CHAPTER 1: INTRODUCTION: THEMES IN THE STUDY OF LIFE

All 3 Powerpoints by: Athira P, Hope C, and Steph J

1.1 THEMES HELP CONNECT THE CONCEPTS OF BIOLOGY

Evolution explains the unity and diversity of life

All the diverse past and present organisms are related through common ancestry

New properties emerge at each level in the biological hierarchy – Emergent Properties

Systems Biology models biological systems and predicts their responses as variables change.

Organisms interact with their environments while exchanging matter and energy

During each energy transformation some energy is converted to thermal energy, which is “lost” as heat

It is a cycle of Energy

Structure and function are correlated at all levels of biological organization

Cell’s are an organism’s basic units of structure and function The cell is the lowest structural level capable

of performing all the activities of life. Prokaryotic – Bacteria & Achaea, lack nucleus

and most cytoplasmic organelles Eukaryotic Cell – All other living organisms,

Nucleus and numerous membrane organelles

The continuity of life is based on heritable Information in the form of DNA

DNA (deoxyribonucleic acid) – the substance of genes

Genes are the units of inheritance which are transmitted from parents to offspring and are located on chromosomes

Biological instructions for the development and functioning of organisms are coded in DNA

Most genes program the cell’s production of proteins

A genome is all the genetic instruction an organism inherits. The human genome is about 3 billion nucleotides long

Research contributing to systems biology Mega-data collection methods such as the automatic

DNA sequencing machines Bioinformatics – provides the computing power,

software, and mathematical models to process and integrate data from enormous data sets

Interdisciplinary research teams with diverse specialists from many scientific fields

Feedback mechanisms regulate biological systems

Negative feedback – an end product slows down a process, often by inhibiting an enzyme

Positive feedback – an end product speeds up its own production

1.2 THE CORE THEME: EVOLUTION ACCOUNTS FOR THE UNITY AND DIVERSITY OF LIFE

Taxonomy is the branch of biology that names organisms and groups into ever broader categories (i.e. genera, family, order, class, phylum, kingdom, and domain) Genus species

Number of kingdoms is debated but it is in three domains currently domain Archaea domain Bacteria domain Eukarya

kingdom protista

Charles Darwin published the Origin of species Descent with modification – prevent forms

evolved from a succession of ancestral forms”

Natural selection Underlying unity seen in the structures

of related species reflects the inheritance of that structure from a common ancestor

1.3 SCIENTISTS USE TWO MAIN FORMS OF INQUIRY IN THEIR STUDY OF NATURE

Science involves inquiry – searching for information by asking and endeavoring to answer questions about nature

Discovery science – careful and verifiable observation and analysis of data

Data – quantitative and qualitative recorded observations

Inductive reasoning – a generalized conclusion drawn from collections of observation

Hypothesis – a tentative answer to a question or explanation of observations using “ if … then” logic

Deductive reasoning – general to specific General hypothesis to specific predictions

of results A hypothesis must be testable and

falsifiable (something that could make the hypothesis untrue)

Hypotheses cannot be proven they can only gain credibility after failed attempts at falsification

Scientific method is rarely adhered to Controlled Experiment – subjects are

divided into an experimental group and a control group. Both groups are treated alike except for the one variable the experiment is trying to test

Scientific inquiry is limited by the requirements that hypotheses be testable and falsifiable and that observations and experimental results must be repeatable

A theory is broader than a hypothesis and is supported by a large body of evidence

Models (including diagrams, graphs, computer programs, and mathematical equations) help explain ideas and processes Is good if fits available data, incorporates new

observations, makes accurate predictions of new experiments

Chapter 2:

The Chemical Context of Life

- 2.1 -Matter consists of chemical elements in pure form and in combinations called compounds

Matter & Elements

Matter is anything that takes up space and has mass.

An element is a substance unable to be broken down to other substances by chemical reactions. 92 elements are known today.

A compound is the combination of two or more elements in a fixed ratio.

Trace elements are elements that an organism must possess in small amounts.

- 2.2 -An element’s properties depend on the

structure of its atoms

Atoms

An atom is the smallest unit of matter that shares the properties of an element.

Atoms are split into even smaller units of matter: subatomic particles. Three kinds of subatomic particles are:

neutrons, protons, and electrons. Protons are positively charged, electrons are

negatively charged, and neutrons are electrically neutral.

Subatomic Particles

Protons and neutrons are packed together in the atomic nucleus at the center of an atom. Electrons form a cloud of negative charge around the nucleus. The attraction between opposite charges are

what keep the electrons where they are. A unit of measurement called the Dalton is

used for atoms and subatomic particles. This was named after the British scientist

John Dalton; he helped to develop the atomic theory.

The Dalton is the same as the atomic mass unit, or amu.

Atomic Number and Atomic Mass

Each element has a unique number of protons, called the atomic number.

The number of neutrons that an element contains can be found from the mass number, the sum of protons plus neutrons in the nucleus of an atom.

The atomic mass of an atom is the total mass of that atom, and because neutrons and protons have masses very close to 1 Dalton, the mass number can be used as an approximate atomic mass.

Isotopes All atoms of a specific element have the same

amount of protons, but some atoms have more neutrons than other atoms of the same element, giving it more mass. These different forms of the atom are called

isotopes of the element. A radioactive isotope is an isotope that has a

nucleus that decays spontaneously, releasing particles and energy.

When the decay of a radioactive isotope leads to a difference in the amount of protons, the atom transforms to an atom of a different element. For example, radioactive carbon decays to create

nitrogen.

The Energy Levels of Electrons

Energy is the ability to cause transformations or changes.

Potential energy is the energy that matter has due to its location or structure. The electrons of an atom have potential energy

due to their arrangement in relation to the nucleus. Electrons are found in different electron

shells. Each electron shell has its own average distance and energy level.

Electron Distribution and Chemical Properties

The chemical behavior of an atom depends mostly on the amount of electrons located in its outermost shell. These electrons are called valence electrons. The outermost shell is called the valence

shell. Incomplete valence shells can lead to

chemically reactive elements. There are three elements (helium, neon, and

argon) that have full valence shells; therefore, they are known to be inert, or chemically unreactive.

Electron Orbitals

The orbital is the three-dimensional area in which an electron is found to spend most of its time in.

Each electron shell has electrons at a specific energy level, distributed among a particular amount of orbitals of different shapes and orientations. The first electron shell has one spherical s orbital

and is called 1s. The second shell has four orbitals: one large s

orbital (2s), and three dumbbell-shaped p orbitals (2p).

No more than two electrons can occupy a single orbital.

- 2.3 -The formation and function of molecules

depend on chemical bonding between atoms

Covalent Bonds

A covalent bond is the sharing of a pair of valence electrons by two atoms. A pair of shared electrons is indicated by a single

bond, while a molecule that shares two pairs of valence electrons is joined together with a double bond.

An atom’s capacity of bonding is called the atom’s valence and is usually equal to the number of unpaired electrons needed to complete the atom’s outermost shell.

Electrons of a polar covalent bond are pulled closer to the more electronegative atom, but if both atoms are the same, they have the same electronegativity, indicating a nonpolar bond.

Ionic Bonds & Weak Chemical Bonds

When a positively charged ion, a cation, attracts a negatively charged ion, an anion, an ionic bond is formed.

Salts, such as NaCl, are compounds formed by ionic bonds.

A hydrogen bond is an attraction between a hydrogen atom with a partial positive charge and an electronegative atom – a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom.

Van der Waals interactions occur between positive and negative molecular regions.

Weak chemical bonds emphasize the shapes of larger molecules and assist molecules to adhere to each other.

- 2.4 -Chemical reactions make and break

bonds

Chemical Reactions & Equilibrium

Chemical reactions are created when changes in the composition of matter are results of the making and breaking of chemical bonds.

All chemical reactions are theoretically reversible. Chemical equilibrium is achieved when the

reactions offset on another. Reactions are still going on, but there is no net

effect on the concentrations of the reactants and products.

Chapter 3: Water and the Fitness of the Environment

3.1 – The polarity of water molecules results in hydrogen

bonding.pp. 46 - 47

Water = H₂OWater has covalent bonds attaching the H

molecules to the O molecule. → HYDROGEN BONDING!

The oxygen has a partial negative charge, and the hydrogens have a partial positive charge.

Oxygen is more electronegative than hydrogen.The electrons of these bonds spend more time

closer to O than H, resulting in polarity.Water’s properties stem from H bonding.

3.2 – Four emergent properties of water contribute to Earth’s

fitness for lifepp. 47 - 52

1. CohesionGlossary definition: The binding together of like

molecules, often by H bonds.Example – water transport in trees:

Trees have water-conducting cells. In each of these cells there is a column of water. Cohesion due to H bonds maintains this column of water. As water evaporates from a leaf (transpiration!), H

bonds causes the departing molecules to tug on molecules farther down.

This upward pull reaches all the way to the roots.

Water can stick to cell walls because of adhesion. This counters downward pull of gravity.

Special Case: Surface Tension Glossary definition: The measure of how difficult

it is to stretch or break the surface of a liquid.Water has a greater surface tension than most

other liquids.An ordered arrangement of water molecules

resides between water and air. These molecules are hydrogen-bonded to

themselves and the molecules underneath them.This creates a “film” on which some organisms

can stand, walk, or run without breaking the surface.

2. Moderation of TemperatureRemember that temperature is a measure of the

average kinetic energy generated by an object’s molecules. Heat is the energy itself.

When two objects of different temperature are brought together:Heat passes from the warmer to the cooler object until

they have the same temperature.In this way, water moderates the temperature of air by

absorbing heat from warmer air and passing this heat to cooler air.

Calorie: the amount of heat it takes to raise the temperature of one gram of water by 1° Celsius.

Kilocalorie: same thing except one gram is changed to a kilogram :)

Special Case: High Specific Heat Glossary definition: The amount of heat that must be absorbed or lost

for one gram of that substance to change its temperature by 1 ° C.

Water has a specific heat of 4.184 J (one calorie equals this many joules).

This helps water to resist drastic changes in temperature upon absorption or loss of heat.

When the temperature of water changes, it absorbs/loses a large amount of heat for each degree of change.

Back to H-bonding: When the temperature of water drops, additional H bonds form. Heat released. When the temperature of water rises, H bonds break. Heat absorbed.

Makes sense because as temperature rises, water molecules are able to move more freely.

Special Case 2: Evaporative CoolingHeat of vaporization: The quantity of heat a liquid must

absorb for one gram of it to be converted from a liquid to a gas.Relation to H-bonds: Hydrogen bonds must be broken in

order for the water molecules to move freely in the gaseous state.

Moderates Earth’s climate.

Evaporative cooling: As liquid evaporates, the surface that remains cools because the molecules with the greatest amount of kinetic energy (the “hottest” molecules) leave as a gas.Maintains temperature in lakes and ponds.Prevents terrestrial organisms from overheating.

3. Insulation of Bodies of Water by Floating Ice WARNING—PREPARE TO BE SHOCKED—SOLID WATER IS LESS

DENSE THAN LIQUID WATER.

Okay, have we all calmed down? Good. Now on to more science.

Water expands instead of contracting when it solidifies, which happens at 0 degrees Celsius.

Molecules form a rigid lattice, and each molecule is bonded to four others.

If ice could sink, all ponds, lakes, and oceans would freeze, and we would not be able to live on this planet.

Instead, when floating over bodies of water, ice acts as an insulator for the water below it, allowing organisms to survive under the surface.

4. (Almost) Universal Solubility If water was truly a universal solvent, it would dissolve any

container, including our cells, so we wouldn’t be alive. End of story.

Solvent (dissolving agent) + solute (substance dissolved) = solution (the homogeneous mixture of two or more substances). Aqueous solution: water is the solvent.

Water molecules dissolve solutes by forming a hydration shell around solute molecules.

Not all compounds have to be ionic in order to dissolve in water (sugar and proteins work) . . . But ionicity does help in most cases. :)

Yes, ionicity is a word.

Special Case: Hydrophilic and Hydrophobic SubstancesHydrophilic substance: Any substance that

has an affinity for water.Substances can be hydrophilic without

dissolving. Some molecules are too large to dissolve, so they become colloids—stable suspensions of fine particles in a liquid.

Hydrophobic substance: Any substance that repels water.

Nonpolar molecules are hydrophobic.

3.3 – Acidic and basic conditions affect living organisms

pp. 54 - 56

Effects of Changes in pH: Acids, Bases, and the pH scale When a hydrogen atom detaches from a water molecule, the

product is hydroxide, or OH-.

The proton bonds to another water molecule, making hydronium, or H3O+.

Acid: a substance that increases the hydrogen ion concentration of a solution.

Base: a substance that reduces the hydrogen ion concentration of a solution.

When H+ and OH- are in equal concentrations, the solution is neutral.

In any aqueous solution, the product of the H+ and OH- concentrations is constant at 10-14 . Every time pH changes by one unit, the difference in concentrations between H+ and OH- changes tenfold. A substance with pH 3 is a thousand times more acidic than a substance with a pH of 6.

Special Case: BuffersBuffers minimize the effects of changes in H+

and OH- concentration.They accept excess hydrogens and donate

needed hydrogens.Weak acid + weak base = buffer.Most buffers are acid-base pairs.Is this reminding you of AP Chem yet?

Threats to Water Quality on Earth

Acid precipitation, carbon dioxide, and other fun stuffAcid precipitation: Rain, snow, or fog with a pH lower than 5.2.

Caused by the burning of fossil fuels – major source of sulfur oxides and nitrous oxides

Damages lakes, streams, and soil.

Greenhouse effect: CO2 is released into the atmosphere. About half of it stays there, preventing heat from escaping into space. CO2 is usually taken up by trees and other organisms as well as

oceans, but when it dissolves in seawater, it forms carbonic acid. This dissociates into bicarbonate and carbonate as well as a lot of protons.

Carbonate concentration decreases as more protons are added to the seawater, which causes damage to corals and lowers the overall pH of the ocean.

And now for something we all love to remember . . . the milk lab.This lab illustrated many properties discussed in this PowerPoint,

including surface tension, polarity, and solubility.

So. To review: We poured some milk into Petri dishes, added drops of food coloring, then dipped a clean cotton swab in the center. As you may recall, nothing happened.

In the next trial, we dipped the cotton swab into dish soap and placed it ever so gently into the milk.

Milk + food coloring + soap = color explosion.

This happens because soap dissolves the fat molecules in the milk, reducing the surface tension and pulling the surface “away” from the spot where the soap-covered cotton swab was dipped into the milk.