Bell High School

Biology Notes

Full course notes for SBI3U, Mr. Ruttan

Richard YeFebruary 21, 2010Last Updated June 12, 2010

TABLE OF CONTENTS

Table of Contents....................................................................................................................1

Digestion and Nutrition..........................................................................................................2

Nutrients.............................................................................................................................2

Components in Human Digestion........................................................................................5

Main processes in Human Digestion...................................................................................7

Notable Digestive Disorders................................................................................................7

Control and Homeostasis....................................................................................................8

Respiration.............................................................................................................................9

Structures in the Respiratory System.................................................................................9

Gas Exchange and the Respiration process.......................................................................11

The human respiratory system..........................................................................................13

The Trachea and Bronchial Tree.......................................................................................14

Diseases of the Respiratory System..................................................................................15

The Circulatory System........................................................................................................16

Blood.................................................................................................................................17

Blood Vessels.....................................................................................................................19

The Heart..........................................................................................................................20

Genetics................................................................................................................................23

Cellular Reproduction.......................................................................................................23

Genes and DNA.................................................................................................................24

Notable Genetic Disorders................................................................................................25

Evolution...............................................................................................................................26

Selection and Speciation...................................................................................................28

The Evolutionary History of Life........................................................................................29

Evolutionary Theory..........................................................................................................30

Classification of Living Things..............................................................................................31

Viruses...............................................................................................................................31

Eubacteria And Archaebacteria.........................................................................................32

Protista..............................................................................................................................32

Plantae...............................................................................................................................33

Animalia.............................................................................................................................34

Fungi.................................................................................................................................35

Tanxomonic Tree...............................................................................................................371

DIGESTION AND NUTRITION

NUTRIENTS

Living things are composed of non-living chemicals.

There are six nutrient chemicals that all life requires. They are:

Proteins Carbohydrates Lipids (fats) Vitamins Minerals Water

Carbohydrates (sugars) are the body’s main source of energy, and the largest component of the diet. Food examples are potatoes, bread, corn, rice and fruits.

The simple sugars (monosaccharides) are C6H12O6 isomers. They are:o Glucose – found in all cells of the body; used for cell respiration. The

chemical test for glucose is Benedict’s Solution.o Fructose – found in fruits and tastes sweeter than glucoseo Galactose – Sugar found in mammalian milk

The disaccharides (“double sugars”) are two monosaccharides linked together. They are:

o Maltose = glucose + glucose; used in making beer / malt flavouro Lactose = glucose + galactose; milk sugaro Sucrose = glucose + fructose; brown and white sugars

The polysaccharides more than two monosaccharides joined together. They are:o Starch – 1000s of glucose molecules joined together; plant storage product.

The chemical test for starch is iodine.o Cellulose – component of cell walls, isomer of starch, cannot be digested by

humans, ingested as roughage. Aids in the elimination of wastes as it holds water; e.g. wood

o Glycogen – principal storage product in animals, stored in liver and muscleso Chitin – forms a hard external skeleton in insects and crustaceans; using in

making strong, non-decomposable surgical thread

Lipids are divided into three groups: fats, oils and waxes; phospholipids and steroids. The function of lipids are:

They can supply energy to the body but are harder to process than carbs An excellent energy storage molecule (the body begins to burn fat after 20 minutes

of exercise) Aids in the absorption of vitamins (some vitamins are not water soluble)

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Serves as insulation from the cold Components of cell membranes; keeps cells from dissolving Aid in the synthesis of hormones; steroid hormones (e.g. testosterone) made from

fat Protects organs inside the body Make the body insoluble and floating (i.e. polar bears have fat to keep warm and

float)

Lipids are composed of three fatty acids and glycerol. Fatty acids are long hydrocarbon chains with an OH-C-O pattern on one end.

A fatty acid

Lipids form when three fatty acids join the three OHs found on glycerol, making the shape on an E. In the digestive tract, the lipid molecules are digested into the smaller component fatty acids and glycerols.

There are many types of lipids:

Saturated fats have C-C single bonds, and have the maximum possible number of hydrogen atoms.

o Usually firm, solid fats found in beef, pork cheese, butter and palm oils.o Names given based on length of carbon chain

Unsaturated fatso C=C are double bonded, lesser amount of hydrogen than saturated fatso Number of C-C single bonds lower; at least one double bondo Better processed by humans. Bendable molecules.o Liquid or soft fats. Found in olive oil, peanut oil, almonds, fish, corn oils and

margarines. Trans fats

o Usually unsaturated fats, if they have a double bond, have hydrogen located on the double bonded carbons that there is a bend in the molecules:

o Trans fats have a trans carbon bond, meaning that the hydrogen atoms are located so that the molecule remains straight:

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Glycerol

o Trans fats are bad for your health, not needed, and cause bad cholesterols to rise, and good ones to fall. Not needed in humans.

Phospholipidso Component of cell membraneso 1 phosphate group + glycerol + 2 fatty acidso Partly soluble, the phosphate region dissolves, but the lipids do not.

Waxes are insoluble in watero Waterproofing agent for plants, animal feathers and fur; i.e. bird’s feathers

are oily to aid drying after diving) Steroids are also lipids

o Carbon-based, multiple ring structureo E.g. estrogens, cholesterol (below), testosterone

Cholesterol is used to make hormones Part of cell membrane Can combine with other fats to form plague, block

blood vessels

Proteins are used to build cell structures and body parts. They are composed of amino acid sequences.

There are 20 essential amino acids. The sequences of these are regulated by genes.o 8 of them are essential, and must be in the diet; the rest can be

manufactured. Proteins include teeth, hair, cell parts, etc.; they are everywhere

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A phospholipid

Structure of an amino acid:

o The amino part is the H-N-H. The carboxyl is the O=C-O-H. The R-group is the variant for amino acids.

o The body cannot store excess amino acids; therefore they must be broken down. The amino group can easily break off and get another H+ ion and form ammonia, NH3. This is very bad news. The kidneys filter it out, combining it with CO2 to form uric acid, which is less toxic than NH3.

Proteins can be shaped as straight (i.e. hair), spiral (spring) (i.e. hair) and countless other folding patterns (crumpled piece of paper). Polypeptides are formed from many amino acids bonding together.

Vitamins enable chemical reactions in the body. A vitamin is an organic compound required as a nutrient in tiny amounts by an organism. They cannot be synthesized in sufficient quantities by an organism, and must be obtained from the diet.

Vitamins are classified by them biological and chemical activity.o Have diverse biochemical functions, including hormones (vitamin D),

antioxidants (vitamin E) and mediators of cell signalling and regulators of cell andtissue grown and differentiation.

Vitamins and their functions:o Vitamin A – night vision, growth of bones and teetho Vitamin B1 – heart function, nerve and muscle function (cell respiration)o Vitamin C – Maintain cells and tissueso Vitamin D – strong teeth and bones, growtho Vitamin E – form red blood cellso Vitamin K – assist in blood clotting, healthy bones

Minerals are elements required by the body in small amounts. They aid enzyme function, electrical balance, generate nerve impulses, help bone structure. They are inorganic. Minerals include:

Calcium – growth of teeth and bones, blood clotting Iodine – proper function of thyroid gland Phosphorus – growth, maintenance of bones and teeth, cell reactions (cell

respiration), e.g. Adenosine triphosphate (ATP) used for cell energy transfer Potassium – needed to make proteins Sodium – muscle contraction, movement of water between cells Iron – transport of oxygen via haemoglobin Macrominerals (present in larger quantity): H, C, N, O, Na, Mg, P, S, Cl, K, Ca, Fe Trace minerals (present in small quantities): B, F, Al, Si, U, Cr, Mn, Co, Ni, Cu, Zn,

As, Se, Mo, I

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Water’s importance in diet cannot be underestimated.

Healthy lifestyles that include exercise and a high fibre diet require plenty of water intake.

Experts suggest that a person drink 8 8-ounce glasses of water/day, 9-13 for those who are exercising.

The body needs water to perform the following functions:o Digest food and dissolve nutrients so that

muscles can move, eyes can move, brain can think (also, hormones in blood).

o Provide a solvent for which nutrients can pass through.

o Regulate body temperatureo Lubricate moving parts (e.g. joints)o Blood is 55% water; body is 70%-80% water

COMPONENTS IN HUMAN DIGESTION

The human digestion system consists of four parts: ingestion, digestion (physical and chemical), absorption, and egestion. Food goes in the mouth and gets expelled down the anus. In between lie the gastrointestinal tract, organs placed one after another, each with specific structure and function.

The mouth’s primary functions are ingestion and digestion, both physical and chemical. After food items are put into the mouth, the teeth chew the food to facilitate easy swallowing. Additionally, smaller food particles allow chemical reactions later on to be more efficient, as there is more area for reaction. Also present is saliva, which lubricates the food for easy swallowing, passes particles to taste buds, giving taste, and contains the enzyme amylase. Amylase digests starch into smaller polysaccharides and glucose. The saliva comes from 6 salivary glands located around the jaw.

Following the mouth is the pharynx, the tube/cavity connecting the mouth with the esophagus, leading to the stomach and the GI tract, and the trachea, leading to the lungs. The pharynx is a connection of the mouth and nose, and is a junction for air to go into the lungs and drink into the stomach.

The trachea is not part of the digestive system. It is here because it is linked to the pharynx. Since water and solids cannot be allowed into the lungs, a small valve, the cartilaginous epiglottis closes the opening of the trachea after swallowing.

The esophagus is the muscular, tubular passage that extends for roughly 30cm, from the pharynx to the stomach. There are two sets of muscles in the esophagus, one set runs laterally, up and down, and the other forms bands around the circumference. The two sets of muscles are necessary for the rhythmic action of peristalsis, which forces chewed food down even when acting against gravity. In this process, the muscles running up and down push the food, which the other set contract and expand to force the food in one direction.

The stomach is a major centre of digestion. It is a J-shaped organ with an adult capacity of about 1.5L. Entry and exit of food is controlled by two sphincters, or circular bands of muscles. At the entry at the end of the esophagus is the cardiac sphincter and at the other end is the pyloric

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Peristalsis

sphincter. Inside the stomach is gastric fluid, which consists of strong hydrochloric acid and digestive enzymes. The acids kill many harmful bacteria and activate the enzyme pepsin, which digests proteins. The stomach’s only role in digestion is to digest these proteins into amino acids in its very acidic environment. Since the stomach itself is made of proteins, measures must be taken to ensure that it doesn’t digest itself. Mucous-secreting glands line the wall, forming a protective coat. A breach in this layer results in a stomach ulcer. Stomach acid escaping into the esophagus causes a pain known as heartburn.

The small intestine is a long (about 5m long), within a narrow diameter of 2.5-3 cm. It is the next stage of digestion, and is the place where most of the absorption takes place as well. The first part of the intestine is known as the duodenum, where the incoming stomach acid is neutralized, and where food is further digested. Enzymes from the pancreas, liver and gallbladder enter here as carbohydrates, proteins and lipids are all digested. Following the duodenum, the small intestine switches to an absorption role. Small noodle-like protrusions called villi increase the surface area and the rate of absorption. On those are even smaller microvilli, which make absorption even more efficient. They are linked to the bloodstream via capillaries, and from there the digested nutrients get distributed all over the body. Similar to the villi are lacteals, which absorb faty acids and glycerol to be distributed via the lymphatic system.

The liver is a multi-functional organ, located in the upper right side of the lower abdominal cavity. Within the digestive system, its primary role is to produce bile, an enzyme that breaks down fats into smaller pieces which other digestive chemicals can better act on. This bile is transported out of the liver through the Hepatic duct. From there, it is generally taken to the gallbladder for storage until needed. The gallbladder is a small sack-like organ located near the liver. Bile enters the GI tract in the duodenum, via the common bile duct. Sometimes, the bile crystallizes in the gallbaldder, forming painful gall stones that block the common bile duct. Other roles of the liver are to control blood sugar (via insulin), deaminatize of amino acids, organize fats, destroy poisons, store iron, store vitamins, make plasma proteins and make heat.

Another enzyme-producing organ is the pancreas. It is a glandular organ, located below the stomach and connected to the duodenum via the pancreatic duct. The pancreas produces the blood sugar-regulating insulin and pancreatic juice which digests carbohydrates, proteins and fats.

Further along the gastrointestinal tract is the large intestine. It is a shorter but wider tube straddling the outside of the small intestine, and is roughly 1.5m long. It is divided into the ascending, transverse, descending and stigmoid portions. It’s function is some further digestion via bacterial cultures present there, absorption of water and vitamins, and the production of faeces. Jutting out the first part of the large intestine is the appendix. It has no known purpose, and is commonly infected.

The final portion of the GI tract is the rectum, coming at the end of the large intestine. It is a 12cm long tube that compresses and stores faeces and activates the urge to defecate. The final step is the anus, which is a sphincter that opens allowing the removal of the excrement.

MAIN PROCESSES IN HUMAN DIGESTION

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NOTABLE DIGESTIVE DISORDERS

Anemia(malabsorbtive)

An iron deficiency in blood results in the lack of hemoglobin to transfer oxygen to cells. This is a result of not enough iron in diet and/or malabsorption. Effects are low stamina, easy fatigue, and difficult blood clots. Treatments are iron supplementation and treatment of underlying cause.

Anorexia Nervosa(psychologicalmalabsorbtive)

A physiological obsession with weight loss resulting in a lack of food intake. Often seen in girls, a common sign is thinking that one is overweight when the opposite is actually true. Effects include extreme weight loss and malnutrition, eating binges, hormonal disturbances, dehydration and death. Treatment is therapy to establish a healthy diet.

Appendicitis(inflammatory)

An infection of the appendix results in it becoming swollen and filled with pus. In some cases, the appendix ruptures, spreading infection. Effects are severe abdominal pain which increases with upward pressure. Fever, nausea, constipation and vomiting may also occur. Treatment is the immediate performance of an appendectomy to remove the appendix in surgery.

Bulimia(psychologicalmalabsorbtive)

Similar to anorexia nervosa, except that food is intaked as usual but then “purged” through induction of vomiting. Additional symptoms may include irritation of esophagus and tooth damage due to the acid.

Celiac Disease(malabsorbtive)

An allergy that affects the small intestine, where the lining of the intestine reacts with gluten. The intestinal wall becomes smooth and hence the body is less able to absorb nutrients. Effects include stunted growth, malnutrition, improper bowel movements, anemia, vitamin deficiencies, mouth ulcers and passing gas. The only treatment is to avoid almost all gluten products (most grains). Vitamin and iron supplements may also be taken.

Gall Stones(inflammatory)

The formation of stones in the gall bladder from an improper chemistry of bile; problems arise when these stones become stuck in the bile ducts. Symptoms are a biliary colic (extreme pain) in the abdomen,

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Polysaccaridesi.e. Starch

Via AmylaseFrom mouth and pancreas

MaltoseIn mouth and small intestine

Via MaltaseFrom mouth and walls ofintestine

MonosaccaridesIn mouth and small intestinei.e. Glucose

ProtiensVia Pepsin and TrypsinPepsin from wall of stomachTrypsin from pancreas

PolypeptidesIn stomach and intestine

Via peptidaseFrom walls i intestine and pancreas

Amino AcidsIn small intestine

FatsVia LipaseFrom walls of intestine and pancreas

Glycerol and Fatty AcidsIn small intestine

which fades and peaks. Treatment are painkillers and the removal of the stones or the entire gall bladder.

Hiatus Hernia(structural)

A protrusion of the stomach into the hole of the diaphragm which the esophagus enters from. Effects are extreme pain, treated by surgery to reverse the problem.

Khawshiokor(malabsorbtive)

An effect of childhood protein malnutrition, but not caloric malnutrition. Effects are generally swelling feet, loss of skin pigment, hair and teeth, and a swelling liver causing a swelled belly. Treatment is the immediate readjustment of diet to give proper nutrition.

Obesity(malabsorbtive)

Excessive caloric intake results in excess fat build up around the belly, thighs, buttock and other parts of the body. Secondary effects include elevated blood pressure, osteoarthritis from higher weight on bones, increased risk of cancer, heart disease and diabetes and many more. The treatment is a regimen of good diet and exercise to burn fat; extreme cases ma be treated with surgery to reduce appetite or absorption of food.

PKU(malabsorbtive)

Phenylketonuria (PKU) is a disease in which the body lacks a means to break down the amino acid phenylalanine. Excess phenylalanine can accumulate near the rain, causing damage; sometimes starting from birth. A carefully controlled diet is the only remedy, but since the body still needs phenylalanine, small amounts still need to be taken. The control can decrease as the body develops resistance to the ill effects.

Tay Sachs(malabsorbtive)

A genetic disorder where a critical enzyme is not produced, causing the buildup of lipids close to the brain. Effects re nervous system damage starting a 6 months of age; spasticity, loss of body functions, blindness and paralysis come late, and death comes within 3 years of onset. However, the later the onset, the longer the survival. There is no cure or treatment for Tay Sachs, however, medicine can be given to control neurological problems.

Stomach Ulcer A hole in the mucous lining in the inside of the stomach causes gastric fluid to react with the stomach ling, generally caused by the bacterium H. pylori which causes low-level infection of the stomach lining. Effects include pain, blood flow in vomit, ac id secretion and broken blood vessels. Using an endoscope, a doctor can see inside and biopsy the stomach, leading to the diagnoses. Treatment is generally antibacterial medication to treat the infection.

CONTROL AND HOMEOSTASIS

The body needs to maintain roughly constant temperature, blood pH and countless other measures critical to our survival. Homeostasis refers to the body’s ability to adjust certain systems based on internal and external factors. For instance, gastric fluid and saliva are produced even before food is ingested; merely seeing food will make people’s mouth water.

Inside the body, and example of homeostasis is the control of blood sugar. Throughout the body there are many sensory systems that tell the control centre (brain) how to respond. The brain then tells an appropriate regulator that will attempt to balance the given system. Blood sugar needs to be maintained at a roughly steady level. After a meal, blood sugar rises due to the new nutrients, stimulating receptors which eventually send signals to the liver to produce insulin, lowering the blood level by making the cells of the liver and muscles more permeable to glucose. This glucose is then stored by the liver as glycogen for further use.

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Correspondingly, a decrease in blood sugar will prompt the production of the hormone glucagon, which causes the glycogen to be converted into glucose, which allows the body to use it immediately. This relationship maintains a healthy blood sugar level.

In the digestive system, hormones regulate the production of food-digesting chemicals. For instance, the activation of secretin by HCl and its subsequent absorption into the bloodstream gets detected by the pancreas, prompting the production of bases to raise the pH of the small intestine. Additionally, another hormone, gastrin, is produced when there is undigested protien in the stomach, prompting the stomach to produce more gastric fluid.

RESPIRATION

Respiration is the process by which oxygen is delivered to the cells and used to break down glucose from food, releasing energy (ATP). It also removes waste product (CO2).

There are 3 stages in Respiration:

1. Breathing – movement of gases between respiratory membranes and the external environment; the act of moving air in (inhale oxygen) and out (exhaling carbon dioxide) of the lungs. Lungs within the body to remain moist, lungs must not be dry.

2. Gas exchange – the swapping of gases between the internal environment (blood) and the external environment (air).

3. Cellular Respiration – the process by which energy is released from food (glucose):a. C6H12O6 + 6O2 6CO2 + 6H2O + 36ATPb. Takes place in the mitochondria in cellsc. Burning of glucose (not actual fire – oxidation)d. Glucose + oxygen carbon dioxide + water + energy

Functions of Respiration:

Bring oxygen into the body and provide a site for transfer into the blood Elimination of carbon dioxide from the body Moving air across vocal cords Putting smells into the nose

The Respiratory System can be divided into two zones:

1. Conducting – tubes and channels that carry gases in and out (nasal cavity, sinuses, pharynx, trachea, bronchi, bronchioles

2. Gas Exchange – tissues where the exchange of gases takes place (very small bronchioles, alveoli, capillaries)

STRUCTURES IN THE RESPIRATORY SYSTEM

Nasal Cavityo Hairs and mucous membranes inside the nose trap dust and unwanted

particleso Mucus moistens air

Turbinates

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o Bony projections increase surface area; better smello Mucus traps dust and moistens airo Lined with capillaries filled with warm blood so air is warmed

Moutho Air can also enter the mouth but does not get as well cleaned, warmed or

moistened due to the smaller surface area. Pharynx

o Tube common to respiratory and digestive systemo Muscular and funnel shapedo Contains tonsils which help fight the entry of pathogenso Contains mucus and cilia (to clean and warm the air).

Sinuseso Sinuses are hollow cavities in the facial bones that connect to the nasal

cavity through narrow channels called Ostia.o The purpose of sinuses are unclear, but there are some theories:

Humidification and filtration of inhaled air Lightens the weight of the skull. Effects vocal resonance/enhances voice Absorb energy of an impact therefore helping to prevent brain injury

(much like the body of a car does in a crash) Epiglottis

o Left shaped piece of cartilageo Seals the opening into the respiratory tract during swallowing

Larynxo Box-like structure, containing the vocal cords (aka voicebox)o 9 pieces of cartilage held together by muscles and ligaments.

Tracheao A hollow tube about 12 cm long, also called the windpipe.o Made of smooth muscle and supported by rights of cartilage. The rings keep

the windpipe from collapsing. The inside is lined with mucus membranes and cilia. Moistens and cleans the air.

Bronchio Trachea branches into two bronchi (right and left) which enter each lung

(note that directions are reversed as if flipping the diagrams right left )

o Smaller diameter, still has cartilage rings; ciliated mucus membranes to clean air.

o Right lung divided into three lobes, left lung two. Bronchioles

o Bronchi continue to branch and spread through the lungso Smaller diameter, no cartilage rings, no cillao Elastic walls which dilate and constrict to allow more or less air through.

Alveolio Microscopic air sacs, like clusters of grapes at the end of bronchioles.o Very thin walled, surrounded by capillaries; site of gas exchange.

Pleurao Double membrane surrounding lungs

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o Outer membrane lines the inner surface of the chest wall and covers the upper surface of the diaphragm

o The inner layer adheres to the lungso Two membranes so close together that only a very thin fluid separates them.

Diaphragmo A thin dome-shaped sheet of muscleo At the level of the bottom of the tibso Separates thoracic cavity from abdominal cavityo Edges connect to the spine at the back, to the lower ribs around the sides

and to the bottom of the breast bone at the front.

GAS EXCHANGE AND THE RESPIRATION PROCESS

The standard equation for cellular respiration is C6H12O6 + 6O2 6CO2 + 6H2O + 36ATP. Of this, the oxygen is inhaled from the air, and the carbon dioxide and water is exhaled. Diffusion is the movement of substances from an area of high concentration to one of low concentration, and respiration uses this to work.

Inspired air is composed of 21% oxygen, 78% nitrogen, <0.05% carbon dioxide and other trace gases. Expired air is composed of 16% oxygen, 78% nitrogen, 55 carbon dioxide and the same trace gases.

Before the alveoli, the composition of air does not change as it is not in contact with respiratory surfaces and the O2 passes into the blood, while CO2 is taken up from the blood. Some of the “dead air” from the tubes will be mixed with the air from the alveoli. After gas exchange the air has a composition of 14.% oxygen, 80% nitrogen, and 5.5% carbon dioxide.

Requirements for Gas Exchange

Gas exchange surface must be large Gas exchange surface must be thin and moist.

o Gas exchange occurs by diffusion, which only occurs when gas is dissolved in water.

Means of transporting bases between the exchange and surface to every cell (i.e. bloodstream) must exist.

Mechanics of breathing

1. Inhalinga. Diaphragm contracts and lowers thus volume of lungs increasedb. Volume of lungs further increased as intercostal muscles contract and ribs

move up and down.c. Increased volume of lungs causes air to rush into the lower pressure area.

2. Expirationa. Diaphragm relaxes, pushing upward thus reducing chest volume.b. Intercostal muscles relax, moves in and down, causing lower chest volume.c. Volume decreased, air pushed out of the lungs.

Breathing out requires no muscle contraction; it is the result of muscle relaxation.

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Nervous system control of breathing

Increased activity means cells require more energy. Energy comes from cellular respiration. Brain (the medulla ablongata part) contains both a CO2 level sensor and an O2 level

sensor which respond to changes in concentrations of CO2 and O2 levels in the blood passing through the brain by increasing and decreasing the breathing rate as necessary.

o Both stimulate breathing, but higher CO2 levels have more effect. The brain sends out impulses to the diaphragm and intercostal muscles to speed up

their action which results in more CO2 out and more O2 in. After exercise the CO2 levels drop, medulla sense this and a signal is sent to slow

down breathing.

Factors Affecting Breathing Rate

Increased altitudeo Increase in altitude results in lower concentration of oxygen.o The body has to breathe more; unacclimated people will suffer from altitude

sickness because less oxygen is taken in per breath. Poorly ventilated room

o Higher concentration of CO2 in the air results increased breathing rate to get rid of the CO2 in blood, because diffusion works less efficiently.

Physical activityo More energy needed means that cellular respiration increases which results

in more required oxygen and gives off carbon dioxide.o The increased of CO2 and decrease of oxygen increases the breathing rate.

A common coldo Increase in breathing activity, but shallower breaths, due to the efficiency of

air movement within the upper passages being reduced by infection.

Lung capacity and volumes

Tidal volumes – the amount of air that moves into the lungs in a normal breath. Inspiratory reserve volume – the extra volume of air that can be inhaled after a

breath. Expiratory reserve volume – the amount of air than can be forced out of the lungs. Vital capacity – the maximum amount of air than can be exhaled after a breath. Residual air capacity – the volume of air that always remains in the lungs. Can only

be removed by opening the chest cavity. Total lung volume – the vital capacity plus the residual air capacity.

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THE HUMAN RESPIRATORY SYSTEM

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THE TRACHEA AND BRONCHIAL TREE

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DISEASES OF THE RESPIRATORY SYSTEM

Bronchitis(inflammatory)

Inflammation of the mucous membrane that lines the bronchi, usually caused by viral infection. Main symptom is a deep cough that brings up grayish or yellowing phlegm, others include breathlessness, wheezing and fever. Smoking, asthma and air pollution are risk factors. Aspirin and cough medication can be used to mask symptoms, but there is no specific treatment.

Bronchial Asthma(inflammatory)

Chronic condition marked by periodic attacks of wheezing and difficulty in breathing. Attacks due to the contraction of muscles in the bronchial walls, generally triggered by allergy. Stress, exercise and infection can also cause attacks. There is no cure, but children often outgrow it. Attacks can be treated or prevented with inhaled drugs (steroids) that relax the muscles walls.

Common Cold(inflammatory)

A group of minor illnesses caused by over hundreds of viruses. The symptoms vary depending on the virus, but are generally runny nose, sore throat, fever, watering eyes, coughing, chills and hoarseness. A very high temperature and general body pains are more likely the flu. The cold cannot be cured, only the body may do that, and only with proper rest. Medication can only mask the symptoms.

COPD(inflammatory/structural)

Chronic obstructive pulmonary disease, a disease referring to chronic bronchitis and emphysema which are coexisting. Generally caused by smoking or other airborne toxins, chronic bronchitis eventually causes damage to the alveoli. This combination of narrowed airways and lost alveoli leads to reduced oxygen intake. Unlike asthma, this is not reversible and often gets worse over time, and a transplant is often the only recourse.

Emphysema(structural)

Disease where the lungs become less and less efficient due to the damage to the alveoli, resulting in decreased surface area and decreased lung capacity due to lowered lung elasticity. Frequent causes include smoking, air pollution, occupational hazards and exceptional force on the lungs (i.e. glassblowing). People who have emphysema often also suffer from asthma or bronchitis. There is no cure, only the progress of the disease can be slowed, via bronchodilator drugs which widen the bronchioles.

Hemoglobin Poisoning(malabsorbtive)

Carbon monoxide poisoning results in hemoglobin absorbing CO and turning into carboxyhaemoglobin. Hemoglobin absorbs carbon monoxide better than it does oxygen, and small amounts of CO in the air will result in lower oxygen absorption. This results in less oxygen being delivered in the blood, causing drowsiness and weakness in lower concentrations and death in higher ones. Treatment is the immediate administration of pure oxygen to flush out the carbon monoxide.

Laryngitis(inflammatory)

Bacterial or viral infection of the larynx, causing general inflammation and swelling of the mucous membrane of the larynx. This causes the vocal cords to be unable to vibrate, resulting in the inability to speak for a few days. This may be an effect of some underlying condition, like cancer or bronchitis. The disease generally heals on its own, but antibiotics can be used to fight possible bacterial infection, and an underlying cause may be treated.

Pleurisy(inflammatory)

Roughening or swelling of one or both of the plural membranes, due to another condition, resulting in difficulty of breathing as the two layers start to rub against each other. Pleurisy is actually a symptom of another disease, generally an infection, but it has become very rare. A fever will indicate an infection, which can be easily treated with

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antibiotics. Painkillers can treat the pain.

Pneumonia(inflammatory)

Not a specific disease, but a general term for several kinds of inflammation of the lungs. Causes include infection and inhalants causing chemical damage to the lungs. In pneumonia, the alveoli swell up and fill with fluid. No single symptom applies to all types pneumonia, but general ones are fever, coughing, chills, sweating, chest pains, cyanosis (bluish tinge to the skin), blood in phlegm and occasionally mental confusion or delirium. Eventually, the body may clear it by itself, or it may cause death, particularly in the old. Treatment is the application of cough medications, antibiotics, painkillers to relieve chest pain and diagnosis and treatment of the underlying condition.

Pneumothorax(structural)

Disease where air leaks out of the lungs into the pleural space, causing the lung to collapse. May be caused by trauma or spontaneously. Symptoms include breathlessness and pain, particularly on one side of the body. A small pneumothorax often clears by itself, but for larger ones a catheter is inserted into the pleural space and the air sucked out as the patient exhales.

Pulmonary Edema(structural)

An edema, or swollen tissue, results from the inefficient pumping action of the left side of the heart. This results in the blood in the pulmonary veins to become damned up, seeping from the blood to the alveoli, resulting in an accumulation of fluid and swollen lungs. The disease starts with increasing breathlessness and coughing up bloody phlegm. Treatment is to relieve the breathlessness fist, usually with morphine to deepen breathing and diuretics to clear the fluid. Action is then taken to strengthen the heart.

Tuberculosis(inflammatory)

A bacterial infection that attacks the lungs, and may move onto the brain, kidneys and bones. The first stage is where the body resists the infection by trapping the bacteria in fibrous capsule that develops around an inflamed area. If bacteria escape, another one is produced, often elsewhere in the body. When the body becomes weak, the still-alive bacteria may escape, developing into the second stage, “consumption”. In this stage, the bacteria multiply rapidly, often in the lungs, reducing the capacity to breathe and causing lung damage. First-stage symptoms are usually mild. The secondary stage may involve slight fever, weight loss, and a tired feeling. Eventually, in a lung infection, shortness of breath and coughing up phlegm develops. If the disease spreads to other organs, it can be fatal. Treatment is a regimen of antibiotics and continual monitoring.

THE CIRCULATORY SYSTEM

The Circulatory System is a system which moves things throughout the body. These things are:

Water Food: vitamins, minerals, glucose, amino acids, glycerol + fatty acids, etc. Oxygen Wastes Hormones Antibodies Drugs

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Carbon dioxide

Why is it necessary?In multi-cellular animals, most cells don’t have direct contact with the external environment and are therefore not in contact with things necessary for life. Therefore, the circulation system takes these things to all body cells. Any cell in the body is probably not more than 2-3 cells away from blood vessels.

The requirement of the circulation system are that is must transport dissolved minerals, must link every cell in the body and must circulate the fluid.

All of these functions are performed by an internal circulatory system with three main components:

1. Fluid: blood and oxygen and nutrients dissolved in fluid2. Vessels: arteries, veins, capillaries3. Pump: the heart

BLOOD

The blood is composed of 55% plasma (which is 95% water, the remainder solutes), and 45% cells (red blood cells 44%, white blood cells 1%, platelets <1%)

Red Blood Cells (aka Erythrocytes) look like a donut without the hole in the middle, but still with a depression. They do not have a nucleus. They are round in order to roll and to not lump together and clot. The depression present in the middle is to increase surface area. There are 4.5-5.5 million of these cells per milliliter of blood, are produced in the bone marrow, and have a lifespan of about 120 days. Dead red blood cells are broken down in the liver and spleen where the iron in them is recycled. The function of the red blood cells is to deliver oxygen to all cells and to take carbon dioxide back to the lungs.

Sickle Cell Anemia: red blood cells become sickle shaped and do not pass through blood vessels as well. Cure is bone marrow transplant or stem cell therapy.

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White Blood Cells are the mainstays of the immune system. They are created in the bone marrow but only have a lifespan of a few hours or days. They defend the body against invaders; a high white blood cell count indicates infection. These cells can squeeze through the walls of blood vessels to reach foreign organisms or sites of injury. There are several types of these cells with different shape, size and appearance of nuclei.

Agranular: lymphocytes produce antibodies; monocytes travel quickly to infected areas and elicit an immune system response.

Granular: basophils prevent unwanted blood clotting; neutrophiles eat foreign organisms; eosinophils are involved in allergic reactions.

Platelets are cells which are really not “alive” at maturity. They are fragments of larger cells with no nucleus, basically sacs filled with thromboplastin which is involved with the clotting of blood. Thromboplastin is a soluble blood-clotting protein. They are the smallest of the blood component parts.

Blood Clotting is the process in which a leak in the blood stream is plugged by chemical processes. When a wall breaks, platelets rupture, releasing thromboplastin.

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Thromboplastin + Calcium (from blood) + prothrombin Thrombin

Thrombin + fibrinogen fibrin clot

Red Blood Cells and platelets stick to the thread-like fibrin; it forms a scab which patches the hole while the skin repairs itself. All compounds of the reaction are present in blood plasma; the starter of the reaction (thromboplastin) is kept separate in the platelets so the reaction only happens when the platelets are ruptured.

A bruise is an injury where blood vessels break and clot inside the body, but the skin is not ruptured so no blood bleeds out.

Blood Types are determined at the moment of conception and do not change. An incompatible blood type which is transfused will kill the patient. An antigen is a marker on the membrane of the cells which identifies them as foreign (or not) and triggers a response. An antibody is a protein formed by the body in response to a foreign substance (antigen), and may be present in blood plasma. Blood types are determined by the antigens present on the membrane of Red Blood Cells.

There are four blood types:

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If antigens and antibodies of the same type come together, they cause the RBCs to clump together. You’re going to probably die if this happens, and there’s nothing you can do about it. If two samples of the same type are mixed, there is no clumping.

Typo O is the universal donor as it has no antigens to react with other blood types. Type AB is the universal recipient as it contains no antibodies to react with antigens.

RH (Rheses) factor: another antigen on RBCs in about 1/6 of people. People with the antigen are Rh positive. Rh negative people have no antigen but do not automatically contain the Rh antibody; they must first be sensitized by receiving some Ph antigen. In pregnancies, there is another problem: if an Rh- mother has an Rh+ child, the baby’s blood can enter the mom’s body, which causes antibodies to be produced. These antibodies can react with the Ph antigen of a second baby. After birth, an Rh- mother is immunized with antibodies which combine with fetal Rh+ antigens and neutralize them before the mother has time to develop her own antibodies.

BLOOD VESSELS

There are three types of blood vessels: arteries, which go away from the heart; veins, which go back; and capillaries, which connect the two.

Arteries are the main transporters of oxygenated blood. Arterioles are smaller arteries whose diameters are adjusted to regulate blood flow. Capillaries are tiny blood vessels one cell thick and diffusion occurs within its walls.

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Veins travel with CO2 rich blood back toward the heart (with exception of the pulmonary vein, which carries O2 rich blood). They are at a lower pressure than arteries. Valves inside the veins help regulate blood flow, with a generally smaller diameter.

Varicose veins form when the valves malfunction and blood builds up. The vessel walls start to sag and protrude out of the skin in an unattractive way. Spider veins occur with smaller vessels.

The Aorta is the most important and largest artery. It exits the heart out the top and takes a u-turn to go back behind the heart. It runs parallel to the spin until the abdomen when it branches off into the arteries in the legs (femoral arteries).

THE HEART

The heart is the size of a person’s fist, and is located to the left side of the cheat. It is suspended in the chest by the large blood vessels connecting to it. It is surrounded by a double membrane sac called the pericardium, and the chambers are lined with a membrane known as the endocardium.

Pulmonary and Systemic Circulation

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LUNGSBODY CELLSR L

O2 Rich Blood - Aorta

Superior and Inferior Vena Cava – O2 Poor Blood

HEART

Pulmonary Artery – O2 Poor Blood

Pulmonary Vein – O2 Rich Blood

Pulmonary circulation involves the heart pumping O2 poor blood to the lungs to be oxygenated, while systemic circulation delivers oxygenated blood to the rest of the body. Another form, pulmonary circulation, supplies the heart itself with blood. Blood flows from the left ventricle through the coronary arteries to the muscle of the heart and back to the right atrium. The coronary arteries branch off the aorta, while the coronary veins bring blood back to the right atrium.

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How the Heart Beats

The SA (sinoatrial) Node is a bundle of nerve tissue in the right atrium. When the SA node is stimulated by the central nervous system, a save of muscle contractions spread out over the right and left atria.

The AV (atrioventricular) Node is a small bundle of nerve tissue in the septum which is stimulated by muscle contractions. The Bundle of His is stimulated by the AV node and in turn stimulate the Purkinje which start contraction from the bottom of the centricle.

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Adrenaline is a hormone which causes the heart rate to rise.

Blood pressure is continuously monitored by bororeceptors, nerves embedded in the walls of arteries. Any rise in pressure is signaled to the medulla at the base of the brain, which issues commands along the ragus and parasumpathetic nerves to correct the situation.

Cardiovascular Risk Profile

Coronary heart disease is a major cause of death in Canada and many other countries. This is a preventable disease. Prevention requires major changes in diet and lifestyle for all Canadians. Some individuals are at a greater risk than others. The more risk factors you have the greater the chance of heart attack or heart disease. Immediate risk factors include smoking, high blood pressure, elevated total and LDL cholesterol, diabetes mellitus and advanced age.

Cigarette smoking is the number one preventable cause of heart attack. Those who smoke a pack of cigarettes per day have twice the risk of heart attack as non-smokers. Stopping smoking reduces the isk of heart attack, heart disease and stroke.

Elevated blood pressure (above 140/90) increases the risk of a stroke and heart attack. Elevated blood pressure can be controlled by both diet and exercise. You should exercise every day.

Blood cholesterol is another factor. If the total cholesterol level is less than 5.0 mmol/L then that is reassuring. A level between 5 and 6 results in twice the risk, but 45% of Canadians are at this level. People should get their level checked at the annual physical. HDL cholesterol is good; LDL is a better indicator of risk. An LDL level above 4.0 mmol/L is a risk factor to having a heart attack.

Diabetes Mellitus: diabetics often have a blood sugar level much higher than it should be. Too much sugar in the blood can cause damage to many parts of the body include blood vessels. Advanced age is perhaps the most powerful risk factor for Cardiovascular disease and cancer, both of which increase exponentially between ages 40 and 80.

Other risk factors include Predisposition/family history, obesity, stress and elevated triglycerides.

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GENETICS

CELLULAR REPRODUCTION

Cells divide to grow the body, maintain the body and repair the body. Cells cannot grow too big or they will become inefficient and may die. For instance, a perfectly cube-shaped cell which doubles each of It’s dimensions decreases by a factor of two. With less surface area for cell respiration and nutrient intake, the cell may not be able to maintain itself and may die. Nutrients also have to travel longer distances to reach the inner parts of a cell if it gets large.

The cell cycle (mitosis):

1. Interphase: this is the time interval between nuclear divisions. The cell increases in mass and the cell duplicates its chromosomes before division. The majority of the time is spent here; the cell is performing it’s function (i.e. muscle cells contract, kidney cells diffuse, etc.).

2. Prophase – the first part of mitosis. The chromosomes become visible; they shorten and lengthen. Centrioles form and move to the poles. Spindle fibers also form and guide the attachment of the centrioles to the chromosomes. The nuclear membrane begins to fade.

3. Metaphase – the second sage of mitosis. Sister chromatids move toward the center of the cell (equatorial plate), and the chromosomes attach to spindle fibres.

4. Anaphase – the third stage of mitosis. Centromeres divide and the sister chromatids (now chromosomes) move to opposite poles of the cell. Same number and type of chromosomes should now be present in both sides.

5. Telophase – the last phase of mitosis. Chromosomes reach the opposite poles of the cells and lengthen. Spindle fibres dissolve, nuclear membrane forms on each chroatin mass.

6. Cytokinesis - the cytoplasm begins to divide as the chromosomes move to opposite poles. Distinct from nuclear division. A furrow develops in animals cells and causes split. In plants, a new cell wall forms down the cell plate.

Meiosis

Meiosis forms gametes, or sex cells (sperm and olvae) There can only be half the usual number of chromosomes in a gamete as they have

to combine to form the zygote. To ensure genetic variation, a process called synapsis or “crossing over” occurs. A

homologous chromosome pair (one from the father, one from the mother) go side by side each other and genetic information is exchanged.

There are two stages to Meiosis: Meiosis I – in this stage, the initial cell splits into two haploid cells each with 23 full

chromosomes. Consists of Prophase I, Metaphase I, Anaphase I and Telophase I, similar to mitosis

Meiosis II – the two haploid cells further divide into four cells with the hapolid number of chromatids (half chromosomes). This again follows Propase II, Metaphase II, Anaphase II and Telophase II.

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In men, 4 sperm cells are formed. However, in women, only one egg (ootid) is formed due to one daughter cell receiving more cytoplasm than the other during Meiosis I and II. The 3 other cells are called polar bodies and are reabsorbed into the body.

Non-disjunction is where the chromosomes fail to separate properly, sending one more chromosome to one daughter cell and one less to the other. This results in monomy and trisomy which are genetic disorders, includes Down’s syndrome.

A cancer is a cell which has lost communication with neighboring cells or otherwise starts to duplicate uncontrollably, forming a tumor. This tumor continues to use the body’s resources, weakening the rest of the body, but often does not perform its usual function. Since cancer cells do not stick to other cells easily, they can metastasize or spread to other parts of the body.

GENES AND DNA

Gregor Mendel, an Austrian monk, developed a set of rules concerning heredity in the 19th

century. Using pea plants, he realized that certain traits of the plants were passed on to the offspring, such as seed shape, flower position and stem length. It was later realized that this was governed by the molecule DNA, which contains all the information needed to create a living thing of a given species with certain traits. This is divided into pairs of chromosomes. All animals have one chromosome from each of their parents. Humans have 46 chromosomes; in 22 pairs plus two sex chromosomes XX indicates a female, XY a male.

Hereditary characteristics are determined by distinct units or factors that occur in pairs. When reproductive cells are produced, the two factors of each pair segregate (separate) are distributed as distinct units, one to each gamete. This is the principle of segregation.

DNA is made up of base pairs. There are four separate molecules that store the information. These are Adenine, Thymine, Guanine and Cytosine. A bonds with T, and G bonds with C. These four molecules form the rungs of a ladder, with phosophase-deoxyribose forming the outside. To be compact, the DNA is tightly compressed in a spiral, forming the double-helix shape.

DNA is first and foremost a series of instructions for making proteins. A series of base pairs responsible for the manufacture of a given protein is called a gene. There can be certain base pair combinations which cause a gene to be different; a different form of a gene is known as an allele. Alleles can be dominant or recessive. Since there are two copies of genes (one in each homologous chromosome pair), they can be different. In some cases, a certain allele may be dominant over a recessive allele. The recessive trait is not used, therefore if one person has one allele for brown eyes dominant over the allele for blue eyes, he will have blue eyes. What the person’s visible traits are is called the phenotype which the combination of alleles in the DNA is expressed as a genotype. Two alleles which are the same are known as homozygous, which two different ones are heterozygous.

To find out the possible phenotype and genotype of the offspring knowing the genotype of the parents, a Punnett Square is used (Y = yellow, y = green)

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The genotype is 0% homozygous yellow : 50% heterozygous yellow : 50% homozygous green. The phenotype is 50% yellow : 50% green.

Punnett squares are also possible with dihybrid crosses where two traits are being evaluated. To do so one must construct a 4x4 grid with every possible combination of alleles in the gametes from each parent along the top and side, like in the following table, between two RrYy parents.

Finally, alleles don’t have to be dominant nor recessive. Two alleles can be co-dominant. For instance, if a plant has a red-flower allele and a white-flower allele which are co-dominant, the plant will have pink flowers.

NOTABLE GENETIC DISORDERS

HemophiliaRecessiveX-Chromosome

Missing two clotting factors, VIII and IX. Bleeding cannot be easily controlled; cuts and bruises may result in death from blood loss. No cure; treatment is the injection of the missing proteins.

Cystic FibrosisRecessiveChromosome 7

Strong difficulty breathing due to excess mucus produced in the lungs. No cure, the only hope is daily beatings to get the mucus out. Also affects pancreas and liver due to the mucus blocking digestive enzyme actions. Drugs and transplant may work.

Sickle-cell AnemiaRecessiveChromosome 4

Red blood cells are sickle-shaped due to malformed hemoglobin. The cells easily clot and cause pain and vessel blockage. Only found in people of black African descent. Cure is a marrow transplant.

Tay-SachsRecessiveChromosome 15

Loss of motor skills, intellectual ability, seizures and death come before age 4 generally as a result of fat buildup in the skull crushing the brain, since the body cannot process the fat due to a missing protein. Tested by the red-spot test in the back of the retina, or behavioral test. Always fatal.

Phenylketonuria (PKU)RecessiveChromosome 12

Inability to metabolize the amino acid PHE. It may accumulate in the brain, crushing it and causing damage. The treatment is a diet very low in PHE, but still with some present as it is still essential to the body.

Huntington’sDominant

Appears in the 40s, starting with mood swings, short-term memory loss, chorea, speed difficulty, shaking and loss of motor control, due to the

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Chromosome 4 accumulation of a different form of the protein Huntingtin. Death is generally due to secondary infection.

Klinefelter’sXXY Chromosomes

Symptoms of this non-disjunction are relatively minor, only less developed male parts and excess breast tissue.

Down SyndromeTrisomy 21

Symptoms include poor motor skills, expanded facial muscle development and lower intellectual ability. The incidence rises dramatically if the mother is over the age of 40. Most common trisomy.

Pata SyndromeTrisomy 13

Severe physical and intellectual defects, including the failure of the brain to divide properly, extra digits, complex heart defects, deformed hands and feet. Babies often die from these defects early.

Edward SyndromeTrisomy 18

A very low rate of survival due to kidney malformations, complex heart defects, severe mental retardation, intestines out of the body, feeding difficulties, etc. Like Down’s incidence rises significantly with mother’s age > 40.

TurnerX chromosome only

The missing second X chromosome may lead to less developed female characteristics, infertility, or it may not have any great effect at all.

Marfan SyndromeDominantChromosome 15

Various symptoms, from large height, weak aorta, nearsightedness, inadequate circulation resulting in numbness and fatigue, and miscellaneous disorders associated with height and poor circulation. Often death occurs due to undiscovered Marfan’s resulting in an aortic aneurism.

Duchenne muscular dystrophy (DMD)RecessiveX-Chromosome

A lead cause of muscle atrophy in males. Muscles start to waste away causing weakness, beginning in the legs and spreading to the arms and upper body. As muscle is replaced by fat, bone structure may malform leading to paralysis. Eventually the heart and breathing muscles are affected causing death from the teens to the mid thirties.

EVOLUTION

Evolution is the change in the genes and allele frequencies of a population from generation to generation via such processes as mutation, natural selection and genetic drift.

The fossil record

The fossil record demonstrates the one time existence of organisms which no longer exist. When arranged in chronological order, changes are found which can only be explained by a series of progressive changes (evolution). There are many types of fossils: entire body frozen in ice, skeletal remains, fossilized wastes or dung, imprints in rocks, amber fossils, petrifaction, tar pit fossils, imprints, molds and casts.

It is impossible to completely piece together the evolutionary history of some organisms. There are some gaps in the fossil record called “missing links”. The missing link between reptiles and birds was filled by the archaeopteryx, which had features from both and could fly.

Comparative Anatomy

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Homologous structures are organs with similar structures but different functions, such as the arm of a human, the bird on a bat and the flipper on a whale.

Vestigial structures are parts which seem to be of no use to them, but were used by its ancestors. In humans, examples are the tailbone and appendix, which were useful to our evolutionary ancestors but not us.

Analogous structures are features of different species that are similar in function but are structurally different. They evolved due to similar environmental challenges, e.g. the wings on birds and insects.

Embryology describes the study of the embryos of different organisms. In vertebrates, the embryos are all remarkably similar between humans, birds, and fish in their early stages, demonstrating some link. For example, humans have gill pouches in early development, which later form the auditory canal.

The Age of the Earth was first calculated by Lord William Thompson Kelvin to be around 40 million years (later revisted to 15-20 million). Pierre Curie discovered radioactive decay in 1903, and it has been useful in determining the age of the Earth, now believed to be around 4.6 billion years. Oldest rocks (Canadian Shield) are around 3.9 billion years old.

Geographic Distribution of Species is when inhabitants of ocean islands resemble forms of the nearest mainland relatives but show some differences, showing that they have evolved from the mainland relatives.

Protective Resemblance shows that the effects of an environmental change on selection patterns. Industrial Melanism was when light colored moths declined in population due to the trees they were on being covered in black soot. They were replaced by back moths.

The DNA mutation rate is about 2 to 4 percent every million years.

Comparative Biochemistry compares the complex molecules and chemical processes shared by organisms and finds incredible similarities in these between various organisms. Closely related species are very similar at the molecular level, and distant species all share essential similarities:

1. Cells are made up of the same basic organic compounds: nucleic acids, lipids, carbohydrates, etc.

2. In all organisms, reactions are controlled by enzymes3. Protein is synthesized from about 20 amino acids.4. Carbohydrates consists of 6-carbon sugars (glucose) and polymers of those

(cellulose, chitin, etc.)5. All cells obtain energy from processing glucose in glycolosis6. All cells contain DNA7. DNA determines the specificity of proteins through compounds like messenger RNA

(mRNA)8. Structures of important lipids, proteins, DNA, RNA, ATP and enzymes are the same.

James Hutton was the founder of modern geology and influenced Darwin. He had a law of Uniformitarianism, where “all parts of physics apply everywhere, and the same principles that govern the universe when it was created still do now.” Geologic time: if Hutton is correct, the Earth must be older than previously thought.

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Genetic Variation – in the 1930s biologists began integrating genetics with Darwin’s ideas on evolution. Sexual reproduction results in the random recombination of thousands of alleles and results in high genetic diversity.

Wilhelm Winberg and Godfrey Hardy came up with the Hardy-Weinburg Principle. Allele frequencies will not change from generation as long as the following conditions are met:

1. Large population2. Mating opportunities are equal3. No mutations occur4. No migration occurs5. No natural selection occurs – all individuals have an equal chance to reproduce

For a gene with two alleles (A and a), the Hardy-Weinburg Principle can be expressed with the equations below (p=frequency for A, q = frequency of allele a):

p+q = 1(p+q)2 = 12

p2 + 2pq + q2 = 1

This can be sued to solve problems dealing with allele frequency.

Domestication and Natural Selection - We can easily breed animals and plants to achieve desirable characteristics. If humans can cause these changes in a short period of time, the environment could cause change in a long period of time.

Genetic Drift

Changes to the allele frequency as a result of chance: such changes are much more pronounced in small populations. In small populations, chance can play a huge role in determining allele frequencies. When a severe event results in a drastic reduction in numbers, a population may experience a bottle-neck effect. A small sample survives to establish a new population, and there allele frequency may differ from the original population. For instances, elephant seals were hunted down to 20 in 1890. They are now at 20000, but they have near total homozygosity.

The founder effect is when a small number of individuals separate from their original population and found a new population.

SELECTION AND SPECIATION

Patterns of Selection

1. Stabilizing Selection – selection against individuals exhibiting variations from the mean.

2. Directional Selection – selections that favor selection toward or against a given trait, away from the current mean.

3. Distributive Selection – selection toward individuals exhibiting variations toward the mean; differences are favored; may cause speciation.

4. Sexual Selection – different reproductive success results from variation in the ability to obtain mates. Results in sexual dimorphism (differences between individuals of

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different sexes within a species) and courtship behaviors. Selection against those who cannot find mates.

Altruism is behavior that decreases the fitness of an individual that is cooperating with a recipient whose fitness is increased. For instance, bees will pass on their own mating opportunities for the good of the colony.

Speciation is the evolutionary formation of a new species. Members or breeding groups which are reproductively isolated from other groups and evolve independently are called species. Reproductive isolating mechanisms are any behavioral, structural or biochemical traits that prevent individuals from different species from mating successfully.

Reproductive Isolating Mechanisms

Pre zygotic:o Ecological isolation – species occupy different habitats or have separate

niches (i.e. Lion and tiger can breed, but they don’t in the wild because they’re not at the same place)

o Temporal isolation – e.g. similar plants bloom during different times to avoid cross-pollination.

o Behavioral Isolation – each species may use different signals for attracting mates

o Mechanical isolation – the parts don’t fit together; structural differences in sex organs

o Genetic isolation – sometimes, sperm and egg of the same species recognize each other via chemical markers. Often, foreign sperm cannot survive inside the female.

Post-zygotico Hybrids cannot mate – prevents the reproduction of offspring from

interspecies reproduction; e.g. hybrid trilliums and mules are sterileo Zygote mortality/hybrid inviability – prevents exchange of alleles between

species

Modes of Speciation

Allopatric speciation is the evolution of populations into separate species as a result of geographic isolation.

Sympatric speciation is the evolution of new species via spontaneous mutation to the degree that they can no longer mate with their compatriots.

THE EVOLUTIONARY HISTORY OF LIFE

Earth and life on earth originated billions of years ago. Science has pieces together initial conditions and events that may have resulted in the origin of life.

The Primordial Earth

Earth formed about 4.6 billion years ago, was very hot. Heat generated by asteroid impacts and radioactivity melted the mantle. Dense elements such as Fe, Ni formed Earth’s core, less dense ones forms the mantle and crust. Hot gasses were present; when temperature falls below 100°C water condenses, rain falls, oceans form.34

Originating Events – Organic Materials

Oparin and Haldare proposed Theory of Primary Abiogenesis in 1930s, stating that the first living things came from non-living things. They did not test their theory. The 1953 Noel Prize winning Harold Urey and Stanley Miller investigate possible reactions that could form molecules of life. Their apparatus modeled the water cycle using a condenser to produce precipitation, a heater to cause evaporation and sparks to simulate lightning; likely present throughout Earth’s early history.

After one week of running, methane was converted to Aldehydes, Carboxylic acids, Urea and simple Amino Acids – organic compounds essential to life. Later, all 20 amino acids were formed, plus vitamis, nitrogen bases of DNA, and essential sugars. This is evidence supporting primary abiogenesis.

Life from Space? Meteoroids found in Australia are rich in amino acids, and many asteroids and comets are rich in organic compounds. These findings provide additional evidence that molecules of life have formed elsewhere. Panspermia takes this further by saying life originated elsewhere in our solar system and came to Earth. A meteor from Mars had bacteria-like fossils on it (later discovered to be false).

Chemical Evolution

In 1977 Sidney Fox was able to spontaneous formation of thermal protienoids, polypeptides that polymerize into cell-like structures, and divide in two, just like natural cells. Julius Rebek (MIT, 1991) created synthetic nucleotide molecules that could replicate themselves, make mistakes and have those mistakes replicated. Earth’s first self-replicating and evolving systems may have been RNA molecules. DNA likely evolved from the reverse transcription of RNA.

Rate of Evolution

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1. Theory of Gradualism attributes large evolutionary changes to the accumulation of many small ones.

2. Punctuated Equilibrium (proposed by Jay Gould, Harvard) attributes these to large steps followed by long periods of stability.

Pathways of Evolution

Divergent evolution occurs when two or more species evolve increasingly different traits, resulting from different selection pressures or genetic drift. Convergent Evolution occurs when two or more species become increasingly similar in phenotype in response to similar pressures.

Adaptive Radiation is the process where divergent evolution proceeds in rapid succession or simultaneously among a number of groups creating 3 or more higher taxa. Coevolution is where one species evolves due to species’ evolution.

Cladistics is a method of assessing evolutionary relationships by compared shard characteristics. Sharing of derived traits by a unique set of organisms suggests they belong to a distinct monophyletic group, having one common ancestor, while those traits shared by organisms outside the group provide no information on evolutionary relationships.

Comparison of amino acid sequences and DNA sequences provide detailed phylogenic relationships by revealing the specific makeup of species and populations. Phylogeny is the evolutionary history of a species. A Phylogenetic Tree (cladogram) is a diagram that depicts the proposed evolutionary relationships of species.

EVOLUTIONARY THEORY

Theories of Organic evolution: three theories historically; the views of modern biologists conbine the second and third.

Lamarck’s Theory (WRONG) proposes that structural variations are due to functional needs – “to use it or lose it”. Use of a structure increases its size, and vice versa (i.e. giraffe’s neck grew based on use). No evidence or support in modern biology.

Theory of Natural Selection

Darwin presented the Theory of Natural Selection in 1859 in his book On the Origin of Species, based on his voyages on the HMS Beagle.

The theory states:

1. All species exhibit structural and functional variation. These affect the chances of survival

2. By the geometric rate of increase (overpopulation) the number of every species tend to become enormously large. Yet the population remains roughly constant because many individuals die (eliminated by enemies, disease, competition, climate, etc.)

3. Involves a “struggle for survival.” Individuals having variations are unsuited to the particular conditions in nature are eliminated, whereas those whose variations are favorable will continue to exist and reproduce.

4. A process of “Natural Selection” is constant for better adapted individuals and the elimination of less well-adapted ones, results in “Evolutionary Change”.

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5. The qualities that promote survival are passed on from generation to generation, thus resulting in “The survival of the Fittest,” and “The Preservation of Favored Races.”

The theory of Natural Selection states that present species have descended with modifications from species that existed in the past. Species are not fixed, unchanging things, but are constantly evolving. Evolution is therefore the constant change that has occurred in our world since its beginning to the present time.

CLASSIFICATION OF LIVING THINGS

We classify organisms based on shared characteristics. Carl Linnaeus came up with the binomial nomenclature system, assigning each organism a two-art scientific using Latin, i.e. Canis familiaris. There are seven main levels of classification:

Kingdom, phylum, class, order, family, genus, species(kings play chess on fine-grained sand)

These are the six kingdoms of organisms:

Eubacteria – single-celled prokaryotes (no nucleus or complex organelles) Archaebacteria – different type of single-celled prokaryotes adapted to live in

extreme conditions. Protista – mostly aquatic single-celled organisms with varying characteristics, can

resemble plants, animals or fungi Fungi – mostly multicellular prokaryotic heterotrophs, decomposers with a cell wall Plantae – autotrophic multicellular prokaryotes producing food via photosynthesis

with a cell wall Animalia – multicellular heterotrophic prokaryotes mostly reproducing sexually

without a cell wall.

One can identify an organism based on its characteristics, following a dichotomous key.

VIRUSES

Viruses are generally not considered “living” because they are so simple. They are only ~100nm long, compared to a blood cell which is 7500nm. Their structure is simple: some genetic information (DNA or RNA) surrounded by a protective protein coat, a capsid. About 95% of the mass is the capsid.

Bacteriophages are “eaters of bacteria” and have a tappole shape with spikes which can latch on to the target cell. Sometimes a lipid membrane, thought to have come from the original cells of the host, coats the virus. This makes them hard to detect by the body’s immune system.

Viruses have no metabolism or structures of any sort. They reproduce by infecting a host cell. The genetic information contained within them are integrated into the host’s DNA and the cell then starts replicating the virus. After the viruses have been produced, they are assembled and the burst out of the host, killing it. The new viruses then go on to infect

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other cells. This process can be called Attachment, Synthesis, Assembly and Release, and is the lytic cycle.

The lysogenic cycle is a more dormant stage. During this time, the DNA is still in the host cells, but the host continues to divide as usual, along with the viral DNA. The cells may eventually go back to the lytic cycle and continue to produce viruses.

Viruses are usually detrimental to the hosts. However, the method for introducing new information into cells has been exploited in gene therapy technique, which hopes to cure genetic illnesses via viruses which contain proper DNA being introduced into the patient.

EUBACTERIA AND ARCHAEBACTERIA

Bacteria are not like viruses – they have a metabolism, more complex structures and are capable of reproducing on their own. Archaebacteria are also not like Eubacteria, as they have certain adaptations which allow them to survive where nothing else can, such as high salinity, methane, or oxygen-free environments.

Bacteria display a few common shaped: spherical (coccus pl. cocci), rod-shaped (bacillus pl. bacilli) and spiral (spirillum pl. spirilla). Bacilli and cocci can form chains or clumps or colonies of two or more.

Bacteria can be divided into obligate aerobes (require oxygen), facultative anaerobes (prefer oxygen) or obligate anaerobes (cannot have oxygen). Fermentation is the process where bacteria get energy without oxygen. Some bacteria (and all archaebacteria) are heterotrophs, in that they need an external source of food. Some are autotrophs, producing their own food (via sunlight).

Bacteria are simple prokaryotes, lacking a nucleus or complex organelles. Eubacteria hay have cell walls, but all archaebacteria do.

All bacteria can reproduce via binary fission. Their DNA replicates, the cell membrane divides and grows, with one identical DNA strand moving to either half, and then the cell splitting into two new cells. Some bacteria can conjugate. Here, two bacteria make cell-to-cell contact via a cytoplasmic bridge. Genetic information is shared along this bridge.

During difficult conditions, bacteria can form endospores, which are tough walls surrounding the genetic material to keep them safe until conditions improve. The bacteria can therefore survive for longer periods of time in difficult situations.

Bacteria can cause a variety of illnesses in humans and other organisms. They can take up the resources of cells, or destroy them, or produce toxins. They can spread from person to person but most can be controlled by antibiotics and the immune system. However, excessive use of antibiotics has led to increased resistance to them by bacteria (natural selection).

However, the majority of bacteria are not harmful. They help in digestion, food production, chemical processes, detoxification, and make up a great part of biomass on earth.

PROTISTA

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Protists are the grab bag of taxonomy. They are all too complex to be considered bacteria, but are too simple to be considered one of the higher groups: plants, animals and fungi. They are all unicellular eukaryotes and prefer aquatic environments. Other than that, they do not have much in common.

Protists can be divided into three groups: plant-like, animal-like and fungi-like.

Plantlike Protists

Euglenophyta (e.g. Euglna) – fresh, pref. stagnant water, flagellated, autotrophic, but can take in food if necessary. Have flagella.

Chrysophyta (e.g. diatoms) – fresh and salt water, encased in shells Pyrrophyta (e.g. dinoflagellates) – have chlorophyll, autotrophic. Important

producers, component of phytoplankton. Cholorophyta (green algae) – fresh, some salt water. Chlorophyll-containing

autotrophs. Some multicellular but non-specialized organisms. Phaeophyta (brown algae) – colder seawater, kelp and seaweed. Multicellular (non-

tissue forming) and autotrophs via chlorophyll. Rhodophyta (red algae) – warmer seawater, some fresh water. Autotrophic via

chlorophyll.

Animal-like Protists (protozoa)

Sarcodina (e.g. Amoeba) – all environments, including in animal intestine; uses pesudopods for movement and food intake

Mastigophora (flagellated protozoans) – all water, including parasitic. Form cysts. Asexual reproduction.

Ciliophora (ciliated protozoans) – most complex of protists, uses cilia for movement. Asexual reproduction.

Sporozoa (e.g. Plasmodium) – no movement, all parasitic. Depends on host for movement and nutrition.

Gymnomycota (fungi-like protists) – i.e. slime molds; Can converge with other cells and behave as one unit.

PLANTAE

Plants are autotrophic, mostly multicellular organisms with developed cells with nuclei and organelles (eukaryotes). They are almost universally autotropic and can produce their own food via photosynthesis.

Plants reproduce following a cycle which is known as the Alternation of Generations. This consists of a diploid and haploid generation. The diploid generation undergoes meiosis to produce haploid gametes. These gametes then form the haploid generation of plants, which produce sperm and eggs, which combine to form a zygote, starting the diploid generation and starting the cycle again.

The non-vascular Bryophytes, such as mosses, are very small as they have no system to transport water and nutrients. Instead, they rely on elongated cells. The vascular Tracheophytes have vessels (xylem transporting water and phloem transporting food) and can therefore grow much larger than their non-vascular counterparts. They follow the

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alternation of generations, and require water for the sperm to meet the egg (however, due to heir small size, a droplet is sufficient).

The next division is between seeded and seedless plants. Seedless plants use spores to reproduce: they have no flowers or seeds. These plants are called Pteridophytes and are composed of ferns. The part of the fern often seen is the frond (leaf) of the sporophyte (diploid) generation. These produce spores which germinate becoming sperm producing and egg producing haploid gametophytes. Sperm are produced in anteridia, eggs in archegonia in the same plant. The hapolid gametophytes are known as prothaluses and they wither away once the sporophyte is produced. There needs to be water for the sperm to meet the egg, but this can be as small as a raindrop.

Of the plants which have seeds, they can have either “naked” seeds (gymnosperms) or enclosed seeds (angiosperms). Their reproductive strategies do not need water, and they are the most recent of the plants. They all have seeds, which contain an embryo, a partially developed plant. The seed shell protects the embryo.

Though spermatophytes can produce asexually, they generally reproduce sexually via the alternation of generations. Seed plants have two reproductive organ types, both male and female.

Gymnosperms produce seeds that are unprotected, or naked, in cone-like structures, as in conifers. Angiosperms produce seeds that are encased in a fruit. In Gymnosperms, the haploid gametophyte generation takes place wholly within the cone. The male cones produce haploid pollen and the female cones produce eggs. When pollen and eggs meet, a zygote is produced, ending the haploid generation. The seed is produced and germinates, producing a new plant.

Angiosperms are the only plants which have flowers. Flowers contain the male and female parts of the plant. The male stamen contains anthers attached to the plant via filaments, and the anthers produce pollen. The female stigma is connected to the plant via the style, which connects it to the ovary, where eggs are stored in ovules. Pollen travels from plant to plant by the wind, insects (such as bees), birds or other organisms. This ensures genetic diversity as pollen travels from plant to plant. The haploid generation is very small, consisting only of the unfertilized egg and pollen. Once the egg has been fertilized, a fruit is formed. This can be from an apple to a very small sac.

Angiosperms can further be divided into two classes: monocots and dicots. This depends on the number of cotyledons there are in the seed. Cotyledons are seed leaves that store carbohydrates for the seedling, and often become the first leaves that form. Seeds that germinate and have their seed split into two are docots; seeds that do not are monocots.

ANIMALIA

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Animals are eukaryotic, multicellular organisms with no rigid cell wall. All are motile for at least part of their life cycle. They range from microscopic to some of the largest creatures on earth. All reproduce sexually and all are heterotrophs. Except for sponges, all have cells which are differentiated into different types of tissues.

Animal Phyla

Porifera (sponges) – sessile with irregular shape present in water, no mouth or digestive tract, relies on filter feeding with no specialized tissues. Mostly sexual reproduction.

Cnidaria (stinging creatures) – motile and sessile at different stages of life (medusoid and polyp forms). Mostly in salt water, sexual and asexual reproduction.

Platyhelminthes (flatworms) – simplest of worms, with no coelom (body cavity). Found in water/parasitic. Flat body, with one digestive opening (no anus). Sexual or asexual reproduction. Simple nervous system with primitive brain.

Rotifera (wheel animals) microscopic, with cilia lining anterior. Mostly freshwater. Nematoda (roundworms) – slender and cylindrical, with coelom and two-ended

digestive tract. Exists in fresh water, with a nervous system and brain. Annelida (segmented worms) – most complex worms with a round segmented body

(i.e. earthworm). Terrestrial and aquatic, with full digestive tract and nervous system. A simple heart exists called the “aortic arch”.

Mollusca (mollusks) – shell present in many forms, muscular “foot”. Soft-bodied, with nervous, digestive and circulatory system, e.g. clams, snails, muscles.

Arthropoda – segmented body (possibly fused), with jointed appendages and exoskeleton. Aquatic and terrestrial; includes insects, spiders and crabs. Have antennae, sexual reproduction, developed circulation, nervous and digestion systems.

Echinodermata (spiny creatures) – many-pointed radial symmetry. Marine. Hard inernal skeleton, water pressure-based muscular system allows for movement. One digestive opening. i.e. starfish, sea cucumbers.

Chordata (chordates) – animals, mostly vertebrates, that have a notochord (a flexible coloum of support present in embryos) during development and a nerve running dorsally. Terrestrial and marine, in all environments.

Chordate Classes

Cephalochordata (lancets) – small marine organisms with a notochord as embryos and adults

Urochordata (tunicates) – small marine animals that are similar in appearance to sponges but have a notochord in embryonic development.

Chondrichthyes (cartilaginous fishes) – bones, including backbone, made of cartilage, for example, sharks and rays. Has fins and tail for navigation and propulsion. Marine.

Osteichthyes (boney fish) – fish that have true bones. With tail and fins for navigation and propulsion. Marine. Two chambered heart with a single loop circulatory system.

Amphibians – adults able to go on land or water, because they have lungs and gills. Eggs need to be placed in water. Three-chambered heart. Skin needs to be kept moist.

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Reptilia (reptiles) – tougher skins do not need to be kept moist. Do not require water to lay eggs. Cold-blooded, with four chambered heart partially divided by the septum.

Aves (birds) – descendants from reptiles, but with hollow bones and wings to enable flight. Warm-blooded and egg-laying. Four chambered heart with complete division by the septum.

Mammalia (mammals) – have a hairy covering, and have mammary glands to feed offspring. All require air. Many give live birth. Four chambered heart with fully dividing septum.

FUNGI

Fungi are eukaryotic, mostly muticellular organisms. They have tough cell walls and reproduce sexually or asexually via spores. Spores are haploid and are produced in sporangia. When a spore germinates, it produces hyphae, the first growth tissue of fungi in the form of microscopic filaments.

Unlike plants, fungi do not photosynthesize and are all heterotrophs. They play important roles as decomposers. They all have rigid cell walls made of chitin or cellulose. Also unlike plants, fungi have no roots, and have very few or no storage cells.

Fungi, unlike many other organisms, digest externally. They release enzymes into the environment which break down organic matter and then take in those digested nutrients.

Fungi can be classified into Mastigomycota, Amastigomycota and Deuteromycota. Mastigomycota produce flagellated motile spores and have cellulose cell walls. They include water molds. Deuteromycota (imperfect fungi) are parasitic and reproduce asexually. Examples include penicillin and the fungi that cause athlete’s foot and yeast infections.

Amastigomycota have chitin in cell walls and produce immotile spores. They are divided into the Zygomycetes (common molds), Ascomycetes (sac fungi, yeast and truffles) and Basidiomycetes (club fungi, mushrooms, shelf fungi). These are all mainly multicellular, with all being able to reproduce sexually or asexually (with the exception of club fungi, which can only reproduce sexually).

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TANXOMONIC TREE

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