopause, a total of 400-500 eggs.

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LAWS OF THERMODYNAMICS

Laws of Thermodynamics

Energy exists in many forms, such as heat, light, chemical energy, and electrical energy. Energy is the ability to bring about change or to do work. Thermodynamics is the study of energy.

First Law of Thermodynamics: Energy can be changed from one form to another, but it cannot be created or destroyed. The total amount of energy and matter in the Universe remains constant, merely changing from one form to another. The First Law of Thermodynamics (Conservation) states that energy is always conserved, it cannot be created or destroyed. In essence, energy can be converted from one form into another.

The Second Law of Thermodynamics states that "in all energy exchanges, if no energy enters or leaves the system, the potential energy of the state will always be less than that of the initial state." This is also commonly referred to as entropy. A watchspring-driven watch will run until the potential energy in the spring is converted, and not again until energy is reapplied to the spring to rewind it. A car that has run out of gas will not run again until you walk 10 miles to a gas station and refuel the car. Once the potential energy locked in carbohydrates is converted into kinetic energy (energy in use or motion), the organism will get no more until energy is input again. In the process of energy transfer, some energy will dissipate as heat. Entropy is a measure of disorder: cells are NOT disordered and so have low entropy. The flow of energy maintains order and life. Entropy wins when organisms cease to take in energy and die.

Potential vs. Kinetic energy

Potential energy, as the name implies, is energy that has not yet been used, thus the term potential. Kinetic energy is energy in use (or motion). A tank of gasoline has a certain potential energy that is converted into kinetic energy by the engine. When the potential is used up, you're outta gas! Batteries, when new or recharged, have a certain potential. When placed into a tape recorder and played at loud volume (the only settings for such things), the potential in the batteries is transformed into kinetic energy to drive the speakers. When the potential energy is all used up, the batteries are dead. In the case of rechargeable batteries, their potential is reelevated or restored.

In the hydrologic cycle, the sun is the ultimate source of energy, evaporating water (in a fashion raising it's potential above water in the ocean). When the water falls as rain (or snow) it begins to run downhill toward sea-level. As the water get closer to sea-level, it's potential energy is decreased. Without the sun, the water would eventually still reach sea-level, but never be evaporated to recharge the cycle.

Chemicals may also be considered from a potential energy or kinetic energy standpoint. One pound of sugar has a certain potential energy. If that pound of sugar is burned the energy is released all at once. The energy released is kinetic energy (heat). So much is released that organisms would burn up if all the energy was released at once. Organisms must release the energy a little bit at a time.

Energy is defined as the ability to do work. Cells convert potential energy, usually in the from of C-C covalent bonds or ATP molecules, into kinetic energy to accomplish cell division, growth, biosynthesis, and active transport, among other things.

Learning Objectives

1. Define energy; be able to state the first and second laws of thermodynamics. 2. Entropy is a measure of the degree of randomness or disorder of systems. Explain how life maintains a high

degree of organization.

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REACTIONS AND ENZYMES

Endergonic and exergonic

Energy releasing processes, ones that "generate" energy, are termed exergonic reactions. Reactions that require energy to initiate the reaction are known as endergonic reactions. All natural processes tend to proceed in such a direction that the disorder or randomness of the universe increases (the second law of thermodynamics).

Oxidation/Reduction

Biochemical reactions in living organisms are essentially energy transfers. Often they occur together, "linked", in what are referred to as oxidation/reduction reactions. Reduction is the gain of an electron. Sometimes we also have H ions along for the ride, so reduction also becomes the gain of H. Oxidation is the loss of an electron (or hydrogen). In oxidation/reduction reactions, one chemical is oxidized, and its electrons are passed (like a hot potato) to another (reduced, then) chemical. Such coupled reactions are referred to as redox reactions. The metabolic processes glycolysis, Kreb's Cycle, and Electron Transport Phosphorylation involve the transfer of electrons (at varying energy states) by redox reactions.

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Catabolism and Anabolism

Anabolism is the total series of chemical reactions involved in synthesis of organic compounds. Autotrophs must be able to manufacture (synthesize) all the organic compounds they need. Heterotrophs can obtain some of their compounds in their diet (along with their energy). For example humans can synthesize 12 of the 20 amino acids, we must obtain the other 8 in our diet. Catabolism is the series of chemical reactions that breakdown larger molecules. Energy is released this way, some of it can be utilized for anabolism. Products of catabolism can be reassembled by anabolic processes into new anabolic molecules.

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Enzymes: Organic Catalysts

Enzymes allow many chemical reactions to occur within the homeostasis constraints of a living system. Enzymes function as organic catalysts. A catalyst is a chemical involved in, but not changed by, a chemical reaction. Many enzymes function by lowering the activation energy of reactions. By bringing the reactants closer together, chemical bonds may be weakened and reactions will proceed faster than without the catalyst.

Enzymes can act rapidly, as in the case of carbonic anhydrase (enzymes typically end in the -ase suffix), which causes the chemicals to react 107 times faster than without the enzyme present. Carbonic anhydrase speeds up the transfer of carbon dioxide from cells to the blood. There are over 2000 known enzymes, each of which is involved with one specific chemical reaction. Enzymes are substrate specific. The enzyme peptidase (which breaks peptide bonds in proteins) will not work on starch (which is broken down by human-produced amylase in the mouth).

Enzymes are proteins. The functioning of the enzyme is determined by the shape of the protein. The arrangement of molecules on the enzyme produces an area known as the active site within which the specific substrate(s) will "fit". It recognizes, confines and orients the substrate in a particular direction.

The induced fit hypothesis suggests that the binding of the substrate to the enzyme alters the structure of the enzyme, placing some strain on the substrate and further facilitating the reaction. Cofactors are nonproteins essential for enzyme activity. Ions such as K+ and Ca+2 are cofactors. Coenzymes are nonprotein organic molecules bound to enzymes near the active site. NAD (nicotinamide adenine dinucleotide).

Enzymatic pathways form as a result of the common occurrence of a series of dependent chemical reactions. In one example, the end product depends on the successful completion of five reactions, each mediated by a specific enzyme. The enzymes in a series can be located adjacent to each

other (in an organelle or in the membrane of an organelle), thus speeding the reaction process. Also, intermediate products tend not to accumulate, making the process more efficient. By removing intermediates (and by inference end products) from the reactive pathway, equilibrium (the tendency of reactions to reverse when concentrations of the products build up to a certain level) effects are minimized, since equilibrium is not attained, and so the reactions will proceed in the "preferred" direction.

Temperature: Increases in temperature will speed up the rate of nonenzyme mediated reactions, and so temperature increase speeds up enzyme mediated reactions, but only to a point. When heated too much, enzymes (since they are proteins dependent on their shape) become denatured. When the temperature drops, the enzyme regains its shape. Thermolabile enzymes, such as those responsible for the color distribution in Siamese cats and color camouflage of the Arctic fox, work better (or work at all) at lower temperatures.

Concentration of substrate and product also control the rate of reaction, providing a biofeedback mechanism.

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Activation, as in the case of chymotrypsin, protects a cell from the hazards or damage the enzyme might cause.

Changes in pH will also denature the enzyme by changing the shape of the enzyme. Enzymes are also adapted to operate at a specific pH or pH range.

Allosteric Interactions may allow an enzyme to be temporarily inactivated. Binding of an allosteric effector changes the shape of the enzyme, inactivating it while the effector is still bound. Such a mechanism is commonly employed in feedback inhibition. Often one of the products, either an end or near-end product act as an allosteric effector, blocking or shunting the pathway.

Competitive Inhibition works by the competition of the regulatory compound and substrate for the binding site. If enough regulatory compound molecules bind to enough enzymes, the pathway is shut down or at least slowed down. PABA, a chemical essential to a bacteria that infects animals, resembles a drug, sulfanilamide, that competes with PABA, shutting down an essential bacterial (but not animal) pathway.

Noncompetitive Inhibition occurs when the inhibitory chemical, which does not have to resemble the substrate, binds to the enzyme other than at the active site. Lead binds to SH groups in this fashion. Irreversible Inhibition occurs when the chemical either permanently binds to or massively denatures the enzyme so that the tertiary structure cannot be restored. Nerve gas permanently blocks pathways involved in nerve message transmission, resulting in death. Penicillin, the first of the "wonder drug" antibiotics, permanently blocks the pathways certain bacteria use to assemble their cell wall components.

Learning Objectives

Reactions that show a net loss in energy are said to be exergonic; reactions that show a net gain in energy are said to be endergonic. Describe an example of each type of chemical reaction from everyday life.

What is meant by a reversible reaction? How might this be significant to living systems? What is the function of metabolic pathways in cellular chemistry? Want more? Try Metabolic Pathways of

Biochemistry. What are enzymes? Explain their importance. Explain what happens when enzymes react with substrates.

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ATP AND BIOLOGICAL ENERGY

The Nature of ATP

Adenosine triphosphate (ATP), the energy currency, transfers energy from chemical bonds to endergonic (energy absorbing) reactions within the cell. Structurally, ATP consists of the adenine nucleotide (ribose sugar, adenine base, and phosphate group, PO4

-2) plus two other phosphate groups.

Energy is stored in the covalent bonds between phosphates, with the greatest amount of energy (approximately 7 kcal/mole) in the bond between the second and third phosphate groups. This covalent bond is known as a pyrophosphate bond.

We can write the chemical reaction for the formation of ATP as:

a) in chemicalese: ADP + Pi + energy ----> ATP

b) in English: Adenosine diphosphate + inorganic Phosphate + energy produces Adenosine Triphosphate

The chemical formula for the expenditure/release of ATP energy can be written as:

a) in chemicalese: ATP ----> ADP + energy + Pi

b) in English Adenosine Triphosphate produces Adenosine diphosphate + energy + inorganic Phosphate

An analogy between ATP and rechargeable batteries is appropriate. The batteries are used, giving up their potential energy until it has all been converted into kinetic energy and heat/unusable energy. Recharged batteries (into which energy has been put) can be used only after the input of additional energy. Thus, ATP is the higher energy form (the recharged battery) while ADP is the lower energy form (the used battery). When the terminal (third) phosphate is cut loose, ATP becomes ADP (Adenosine diphosphate; di= two), and the stored energy is released for some biological process to utilize. The input of additional energy (plus a phosphate group) "recharges" ADP into ATP (as in my analogy the spent batteries are recharged by the input of additional energy).

How to Make ATP

Two processes convert ADP into ATP: 1) substrate-level phosphorylation; and 2) chemiosmosis. Substrate-level

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phosphorylation occurs in the cytoplasm when an enzyme attaches a third phosphate to the ADP (both ADP and the phosphates are the substrates on which the enzyme acts).

Chemiosmosis, involves more than the single enzyme of substrate-level phosphorylation. Enzymes in chemiosmotic synthesis are arranged in an electron transport chain that is embedded in a membrane. In eukaryotes this membrane is in either the chloroplast or mitochondrion. According to the chemiosmosis hypothesis proposed by Peter Mitchell in 1961, a special ATP-synthesizing enzyme is also located in the membranes. Mitchell would later win the Nobel Prize for his work.

During chemiosmosis in eukaryotes, H+ ions are pumped across an organelle membrane by membrane "pump proteins" into a confined space (bounded by membranes) that contains numerous hydrogen ions. The energy for the pumping comes from the coupled oxidation-reduction reactions in the electron transport chain. Electrons are passed from one membrane-

bound enzyme to another, losing some energy with each transfer (as per the second law of thermodynamics). This "lost" energy allows for the pumping of hydrogen ions against the concentration gradient (there are fewer hydrogen ions outside the confined space than there are inside the confined space). The confined hydrogens cannot pass back through the membrane. Their only exit is through the ATP synthesizing enzyme that is located in the confining membrane. As the hydrogen passes through the ATP synthesizing enzyme, energy from the enzyme is used to attach a third phosphate to ADP, converting it to ATP.

Usually the terminal phosphate is not simply removed, but instead is attached to another molecule. This process is known as phosphorylation.

W + ATP -----> W~P + ADP where W is any compound, for example:

glucose + ATP -----> glucose~P + ADP

Glucose can be converted into Glucose-6-phosphate by the addition of the phosphate group from ATP.

ATP serves as the biological energy company, releasing energy for both anabolic and catabolic processes and being recharged by energy generated from other catabolic reactions.

Learning Objectives

Describe the components, organization, and functions of an electron transport system. ATP is composed of ribose, a five-carbon sugar, three phosphate groups, and adenine , a nitrogen-containing

compound (also known as a nitrogenous base). What class of organic macromolecules is composed of monomers similar to ATP?

ATP directly or indirectly delivers energy to almost all metabolic pathways. Explain the functioning of the ATP/ADP cycle.

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Adding a phosphate to a molecule is called phosphorylation. What two methods do cells use to phosphorylate ADP into ATP?

CELLULAR METABOLISM AND FERMENTATION

Glycolysis, the Universal Process

Nine reactions, each catalyzed by a specific enzyme, makeup the process we call glycolysis. ALL organisms have glycolysis occurring in their cytoplasm.

At steps 1 and 3 ATP is converted into ADP, inputting energy into the reaction as well as attaching a phosphate to the glucose. At steps 6 and 9 ADP is converted into the higher energy ATP. At step 5 NAD+ is converted into NADH + H+.

The process works on glucose, a 6-C, until step 4 splits the 6-C into two 3-C compounds. Glyceraldehyde phosphate (GAP, also known as phosphoglyceraldehyde, PGAL) is the more readily used of the two. Dihydroxyacetone phosphate can be converted into GAP by the enzyme Isomerase. The end of the glycolysis process yields two pyruvic acid (3-C) molecules, and a net gain of 2 ATP and two NADH per glucose.

Anaerobic Pathways

Under anaerobic conditions, the absence of oxygen, pyruvic acid can be routed by the organism into one of three pathways: lactic acid fermentation, alcohol fermentation, or cellular (anaerobic) respiration. Humans cannot ferment alcohol in their own bodies, we lack the genetic information to do so. These biochemical pathways, with their myriad reactions catalyzed by reaction-specific enzymes all under genetic control, are extremely complex. We will only skim the surface at this time and in this course.

Alcohol fermentation is the formation of alcohol from sugar. Yeast, when under anaerobic conditions, convert glucose to pyruvic acid via the glycolysis pathways, then go one step farther, converting pyruvic acid into ethanol, a C-2 compound.

Many organisms will also ferment pyruvic acid into, other chemicals, such as lactic acid. Humans ferment lactic acid in muscles where oxygen becomes depleted, resulting in localized anaerobic conditions. This lactic acid causes the muscle stiffness couch-potatoes feel after beginning exercise programs. The stiffness goes away after a few days since the cessation of strenuous activity allows aerobic conditions to return to the muscle, and the lactic acid can be converted into ATP via the normal aerobic respiration pathways.

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Aerobic Respiration

When oxygen is present (aerobic conditions), most organisms will undergo two more steps, Kreb's Cycle, and Electron Transport, to produce their ATP. In eukaryotes, these processes occur in the mitochondria, while in prokaryotes they occur in the cytoplasm.

Acetyl Co-A: The Transition Reaction

Pyruvic acid is first altered in the transition reaction by removal of a carbon and two oxygens (which form carbon dioxide). When the carbon dioxide is removed, energy is given off, and NAD+ is converted into the higher energy form NADH. Coenzyme A attaches to the remaining 2-C (acetyl) unit, forming acetyl Co-A. This process is a prelude to the Kreb's Cycle.

Kreb's Cycle (aka Citric Acid Cycle)

The Acetyl Co-A (2-C) is attached to a 4-C chemical (oxaloacetic acid). The Co-A is released and returns to await another pyruvic acid. The 2-C and 4-C make another chemical known as Citric acid, a 6-C. Kreb's Cycle is also known as the Citric Acid Cycle. The process after Citric Acid is essentially removing carbon dioxide, getting out energy in the form of ATP, GTP, NADH and FADH2, and lastly regenerating the cycle. Between Isocitric Acid and -Ketoglutaric Acid, carbon dioxide is given off and NAD+ is converted into NADH. Between -Ketoglutaric Acid and Succinic Acid the release of carbon dioxide and reduction of NAD+ into NADH happens again, resulting in a 4-C chemical, succinic acid. GTP (Guanine Triphosphate, which transfers its energy to ATP) is also formed here (GTP is formed by attaching a phosphate to GDP).

The remaining energy carrier-generating steps involve the shifting of atomic arrangements within the 4-C molecules. Between Succinic Acid and Fumaric Acid, the molecular shifting releases not enough energy to make ATP or NADH outright, but instead this energy is captured by a new energy carrier, Flavin adenine dinucleotide (FAD). FAD is reduced by the addition of two H's to become FADH2. FADH2 is not as rich an energy carrier as NADH, yielding less ATP than the latter.

The last step, between Malic Acid and Oxaloacetic Acid reforms OA to complete the cycle. Energy is given off and trapped by the reduction of NAD+ to NADH. The carbon dioxide released by cells is generated by the Kreb's Cycle, as are the energy carriers (NADH and FADH2) which play a role in the next step.

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Electron Transport Phosphorylation

Whereas Kreb's Cycle occurs in the matrix of the mitochondrion, the Electron Transport System (ETS) chemicals are embedded in the membranes known as the cristae. Kreb's cycle completely oxidized the carbons in the pyruvic acids, producing a small amount of ATP, and reducing NAD and FAD into higher energy forms. In the ETS those higher energy forms are cashed in, producing ATP. Cytochromes are molecules that pass the "hot potatoes" (electrons) along the ETS chain. Energy released by the "downhill" passage of electrons is captured as ATP by ADP molecules. The ADP is reduced by the gain of electrons. ATP formed in this way is made by the process of oxidative phosphorylation. The mechanism for the oxidative phosphorylation process is the gradient of H+ ions discovered across the inner mitochondrial membrane. This mechanism is known as chemiosmotic coupling. This involves both chemical and transport processes. Drops in the potential energy of electrons moving down the ETS chain occur at three points. These points turn out to be where ADP + P are converted into ATP. Potential energy is captured by ADP and stored in the pyrophosphate bond. NADH enters the ETS chain at the beginning, yielding 3 ATP per NADH. FADH2 enters at Co-Q, producing only 2 ATP per FADH2.

Catabolism and Anabolism

Catabolism is the breaking down of complex molecules (triglycerides and polysaccharides). Anabolism is the building up of molecules for energy storage.

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PHOTOSYNTHESIS

What is Photosynthesis?

Photosynthesis is the process by which plants, some bacteria, and some protistans use the energy from sunlight to produce sugar, which cellular respiration converts into ATP, the "fuel" used by all living things. The conversion of unusable sunlight energy into usable chemical energy, is associated with the actions of the green pigment chlorophyll. Most of the time, the photosynthetic process uses water and releases the oxygen that we absolutely must have to stay alive. Oh yes, we need the food as well!

We can write the overall reaction of this process as:

6H2O + 6CO2 ----------> C6H12O6+ 6O2

Most of us don't speak chemicalese, so the above chemical equation translates as:

six molecules of water plus six molecules of carbon dioxide produce one molecule of sugar plus six molecules of oxygen

Leaves and Leaf Structure

Plants are the only photosynthetic organisms to have leaves (and not all plants have leaves). A leaf may be viewed as a solar collector crammed full of photosynthetic cells.

The raw materials of photosynthesis, water and carbon dioxide, enter the cells of the leaf, and the products of photosynthesis, sugar and oxygen, leave the leaf.

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Water enters the root and is transported up to the leaves through specialized plant cells known as xylem (pronounces zigh-lem). Land plants must guard against drying out (desiccation) and so have evolved specialized structures known as stomata to allow gas to enter and leave the leaf. Carbon dioxide cannot pass through the protective waxy layer covering the leaf (cuticle), but it can enter the leaf through an opening (the stoma; plural = stomata; Greek for hole) flanked by two guard cells. Likewise, oxygen produced during photosynthesis can only pass out of the leaf through the opened stomata. Unfortunately for the plant, while these gases are moving between the inside and outside of the leaf, a great deal water is also lost. Cottonwood trees, for example, will lose 100 gallons of water per hour during hot desert days. Carbon dioxide enters single-celled and aquatic autotrophs through no specialized structures.

The Nature of Light

White light is separated into the different colors (=wavelengths) of light by passing it through a prism. Wavelength is defined as the distance from peak to peak (or trough to trough). The energy of is inversely proportional to the wavelength: longer wavelengths have less energy than do shorter ones.

The order of colors is determined by the wavelength of light. Visible light is one small part of the electromagnetic spectrum. The longer the wavelength of visible light, the more red the color. Likewise the shorter wavelengths are towards the violet side of the spectrum. Wavelengths longer than red are referred to as infrared, while those shorter than violet are ultraviolet.

Light behaves both as a wave and a particle. Wave properties of light include the bending of the wave path when passing from one material (medium) into another (i.e. the prism, rainbows, pencil in a glass-of-water, etc.). The particle properties are demonstrated by the photoelectric effect. Zinc exposed to ultraviolet light becomes positively charged because light energy forces electrons from the zinc. These electrons can create an electrical current. Sodium, potassium and selenium have critical wavelengths in the visible light range. The critical wavelength is the maximum wavelength of light (visible or invisible) that creates a photoelectric effect.

Chlorophyll and Accessory Pigments

A pigment is any substance that absorbs light. The color of the pigment comes from the wavelengths of light reflected (in other words, those not absorbed). Chlorophyll, the green pigment common to all photosynthetic cells, absorbs all wavelengths of visible light except green, which it reflects to be detected by our eyes. Black pigments absorb all of the wavelengths that strike them. White pigments/lighter colors reflect all or almost all of the energy striking them. Pigments have their own characteristic absorption spectra, the absorption pattern of a given pigment.

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Chlorophyll is a complex molecule. Several modifications of chlorophyll occur among plants and other photosynthetic organisms. All photosynthetic organisms (plants, certain protistans, prochlorobacteria, and cyanobacteria) have chlorophyll a. Accessory pigments absorb energy that chlorophyll a does not absorb. Accessory pigments include chlorophyll b (also c, d, and e in algae and protistans), xanthophylls, and carotenoids (such as beta-carotene). Chlorophyll a absorbs its energy from the Violet-Blue and Reddish orange-Red wavelengths, and little from the intermediate (Green-Yellow-Orange) wavelengths.

Carotenoids and chlorophyll b absorb some of the energy in the green wavelength. Why not so much in the orange and yellow wavelengths? Both chlorophylls also absorb in the orange-red end of the spectrum (with longer wavelengths and lower energy). The origins of photosynthetic organisms in the sea may account for this. Shorter wavelengths (with more energy) do not penetrate much below 5 meters deep in sea water. The ability to absorb some energy from the longer (hence more penetrating) wavelengths might have been an advantage to early photosynthetic algae that were not able to be in the upper (photic) zone of the sea all the time.

The action spectrum of photosynthesis is the relative effectiveness of different wavelengths of light at generating electrons. If a pigment absorbs light energy, one of three things will occur. Energy is dissipated as heat. The energy may be emitted immediately as a longer wavelength, a phenomenon known as fluorescence. Energy may trigger a chemical reaction, as in photosynthesis. Chlorophyll only triggers a chemical reaction when it is associated with proteins embedded in a membrane (as in a chloroplast) or the membrane infoldings found in photosynthetic prokaryotes such as cyanobacteria and prochlorobacteria.

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The structure of the chloroplast and photosynthetic membranes

The thylakoid is the structural unit of photosynthesis. Both photosynthetic prokaryotes and eukaryotes have these flattened sacs/vesicles containing photosynthetic chemicals. Only eukaryotes have chloroplasts with a surrounding membrane.

Thylakoids are stacked like pancakes in stacks known collectively as grana. The areas between grana are referred to as stroma. While the mitochondrion has two membrane systems, the chloroplast has three, forming three compartments.

Stages of Photosynthesis

Photosynthesis is a two stage process. The first process is the Light Dependent Process (Light Reactions), requires the direct energy of light to make energy carrier molecules that are used in the second process. The Light Independent Process (or Dark Reactions) occurs when the products of the Light Reaction are used to form C-C covalent bonds of carbohydrates. The Dark Reactions can usually occur in the dark, if the energy carriers from the light process are present. Recent evidence suggests that a major enzyme of the Dark Reaction is indirectly stimulated by light, thus the term Dark Reaction is somewhat of a misnomer. The Light Reactions occur in the grana and the Dark Reactions take place in the stroma of the chloroplasts.

Light Reactions

In the Light Dependent Processes (Light Reactions) light strikes chlorophyll a in such a way as to excite electrons to a higher energy state. In a series of reactions the energy is converted (along an electron transport process) into ATP and NADPH. Water is split in the process, releasing oxygen as a by-product of the reaction. The ATP and NADPH are used to make C-C bonds in the Light Independent Process (Dark Reactions).

In the Light Independent Process, carbon dioxide from the atmosphere (or water for aquatic/marine organisms) is captured and modified by the addition of Hydrogen to form carbohydrates (general formula of carbohydrates is [CH2O]n). The incorporation of carbon dioxide into organic compounds is known as carbon fixation. The energy for this comes from the first phase of the photosynthetic process. Living systems cannot directly utilize light energy, but can, through a complicated series of reactions, convert it into C-C bond energy that

can be released by glycolysis and other metabolic processes.

Photosystems are arrangements of chlorophyll and other pigments packed into thylakoids. Many Prokaryotes have only one photosystem, Photosystem II (so numbered because, while it was most likely the first to evolve, it was the second one discovered). Eukaryotes have Photosystem II plus Photosystem I. Photosystem I uses chlorophyll a, in the form referred to as P700. Photosystem II uses a form of chlorophyll a known as P680. Both "active" forms of chlorophyll a function in

photosynthesis due to their association with proteins in the thylakoid membrane.

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Photophosphorylation is the process of converting energy from a light-excited electron into the pyrophosphate bond of an ADP molecule. This occurs when the electrons from water are excited by the light in the presence of P680. The energy transfer is similar to the chemiosmotic electron transport occurring in the mitochondria. Light energy causes the removal of an electron from a molecule of P680 that is part of Photosystem II. The P680 requires an electron, which is taken from a water molecule, breaking the water into H+ ions and O-2 ions. These O-2 ions combine to form the diatomic O2 that is released. The electron is "boosted" to a higher energy state and attached to a primary electron acceptor, which begins a series of redox reactions, passing the electron through a series of electron carriers, eventually attaching it to a molecule in Photosystem I. Light acts on a molecule of P700 in Photosystem I, causing an electron to be "boosted" to a still higher potential. The electron is attached to a different primary electron acceptor (that is a different molecule from the one associated with Photosystem II). The electron is passed again through a series of redox reactions, eventually being attached to NADP+ and H+ to form NADPH, an energy carrier needed in the Light Independent Reaction. The electron from Photosystem II replaces the excited electron in the P700 molecule. There is thus a continuous flow of electrons from water to NADPH. This energy is used in Carbon Fixation. Cyclic Electron Flow occurs in some eukaryotes and primitive photosynthetic bacteria. No NADPH is produced, only ATP. This occurs when cells may require additional ATP, or when there is no NADP+ to reduce to NADPH. In Photosystem II, the pumping to H ions into the thylakoid and the conversion of ADP + P into ATP is driven by electron gradients established in the thylakoid membrane.

Chemiosmosis as it operates in photophosphorylation within a chloroplast

Halobacteria, which grow in extremely salty water, are facultative aerobes, they can grow when oxygen is absent. Purple pigments, known as retinal (a pigment also found in the human eye) act similar to chlorophyll. The complex of retinal and membrane proteins is known as bacteriorhodopsin, which generates electrons which establish a proton gradient that powers an ADP-ATP pump, generating ATP from sunlight without chlorophyll. This supports the theory that chemiosmotic processes are universal in their ability to generate ATP.

Dark Reaction

Carbon-Fixing Reactions are also known as the Dark Reactions (or Light Independent Reactions). Carbon dioxide enters single-celled and aquatic autotrophs through no specialized structures, diffusing into the cells. Land plants must guard against drying out (desiccation) and so have evolved specialized structures known as stomata to allow gas to enter and leave the leaf. The Calvin Cycle occurs in the stroma of chloroplasts (where would it occur in a prokaryote?). Carbon dioxide is captured by the chemical ribulose biphosphate (RuBP). RuBP is a 5-C chemical. Six molecules of carbon dioxide enter the Calvin Cycle, eventually producing one molecule of glucose. The reactions in this process were worked out by Melvin Calvin (shown below).

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The first steps in the Calvin cycle.

The first stable product of the Calvin Cycle is phosphoglycerate (PGA), a 3-C chemical. The energy from ATP and NADPH energy carriers generated by the photosystems is used to attach phosphates to (phosphorylate) the PGA. Eventually there are 12 molecules of glyceraldehyde phosphate (also known as phosphoglyceraldehyde or PGAL, a 3-C), two of which are removed from the cycle to make a glucose. The remaining PGAL molecules are converted by ATP energy to reform 6 RuBP molecules, and thus start the cycle again. Remember the complexity of life, each reaction in this process, as in Kreb's Cycle, is catalyzed by a different reaction-specific enzyme.

C-4 Pathway

Some plants have developed a preliminary step to the Calvin Cycle (which is also referred to as a C-3 pathway), this preamble step is known as C-4. While most C-fixation begins with RuBP, C-4 begins with a new molecule, phosphoenolpyruvate (PEP), a 3-C chemical that is converted into oxaloacetic acid (OAA, a 4-C chemical) when carbon dioxide is combined with PEP. The OAA is converted to Malic Acid and then transported from the mesophyll cell into the bundle-sheath cell, where OAA is broken down into PEP plus carbon dioxide. The carbon dioxide then enters the Calvin Cycle, with PEP returning to the mesophyll cell. The resulting sugars are now adjacent to the leaf veins and can readily be transported throughout the plant.

The capture of carbon dioxide by PEP is ediated by the enzyme PEP carboxylase, which has a stronger affinity for carbon dioxide than does RuBP carboxylase When carbon dioxide levels decline below the

threshold for RuBP carboxylase, RuBP is catalyzed with oxygen instead of carbon dioxide. The product of that reaction forms glycolic acid, a chemical that can be broken down by photorespiration, producing neither NADH nor ATP, in effect dismantling the Calvin Cycle. C-4 plants, which often grow close together, have had to adjust to decreased levels of carbon dioxide by artificially raising the carbon dioxide concentration in certain cells to prevent photorespiration. C-4 plants evolved in the tropics and are adapted to higher temperatures than are the C-3 plants found at higher latitudes. Common C-4 plants include crabgrass, corn, and sugar cane. Note that OAA and Malic Acid also have functions in other processes, thus the chemicals would have

been present in all plants, leading scientists to hypothesize that C-4 mechanisms evolved several times independently in response to a similar environmental condition, a type of evolution known as convergent evolution.

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We can see anatomical differences between C3 and C4 leaves.

The Carbon Cycle

Plants may be viewed as carbon sinks, removing carbon dioxide from the atmosphere and oceans by fixing it into organic chemicals. Plants also produce some carbon dioxide by their respiration, but this is quickly used by photosynthesis. Plants also convert energy from light into chemical energy of C-C covalent bonds. Animals are carbon dioxide producers that derive their energy from carbohydrates and other chemicals produced by plants by the process of photosynthesis.

The balance between the plant carbon dioxide removal and animal carbon dioxide generation is equalized also by the formation of carbonates in the oceans. This removes excess carbon dioxide from the air and water (both of which are in equilibrium with regard to carbon dioxide). Fossil fuels, such as petroleum and coal, as well as more recent fuels such as peat and wood generate carbon dioxide when burned. Fossil fuels are formed ultimately by organic processes, and represent also a tremendous carbon sink. Human activity has greatly increased the concentration of carbon dioxide in air. This increase has led to global warming, an increase in temperatures around the world, the Greenhouse Effect. The increase in carbon dioxide and other pollutants in the air has also led to acid rain, where water falls through polluted air and chemically combines with carbon dioxide, nitrous oxides, and sulfur oxides, producing rainfall with pH as low as 4. This results in fish kills and changes in soil pH which can alter the natural vegetation and uses of the land. The Global Warming problem can lead to melting of the ice caps in Greenland and Antarctica, raising sea-level as much as 120 meters. Changes in sea-level and temperature would affect climate changes, altering belts of grain production and rainfall patterns.

Learning Objectives

After completing this chapter you should be able to:

Study the general equation for photosynthesis and be able to indicate in which process each reactant is used and each product is produced.

List the two major processes of photosynthesis and state what occurs in those sets of reactions. Distinguish between organisms known as autotrophs and those known as heterotrophs as pertains to their modes

of nutrition. Explain the significance of the ATP/ADP cycle. Describe the nature of light and how it is associated with the release of electrons from a photosystem. Describe how the pigments found on thylakoid membranes are organized into photosystems and how they relate

to photon light energy.

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Describe the role that chlorophylls and the other pigments found in chloroplasts play to initiate the light-dependent reactions.

Describe the function of electron transport systems in the thylakoid membrane. Explain the role of the two energy-carrying molecules produced in the light-dependent reactions (ATP and

NADPH) in the light-independent reactions. Describe the Calvin-Benson cycle in terms of its reactants and products. Explain how C-4 photosynthesis provides an advantage for plants in certain environments. Describe the phenomenon of acid rain, and how photosynthesis relates to acid rain and the carbon cycle..

Review Questions

1. The organic molecule produced directly by photosynthesis is: a) lipids; b) sugar; c) amino acids; d) DNA

2. The photosynthetic process removes ___ from the environment. a) water; b) sugar; c) oxygen; d) chlorophyll; e) carbon dioxide

3. The process of splitting water to release hydrogens and electrons occurs during the _____ process. a) light dependent; b) light independent; c) carbon fixation; d) carbon photophosphorylation; e) glycolysis

4. The process of fixing carbon dioxide into carbohydrates occurs in the ____ process. a) light dependent; b) light independent; c) ATP synthesis; d) carbon photophosphorylation; e) glycolysis

5. Carbon dioxide enters the leaf through ____. a) chloroplasts; b) stomata: c) cuticle; d) mesophyll cells; e) leaf veins

6. The cellular transport process by which carbon dioxide enters a leaf (and by which water vapor and oxygen exit) is ___. a) osmosis; b) active transport; c. co- transport; d) diffusion; e) bulk flow

7. Which of the following creatures would not be an autotroph? a) cactus; b) cyanobacteria; c) fish; d) palm tree; e) phytoplankton

8. The process by which most of the world's autotrophs make their food is known as ____. a) glycolysis; b) photosynthesis; c) chemosynthesis; d) herbivory; e) C-4 cycle

9. The process of ___ is how ADP + P are converted into ATP during the Light dependent process. a) glycolysis; b) Calvin Cycle; c) chemiosmosis; d) substrate-level phosphorylation; e) Kreb's Cycle

10. Once ATP is converted into ADP + P, it must be ____. a) disassembled into components (sugar, base, phosphates) and then ressembled; b) recharged by chemiosmosis; c) converted into NADPH; d) processed by the glycolysis process; e) converted from matter into energy.

11. Generally speaking, the longer the wavelenght of light, the ___ the available energy of that light. a) smaller; b) greater; c) same

12. The section of the electromagnetic spectrum used for photosynthesis is ___. a) infrared; b) ultraviolet; c) x-ray; d) visible light; e) none of the above

13. The colors of light in the visible range (from longest wavelength to shortest) is ___. a) ROYGBIV; b) VIBGYOR; c) GRBIYV; d) ROYROGERS; e) EBGDF

14. The photosynthetic pigment that is essential for the process to occur is ___. a) chlorophyll a; b) chlorophyll b; c) beta carotene; d) xanthocyanin; e) fucoxanthin

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15. When a pigment reflects red light, _____. a) all colors of light are absorbed; b) all col;ors of light are reflected; c) green light is reflected, all others are absorbed; d) red light is reflected, all others are absorbed; e) red light is absorbed after it is reflected into the internal pigment molecules.

16. Chlorophyll a absorbs light energy in the ____color range. a) yellow-green; b) red-organge; c) blue violet; d) a and b; e) b and c.

17. A photosystem is ___. a) a collection of hydrogen-pumping proteins; b) a collection of photosynthetic pigments arranged in a thylakjoid membrane; c) a series of electron-accepting proteins arranged in the thylakoid membrane; d. found only in prokaryotic organisms; e) multiple copies of chlorophyll a located in the stroma of the chloroplast.

18. The individual flattened stacks of membrane material inside the chloroplast are known as ___. a) grana; b) stroma; c) thylakoids; d) cristae; e) matrix

19. The fluid-filled area of the chloroplast is the ___. a) grana; b) stroma; c) thylakoids; d) cristae; e) matrix

20. The chloroplast contains all of these except ___. a) grana; b) stroma; c) DNA; d) membranes; e) endoplasmic reticulum

21. The chloroplasts of plants are most close in size to __. a) unfertilized human eggs; b) human cheek cells; c) human nerve cells; d) bacteria in the human mouth; e) viruses

22. Which of these photosynthetic organisms does not have a chloroplast? a) plants; b) red algae; c) cyanobacteria; d) diatoms; e) dinoflagellates

23. The photoelectric effect refers to ____. a) emission of electrons from a metal when energy of a critical wavelength strikes the metal; b) absorbtion of electrons from the surrounding environment when energy of a critical wavelength is nearby; c) emission of electrons from a metal when struck by any wavelength of light; d) emission of electrons stored in the daytime when stomata are open at night; e) release of NADPH and ATP energy during the Calvin Cycvle when light iof a specific wavelength strikes the cell.

24. Light of the green wavelengths is commonly absorbed by which accessory pigment? a) chlorophyll a; b) chlorophyll b; c) phycocyanin; d) beta carotene

25. The function of the electron transport proteins in the thyakoid membranes is ___. a) production of ADP by chemiosmosis; b) production of NADPH by substrate-level phosphorylation; c) pumping of hydrogens into the thylakoid space for later generation of ATP by chemiosmosis; d) pumping of hydrogens into the inner cristae space for later generation of ATP by chemiosmosis; e) preparation of water for eventual incorporation into glucose

26. ATP is known as the energy currency of the cell because ____. a) ATP is the most readily usable form of energy for cells; b) ATP passes energy along in an electron transport chain; c) ATP energy is passed to NADPH; d) ATP traps more energy than is produced in its formation; e) only eukaryotic cells use this energy currency.

27. Both cyclic and noncyclic photophosphorylation produce ATP. We can infer that the purpose of ATP in photosynthesis is to ____. a) supply hydrogen to the carbohydrate; b) supply carbon to the carbohydrate; c) supply energy that can be used to form a carbohydrate; d) transfer oxygens from the third phosphate group to the carbohydrate molecule; e) convert RuBP into PGA

28. The role of NADPH in oxygen-producing photosynthesis is to ____. a) supply hydrogen to the carbohydrate; b) supply carbon to the carbohydrate; c) supply energy that can be used to form a carbohydrate; d) transfer oxygens from the third phosphate group to the carbohydrate molecule; e) convert RuBP into PGA.

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29. The dark reactions require all of these chemicals to proceed except ___. a) ATP; b) NADPH; c) carbon dioxide; d) RUBP; e) oxygen

30. The first stable chemical formed by the Calvin Cycle is _____. a) RUBP; b) RU/18; c) PGA; d) PGAL; e) Rubisco

31. The hydrogen in the carbohydrate produced by the Calvin Cycle comes from ___ a.) ATP; b) NADPH; c) the environment if the pH is very acidic; d) a and b; e) a and c

32. The carbon incorporated into the carbohydrate comes from ___. a) ATP; b) NADPH; c) carbon dioxide; d) glucose; e) organic molecules

33. C-4 photosynthesis is so named because _____. a) it produces a three carbon compound as the first stable product of photosynthesis; b) it produces a four carbon compound as the first stable produc of photosynthesis; c) it produces four ATP and four NADPH molecules for carbon fixation.; d) there are only four steps in this form of carbon fixation into carbohydrate.

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INTRODUCTION TO GENETICS

Heredity, Historical Perspective

For much of human history people were unaware of the scientific details of how babies were conceived and how heredity worked. Clearly they were conceived, and clearly there was some hereditary connection between parents and children, but the mechanisms were not readily apparent. The Greek philosophers had a variety of ideas: Theophrastus proposed that male flowers caused female flowers to ripen; Hippocrates speculated that "seeds" were produced by various body parts and transmitted to offspring at the time of conception, and Aristotle thought that male and female semen mixed at conception. Aeschylus, in 458 BC, proposed the male as the parent, with the female as a "nurse for the young life sown within her".

During the 1700s, Dutch microscopist Anton van Leeuwenhoek (1632-1723) discovered "animalcules" in the sperm of humans and other animals. Some scientists speculated they saw a "little man" (homunculus) inside each sperm. These scientists formed a school of thought known as the "spermists". They contended the only contributions of the female to the next generation were the womb in which the homunculus grew, and prenatal influences of the womb. An opposing school of thought, the ovists, believed that the future human was in the egg, and that sperm merely stimulated the growth of the egg. Ovists thought women carried eggs containing boy and girl children, and that the gender of the offspring was determined well before conception.

Pangenesis was an idea that males and females formed "pangenes" in every organ. These pangenes subsequently moved through their blood to the genitals and then to the children. The concept originated with the ancient Greeks and influenced biology until little over 100 years ago. The terms "blood relative", "full-blooded", and "royal blood" are relicts of pangenesis. Francis Galton, Charles Darwin's cousin, experimentally tested and disproved pangenesis during the 1870s.

Blending theories of inheritance supplanted the spermists and ovists during the 19th century. The mixture of sperm and egg resulted in progeny that were a "blend" of two parents' characteristics. Sex cells are known collectively as gametes (gamos, Greek, meaning marriage). According to the blenders, when a black furred animal mates with white furred animal, you would expect all resulting progeny would be gray (a color intermediate between black and white). This is often not the case. Blending theories ignore characteristics skipping a generation. Charles Darwin had to deal with the implications of blending in his theory of evolution. He was forced to recognize blending as not important (or at least not the major principle), and suggest that science of the mid-1800s had not yet got the correct answer. That answer came from a contemporary, Gregor Mendel, although Darwin apparently never knew of Mendel's work.

The Monk and his peas

An Austrian monk, Gregor Mendel, developed the fundamental principles that would become the modern science of genetics. Mendel demonstrated that heritable properties are parceled out in discrete units, independently inherited. These eventually were termed genes.

Mendel reasoned an organism for genetic experiments should have:

1. a number of different traits that can be studied 2. plant should be self-fertilizing and have a flower structure that limits accidental

contact 3. offspring of self-fertilized plants should be fully fertile.

Mendel's experimental organism was a common garden pea (Pisum sativum), which has a flower that lends itself to self-pollination. The male parts of the flower are termed the anthers. They produce pollen, which contains the male gametes (sperm). The female parts of the flower are the stigma, style, and ovary. The egg (female gamete) is produced in the ovary. The process of pollination (the transfer of pollen from anther to stigma) occurs prior to the opening of the pea flower. The pollen grain grows a pollen tube which allows the sperm to travel through the stigma and style, eventually

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reaching the ovary. The ripened ovary wall becomes the fruit (in this case the pea pod). Most flowers allow cross-pollination, which can be difficult to deal with in genetic studies if the male parent plant is not known. Since pea plants are self-pollinators, the genetics of the parent can be more easily understood. Peas are also self-compatible, allowing self-fertilized embryos to develop as readily as out-fertilized embryos. Mendel tested all 34 varieties of peas available to him through seed dealers. The garden peas were planted and studied for eight years. Each character studied had two distinct forms, such as tall or short plant height, or smooth or wrinkled seeds. Mendel's experiments used some 28,000 pea plants.

Some of Mendel's traits as expressed in garden peas

Mendel's contribution was unique because of his methodical approach to a definite problem, use of clear-cut variables and application of mathematics (statistics) to the problem. Gregor Using pea plants and statistical methods, Mendel was able to demonstrate that traits were passed from each parent to their offspring through the inheritance of genes.

Mendel's work showed:

1. Each parent contributes one factor of each trait shown in offspring. 2. The two members of each pair of factors segregate from each other during gamete formation. 3. The blending theory of inheritance was discounted. 4. Males and females contribute equally to the traits in their offspring. 5. Acquired traits are not inherited.

Principle of Segregation

Mendel studied the inheritance of seed shape first. A cross involving only one trait is referred to as a monohybrid cross. Mendel crossed pure-breeding (also referred to as true-breeding) smooth-seeded plants with a variety that had always produced wrinkled seeds (60 fertilizations on 15 plants). All resulting seeds were smooth. The following year, Mendel planted these seeds and allowed them to self-fertilize. He recovered 7324 seeds: 5474 smooth and 1850 wrinkled. To help with record keeping, generations were labeled and numbered. The parental generation is denoted as the P1 generation.

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The offspring of the P1 generation are the F1 generation (first filial). The self-fertilizing F1 generation produced the F2 generation (second filial).

Inheritance of two alleles, S and s, in peas.

Punnett square explaining the behavior of the S and s alleles. P1: smooth X wrinkled

F1 : all smooth

F2 : 5474 smooth and 1850 wrinkled

Meiosis, a process unknown in Mendel's day, explains how the traits are inherited.

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Mendel studied seven traits which appeared in two discrete forms, rather than continuous characters which are often difficult to distinguish. When "true-breeding" tall plants were crossed with "true-breeding" short plants, all of the offspring were tall plants. The parents in the cross were the P1 generation, and the offspring represented the F1 generation. The trait referred to as tall was considered dominant, while short was recessive. Dominant traits were defined by Mendel as those which appeared in the F1 generation in crosses between true-breeding strains. Recessives were those which "skipped" a generation, being expressed only when the dominant trait is absent. Mendel's plants exhibited complete dominance, in which the phenotypic expression of alleles was either dominant or recessive, not "in between".

When members of the F1 generation were crossed, Mendel recovered mostly tall offspring, with some short ones also occurring. Upon statistically analyzing the F2 generation, Mendel determined the ratio of tall to short plants was approximately 3:1. Short plants have skipped the F1 generation, and show up in the F2 and succeeding generations. Mendel concluded that the traits under study were governed by discrete (separable) factors. The factors were inherited in pairs, with each generation having a pair of trait factors. We now refer to these trait factors as alleles. Having traits inherited in pairs allows for the observed phenomena of traits "skipping" generations.

Summary of Mendel's Results:

1. The F1 offspring showed only one of the two parental traits, and always the same trait. 2. Results were always the same regardless of which parent donated the pollen (was male). 3. The trait not shown in the F1 reappeared in the F2 in about 25% of the offspring. 4. Traits remained unchanged when passed to offspring: they did not blend in any offspring but behaved as separate

units. 5. Reciprocal crosses showed each parent made an equal contribution to the offspring.

Mendel's Conclusions:

1. Evidence indicated factors could be hidden or unexpressed, these are the recessive traits.

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2. The term phenotype refers to the outward appearance of a trait, while the term genotype is used for the genetic makeup of an organism.

3. Male and female contributed equally to the offsprings' genetic makeup: therefore the number of traits was probably two (the simplest solution).

4. Upper case letters are traditionally used to denote dominant traits, lower case letters for recessives.

Mendel reasoned that factors must segregate from each other during gamete formation (remember, meiosis was not yet known!) to retain the number of traits at 2. The Principle of Segregation proposes the separation of paired factors during gamete formation, with each gamete receiving one or the other factor, usually not both. Organisms carry two alleles for every trait. These traits separate during the formation of gametes.

Dihybrid Crosse

When Mendel considered two traits per cross (dihybrid, as opposed to single-trait-crosses, monohybrid), The resulting (F2) generation did not have 3:1 dominant:recessive phenotype ratios. The two traits, if considered to inherit independently, fit into the principle of segregation. Instead of 4 possible genotypes from a monohybrid cross, dihybrid crosses have as many as 16 possible genotypes.

Mendel realized the need to conduct his experiments on more complex situations. He performed experiments tracking two seed traits: shape and color. A cross concerning two traits is known as a dihybrid cross.

Crosses With Two Traits

Smooth seeds (S) are dominant over wrinkled (s) seeds.

Yellow seed color (Y) is dominant over green (g).

Again, meiosis helps us understand the behavior of alleles.

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Methods, Results, and Conclusions

Mendel started with true-breeding plants that had smooth, yellow seeds and crossed them with true-breeding plants having green, wrinkled seeds. All seeds in the F1 had smooth yellow seeds. The F2 plants self-fertilized, and produced four phenotypes:

315 smooth yellow

108 smooth green

101 wrinkled yellow

32 wrinkled green

Mendel analyzed each trait for separate inheritance as if the other trait were not present. The 3:1 ratio was seen separately and was in accordance with the Principle of Segregation. The segregation of S and s alleles must have happened independently of the segregation of Y and y alleles. The chance of any gamete having a Y is 1/2; the chance of any one gamete having a S is 1/2.The chance of a gamete having both Y and S is the product of their individual chances (or 1/2 X 1/2 = 1/4). The chance of two gametes forming any given genotype is 1/4 X 1/4 (remember, the product of their individual chances). Thus, the Punnett Square has 16 boxes. Since there are more possible combinations to produce a smooth yellow phenotype (SSYY, SsYy, SsYY, and SSYy), that phenotype is more common in the F2.

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From the results of the second experiment, Mendel formulated the Principle of Independent Assortment -- that when gametes are formed, alleles assort independently. If traits assort independent of each other during gamete formation, the results of the dihybrid cross can make sense. Since Mendel's time, scientists have discovered chromosomes and DNA. We now interpret the Principle of Independent Assortment as alleles of genes on different chromosomes are inherited independently during the formation of gametes. This was not known to Mendel.

Punnett squares deal only with probability of a genotype showing up in the next generation. Usually if enough offspring are produced, Mendelian ratios will also be produced.

Step 1 - definition of alleles and determination of dominance.

Step 2 - determination of alleles present in all different types of gametes.

Step 3 - construction of the square.

Step 4 - recombination of alleles into each small square.

Step 5 - Determination of Genotype and Phenotype ratios in the next generation.

Step 6 - Labeling of generations, for example P1, F1, etc.

While answering genetics problems, there are certain forms and protocols that will make unintelligible problems easier to do. The term "true-breeding strain" is a code word for homozygous. Dominant alleles are those that show up in the next generation in crosses between two different "true-breeding strains". The key to any genetics problem is the recessive phenotype (more properly the phenotype that represents the recessive genotype). It is that organism whose genotype can be determined by examination of the phenotype. Usually homozygous dominant and heterozygous individuals have identical phenotypes (although their genotypes are different). This becomes even more important in dihybrid crosses.

Mutations

Hugo de Vries, one of three turn-of-the-century scientists who rediscovered the work of Mendel, recognized that occasional abrupt, sudden changes occurred in the patterns of inheritance in the primrose plant. These sudden changes he termed mutations. De Vries proposed that new alleles arose by mutations. Charles Darwin, in his Origin of Species, was unable to describe how heritable changes were passed on to subsequent generations, or how new adaptations arose. Mutations provided answers to problems of the appearance of novel adaptations. The patterns of Mendelian inheritance explained the perseverance of rare traits in organisms, all of which increased variation, as you recall that was a major facet of Darwin's theory.

Mendel's work was published in 1866 but not recognized until the early 1900s when three scientists independently verified his principles, more than twenty years after his death. Ignored by the scientific community during his lifetime, Mendel's work is now a topic enjoyed by generations of biology students (;))

Genetic Terms

Definitions of terms. While we are discussing Mendel, we need to understand the context of his times as well as how his work fits into the modern science of genetics.

Gene - a unit of inheritance that usually is directly responsible for one trait or character.

Allele - an alternate form of a gene. Usually there are two alleles for every gene, sometimes as many a three or four.

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Homozygous - when the two alleles are the same.

Heterozygous - when the two alleles are different, in such cases the dominant allele is expressed.

Dominant - a term applied to the trait (allele) that is expressed irregardless of the second allele.

Recessive - a term applied to a trait that is only expressed when the second allele is the same (e.g. short plants are homozygous for the recessive allele).

Phenotype - the physical expression of the allelic composition for the trait under study.

Genotype - the allelic composition of an organism.

Punnett squares - probability diagram illustrating the possible offspring of a mating.

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GENE INTERACTIONS

Finding the Genes

Between 1884 (the year Mendel died) and 1888 details of mitosis and meiosis were reported, the cell nucleus was identified as the location of the genetic material, and "qualities" were even proposed to be transmitted on chromosomes to daughter cells at mitosis. In 1903 Walter Sutton and Theodore Boveri formally proposed that chromosomes contain the genes. The Chromosome Theory of Inheritance is one of the foundations of genetics and explains the physical reality of Mendel's principles of inheritance.

The location of many genes (Mendel's factors) was determined by Thomas Hunt Morgan and his coworkers in the early 1900's. Morgan's experimental organism was the fruit fly (Drosophila melanogaster). Fruit flies are ideal organisms for genetics, having a small size, ease of care, susceptibility to mutations, and short (7-9 day) generation time. The role of chromosomes in determination of sex was deduced by Morgan from work on fruit flies.

During Metaphase I, homologous chromosomes will line up. A karyotype can be made by cutting and arranging photomicrographs of the homologous chromosomes thus revealed at Metaphase I. Two types of chromosome pairs occur. Autosomes resemble each other in size and placement of the centromere, for example pairs of chromosome 21 are the same size, while pairs of chromosome 9 are of a different size from pair 21. Sex chromosomes may differ in their size, depending on the species of the organism they are from. In humans and Drosophila, males have a smaller sex chromosome, termed the Y, and a larger one, termed the X. Males are thus XY, and are termed heterogametic. Females are XX, and are termed homogametic. In grasshoppers, which Sutton studied in discovering chromosomes, there is no Y, only the X chromosome in males. Females are XX, while males are denoted as XO. Other organisms (notably birds, moths and butterflies) have males homogametic and females heterogametic. Males (if heterogametic) contribute either an X or Y to the offspring, while females contribute either X. The male thus determines the sex of the offspring. Remember that in meiosis, each chromosome is replicated and one copy sent to each gamete.

Morgan discovered a mutant eye color and attempted to use this mutant as a recessive to duplicate Mendel's results. He failed, instead of achieving a 3:1 F2 ratio the ratio was closer to 4:1 (red to white). Most mutations are usually recessive, thus the appearance of the white mutant presented Morgan a chance to test Mendel's ratios on animals. The F1 generation also had no white eyed females. Morgan hypothesized that the gene for eye color was only on the X chromosome, specifically in that region of the X that had no corresponding region on the Y. White eyed fruit flies were also more likely to die prior to adulthood, thus explaining the altered ratios. Normally eyes are red, but a variant (white) eyed was detected and used in genetic study. Cross a homozygous white eyed male with a homozygous red eyed female, and all the offspring have red eyes. Red is dominant over white. However, cross a homozygous white eyed female with a red eyed male, and the unexpected results show all the males have white eyes and all the females red eyes. This can be explained if the eye color gene is on the X chromosome.

Explanation

If the gene for eye color is on the X chromosome, the red eyed male in the second cross will pass his red eyed X to only his daughters, who in turn received only a recessive white-carrying X from their mother. Thus all females had red eyes like their father. Since the male fruit fly passes only the Y to his sons, their eye color is determined entirely by the single X chromosome they receive from their mother (in this case white). Thus all the males in the second cross were white eyed.

These experiments introduced the concept of sex-linkage, the occurrence of genes on that part of the X that lack a corresponding location on the Y. Sex-linked recessives (such as white eyes in fruit

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flies, hemophilia, baldness, and colorblindness in humans) occur more commonly in males, since there is no chance of them being heterozygous. Such a condition is termed hemizygous.

Characteristics of X-linked Traits

1. Phenotypic expression more common in males

2. Sons cannot inherit the trait from their fathers, but daughters can.

Sons inherit their Y chromosome from their father.

Only a few genes have been identified on the Y chromosome, among them the testis-determining factor (TDF) that promotes development of the male phenotype.

Barr bodies are interpreted as inactivated X chromosomes in mammalian females. Since females have two X chromosomes, the Lyon hypothesis suggests that one or the other X is inactivated in each somatic (non-reproductive) cell during embryonic development. Cells mitotically produced from these embryonic cells likewise have the same inactivated X chromosome.

Calico cats (sometimes called tortoiseshell) are almost always female since the calico trait is caused by some areas of the cat's fur expressing one allele and others expressing the other color. Can there be a male tortoiseshell cat? How would such a cat get its genes? Remember that fur color in cats is a sex-linked feature. Would the male calico be fertile or sterile?

The Modern View of the Gene

While Mendel discussed traits, we now know that genes are segments of the DNA that code for specific proteins. These proteins are responsible for the expression of the phenotype. The basic principles of segregation and independent assortment as worked out by Mendel are applicable even for sex-linked traits.

Codominant alleles

Codominant alleles occur when rather than expressing an intermediate phenotype, the heterozygotes express both homozygous phenotypes. An example is in human ABO blood types, the heterozygote AB type manufactures antibodies to both A and B types. Blood Type A people manufacture only anti-B antibodies, while type B people make only anti-A antibodies. Codominant alleles are both expressed. Heterozygotes for codominant alleles fully express both alleles. Blood

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type AB individuals produce both A and B antigens. Since neither A nor B is dominant over the other and they are both dominant over O they are said to be codominant.

Incomplete dominance

Incomplete dominance is a condition when neither allele is dominant over the other. condition is recognized by the heterozygotes expressing an intermediate phenotype relative to the parental phenotypes. If a red flowered plant is crossed with a white flowered one, the progeny will all be pink. When pink is crossed with pink, the progeny are 1 red, 2 pink, and 1 white.

Flower color in snapdragons is an example of this pattern. Cross a true-breeding red strain with a true-breeding white strain and the F1 are all pink (heterozygotes). Self-fertilize the F1 and you get an F2 ratio of 1 red: 2 pink: 1 white. This would not happen if true blending had occurred (blending cannot explain traits such as red or white skipping a generation and pink flowers crossed with pink flowers should produce ONLY pink flowers).

Multiple alleles

Many genes have more than two alleles (even though any one diploid individual can only have at most two alleles for any gene), such as the ABO blood groups in humans, which are an example of multiple alleles. Multiple alleles result from different mutations of the same gene. Coat color in rabbits is determined by four alleles. Human ABO blood types are determined by alleles A, B, and O. A and B are codominants which are both dominant over O. The only possible genotype for a type O person is OO. Type A people have either AA or AO genotypes. Type B people have either BB or BO genotypes. Type AB have only the AB (heterozygous) genotype. The A and B alleles of gene I produce slightly different glycoproteins (antigens) that are on the surface of each cell. Homozygous A individuals have only the A antigen, homozygous B individuals have only the B antigen, homozygous O individuals produce neither antigen, while a fourth phenotype (AB) produces both A and B antigens.

Interactions among genes

While one gene may make only one protein, the effects of those proteins usually interact (for example widow's peak may be masked by expression of the baldness gene). Novel phenotypes often result from the interactions of two genes, as in the case of the comb in chickens. The single comb is produced only by the rrpp genotype. Rose comb (b) results from R_pp. (_ can be either R or r). Pea comb (c) results from rrP_. Walnut comb, a novel phenotype, is produced when the genotype has at least one dominant of each gene (R_P_).

Epistasis

Epistasis is the term applied when one gene interferes with the expression of another (as in the baldness/widow's peak mentioned earlier). Bateson reported a different phenotypic ratio in sweet pea than could be explained by simple Mendelian inheritance. This ratio is 9:7 instead of the 9:3:3:1 one would expect of a dihybrid cross between heterozygotes. Of the two genes (C and P), when either is homozygous recessive (cc or pp) that gene is epistatic to (or hides) the other. To get purple flowers one must have both C and P alleles present.

Environment and Gene Expression

Phenotypes are always affected by their environment. In buttercup (Ranunculus peltatus), leaves below water-level are finely divided and those above water-level are broad, floating, photosynthetic leaf-like leaves. Siamese cats are darker on

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their extremities, due to temperature effects on phenotypic expression. Expression of phenotype is a result of interaction between genes and environment. Siamese cats and Himalayan rabbits both animals have dark colored fur on their extremities. This is caused by an allele that controls pigment production being able only to function at the lower temperatures of those extremities. Environment determines the phenotypic pattern of expression.

Polygenic Inheritance

Polygenic inheritance is a pattern responsible for many features that seem simple on the surface. Many traits such as height, shape, weight, color, and metabolic rate are governed by the cumulative effects of many genes. Polygenic traits are not expressed as absolute or discrete characters, as was the case with Mendel's pea plant traits. Instead, polygenic traits are recognizable by their expression as a gradation of small differences (a continuous variation). The results form a bell shaped curve, with a mean value and extremes in either direction.

Height in humans is a polygenic trait, as is color in wheat kernels. Height in humans is NOT discontinuous. If you line up the entire class a continuum of variation is evident, with an average height and extremes in variation (very short [vertically challenged?] and very tall [vertically enhanced]). Traits showing continuous variation are usually controlled by the additive effects of two or more separate gene pairs. This is an example of polygenic inheritance. The inheritance of EACH gene follows Mendelian rules.

Usually polygenic traits are distinguished by

1. Traits are usually quantified by measurement rather than counting. 2. Two or more gene pairs contribute to the phenotype. 3. Phenotypic expression of polygenic traits varies over a wide range.

Human polygenic traits include

1. Height 2. SLE (Lupus) Weight 3. Eye Color) 4. Intelligence 5. Skin Color 6. Many forms of behavior

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Pleiotropy

Pleiotropy is the effect of a single gene on more than one characteristic. An example is the "frizzle-trait" in chickens. The primary result of this gene is the production of defective feathers. Secondary results are both good and bad; good include increased adaptation to warm temperatures, bad include increased metabolic rate, decreased egg-laying, changes in heart, kidney and spleen. Cats that are white with blue eyes are often deaf, white cats with a blue and an yellow-orange eye are deaf on the side with the blue eye. Sickle-cell anemia is a human disease originating in warm lowland tropical areas where malaria is common. Sickle-celled individuals suffer from a number of problems, all of which are pleiotropic effects of the sickle-cell allele.

Genes and Chromosomes

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Linkage occurs when genes are on the same chromosome. Remember that sex-linked genes are on the X chromosome, one of the sex chromosomes. Linkage groups are invariably the same number as the pairs of homologous chromosomes an organism possesses. Recombination occurs when crossing-over has broken linkage groups, as in the case of the genes for wing size and body color that Morgan studied. Chromosome mapping was originally based on the frequencies of recombination between alleles.

Since mutations can be induced (by radiation or chemicals), Morgan and his coworkers were able to cause new alleles to form by subjecting fruit flies to mutagens (agents of mutation, or mutation generators). Genes are located on specific regions of a certain chromosome, termed the gene locus (plural: loci). A gene therefore is a specific segment of the DNA molecule.

Alfred Sturtevant, while an undergraduate student in Morgan's lab, postulated that crossing-over would be less common between genes adjacent to each other on the same chromosome and that it should be possible to plot the sequence of genes along a fruit fly chromosome by using crossing-over frequencies. Distances on gene maps are expressed in map units (one map unit = 1 recombinant per 100 fertilized eggs; or a 1% chance of recombination).

The map for Drosophila melanogaster chromosomes is well known Note that eye color and aristae length are far apart, as indicated by the occurrence of more recombinants (crossing-overs) between them, while wing length is closer to eye shape (as indicated by the low frequency of recombination between these two features).

Figure A illustrates the fruit fly chromosomes at metaphase; figure B shows a polytene chromosome.

Chromosome Abnormalities

Chromosome abnormalities include inversion, insertion, duplication, and deletion. These are types of mutations. Since DNA is information, and information typically has a beginning point, an inversion would produce an inactive or altered protein. Likewise deletion or duplication will alter the gene product.

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DNA AND MOLECULAR GENETICS

The physical carrier of inheritance

While the period from the early 1900s to World War II has been considered the "golden age" of genetics, scientists still had not determined that DNA, and not protein, was the hereditary material. However, during this time a great many genetic discoveries were made and the link between genetics and evolution was made.

Friedrich Meischer in 1869 isolated DNA from fish sperm and the pus of open wounds. Since it came from nuclei, Meischer named this new chemical, nuclein. Subsequently the name was changed to nucleic acid and lastly to deoxyribonucleic acid (DNA). Robert Feulgen, in 1914, discovered that fuchsin dye stained DNA. DNA was then found in the nucleus of all eukaryotic cells.

During the 1920s, biochemist P.A. Levene analyzed the components of the DNA molecule. He found it contained four nitrogenous bases: cytosine, thymine, adenine, and guanine; deoxyribose sugar; and a phosphate group. He concluded that the basic unit (nucleotide) was composed of a base attached to a sugar and that the phosphate also attached to the sugar. He (unfortunately) also erroneously concluded that the proportions of bases were equal and that there was a tetranucleotide that was the repeating structure of the molecule. The nucleotide, however, remains as the fundemantal unit (monomer) of the nucleic acid polymer. There are four nucleotides: those with cytosine (C), those with guanine (G), those with adenine (A), and those with thymine (T).

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During the early 1900s, the study of genetics began in earnest: the link between Mendel's work and that of cell biologists resulted in the chromosomal theory of inheritance; Garrod proposed the link between genes and "inborn errors of metabolism"; and the question was formed: what is a gene? The answer came from the study of a deadly infectious disease: pneumonia. During the 1920s Frederick Griffith studied the difference between a disease-causing strain of the pneumonia causing bacteria (Streptococcus peumoniae) and a strain that did not cause pneumonia. The pneumonia-

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causing strain (the S strain) was surrounded by a capsule. The other strain (the R strain) did not have a capsule and also did not cause pneumonia. Frederick Griffith (1928) was able to induce a nonpathogenic strain of the bacterium Streptococcus pneumoniae to become pathogenic. Griffith referred to a transforming factor that caused the non-pathogenic bacteria to become pathogenic. Griffith injected the different strains of bacteria into mice. The S strain killed the mice; the R strain did not. He further noted that if heat killed S strain was injected into a mouse, it did not cause pneumonia. When he combined heat-killed S with Live R and injected the mixture into a mouse (remember neither alone will kill the mouse) that the mouse developed pneumonia and died. Bacteria recovered from the mouse had a capsule and killed other mice when injected into them!

Hypotheses:

1. The dead S strain had been reanimated/resurrected.

2. The Live R had been transformed into Live S by some "transforming factor".

Further experiments led Griffith to conclude that number 2 was correct.

In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty revisited Griffith's experiment and concluded the transforming factor was DNA. Their evidence was strong but not totally conclusive. The then-current favorite for the hereditary material was protein; DNA was not considered by many scientists to be a strong candidate.

The breakthrough in the quest to determine the hereditary material came from the work of Max Delbruck and Salvador Luria in the 1940s. Bacteriophage are a type of virus that attacks bacteria, the viruses that Delbruck and Luria worked with were those attacking Escherichia coli, a bacterium found in human intestines. Bacteriophages consist of protein coats covering DNA. Bacteriophages infect a cell by injecting DNA into the host cell. This viral DNA then "disappears" while taking over the bacterial machinery and beginning to make new virus instead of new bacteria. After 25 minutes the host cell bursts, releasing hundreds of new bacteriophage. Phages have DNA and protein, making them ideal to resolve the nature of the hereditary material.

In 1952, Alfred D. Hershey and Martha Chase (click the link to view details of their experiment) conducted a series of experiments to determine whether protein or DNA was the hereditary material. By labeling the DNA and protein with different (and mutually exclusive) radioisotopes, they would be able to determine which chemical (DNA or protein) was getting into the bacteria. Such material must be the hereditary material (Griffith's transforming agent). Since DNA contains Phosphorous (P) but no Sulfur (S), they tagged the DNA with radioactive Phosphorous-32. Conversely, protein lacks P but does have S, thus it could be tagged with radioactive Sulfur-35. Hershey and Chase found that the radioactive S remained outside the cell while the radioactive P was found inside the cell, indicating that DNA was the physical carrier of heredity.

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The Structure of DNA

Erwin Chargaff analyzed the nitrogenous bases in many different forms of life, concluding that the amount of purines does not always equal the amount of pyrimidines (as proposed by Levene). DNA had been proven as the genetic material by the Hershey-Chase experiments, but how DNA served as genes was not yet certain. DNA must carry information from parent cell to daughter cell. It must contain information for replicating itself. It must be chemically stable, relatively unchanging. However, it must be capable of mutational change. Without mutations there would be no process of evolution.

Many scientists were interested in deciphering the structure of DNA, among them were Francis Crick, James Watson, Rosalind Franklin, and Maurice Wilkens. Watson and Crick gathered all available data in an attempt to develop a model of DNA structure. Franklin took X-ray diffraction photomicrographs of crystalline DNA extract, the key to the puzzle. The data known at the time was that DNA was a long molecule, proteins were helically coiled (as determined by the work of Linus Pauling), Chargaff's base data, and the x-ray diffraction data of Franklin and Wilkens.

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Ball and stick model of DNA.

X-ray diffraction photograph of the DNA double helix.

James Watson (L) and Francis Crick (R), and the model they built of the structure of DNA.

DNA is a double helix, with bases to the center (like rungs on a ladder) and sugar-phosphate units along the sides of the helix (like the sides of a twisted ladder). The strands are complementary (deduced by Watson and Crick from Chargaff's data, A pairs with T and C pairs with G, the pairs held together by hydrogen bonds). Notice that a double-ringed purine is always bonded to a single ring pyrimidine. Purines are Adenine (A) and Guanine (G). We have encountered Adenosine triphosphate (ATP) before, although in that case the sugar was ribose, whereas in DNA it is deoxyribose. Pyrimidines are Cytosine (C) and Thymine (T). The bases are complementary, with A on one side of the molecule you only get T on the other side, similarly with G and C. If we know the base sequence of one strand we know its complement.

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The ribbon model of DNA.

DNA Replication

DNA was proven as the hereditary material and Watson et al. had deciphered its structure. What remained was to determine how DNA copied its information and how that was expressed in the phenotype. Matthew Meselson and Franklin W. Stahl designed an experiment to determine the method of DNA replication. Three models of replication were considered likely.

1. Conservative replication would somehow produce an entirely new DNA strand during replication.

2. Semiconservative replication would produce two DNA molecules, each of which was composed of one-half of the parental DNA along with an entirely new complementary strand. In other words the new DNA would consist of one new and one old strand of DNA. The existing strands would serve as complementary templates for the new strand.

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3. Dispersive replication involved the breaking of the parental strands during replication, and somehow, a reassembly of molecules that were a mix of old and new fragments on each strand of DNA.

The Meselson-Stahl experiment involved the growth of E. coli bacteria on a growth medium containing heavy nitrogen (Nitrogen-15 as opposed to the more common, but lighter molecular weight isotope, Nitrogen-14). The first generation of bacteria was grown on a medium where the sole source of N was Nitrogen-15. The bacteria were then transferred to a medium with light (Nitrogen-14) medium. Watson and Crick had predicted that DNA replication was semi-conservative. If it was, then the DNA produced by bacteria grown on light medium would be intermediate between heavy and light. It was.

DNA replication involves a great many building blocks, enzymes and a great deal of ATP energy (remember that after the S phase of the cell cycle cells have a G phase to regenerate energy for cell division). Only occurring in a cell once per (cell) generation, DNA replication in humans occurs at a rate of 50 nucleotides per second, 500/second in prokaryotes. Nucleotides have to be assembled and available in the nucleus, along with energy to make bonds between nucleotides. DNA polymerases unzip the helix by breaking the H-bonds between bases. Once the polymerases have opened the molecule, an area known as the replication bubble forms (always initiated at a certain set of nucleotides, the origin of replication). New nucleotides are placed in the fork and link to the corresponding parental nucleotide already there (A with T, C with G). Prokaryotes open a single replication bubble, while eukaryotes have multiple bubbles. The entire length of the DNA molecule is replicated as the bubbles meet.

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Since the DNA strands are antiparallel, and replication proceeds in the 5' to 3' direction on EACH strand, one strand will form a continuous copy, while the other will form a series of short Okazaki fragments.

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PROTEIN SYNTHESIS

One-gene-one-protein

During the 1930s, despite great advances, geneticists had several frustrating questions yet to answer:

What exactly are genes?

How do they work?

What produces the unique phenotype associated with a specific allele?

Answers from physics, chemistry, and the study of infectious disease gave rise to the field of molecular biology. Biochemical reactions are controlled by enzymes, and often are organized into chains of reactions known as metabolic pathways. Loss of activity in a single enzyme can inactivate an entire pathway.

Archibald Garrod, in 1902, first proposed the relationship through his study of alkaptonuria and its association with large quantities "alkapton". He reasoned unaffected individuals metabolized "alkapton" (now called homogentistic acid) to other products so it would not buildup in the urine. Garrod suspected a blockage of the pathway to break this chemical down, and proposed that condition as "an inborn error of metabolism". He also discovered alkaptonuria was inherited as a recessive Mendelian trait.

George Beadle and Edward Tatum during the late 1930s and early 1940s established the connection Garrod suspected between genes and metabolism. They used X rays to cause mutations in strains of the mold Neurospora. These mutations affected a single genes and single enzymes in specific metabolic pathways. Beadle and Tatum proposed the "one gene one enzyme hypothesis" for which they won the Nobel Prize in 1958.

Since the chemical reactions occurring in the body are mediated by enzymes, and since enzymes are proteins and thus heritable traits, there must be a relationship between the gene and proteins. George Beadle, during the 1940s, proposed that mutant eye colors in Drosophila was caused by a change in one protein in a biosynthetic pathway.

In 1941 Beadle and coworker Edward L. Tatum decided to examine step by step the chemical reactions in a pathway. They used Neurospora crassa as an experimental organism. It had a short life-cycle and was easily grown. Since it is haploid for much of its life cycle, mutations would be immediately expressed. The meiotic products could be easily inspected. Chromosome mapping studies on the organism facilitated their work. Neurospora can be grown on a minimal medium, and it's nutrition could be studied by its ability to metabolize sugars and other chemicals the scientist could add or delete from the mixture of the medium. It was able to synthesize all of the amino acids and other chemicals needed for it to grow, thus mutants in synthetic pathways would easily show up. X-rays induced mutations in Neurospora, and the mutated spores were placed on growth media enriched with all essential amino acids. Crossing the mutated fungi with non-mutated forms produced spores which were then grown on media supplying only one of the 20 essential amino acids. If a spore lacked the ability to synthesize a particular amino acid, such as Pro (proline), it would only grow if the Proline was in the growth medium. Biosynthesis of amino acids (the building blocks of proteins) is a complex process with many chemical reactions mediated by enzymes, which if mutated would shut down the pathway, resulting in no-growth. Beadle and Tatum proposed the "one gene one enzyme" theory. One gene codes for the production of one protein. "One gene one enzyme" has since been modified to "one gene one polypeptide" since many proteins (such as hemoglobin) are made of more than one polypeptide.

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The Structure of Hemoglobin

Linus Pauling used electrophoresis to separate hemoglobin molecules. Sickle-cell anemia (h) is a recessive allele in which a defective hemoglobin is made, ultimately causing pain and death to those individuals homozygous recessive for the trait. Pauling reasoned that if Beadle and Tatum were correct, there should be a slight (but detectable) difference between the structure of a normal (HH) and sickle cell (hh) hemoglobin due to genetic differences. Heterozygotes (Hh, also sampled by Pauling) make both normal and "sickle cell" hemoglobins. Later, Vernon Ingram discovered that the normal and sickle-cell hemoglobins differ by only 1 (out of a total of 300) amino acids.

Viruses Contain DNA

The coats of viruses act as antigens, initiating an antigen-specific antibody response. Remember that vaccines work by either prompting the immune system to make antibodies or by supplying antibodies. If a virus (or anything else for that matter) mutates its antigens, the immune system is forever playing catch-up.

RNA Links the Information in DNA to the Sequence of Amino Acids in Protein

Ribonucleic acid (RNA) was discovered after DNA. DNA, with exceptions in chloroplasts and mitochondria, is restricted to the nucleus (in eukaryotes, the nucleoid region in prokaryotes). RNA occurs in the nucleus as well as in the cytoplasm (also remember that it occurs as part of the ribosomes that line the rough endoplasmic reticulum).

Scientists for some time had suspected such a link between DNA and proteins. Cells of developing embryos contain high levels of RNA. Rapidly growing E. coli has half its mass as ribosomes. Ribosomes are 2/3 RNA (a type of RNA known as ribosomal RNA or rRNA) and 1/3 protein. RNA is synthesized from viral DNA in an infected cell before protein synthesis begins. Some viruses, for example Tobacco Mosaic Virus (TMV) have RNA in place of DNA. If RNA extracted from a virus was injected into a host cell the cell began to make new viruses. Clearly RNA was involved in protein synthesis.

Crick's central dogma. Information flow (with the exception of reverse transcription) is from DNA to RNA via the process of transcription, and thence to protein via translation. Transcription is the making of an RNA molecule off a DNA template. Translation is the construction of an amino acid sequence (polypeptide) from an RNA molecule. Although originally called dogma, this idea has been tested repeatedly with almost no exceptions to the rule being found (save retroviruses).

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Messenger RNA (mRNA) is the blueprint for construction of a protein. Ribosomal RNA (rRNA) is the construction site where the protein is made. Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time.

RNA has ribose sugar instead of deoxyribose sugar. The base uracil (U) replaces thymine (T) in RNA. Most RNA is single stranded, although tRNA will form a "cloverleaf" structure due to complementary base pairing.

Transcription: making an RNA copy of a DNA sequence

RNA polymerase opens the part of the DNA to be transcribed. Only one strand of DNA (the template strand) is transcribed. RNA nucleotides are available in the region of the chromatin (this process only occurs during Interphase) and are linked together similar to the DNA process.

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The Genetic Code: Translation of RNA code into protein

The code consists of at least three bases, according to astronomer George Gamow. To code for the 20 essential amino acids a genetic code must consist of at least a 3-base set (triplet) of the 4 bases. If one considers the possibilities of arranging four things 3 at a time (4X4X4), we get 64 possible code words, or codons (a 3-base sequence on the mRNA that codes for either a specific amino acid or a control word).

The genetic code was broken by Marshall Nirenberg and Heinrich Matthaei, a decade after Watson and Crick's work. Nirenberg discovered that RNA, regardless of its source organism, could initiate protein synthesis when combined with contents of broken E. coli cells. By adding poly-U to each of 20 test-tubes (each tube having a different "tagged" amino acid) Nirenberg and Matthaei were able to determine that the codon UUU (the only one in poly-U) coded for the amino acid phenylalanine.

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Likewise, an artificial mRNA consisting of alternating A and C bases would code for alternating amino acids histidine and threonine. Gradually, a complete listing of the genetic code codons was developed.

The genetic code consists of 61 amino-acid coding codons and three termination codons, which stop the process of translation. The genetic code is thus redundant (degenerate in the sense of having multiple states amounting to the same thing), with, for example, glycine coded for by GGU, GGC, GGA, and GGG codons. If a codon is mutated, say from GGU to CGU, is the same amino acid specified?

Protein Synthesis

Prokaryotic gene regulation differs from eukaryotic regulation, but since prokaryotes are much easier to work with, we focus on prokaryotes at this point. Promoters are sequences of DNA that are the start signals for the transcription of mRNA. Terminators are the stop signals. mRNA molecules are long (500- 10,000 nucleotides).

Ribosomes are the organelle (in all cells) where proteins are synthesized. They consist of two-thirds rRNA and one-third protein. Ribosomes consist of a small (in E. coli , 30S) and larger (50S) subunits. The length of rRNA differs in each. The 30S unit has 16S rRNA and 21 different proteins. The 50S subunit consists of 5S and 23S rRNA and 34 different proteins. The smaller subunit has a binding site for the mRNA. The larger subunit has two binding sites for tRNA.

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Transfer RNA (tRNA) is basically cloverleaf-shaped. tRNA carries the proper amino acid to the ribosome when the codons call for them. At the top of the large loop are three bases, the anticodon, which is the complement of the codon. There are 61 different tRNAs, each having a different binding site for the amino acid and a different anticodon. For the codon UUU, the complementary anticodon is AAA. Amino acid linkage to the proper tRNA is controlled by the aminoacyl-tRNA synthetases. Energy for binding the amino acid to tRNA comes from ATP conversion to adenosine monophosphate (AMP).

Translation is the process of converting the mRNA codon sequences into an amino acid sequence. The initiator codon (AUG) codes for the amino acid N-formylmethionine (f-Met). No transcription occurs without the AUG codon. f-Met is always the first amino acid in a polypeptide chain, although frequently it is removed after translation. The intitator tRNA/mRNA/small ribosomal unit is called the initiation complex. The larger subunit attaches to the initiation complex. After the initiation phase the message gets longer during the elongation phase.

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New tRNAs bring their amino acids to the open binding site on the ribosome/mRNA complex, forming a peptide bond between the amino acids. The complex then shifts along the mRNA to the next triplet, opening the A site. The new tRNA enters at the A site. When the codon in the A site is a termination codon, a releasing factor binds to the site, stopping translation and releasing the ribosomal complex and mRNA.

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Often many ribosomes will read the same message, a structure known as a polysome forms. In this way a cell may rapidly make many proteins.

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Mutations Redefined

We earlier defined mutations as any change in the DNA. We now can refine that definition: a mutation is a change in the DNA base sequence that results in a change of amino acid(s) in the polypeptide coded for by that gene. Alleles are alternate sequences of DNA bases (genes), and thus at the molecular level the products of alleles differ (often by only a single amino acid, which can have a ripple effect on an organism by changing ). Addition, deletion, or addition of nucleotides can alter the polypeptide. Point mutations are the result of the substitution of a single base. Frame-shift mutations occur when the reading frame of the gene is shifted by addition or deletion of one or more bases. With the exception of mitochondria, all organisms use the same genetic code. Powerful evidence for the common ancestry of all living things.

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POPULATION ECOLOGY

Ecology

In previous chapters/units we have concentrated on the biology of the individual cell, tissue, and organism. There are levels of organization above the individual organism that will be the subject of this unit. Individual organisms are grouped into populations, which in turn form communities, which form ecosystems. Ecosystems make up the biosphere, which includes all life on Earth. If there is life on other planets, will we need another level of organization?

Biosphere: The sum of all living things taken in conjunction with their environment. In essence, where life occurs, from the upper reaches of the atmosphere to the top few meters of soil, to the bottoms of the oceans. We divide the earth into atmosphere (air), lithosphere (earth), hydrosphere (water), and biosphere (life).

Ecosystem: The relationships of a smaller groups of organisms with each other and their environment. Scientists often speak of the interrelatedness of living things. Since, according to Darwin's theory, organisms adapt to their environment, they must also adapt to other organisms in that environment. We can discuss the flow of energy through an ecosystem from photosynthetic autotrophs to herbivores to carnivores.

Community: The relationships between groups of different species. For example, the desert communities consist of rabbits, coyotes, snakes, birds, mice and such plants as sahuaro cactus (Carnegia gigantea), Ocotillo, creosote bush, etc. Community structure can be disturbed by such things as fire, human activity, and over-population.

Species: Groups of similar individuals who tend to mate and produce viable, fertile offspring. We often find species described not by their reproduction (a biological species) but rather by their form (anatomical or form species).

Populations: Groups of similar individuals who tend to mate with each other in a limited geographic area. This can be as simple as a field of flowers, which is separated from another field by a hill or other area where none of these flowers occur.

Individuals: One or more cells characterized by a unique arrangement of DNA "information". These can be unicellular or multicellular. The multicellular individual exhibits specialization of cell types and division of labor into tissues, organs, and organ systems.

Ecology is the study how organisms interact with each other and their physical environment. These interactions are often quite complex. Human activity frequently disturbs living systems and affects these interactions. Ecological predictions are, of a consequence, often more general than we would like.

Population Growth

A population is a group of individuals of the same species living in the same geographic area. The study of factors that affect growth, stability, and decline of populations is population dynamics. All populations undergo three distinct phases of their life cycle:

1. growth 2. stability

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3. decline

Population growth occurs when available resources exceed the number of individuals able to exploit them. Reproduction is rapid, and death rates are low, producing a net increase in the population size.

Population stability is often proceeded by a "crash" since the growing population eventually outstrips its available resources. Stability is usually the longest phase of a population's life cycle.

Decline is the decrease in the number of individuals in a population, and eventually leads to population extinction.

Factors Influencing Population Growth

Nearly all populations will tend to grow exponentially as long as there are resources available. Most populations have the potential to expand at an exponential rate, since reproduction is generally a multiplicative process. Two of the most basic factors that affect the rate of population growth are the birth rate, and the death rate. The intrinsic rate of increase is the birth rate minus the death rate.

Two modes of population growth. The Exponential curve (also known as a J-curve) occurs when there is no limit to population size. The Logistic curve (also known as an S-curve) shows the effect of a limiting factor (in this case the carrying capacity of the environment).

Population Growth Potential Is Related to Life History

The age within it's individual life cycle at which an organism reproduces affects the rate of population increase. Life history refers to the age of sexual maturity, age of death, and other events in that individual's lifetime that influence reproductive traits. Some organisms grow fast, reproduce quickly, and have abundant offspring each reproductive cycle. Other organisms grow slowly, reproduce at a late age, and have few offspring per cycle. Most organisms are intermediate to these two extremes.

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Age structure refers to the relative proportion of individuals in each age group of a population. Populations with more individuals aged at or before reproductive age have a pyramid-shaped age structure graph, and can expand rapidly as the young mature and breed. Stable populations have relatively the same numbers in each of the age classes.

Comparison of the population age structure in the United States and Mexico. Note the demographic bulge in the Mexican population. The effects of this bulge will be felt for generations. 

Human populations are in a growth phase. Since evolving about 200,000 years ago, our species has proliferated and spread over the Earth. Beginning in 1650, the slow population increases of our species exponentially increased. New technologies for hunting and farming have enabled this expansion. It took 1800 years to reach a total population of 1 billion, but only 130 years to reach 2 billion, and a mere 45 years to reach 4 billion.

Despite technological advances, factors influencing population growth will eventually limit expansion of human population. These will involve limitation of physical and biological resources as world population increased to over six billion in 1999. The 1987 population was estimated at a puny 5 billion.

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Human population growth over the past 10,000 years. Note the effects of worldwide disease (the Black death) and technological advances on the population size.

Populations Transition Between Growth and Stability

Limits on population growth can include food supply, space, and complex interactions with other physical and biological factors (including other species). After an initial period of exponential growth, a population will encounter a limiting factor that will cause the exponential growth to stop. The population enters a slower growth phase and may eventually stabilize at a fairly constant population size within some range of fluctuation. This model fits the logistic growth model. The carrying capacity is the point where population size levels off.

Several Basic Controls Govern Population Size

The environment is the ultimate cause of population stabilization. Two categories of factors are commonly used: physical environment and biological environment. Three subdivisions of the biological environment are competition, predation, and symbiosis.

Physical environment factors include food, shelter, water supply, space availability, and (for plants) soil and light. One of these factors may severely limit population size, even if the others are not as constrained. The Law of the Minimum states that population growth is limited by the resource in the shortest supply.

The biological role played by a species in the environment is called a niche. Organisms/populations in competition have a niche overlap of a scarce resource for which they compete. Competitive exclusion occurs between two species when competition is so intense that one species completely eliminates the second species from an area. In nature this is rather rare. While owls and foxes may compete for a common food source, there are alternate sources of food available. Niche overlap is said to be minimal.

Paramecium aurelia has a population nearly twice as large when it does not have to share its food source with a competing species. Competitive release occurs when the competing species is no longer present and its constraint on the winner's population size is removed.

Predators kill and consume other organisms. Carnivores prey on animals, herbivores consume plants. Predators usually limit the prey population, although in extreme cases they can drive the prey to extinction. There are three major reasons why predators rarely kill and eat all the prey:

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1. Prey species often evolve protective mechanisms such as camouflage, poisons, spines, or large size to deter predation.

2. Prey species often have refuges where the predators cannot reach them. 3. Often the predator will switch its prey as the prey species becomes lower in abundance: prey switching.

Fluctuations in predator (wolf) and prey (moose) populations over a 40-year span. Note the effects of declines in the wolf population in the late 1960s and again in the early 1980s on the moose population.

Symbiosis has come to include all species interactions besides predation and competition.

Mutualism is a symbiosis where both parties benefit, for example algae (zooxanthellae) inside reef-building coral.

Parasitism is a symbiosis where one species benefits while harming the other. Parasites act more slowly than predators and often do not kill their host.

Commensalism is a symbiosis where one species benefits and the other is neither harmed nor gains a benefit: Spanish moss on trees, barnacles on crab shells.

Amensalism is a symbiosis where members of one population inhibit the growth of another while being unaffected themselves.

The Real World Has a Complex Interaction of Population Controls

Natural populations are not governed by a single control, but rather have the combined effects of many controls simultaneously playing roles in determining population size. If two beetle species interact in the laboratory, one result occurs; if a third species is introduced, a different outcome develops. The latter situation is more like nature, and changes in one population may have a domino effect on others.

Which factors, if either, is more important in controlling population growth: physical or biological? Physical factors may play a dominant role, and are called density independent regulation, since population density is not a factor The other extreme has biological factors dominant, and is referred to as density dependent regulation,

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since population density is a factor. It seems likely that one or the other extreme may dominate in some environments, with most environments having a combination control.

Population Decline and Extinction

Extinction is the elimination of all individuals in a group. Local extinction is the loss of all individuals in a population. Species extinction occurs when all members of a species and its component populations go extinct. Scientists estimate that 99% of all species that ever existed are now extinct. The ultimate cause of decline and extinction is environmental change. Changes in one of the physical factors of the environment may cause the decline and extinction; likewise the fossil record indicates that some extinctions are caused by migration of a competitor.

Dramatic declines in human population happen periodically in response to an infectious disease. Bubonic plague infections killed half of Europe's population between 1346 and 1350, later plagues until 1700 killed one quarter of the European populace. Smallpox and other diseases decimated indigenous populations in North and South America.

Human Impact

Human populations have continued to increase, due to use of technology that has disrupted natural populations. Destabilization of populations leads to possible outcomes:

population growth as previous limits are removed population decline as new limits are imposed

Agriculture and animal domestication are examples of population increase of favored organisms. In England alone more than 300,000 cats are put to sleep per year, yet before their domestication, the wild cat ancestors were rare and probably occupied only a small area in the Middle East.

Pollution

Pollutants generally are (unplanned?) releases of substances into the air and water. Many lakes often have nitrogen and phosphorous as limiting nutrients for aquatic and terrestrial plants. Runoff from agricultural fertilizers increases these nutrients, leading to runaway plant growth, or eutrophication. Increased plant populations eventually lead to increased bacterial populations that reduce oxygen levels in the water, causing fish and other organisms to suffocate.

Pesticides and Competition

Removal of a competing species can cause the ecological release of a population explosion in that species competitor. Pesticides sprayed on wheat fields often result in a secondary pest outbreak as more-tolerant-to-pesticide species expand once less tolerant competitors are removed.

Removal of Predators

Predator release is common where humans hunt, trap, or otherwise reduce predator populations, allowing the prey population to increase. Elimination of wolves and panthers have led to increase in their natural prey: deer. There are more deer estimated in the United States than there were when Europeans arrived. Large deer populations often cause over grazing that in turn leads to starvation of the deer.

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Introduction of New Species

Introduction of exotic or alien non-native species into new areas is perhaps the greatest single factor to affect natural populations. More than 1500 exotic insect species and more than 25 families of alien fish have been introduced into North America; in excess of 3000 plant species have also been introduced. The majority of accidental introductions may fail, however, once an introduced species becomes established, its population growth is explosive. Kudzu, a plant introduced to the American south from Japan, has taken over large areas of the countryside.

Altering Population Growth

Humans can remove or alter the constraints on population sizes, with both good and bad consequences. On the negative side, about 17% of the 1500 introduced insect species require the use of pesticides to control them. For example, African killer bees are expanding their population and migrating from northward from South America. These killer bees are much more aggressive than the natives, and destroy native honeybee populations.

On a positive note, human-induced population explosions can provide needed resources for growing human populations. Agriculture now produces more food per acre, allowing and sustaining increased human population size.

Human action is causing the extinction of species at thousands of times the natural rate. Extinction is caused by alteration of a population's environment in a harmful way. Habitat disruption is the disturbance of the physical environment of a species, for example cutting a forest or draining wetlands. Habitat disruption in currently the leading cause of extinction.

Changes in the biological environment occur in three ways.

1. Species introduction: An exotic species is introduced into an area where it may have no predfators to control its population size, or where it can gratly out compete native organisms. Examples include zebra mussels introduced into Lake Erie, and lake trout released into Yellowstone Lake where they are threatening the native cutthroat trout populations.

2. Overhunting: When a predator population increases or becomes more efficient at killing the prey, the prey population may decline or go extinct. Examples today include big game hunting, which has in many places reduced the predator (or in this case prey) population. In human prehistory we may have caused the extinction of the mammoths and mastodons due to increased human hunting skill.

3. Secondary extinction: Loss of food species can cause migration or extinction of any species that depends largely or solely on that species as a food source.

Overkill is the shooting, trapping, or hunting of a species usually for sport or economic reasons. Unfortunately, this cannot eliminate "pest" species like cockroaches and mice due to their large population sizes and capacity to reproduce more rapidly than we can eliminate them. However, many large animals have been eliminated or had their populations drastically reduced (such as tigers, elephants, and leopards).

The death of one species or population can cause the decline or elimination of others, a process known as secondary extinction. Destruction of bamboo forests in China, the food for the giant panda, may cause the extinction of the panda. The extinction of the dodo bird has caused the Calviera tree to become unable to reproduce since the dodo ate the fruit and processed the seeds of that tree.

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Giant pandas eat an estimated 10,000 pounds of bamboo per panda per year.

Populations Have a Minimum Viable Size

Even if a number of individuals survive, the population size may become too small for the species to continue. Small populations may have breeding problems. They are susceptible to random environmental fluctuations and genetic drift to a greater degree than are larger populations. The chance of extinction increases exponentially with decreasing population size.

The minimum viable population (MVP) is the smallest population size that can avoid extinction by the two reasons listed above. If no severe environmental fluxes develop for a long enough time, a small population will recover. The MVP depends heavily on reproductive rates of the species.

Range and Density

Populations tend to have a maximum density near the center of their geographic range. Geographic range is the total area occupied by the species. Outlying zones, where conditions are less optimal, include the zone of physiological stress (where individuals are rare), and eventually the zone of intolerance (where individuals are not found).

The environment is usually never uniform enough to support uniform distribution of a species. Species thus have a dispersion pattern. Three patterns found include uniform, clumped, and random.

Geographic ranges of species are dynamic, over time they can contract or expand due to environmental change or human activity. Often a species will require another species' presence, for example Drosophila in Hawaii. Species ranges can also expand due to human actions: brown trout are now found worldwide because of the spread of trout fishing.

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COMMUNITY AND ECOSYSTEM DYNAMICS

Definitions

A community is the set of all populations that inhabit a certain area. Communities can have different sizes and boundaries. These are often identified with some difficulty.

An ecosystem is a higher level of organization the community plus its physical environment. Ecosystems include both the biological and physical components affecting the community/ecosystem. We can study ecosystems from a structural view of population distribution or from a functional view of energy flow and other processes.

Community Structure

Ecologists find that within a community many populations are not randomly distributed. This recognition that there was a pattern and process of spatial distribution of species was a major accomplishment of ecology. Two of the most important patterns are open community structure and the relative rarity of species within a community.

Do species within a community have similar geographic range and density peaks? If they do, the community is said to be a closed community, a discrete unit with sharp boundaries known as ecotones. An open community, however, has its populations without ecotones and distributed more or less randomly.

In a forest, where we find an open community structure, there is a gradient of soil moisture. Plants have different tolerances to this gradient and occur at different places along the continuum. Where the physical environment has abrupt transitions, we find sharp boundaries developing between populations. For example, an ecotone develops at a beach separating water and land.

Open structure provides some protection for the community. Lacking boundaries, it is harder for a community to be destroyed in an all or nothing fashion. Species can come and go within communities over time, yet the community as a whole persists. In general, communities are less fragile and more flexible than some earlier concepts would suggest.

Most species in a community are far less abundant than the dominant species that provide a community its name: for example oak-hickory, pine, etc. Populations of just a few species are dominant within a community, no matter what community we examine. Resource partitioning is thought to be the main cause for this distribution.

Classification of Communities

There are two basic categories of communities: terrestrial (land) and aquatic (water). These two basic types of community contain eight smaller units known as biomes. A biome is a large-scale category containing many communities of a similar nature, whose distribution is largely controlled by climate

Terrestrial Biomes: tundra, grassland, desert, taiga, temperate forest, tropical forest. Aquatic Biomes: marine, freshwater.

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Major terrestrial biomes.

Terrestrial Biomes

Tundra and Desert

The tundra and desert biomes occupy the most extreme environments, with little or no moisture and extremes of temperature acting as harsh selective agents on organisms that occupy these areas. These two biomes have the fewest numbers of species due to the stringent environmental conditions. In other words, not everyone can live there due to the specialized adaptations required by the environment.

Tropical Rain Forests

Tropical rain forests occur in regions near the equator. The climate is always warm (between 20° and 25° C) with plenty of rainfall (at least 190 cm/year). The rain forest is probably the richest biome, both in diversity and in total biomass. The tropical rain forest has a complex structure, with many levels of life. More than half of all terrestrial species live in this biome. While diversity is high, dominance by a particular species is low.

While some animals live on the ground, most rain forest animals live in the trees. Many of these animals spend their entire life in the forest canopy. Insects are so abundant in tropical rain forests that the majority have not yet been identified. Charles Darwin noted the number of species found on a single tree, and suggested the richness of the rain forest would stagger the future systematist with the size of the catalogue of animal species found there. Termites are critical in the decomposition and nutrient cycling of wood. Birds tend to be brightly colored, often making them sought after as exotic pets. Amphibians and reptiles are well represented. Lemurs, sloths, and monkeys feed on fruits in tropical rain forest trees. The largest carnivores are the cats (jaguars in South

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America and leopards in Africa and Asia). Encroachment and destruction of habitat put all these animals and plants at risk.

Epiphytes are plants that grow on other plants. These epiphytes have their own roots to absorb moisture and minerals, and use the other plant more as an aid to grow taller. Some tropical forests in India, Southeast Asia, West Africa, Central and South American are seasonal and have trees that shed leaves in dry season. The warm, moist climate supports high productivity as well as rapid decomposition of detritus.

With its yearlong growing season, tropical forests have a rapid cycling of nutrients. Soils in tropical rain forests tend to have very little organic matter since most of the organic carbon is tied up in the standing biomass of the plants. These tropical soils, termed laterites, make poor agricultural soils after the forest has been cleared.

About 17 million hectares of rain forest are destroyed each year (an area equal in size to Washington state). Estimates indicate the forests will be destroyed (along with a great part of the Earth's diversity) within 100 years. Rainfall and climate patterns could change as a result.

Temperate Forests

The temperate forest biome occurs south of the taiga in eastern North America, eastern Asia, and much of Europe. Rainfall is abundant (30-80 inches/year; 75-150 cm) and there is a well-defined growing season of between 140 and 300 days. The eastern United States and Canada are covered (or rather were once covered) by this biome's natural vegetation, the eastern deciduous forest. Dominant plants include beech, maple, oak; and other deciduous hardwood trees. Trees of a deciduous forest have broad leaves, which they lose in the fall and grow again in the spring..

Sufficient sunlight penetrates the canopy to support a well-developed understory composed of shrubs, a layer of herbaceous plants, and then often a ground cover of mosses and ferns. This stratification beneath the canopy provides a numerous habitats for a variety of insects and birds. The deciduous forest also contains many members of the rodent family, which serve as a food source for bobcats, wolves, and foxes. This area also is a home for deer and black bears. Winters are not as cold as in the taiga, so many amphibian and reptiles are able to survive.

Shrubland (Chaparral)

The shrubland biome is dominated by shrubs with small but thick evergreen leaves that are often coated with a thick, waxy cuticle, and with thick underground stems that survive the dry summers and frequent fires. Shrublands occur in parts of South America, western Australia, central Chile, and around the Mediterranean Sea. Dense shrubland in California, where the summers are hot and very dry, is known as chaparral. This Mediterranean-type shrubland lacks an understory and ground litter, and is also highly flammable. The seeds of many species require the heat and scarring action of fire to induce germination.

Grasslands

Grasslands occur in temperate and tropical areas with reduced rainfall (10-30 inches per year) or prolonged dry seasons. Grasslands occur in the Americas, Africa, Asia, and Australia. Soils in this region are deep and rich and are excellent for agriculture. Grasslands are almost entirely devoid of trees, and can support large herds of grazing animals. Natural grasslands once covered over 40 percent of the earth's land surface. In temperate areas where rainfall is between 10 and 30 inches a year, grassland is the climax community because it is too wet for desert and too dry for forests.

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Most grasslands have now been utilized to grow crops, especially wheat and corn. Grasses are the dominant plants, while grazing and burrowing species are the dominant animals. The extensive root systems of grasses allows them to recover quickly from grazing, flooding, drought, and sometimes fire.

Temperate grasslands include the Russian steppes, the South American pampas, and North American prairies. A tall-grass prairie occurs where moisture is not quite sufficient to support trees.

Animal life includes mice, prairie dogs, rabbits, and animals that feed on them (hawks and snakes). Prairies once contained large herds of buffalo and pronghorn antelope, but with human activity these once great herds have dwindled.

The savanna is a tropical grassland that contains some trees. The savanna contains the greatest variety and numbers of herbivores (antelopes, zebras, and wildebeests, among others). This environment supports a large population of carnivores (lions, cheetahs, hyenas, and leopards). Any plant litter not consumed by grazers is attacked by termites and other decomposers. Once again, human activities are threatening this biome, reducing the range for herbivores and carnivores. Will extinction of the great cats be a result?

Deserts

Deserts are characterized by dry conditions (usually less than 10 inches per year; 25 cm) and a wide temperature range. The dry air leads to wide daily temperature fluctuations from freezing at night to over 120 degrees during the day. Most deserts occur at latitudes of 30o N or S where descending air masses are dry. Some deserts occur in the rainshadow of tall mountain ranges or in coastal areas near cold offshore currents. Plants in this biome have developed a series of adaptations (such as succulent stems, and small, spiny, or absent leaves) to conserve water and deal with these temperature extremes. Photosynthetic modifications (CAM) are another strategy to life in the drylands.

The Sahara and a few other deserts have almost no vegetation. Most deserts, however, are home to a variety of plants, all adapted to heat and lack of abundant water (succulents and cacti).. Animal life of the Sonoran desert includes arthropods (especially insects and spiders), reptiles (lizards and snakes), running birds (the roadrunner of the American southwest and Warner Brothers cartoon fame), rodents (kangaroo rat and pack rat), and a few larger birds and mammals (hawks, owls, and coyotes).

Taiga (Boreal Forest)

The taiga (pronounced "tie-guh") is a coniferous forest extending across most of the northern area of northern Eurasia and North America. This forest belt also occurs in a few other areas, where it has different names: the montane coniferous forest when near mountain tops; and the temperate rain forest along the Pacific Coast as far south as California. The taiga receives between 10 and 40 inches of rain per year and has a short growing season. Winters are cold and short, while summers tend to be cool. The taiga is noted for its great stands of spruce, fir, hemlock, and pine. These trees have thick protective leaves and bark, as well as needlelike (evergreen) leaves can withstand the weight of accumulated snow. Taiga forests have a limited understory of plants, and a forest floor covered by low-lying mosses and lichens. Conifers, alders, birch and willow are common plants; wolves, grizzly bears, moose, and caribou are common animals. Dominance of a few species is pronounced, but diversity is low when compared to temperate and tropical biomes.

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Tundra

The tundra, covers the northernmost regions of North America and Eurasia, about 20% of the Earth's land area. This biome receives about 20 cm (8-10 inches) of rainfall annually. Snow melt makes water plentiful during summer months. Winters are long and dark, followed by very short summers. Water is frozen most of the time, producing frozen soil, permafrost. Vegetation includes no trees, but rather patches of grass and shrubs; grazing musk ox, reindeer, and caribou exist along with wolves, lynx, and rodents. A few animals highly adapted to cold live in the tundra year-round (lemming, ptarmigan). During the summer the tundra hosts numerous insects and migratory animals. The ground is nearly completely covered with sedges and short grasses during the short summer. There are also plenty of patches of lichens and mosses. Dwarf woody shrubs flower and produce seeds quickly during the short growing season. The alpine tundra occurs above the timberline on mountain ranges, and may contain many of the same plants as the arctic tundra.

Climate, Altitude and Terrestrial Biomes

Climate controls biome distribution by an altitudinal gradient and a latitudinal gradient. With increases of either altitude or latitude, cooler and drier conditions occur. Cooler conditions can cause aridity since cooler air can hold less water vapor than can warmer air.

Deserts can occur in warm areas due to a blockage of air circulation patterns that form a rain shadow, or from atmospheric circulation patters. Warm air rises, producing low pressure areas. Cooler air sinks, producing high pressure areas. The tropics tend to be atmospheric low pressure zones the arctic areas atmospheric highs. Relative humidity is a measure of how much water an air mass at a given temperature can hold. In short, warm air can hold more moisture than can cold air. This basic physical feature of air helps explain the distribution of some of the world's great deserts.

The warm, moist air masses in the tropics rise upward in the atmosphere as they heat. The pressure of air rising forces air in the upper atmosphere to flow away north and south. This air at higher elevations is cooler and loses much of its moisture as rainfall. When the air masses begin to descend they heat up and begin to draw moisture from the lands they descend upon, at 30 degrees north and south of the equator. Many of the world's deserts are at approximately 30 degrees latitude.

Rain shadow deserts also form when cool, dry air masses descend after passing over a tall mountain range, such as the Coast Range and Sierras in California. The Sonoran desert in Arizona is a doubly caused desert, being at 30 degrees latitude as well as in the rain shadow of California mountains.

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Global Wind Patterns

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Aquatic Biomes

Conditions in water are generally less harsh than those on land. Aquatic organisms are buoyed by water support, and do not usually have to deal with desiccation. Despite covering 71% of the Earth's surface, areas of the open ocean are a vast aquatic desert containing few nutrients and very little life. Clear-cut biome distinctions in water, like those on land, are difficult to make. Dissolved nutrients controls many local aquatic distributions. Aquatic communities are classified into: freshwater (inland) communities and marine (saltwater or oceanic)

communities.

The Marine Biome

The marine biome contains more dissolved minerals than the freshwater biome. Over 70% of the Earth's surface is covered in water, by far the vast majority of that being saltwater. There are two basic categories to this biome: benthic and pelagic. Benthic communities (bottom dwellers) are subdivided by depth: the shore/shelf and deep sea. Pelagic communities (swimmers or floaters suspended in the water column) include planktonic (floating) and

nektonic (swimming) organisms. The upper 200 meters of the water column is the euphotic zone to which light can penetrate.

Coastal Communities

Estuaries are bays where rivers empty into the sea. Erosion brings down nutrients and tides wash in salt water; forms nutrient trap. Estuaries have high production for organisms that can tolerate changing salinity. Estuaries are called "nurseries of the sea" because many young marine fish develop in this protected environment before moving as adults into the wide open seas.

Seashores

Rocky shorelines offer anchorage for sessile organisms. Seaweeds are main photosynthesizers and use holdfasts to anchor. Barnacles glue themselves to stone. Oysters and mussels attach themselves by threads. Limpets and periwinkles either hide in crevices or fasten flat to rocks.

Sandy beaches and shores are shifting strata. Permanent residents therefore burrow underground. Worms live permanently in tubes. Amphipods and ghost crabs burrow above high tide and feed at night.

Coral Reefs

Areas of biological abundance in shallow, warm tropical waters. Stony corals have calcium carbonate exoskeleton and may include algae. Most form colonies; may associate with zooxanthellae dinoflagellates. Reef is densely populated with animal life. The Great Barrier Reef of Australia suffers from heavy predation by crown-of-thorns sea star, perhaps because humans have harvested its predator, the giant triton.

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Oceans

Oceans cover about three-quarters of the Earth's surface. Oceanic organisms are placed in either pelagic (open water) or benthic (ocean floor) categories. Pelagic division is divided into neritic and three levels of pelagic provinces. Neritic province has greater concentration of organisms because sunlight penetrates; nutrients are found here. Epipelagic zone is brightly lit, has much photosynthetic phytoplankton, that support zooplankton that are food for fish, squid, dolphins, and whales. Mesopelagic zone is semi-dark and contains carnivores; adapted organisms tend to be translucent, red colored, or luminescent; for example: shrimps, squids, lantern and hatchet fishes. The bathypelagic zone is completely dark and largest in size; it has strange-looking fish. Benthic division includes organisms on continental shelf (sublittoral), continental slope (bathyal), and the abyssal plain.

Sublittoral zone harbors seaweed that becomes sparse where deeper; most dependent on slow rain of plankton and detritus from sunlit water above. Bathyal zone continues with thinning of sublittoral organisms. Abyssal zone is mainly animals at soil-water interface of dark abyssal plain; in spite of high pressure, darkness and coldness, many invertebrates thrive here among sea urchins and tubeworms.

Thermal vents along oceanic ridges form a very unique community. Molten magma heats seawater to 350oC, reacting with sulfate to form hydrogen sulfide (H2S). Chemosynthetic bacteria obtain energy by oxidizing hydrogen sulfide. The resulting food chain supports a community of tubeworms and clams.

 

The Freshwater Biome

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The freshwater biome is subdivided into two zones: running waters and standing waters. Larger bodies of freshwater are less prone to stratification (where oxygen decreases with depth). The upper layers have abundant oxygen, the lowermost layers are oxygen-poor. Mixing between upper and lower layers in a pond or lake occurs during seasonal changes known as spring and fall overturn.

Lakes are larger than ponds, and are stratified in summer and winter. The epilimnion is the upper surface layer. It is warm in summer. The hypolimnion is the cold lower layer. A sudden drop in temperature occurs at the middle of the thermocline. Layering prevents mixing between the lower hypolimnion (rich in nutrients) and the upper epilimnion (which has oxygen absorbed from its surface). The epilimnion warms in spring and cools in fall, causing a temporary mixing. As a consequence, phytoplankton become more abundant due to the increased

amounts of nutrients.

Life zones also exist in lakes and ponds. The littoral zone is closest to shore. The limnetic zone is the sunlit body of the lake. Below the level of sunlight penetration is the dark profundal zone. At the soil-water interface we find the benthic zone. The term benthos is applied to animals and other organisms that live on or in the benthic zone.

Rapidly flowing, bubbling streams have insects and fish adapted to oxygen-rich water. Slow moving streams have aquatic life more similar to lake and pond life.

Community Density and Stability

Communities are made up of species adapted to the conditions of that community. Diversity and stability help define a community and are important in environmental studies. Species diversity decreases as we move away from the tropics. Species diversity is a measure of the different types of organisms in a community (also referred to as species richness). Latitudinal diversity gradient refers to species richness decreasing steadily going away from the equator. A hectare of tropical rain forest contains 40-100 tree species, while a hectare of temperate zone forest contains 10-30 tree species. In marked contrast, a hectare of taiga contains only a paltry 1-5 species! Habitat destruction in tropical countries will cause many more extinctions per hectare than it would in higher latitudes.

Environmental stability is greater in tropical areas, where a relatively stable/constant environment allows more different kinds of species to thrive. Equatorial communities are older because they have been less disturbed by glaciers and other climate changes, allowing time for new species to evolve. Equatorial areas also have a longer growing season.

The depth diversity gradient is found in aquatic communities. Increasing species richness with increasing water depth. This gradient is established by environmental stability and the increasing availability of nutrients.

Community stability refers to the ability of communities to remain unchanged over time. During the 1950s and 1960s, stability was equated to diversity: diverse communities were also stable communities. Mathematical

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modeling during the 1970s showed that increased diversity can actually increase interdependence among species and lead to a cascade effect when a keystone species is removed. Thus, the relation is more complex than previously thought.

Change in Communities Over Time

Biological communities, like the organisms that comprise them, can and do change over time. Ecological time focuses on community events that occur over decades or centuries. Geological time focuses on events lasting thousands of years or more.

Community succession is the sequential replacement of species by immigration of new species and local extinction of older ones following a disturbance that creates unoccupied habitats for colonization. The initial rapid colonizer species are the pioneer community. Eventually a climax community of more or less stable but slower growing species eventually develops.

During succession productivity declines and diversity increases. These trends tend to increase the biomass (total weight of living tissue) in a community. Succession occurs because each community stage prepares the environment for the stage following it.

Primary succession begins with bare rock and takes a very long time to occur. Weathering by wind and rain plus the actions of pioneer species such as lichens and mosses begin the buildup of soil. Herbaceous plants, including the grasses, grow on deeper soil and shade out shorter pioneer species. Pine trees or deciduous trees eventually take root and in most biomes will form a climax community of plants that are stabile in the environment. The young produced by climax species can live in that environment, unlike the young produced by successional species.

Secondary succession occurs when an environment has been disturbed, such as by fire, geological activity, or human intervention (farming or deforestation in most cases). This form of succession often begins in an abandoned field with soil layers already in place. Compared to primary succession, which must take long periods of time to build or accumulate soil, secondary succession occurs rapidly. The herbaceous pioneering plants give way to pines, which in turn may give way to a hardwood deciduous forest (in the classical old field succession models developed in the eastern deciduous forest biome).

Early researchers assumed climax communities were determined for each environment. Today we recognize the outcome of competition among whatever species are present as establishing the climax community.

Climax communities tend to be more stable than successional communities. Early stages of succession show the most growth and are most productive. Pioneer communities lack diversity, make poor use of inputs, and lose heat and nutrients. As succession proceeds, species variety increases and nutrients are recycled more. Climax communities make fuller use of inputs and maintain themselves, thus, they are more stable. Human activity (such as clearing a climax forest community to establish a farm field consisting of a cultivated pioneering species, say corn or wheat) replaces climax communities with simpler communities.

Communities are composed of species that evolve, so the community must also evolve. Comparing marine communities of 500 million years ago with modern communities shows modern communities composed of quite different organisms. Modern communities also tend to be more complex, although this may be a reflection of the nature of the fossil record as well as differences between biological and fossil species.

Disturbance of a Community

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The basic effect of human activity on communities is community simplification, an overall reduction of species diversity. Agriculture is a purposeful human intervention in which we create a monoculture of a single favored (crop) species such as corn. Most of the agricultural species are derived from pioneering communities.

Inadvertent human intervention can simplify communities and produce stressed communities that have fewer species as well as a superabundance of some species. Disturbances favor early successional (pioneer) species that can grow and reproduce rapidly.

Ecosystems and Communities

Ecosystems include both living and nonliving components. These living, or biotic, components include habitats and niches occupied by organisms. Nonliving, or abiotic, components include soil, water, light, inorganic nutrients, and weather. An organism's place of residence, where it can be found, is its habitat. A niche is is often viewed as the role of that organism in the community, factors limiting its life, and how it acquires food.

Producers, a major niche in all ecosystems, are autotrophic, usually photosynthetic, organisms. In terrestrial ecosystems, producers are usually green plants. Freshwater and marine ecosystems frequently have algae as the dominant producers.

Consumers are heterotrophic organisms that eat food produced by another organism. Herbivores are a type of consumer that feeds directly on green plants (or another type of autotroph). Since herbivores take their food directly from the producer level, we refer to them as primary consumers. Carnivores feed on other animals (or another type of consumer) and are secondary or tertiary consumers. Omnivores, the feeding method used by humans, feed on both plants and animals. Decomposers are organisms, mostly bacteria and fungi that recycle nutrients from decaying organic material. Decomposers break down detritus, nonliving organic matter, into inorganic matter. Small soil organisms are critical in helping bacteria and fungi shred leaf litter and form rich soil.

Even if communities do differ in structure, they have some common uniting processes such as energy flow and matter cycling. Energy flows move through feeding relationships. The term ecological niche refers to how an organism functions in an ecosystem. Food webs, food chains, and food pyramids are three ways of representing energy flow.

Producers absorb solar energy and convert it to chemical bonds from inorganic nutrients taken from environment. Energy content of organic food passes up food chain; eventually all energy is lost as heat, therefore requiring continual input. Original inorganic elements are mostly returned to soil and producers; can be used again by producers and no new input is required.

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Energy flow in ecosystems, as with all other energy, must follow the two laws of thermodynamics. Recall that the first law states that energy is neither created nor destroyed, but instead changes from one form to another (potential to kinetic). The second law mandates that when energy is transformed from one form to another, some usable energy is lost as heat. Thus, in any food chain, some energy must be lost as we move up the chain.

The ultimate source of energy for nearly all life is the Sun. Recently, scientists discovered an exception to this once unchallenged truism: communities of organisms around ocean vents where food chain begins with chemosynthetic bacteria that oxidize hydrogen sulfide generated by inorganic chemical reactions inside the Earth's crust. In this special case, the source of energy is the internal heat engine of the Earth.

Food chains indicate who eats whom in an ecosystem. Represent one path of energy flow through an ecosystem. Natural ecosystems have numerous interconnected food chains. Each level of producer and consumers is a trophic level. Some primary consumers feed on plants and make grazing food chains; others feed on detritus.

The population size in an undisturbed ecosystem is limited by the food supply, competition, predation, and parasitism. Food webs help determine consequences of perturbations: if titmice and vireos fed on beetles and earthworms, insecticides that killed beetles would increase competition between birds and probably increase predation of earthworms, etc.

The trophic structure of an ecosystem forms an ecological pyramid. The base of this pyramid represents the producer trophic level. At the apex is the highest level consumer, the top predator. Other pyramids can be recognized in an ecosystem. A pyramid of numbers is based on how many organisms occupy each trophic level. The pyramid of biomass is calculated by multiplying the average weight for organisms times the number of organisms at each trophic level. An energy pyramid illustrates the amounts of energy available at each successive trophic level. The energy pyramid always shows a decrease moving up trophic levels because:

Only a certain amount of food is captured and eaten by organisms on the next trophic level. Some of food that is eaten cannot be digested and exits digestive tract as undigested waste. Only a portion of digested food becomes part of the organism's body; rest is used as source of energy.

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Substantial portion of food energy goes to build up temporary ATP in mitochondria that is then used to synthesize proteins, lipids, carbohydrates, fuel contraction of muscles, nerve conduction, and other functions.

Only about 10% of the energy available at a particular trophic level is incorporated into tissues at the next level. Thus, a larger population can be sustained by eating grain than by eating grain-fed animals since 100 kg of grain would result in 10 human kg but if fed to cattle, the result, by the time that reaches the human is a paltry 1 human kg!

A food chain is a series of organisms each feeding on the one preceding it. There are two types of food chain: decomposer and grazer. Grazer food chains begin with algae and plants and end in a carnivore. Decomposer chains are composed of waste and decomposing organisms such as fungi and bacteria.

Energy flow and the relative proportions of various levels in the food chain..

Food chains are simplifications of complex relationships. A food web is a more realistic and accurate depiction of energy flow. Food webs are networks of feeding interactions among species.

The food pyramid provides a detailed view of energy flow in an ecosystem. The first level consists of the producers (usually plants). All higher levels are consumers. The shorter the food chain the more energy is available to organisms.

Most humans occupy a top carnivore role, about 2% of all calories available from producers ever reach the tissues of top carnivores. Leakage of energy occurs between each feeding level. Most natural ecosystems therefore do not have more than five levels to their food pyramids. Large carnivores are rare because there is so little energy available to them atop the pyramid.

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Food generation by producers varies greatly between ecosystems. Net primary productivity (NPP) is the rate at which producer biomass is formed. Tropical forests and swamps are the most productive terrestrial ecosystems. Reefs and estuaries are the most productive aquatic ecosystems. All of these productive areas are in danger from human activity. Humans redirect nearly 40% of the net primary productivity and directly or indirectly use nearly 40% of all the land food pyramid. This energy is not available to natural populations.

Learning Objectives

Be able to describe the major terrestrial biomes and the types of plants and animals occurring there. Relate the effect of increasing altitude as one goes up a mountain to biome changes seen as one moves

north of the equator toward the polar regions. Distinguish the different regions within the marine ecosystems. Be able to describe a food chain in detail, with some indication of the relative proportions of organisms

at each trophic level.

Biogeochemical Cycles

More than thirty chemical elements are cycled through the environment by biogeochemical cycles. There are six important biogeochemical cycles that transport carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorous. Recall that these six elements comprise the bulk of atoms in living things. Carbon, the most abundant element in the human body, is not the most common element in the crust, silicon is.

The Phosphorus Cycle

Weathering of rocks makes phosphate ions (PO4

= and HPO4=) available to

plants through uptake from the soil. The mineral apatite contains a small amount of phosphorous, although this is enough for all living things to utilize. Runoff returns phosphates to aquatic systems and sediment. Organisms use phosphate in phospholipids, ATP, teeth, bones, and shells. Phosphate is a limiting nutrient because most of it is being currently used in organisms. The inorganic source, apatite, is a rare mineral, further limiting the input of this essential nutrient.

Humans mine phosphate ores for use in fertilizer, as an animal feed supplement, and for detergents. Detergents, untreated human and animal wastes, and fertilizers from cropland add excess phosphate to water often causing population explosions (algal blooms) in lakes..

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The Nitrogen Cycle

Atmospheric nitrogen gas (N2), the major portion of our modern atmosphere, is unfortunately in a form that is not usable by plants and most other organisms. Plants therefore depend on various types of nitrogen-fixing bacteria to take up nitrogen gas and make it available to them as some form of organic nitrogen. Nitrogen fixation occurs when nitrogen gas is chemically reduced and nitrogen is added to organic compounds. Atmospheric nitrogen is converted to ammonium (NH4

+) by some cyanobacteria in aquatic ecosystems and by nitrogen-fixing bacteria in the nodules on roots of legume (beans, peas, clover, etc.) plants in terrestrial ecosystems. Plants take up both NH4

+ and nitrate (NO3-) from soil. The nitrate (NO3

-) is enzymatically reduced to ammonium (NH4

+) and used in the production of both amino acids and nucleic acids.

Nitrification is the inorganic production of nitrates. Nitrogen gas (N2) is converted to nitrate (NO3-) by cosmic

radiation, meteor trails, and lightning in the atmosphere. Human technology can now manufacture nitrates for use in fertilizers. In soil, bacteria convert ammonium (NH4

+) to nitrate (NO3-) by a two-step process. Nitrite-

producing bacteria convert ammonia to nitrite (NO2-). Next, nitrate-producing bacteria convert nitrite to nitrate.

These two groups of bacteria are called nitrifying bacteria.

Denitrification is conversion of nitrate to nitrous oxide and nitrogen gas back to atmosphere. This is done by denitrifying bacteria in both aquatic and terrestrial ecosystems. The process of denitrification almost, but not completely, counterbalances nitrogen fixation.

The Carbon Cycle

There is a relationship between the two major metabolic processes of photosynthesis and cellular respiration. Cellular respiration releases carbon dioxide, which is used as a raw material in photosynthesis. Photosynthesis in turn releases oxygen used in respiration. Animals and other heterotrophs depend on green organisms for organic food, energy, and oxygen. In the carbon cycle, organisms exchange carbon dioxide with the atmosphere. On land, plants take up carbon dioxide via photosynthesis and incorporate it into food used by themselves and heterotrophs. When organisms respire, some of this carbon is returned to the atmosphere in the molecules of carbon dioxide. In aquatic ecosystems, carbon dioxide from air combines with water to give carbonic acid, which breaks down to bicarbonate ions. Bicarbonate ions are a source of carbon for algae. When aquatic organisms respire, they release carbon dioxide that becomes bicarbonate (HCO3). The amount of bicarbonate in water is in equilibrium with amount of carbon dioxide in air.

Living and dead organisms are reservoirs of carbon in carbon cycle. More than 800 billion tons of carbon are in the world's biota, mainly in cells of trees. An additional 1,000 to 3,000 billion tons of carbon occurs in plant and animal remains in the soil. Fossil fuels, such as coal, petroleum, and natural gas, were formed during various times of the geologic past when exceptional amount of organic matter were rapidly buried in an environment that locally lacked biologic activity. Inorganic calcium carbonate (the minerals calcite and aragonite, CaCO3) accumulates in limestone and the calcite of shells.

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Human burning of fossil fuels and wood has increased the amount of carbon dioxide released into atmosphere to 42 billion metric tons in only 22 years. Since human activity in 22 years probably released 78 billion metric tons, 36 billion metric tons were probably absorbed in oceans. Increased carbon dioxide levels may increase the greenhouse effect, where such gases allow the Sun's radiant energy to pass through to Earth where it is absorbed and reradiated as heat. Instead of radiating from the earth back into space, this heat is then trapped on Earth, perhaps causing or contributing to global warming.

. The global carbon cycle..

Excess output occurs when biomass is suddenly released, such as in slash and burn agriculture. Excess input commonly occurs from agricultural increase in organic fertilizer and other nutrients into an ecosystem. Generally speaking, the faster matter cycles, the faster it can recover from human intervention.

Recently, speculation has centered on the interconnection of biogeochemical cycles and their possible roles in a "superorganism" that James Lovelock has called Gaia, after the ancient Greek Earth goddess. While an intriguing notion, the degree of organization of these cycles is not as complex or integrated as the cells in a body. Gaia remains controversial hypothesis that continues to generate speculation and research both pro and con.

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