John I., Steven K., Joseph S.

Table of Contents
1. Metabolic Processes
1.1 PROPERTIES OF WATER 1.2 TYPES OF REACTIONS 1.3 FUNCTIONAL GROUP STRUCTURES 1.4 MACROMOLECULES 1.4.1 CARBOHYDRATES 1.4.2 LIPIDS 1.4.3 AMINO ACIDS 1.4.4 PROTEINS 1.4.5 NUCLEIC ACIDS 1.5 LAWS OF THERMODYNAMICS 1.6 ANABOLIC AND CATABOLIC REACTIONS 1.7 ENZYMES 1.7.1 ENZYME INHIBITION 1.8 CELLULAR RESPIRATION GLYCOLYSIS PYRUVATE O XIDATION KREBS CYCLE ELECTRON TRANSPORT CHAIN TOTAL YIELD OF CELLULAR RESPIRATION 1.9 ANAEROBIC RESPIRATION 1.10 PHOTOSYNTHESIS 1.10.1 (D) ELECTRON TRANSPORT 1.10.2 (D) CALVIN CYCLE 1.10.3 LIGHT DEPENDANT REACTIONS 1.10.4 LIGHT INDEPENDENT REACTIONS 1.10.5 (A) PHOTOSYNTHESIS VS . CELLULAR RESPIRATION 1.8.1 1.8.2 1.8.3 1.8.4 1.8.5

2. Homeostasis
2.1 THERMOREGULATION 2.2 URINARY SYSTEM 2.2.1 STRUCTURE 2.2.2 NEPHRON 2.2.3 THE FORMATION OF URINE 2.2.4 WATER BALANCE 2.3 ENDOCRINE SYSTEM 2.3.1 PROTEIN VS. STEROID HORMONE 2.3.2 PITUITARY GLAND 2.3.3 PITUITARY CHART 2.3.4 SUGAR LEVELS 2.3.5 STRESS RESPONSE 2.3.6 THYROID GLAND 2.3.7 REPRODUCTIVE SYSTEM 2.4 NERVOUS SYSTEM 2.4.1 DIVISIONS 2.4.2 HOW THE NEURON WORKS 2.4.3 THE SPINAL CORD 2.4.4 THE BRAIN

3. Genetics
3.1 DNA STRUCTURE 3.2 DNA REPLICATION 3.2.1 UNWINDING OF DNA 3.2.2 BUILDING THE COMPLEMENTARY STRANDS 3.2.3 COMPLETION 3.3 CENTRAL DOGMA 3.4 PROTEIN SYNTHESIS 3.4.1 TRANSCRIPTION 3.4.2 TRANSLATION 3.5 CONTROL MECHANISMS 3.5.1 3.5.2 CONTROL MECHANISMS IN EUKARYOTES CONTROL MECHANISMS IN PROKARYOTES LAC OPERON TRP OPERON

3.5.3 3.5.4 3.6 MUTATIONS 3.6.1 TYPES OF MUTATIONS 3.7 IMPORTANT SCIENTISTS 3.7.1 EARLY SCIENTISTS 3.7.2 MESELSON AND STAHL

John I., Steven K., Joseph S.

4. Evolution
4.1 CONTRIBUTIONS OF CHARLES DARWIN 4.2 EVIDENCE FOR EVOLUTION 4.3 RANDOM CHANGE 4.4 TYPES OF SELECTION 4.5 REPRODUCTIVE ISOLATING MECHANISM 4.6 HARDY-WEINBERG EQUILIBRIUM 4.7 SPECIATION

5. Population Density
5.1 DEFINITIONS 5.2 MARK AND RECAPTURE PROBLEMS 5.3 POPULATION DENSITY PROBLEMS 5.4 CHANGES IN POPULATION SIZE 5.5 POPULATION GROWTH MODELS 5.6 FACTORS E FFECTING POPULATION CHANGE 5.7 INTERACTION WITHIN A COMMUNITY

6. Appendix
6.1 6.1.1 6.1.2 6.1.3 6.1.4 6.2 6.2.1 6.2.2 6.2.3 6.2.4 6.2.5 6.3 6.3.1 TRANSLATION 6.3.2 LACI OPERON 6.3.3 TRP OPERON 6.4 REPRODUCTIVE SYSTEM - DIAGRAMS OVERVIEW NEPHRON URINE FORMATION STRESS RESPONSE REFLEX ARC PROTEIN FORMATION GLYCOLYSIS KREBS CYCLE CELLULAR RESPIRATION VS. P HOTOSYNTHESIS

Biology Review Guide

1. Metabolic Processes
1.1 Properties of Water 1) Water is liquid at room temperature: Water does not boil and become a gas until a temperature of 100C due to hydrogen bonding 2) Water is the universal solvent for polar molecules and thereby facilitates chemical reactions: Ions and molecules that associate with water are hydrophilic (water-loving); polar molecules are hydrophilic. Non polar molecules do not dissolve in water and are hydrophobic (water-fearing) 3) Water clings: Due to hydrogen bonding, water is cohesive and allows for higher surface tension Hydrogen bonds with polar molecules allow water to be adhesive - capillary action which allows for water to creep narrow areas and yet flow freely 4) The temperature of liquid water rises and falls slowly, preventing sudden or drastic changes: Hydrogen bonding causes water to absorb a lot of heat before the temperature increases 5) Water has a high heat of vaporization, keeping the body from overheating: Takes a large amount of heat to turn into steam and takes a lot to evaporate sweat in mammals 6) Frozen water is less dense than liquid water: Highest density of water is at 4C Hydrogen bonds become very rigid and form a crystallite lattice Ice floats on water allowing for bodies of water to sustain life 1.2 Types of Reactions: Three major types of chemical reactions that break apart and build materials: Redox, an oxidization reduction reaction, which transfers electrons between molecules Hydrolysis reaction, in which molecules react with H2O to break up large molecules (decomposition) Condensation (hydration synthesis reaction) in which molecules react to form H2O as a by-product and create larger molecules 1.3 Functional Group Structures

1.4 Macromolecules 1.4.1 Carbohydrates Composed of C, H, and O in a fixed ratio. Monomer of a carbohydrate is a monosaccharide Monosaccharide carbohydrates made up of single saccharide (CnH2nOn) A sugar with 3 carbons = triose E.g. pyruvate A sugar with 5 carbons = pentose E.g. ribose, deoxyribose A sugar with 6 carbons = hexose E.g. glucose, fructose, galactose Differences between glucose and galactose isomers: Carbon-4: hydrogen on top and hydroxyl on bottom (glucose) or hydrogen on bottom and hydroxyl on top (galactose) NOTE: if hydroxyl group is on top of carbon-1, the molecule is . If hydroxyl on bottom, the molecule is Monosaccharides are linear structures in dry state and form ring structures in dissolved water Disaccharide: a group of carbohydrates made of two monosaccharides; double sugar Formation: sugars are joined together by condensation/dehydration synthesis reactions that form glycosidic linkages (covalent bonds) between hydroxyl groups E.g. maltose (glucose-glucose), sucrose/table sugar (glucose-fructose), lactose (glucose-galactose) Polysaccharide: three or more sugars joined by glycosidic linkages between hydroxyl groups Function: these large chains of glucose act as good storage forms for glucose o E.g. glycogen (storage molecule for animals), starch (storage molecules for plants), cellulose (structural polysaccharides for plants), chitin (structural polysaccharide) o These are all polymers of glucose that are linked together in different ways Starch TEXTBOOK PAGE 31 FIGURE 9 Amylose o 1-4 glycosidic linkages o Straight chain Amylopectin o 1-4 glycosidic linkages AND 1-6 glycosidic linkages (forms a branch) Glycogen TEXTBOOK PAGE 32 FIGURE 10 Contains 1-4 glycosidic linkages and many 1-6 glycosidic linkages (on every branch) Food storage in animals Cellulose TEXTBOOOK PAGE 32 FIGURE 11 bonds form between glucose molecules which cannot be broken down by human enzymes Becomes fibre in our diets Used as structural support because of hydrogen bonding.

1.4.2 Lipids: Composed of C, H and O atoms with a very low ratio of O Formation: hydrocarbons link to form long chains that can vary in length (12 to 24 carbons long) Hydrocarbon chains are hydrophobic as there are more non polar C-H bonds than polar O-H bonds Groups of lipids: fatty acids, glycerides, phospholipids, waxes, steroids A) Fatty Acids Carboxyl group at the end Types: saturated (solid at room temperature) and unsaturated (liquid at room temperature) Unsaturated: monounsaturated (one double bond between carbons), polyunsaturated (two or more double bonds between carbons) B) Glycerides Formation: when fatty acids join a glycerol backbone through condensation reactions between the carboxyl group of the fatty acid and the hydroxyl group of the glycerol forming an ester linkage Function: most fats we eat, how the body stores fat C) Phospholipids Glycerol with two fatty acids and a phosphate group attached to the glycerol backbone When phospholipids interact, they align themselves so that their polar phosphate head groups stay together and their non polar fatty acid tails stay together Function: often form a double layer (lipid bilayer) that forms cell membranes or spherical micelles D) Waxes Long chain of fatty acids joined to alcohol or carbon rings Function: water proof coatings (i.e. leaves and feathers) E) Steroids Four fused hydrocarbon rings with several different possible functional groups Function: cholesterol (adds rigidity to membranes), hormones (i.e. testosterone, estrogen, progesterone , adrenaline) 1.4.3 Amino Acids: There are 20 different amino acids and they all have the same basic structure: The backbone of the amino acid is constant: one central carbon atom, amino group carboxyl group This backbone is bound to an R group (radical group changes for each of the 20 amino acids) Formation: amino acids can join by condensation/dehydration synthesis reactions to form dipeptides and polypeptides with peptide bonds (covalent bonds between carboxyl and amino groups of adjacent amino acids) Breakdown: breakage of a peptide bond involves the addition of a molecule of water hydrolysis 1.4.4 Proteins: polymers of monomer amino acids Polypeptide: when many amino acids are bonded together to form a long amino acid chain Protein: polypeptides with a specific structure and function Function: enzymes, hormones, channels, structural elements, carriers, messengers, energy: last resort Structure TEXTBOOK PAGE 44 (see next page) a) Primary: sequence of amino acids in a polypeptide strand

b) Secondary: hydrogen bonds that form with nearby amino acids fold the polypeptide into helices and pleaded sheets c) Tertiary: polypeptides fold further and are stabilized by R group-R group interactions d) Quaternary: the clustering of two more polypeptides in tertiary structure A proteins shape determines its function. If the protein does not have the right shape, it cannot perform its function A proteins shape is called its conformation If a protein loses its conformation then it is said to be denatured and therefore loses its function (See Appendix 6.1.1 Protien synthesis)

1.4.5 Nucleic Acids: DNA and RNA composed of monomer nucleotides (composed of a sugar, base and phosphate) DNA: deoxyribose + adenine/guanine/cytosine/thymine RNA: ribose + adenine/guanine/cytosine/uracil Purines (have an extra ring): adenine and guanine Pyrimidines: cytosine and thymine Formation: nucleotide subunits linked together by a series of enzymes that create covalent bonds between phosphates and the hydroxyl on carbon-3 of the sugar of the adjacent nucleotide (phosphodiester bond) DNA: condensation/dehydration synthesis reaction DNA: composed of two strands wound around each other in a double helix and held together by hydrogen bonds Function: used by organisms to store hereditary information that determines structural and functional characteristics; the only molecules that can produce identical copies of themselves and in doing so, allow organisms to reproduce 1.5 Laws of Thermodynamics: 1) Energy cannot be created or destroyed, but can be transformed from one form to another 2) Energy cannot be transformed from one form to another without loss of useful energy (Law of Entropy)

Exothermic vs. Endothermic Reactions:

Exothermic reaction reaction that releases energy Endothermic reaction reaction that absorbs energy

1.6 Anabolic and Catabolic Reactions: Anabolic Reactions: Requires the use of energy to build larger molecules from smaller subunits Condensation reaction (dehydration synthesis) joining up of two subunits by removing a water molecule Catabolic Reactions: Release of energy by breaking down polymers into shorter polymers. Hydrolysis reaction covalent bonds that are broken down by the addition of water molecules. 1.7 Enzymes Enzymes are protein catalysts (speed up chemical reactions without being consumed) Enzymes speed up reactions by lowering activation energy Living cells cannot tolerate high heat, therefore enzymes are necessary for decreasing the amount of thermal energy Tertiary and quaternary proteins with complex 3D shapes (conformation) They are substrate (the reactant the enzyme binds to) specific The names of the enzymes end in ase, i.e. maltase which catalyzes maltose

How do enzymes work? The substrate binds to the enzyme at the active/binding site and slight change in conformation occurs, this is called an induced fit The combination of the enzyme and substrate is called an ENZYME-SUBSTRATE COMPLEX The complex is held together by hydrogen bonds and weak ionic bonds, effectively locking the substrate in place This process enables the enzyme to interact chemically with the substrate

Enzyme Activity: Temperature and pH will affect enzyme activity and will increase enzyme activity to a critical point after which these factors will negatively affect the performance of the enzyme by denaturing the protein Enzymes have an optimal pH and temperature range in which they work best (ex. pepsin, trypsin) Some enzymes work with the help of substances called coenzymes, these bind to the active site of the substrate

1.7.1 Enzyme Inhibition Competitive Inhibition: substances that compete with the substrate for the active site on the enzyme Non-competitive Inhibition: substances that attach to the binding site (another part of the enzyme), causing a change in shape, making the enzyme less likely to accept its substrate (ex. DDT)

Allosteric Regulations: Cells must control enzyme activity to coordinate cellular functions Allosteric sites are receptor sites that are used to either stimulate or inhibit an enzymes activity An allosteric activator stabilizes the protein and keeps the active site available for their substrates An allosteric inhibitor stabilizes the inactive form of the enzyme

Feedback Inhibition: A method of metabolic control in which a product later on in the sequence of a reaction steps allosterically inhibits an enzyme needed earlier in the sequence Feedback inhibition is one of the most common control mechanisms in metabolic processes

1.8 Cellular Respiration C6H12O6 + 6O2 6H2O + 6CO2

1.8.1 Glycolysis: Occurs in cytoplasm 10 steps; converting glucose (6C) to 2 pyruvate (3C) Essentially, the combustion of glucose via a series of about 20 reactions, with each step catalyzed by a different enzyme Glucose itself cannot be used to create the work in a living system and we must make ATP from it Organisms can break the covalent bonds in this molecule and rearrange them into new configurations (via a series of enzyme controlled redox reactions) Glucose is oxidized to CO2 and O2 is reduced to H2O

This is an exothermic reaction, so energy is released

Some Enzyme Basics: -kinase: transfers phosphate group from high energy donor to target molecule (substrate) -isomerase: it rearranges the structure of the isomer -mutase: differs from isomerise because only moves functional groups -dehydrogenase: is an enzyme that oxidizes a substrate by transferring one or more H- to an acceptor molecule (Glycolysis - See Appendix 6.1.2) 1.8.2 Pyruvate Oxidation Prepares pyruvate for entry into the Krebs Cycle 2 pyruvate go in, loses CO2, becomes oxidized and leaves as acetyl-CoA

1.8.3 Krebs Cycle Takes acetyl-CoA and produces many NADH that can be used in the electron transport chain (See Appendix 6.1.3) 1.8.4 Electron Transport Chain Chain of electron carriers that reaches a final proton acceptor (oxygen) that creates water from oxygen and hydrogen Creates a proton gradient that passes through ATP synthase to take ADP + Pi and form ATP

1.8.5 Total Yield of Cellular Respiration

1.9 Anaerobic respiration Fermentation

1.10 Photosynthesis 6H2O + 6CO2 C6H12O6 + 6O2 Photosynthesis involves the use of energy from light to form carbohydrates Autotrophs: organisms that manufacture their own food Autotrophs form the base of the food chain because heterotrophs depend on them

See 1.10.3 & 1.10.4

1.10.1 Electron flow chain & 1.10.2 Calvin Cycle

1.10.3 Light Dependent Reactions

1.10.4 Light Independent Reactions

2. Homeostasis
Positive Feedback: stimulus causes response that increases (i.e. the birth process) Negative Feedback: reaction that reduces the stimulus on its effects

2.1 Thermoregulation:

2.2 Urinary System: 2.2.1 Structure a) Renal Arteries: branch from the aorta that carry blood to the kidneys b) Renal Veins: return blood from kidneys to the inferior vena cava c) Kidneys: fist shaped organ that weigh 0.25 kg each and hold as much as 25% of the bodys blood at any time i. Cortex: outer layer of kidney ii. Medulla: area inside the cortex iii. Renal Pelvis: area where kidney joins the ureter d) Ureter: tubes that conduct urine from the kidneys t the bladder e) Bladder: organ that stores urine f) Urethra: tube that carries urine from the bladder to the exterior of the body 2.2.2 Nephron functional unit of the kidney a) Afferent Arteriole: small branches that carry blood to the glomerulus b) Glomerulus: high pressure capillary bed that is the site of filtration c) Efferent Arterioles: small branches that carry blood away from the glomerulus to a capillary net d) Peritubular Capillaries: network of small blood vessels that surround the nephron e) Bowmans Capsule: cuplike structure that surrounds the glomerulus f) Proximal Tubule: section of the nephron joining Bowmans capsule with the Loop of Henle g) Loop of Henle: carries filtrate from the proximal tubule to the distal tubule

h) Distal Tubule: conducts urine from the Loop of Henle to the collecting duct i) Collecting Duct: tube that carries urine from nephron to the pelvis of a kidney (See appendix 6.2.2) 2.2.3 The Formation of Urine Filtration: movement of fluid and water from the blood into Bowmans Capsule Reabsorption: involves the transfer of essential solutes and water from the nephron back into the blood Secretion: involves the movement of materials from the blood back to the nephron (See appendix 6.2.3)

2.2.4 Water Balance Osmoreceptors: Specialized nerve cells in the hypothalamus that detect changes in osmotic pressure of the blood and surrounding extracellular fluid. These two hormones control the kidney: 1. Antidiuretic Hormone (ADH) Affects permeability of collecting duct becomes more permeable to water Causes more water to be reabsorbed produce more concentrated urine Produced by specialized cells in the hypothalamus Stored in pituitary gland and released into the blood 2. Aldosterone Released from the adrenal glands Steroid hormone that adjusts final concentration of sodium (Na+) and potassium (K+) o Stimulates secretion of K+ from blood into distal tubule less K+ in the blood o Causes Na+ to be reabsorbed from the distal tubule into the blood more water moves out of nephron by osmosis and blood volume and blood pressure are regulated 2.3 Endocrine System: 2.3.1 Protein Hormone vs. Steroid Hormone

2.3.2 Pituitary Gland Small gland located at the bottom of the hypothalamus gland at the base of the brain Known as the master gland as it coordinate and connects the endocrine and nervous systems
Pituitary Lobe Anterior Hormone Growth Hormone (GH) Prolactin (PRL) Follicle stimulating & luteinizing hormones Thyroid stimulating hormone (TSH) ACTH Function Promotes growth Stimulates and maintains milk production in lactating females Stimulates follicle development in ovaries (females). Promotes development of sperm cells in testes (males). Stimulates release of thyroxine (regulates cell metabolism) from the thyroid Stimulates release of hormones involved in stress response

Posterior

ADH Oxytocin

Increases water reabsorption in kidneys Initiates strong contractions. Triggers milk release, lactating

2.3.4 Sugar Levels Insulin: hormone produced by pancreas beta islet cells Released when blood sugar levels increase Promotes the uptake of glucose by liver, muscle, and other organ cells In the liver, glucose is converted into glycogen to reduce glucose levels in the blood Glucagon: hormone produced by pancreas alpha islet cells Released when blood sugar levels drop Promotes the conversion of glycogen into glucose Promotes the release of glucose from liver cells into blood to increase blood sugar levels

Diabetes: Type 1: pancreas is unable to produce insulin due to early degeneration of beta islet cells. Patients take insulin to live. Type 2: decreased insulin production or ineffective use insulin. Can be controlled with diet, exercise and oral pills Gestational Diabetes: temporary condition affecting 4% of pregnancies Hyperglycemia: high blood sugar Hypoglycemia: low blood sugar 2.3.5 Stress Response a) Adrenal Medulla Regulated by the nervous system Produces 2 hormones: epinephrine (adrenaline) & norepinephrine (noradrenaline) for short term stress response During period of stress, sympathetic nerves stimulate adrenal medulla to release epinephrine and norepinephrine into the blood Causes glycogen in liver and muscle cells to be converted to glucose (readily usable form of energy) b) Adrenal Cortex Regulated by hormones Produces three different types of associated with long term response: 1. Glucocorticoids: associated with blood glucose levels (i.e. Cortisol: increases amino acids in blood) 2. Mineralocorticoid: important for salt and water metabolism (i.e. Aldosterone: greater H2O and Na+ reabsorption) 3. Sex hormones: controls sexual development (i.e. testosterone) * Sex hormones are not made by the adrenal glands, but are mentioned because of they are part of the stress response (See appendix 6.2.5) 2.3.6 Thyroid Gland located at the base of the neck, below the larynx: Hormones: o Thyroxine (T4): 4 iodine atoms Triiodothyronine (T3): 3 iodine atoms

o Calcitonin: acts on bones (absorbs Ca2+ from blood to bones) T3 and T4 hormones influence body metabolism and growth and differentiation of tissues HYPERTHYROIDISM higher levels of T4 increase the oxidization of sugars and other nutrients o 60% of glucose = heat; 40% of glucose = transferred to ATP HYPOTHYROIDISM lower levels of T4 decrease the oxidization of sugars and other nutrients o Excess blood sugar is converted to glycogen o Once glycogen storages are filled, excess blood sugar is converted to fat o Cause muscle weakness, cold intolerance, dry skin and hair Iodine is an important component in T3 and T4 Iodine is actually transported from the blood into the follicle cells of the thyroid Iodine in the thyroid is 25 times greater than that in the blood Problems arise when iodine levels begin to fall GOITER: when inadequate amounts of iodine are obtained from diet causes thyroid to enlarge
Low iodine atoms T4 secretion drops More TSH produced Thyroid is stim- Cells of thyroid continue Thyroid ulated more to develop enlarges

2.3.7 Reproductive System

2.4 Nervous System 2.4.1 Divisions

2.4.2 How the Neuron Works Neuron at rest: Outside of neuron is positively charged compared to inside Outside neuron are high concentrations of Na+ and Cl- and low concentrations of K+ and vice versa When cell gates open, Na+ is moving in and K+ is moving out, thus causing the cell to become more positive At rest cell has resting potential of -70mV Depolarization: when a neuron is sufficiently stimulated (neurotransmitters), a wave of depolarization starts Gates of K+ close and gates of Na+ open and thus only Na+ can enter the cell, causing the cell to become positive Depolarization of one part causes gates of the next section to open, and this continues along the axon Active potential is the change in charge. Action potential occurs along the dendrites and the cell body and the axon Repolarization: causes the Na+ channels to close and the K+ channels to reopen K+ moves through the channels and Na+ cannot move in Na+ is actively transported out until the resting potential is reached Happens very quickly (many impulses are sent per second) Brief time between triggers is called the retractory period Speed is increased with a fatty layer, the myelin sheath. Schwann cells are important for repair of damaged tissue Impulses jump via gaps along the neuron called the Nodes of Ranvier All-or-None Principal Sensory neurons are stimulated by chemicals, light, heat, mechanical distortion of the membrane Motor neurons and neurons of the Central Nervous System are stimulated by neurotransmitters If the axon is stimulated enough it will send an impulse down the length of the axon Strength of the impulse is always the same The Central Nervous System: Consists of the brain and spinal cord Cerebrospinal fluid circulates between layers of the brain and spinal cord Acts as a shock absorber and a transport medium Cerebrospinal fluid from the spinal cord can be used to diagnose bacterial and viral infections, the process is called a lumbar puncture/spinal tap

2.4.3 The Spinal Cord Carries sensory nerve messages from receptors to the brain and relays motor nerve messages from the brain to muscles, organs, glands The spinal cord emerges from the skull through an opening called the FORAMEN MAGNUM and down through a canal into the backbone (See appendix 6.2.7) 2.4.4 The Brain Brain is surrounded by meninges a tough 3 layer protective membrane forming the blood brain barrier: a) Dura mater: outer membrane b) Arachnoid mater: middle membrane c) Pia mater: inner layer

Parts of the Brain The parts of the brain include the hindbrain, midbrain and forebrain 1) Hindbrain: primitive basic life functions Controls breathing, heartbeat, blood pressure a) Medulla Oblongata: relay centre connecting higher brain and sensory neurons to motor pathways Heart rate, breathing, blood vessel diameter b) Cerebellum: white matter (myelinated) and outer cortex, grey matter (unmyelinated) highly folded Nerve tracts connect to motor area of cerebral cortex Receives inputs from all areas of body Coordinates/maintains fine control of all motor actions and activities Controls posture and equilibrium Damage affects motor skills, balance, speech c) Pons: bridge between the medulla and the midbrain Connects two sides of cerebellum and connects to relay centres of cerebrum and midbrain 2) Midbrain: above Pons Four small bundles of grey matter relay centres Some white matter connects pons, cerebellum, spinal cord, and parts of cerebrum Bridge between hindbrain and forebrain 3) Forebrain: a) Cerebrum: largest part of human brain 2 hemispheres: left and right 4 lobes: frontal, parietal, occipital, temporal b) Thalamus: relay centre for nerve impulses going to cerebrum Consciousness and the perception of pain c) Hypothalamus: control centre for many vital functions of the autonomic nervous system Temperature regulation, water balance, hunger, thirst, sex drive Also release neurohormones which regulate the anterior pituitary gland

3. Genetics
3.1 DNA Structure

3.2 DNA Replication 3.2.1 Unwinding the DNA Protiens bind to replicate origin (prokaryotes=1 site, Eukaryotes=multiple sites) DNA helicase unwinds the double helix by breaking the hydrogen bonds between the complementary base pairs SSBs (single standard binding protein): Bind the exposed DNA strands and blocks hydrogen bonding DNA gyrase: Relieves tension brought about by the unwinding of the DNA strands Gyrase cuts both strands of DNA allowing them to swivel and then reseals them The junction where the DNA strands are still joined is called the replication fork (prokaryotes=1 fork Eukaryotes= many forks) When two replication forks are near each other a replication bubble forms DNA replication proceeds towards the direction of the replication fork on one strand and away from the foron on the other strand. 3.2.2 Building the complementary strands RNA Primer: sequence of 10-60 bases that anneals to the template strand for the purpose of initiating DNA replication o Primer is made by enzyme primase DNA polymerase III: builds complementary strand using template as a guide DNA is synthesized in the 5 to 3 direction Nucleotide bonds are added to the 3 end of the elongating strand. DNA polymerase only functions under certain conditions the leading strand uses 3 to 5 template strand as a guide and builds the complementary strand continuously The lagging strand is synthesized discontinuously in short fragments in the opposite direction to the replication fork Primers are continuously added as the replication fork forms along the DNA parent strand. DNA polymerase builds in short segments called Okazaki fragments

3.2.3 Completion DNA Polymerase 1: Removes the RNA primers from the leading strand and the fragments of the lagging strand and replaces them with the appropriate nucleotides. DNA ligase joins the Okazaki fragments into one strand by phosphodeister bonds. As two new strands of DNA form, two double stranded DNA molecules are produced that automatically twist into a helix. As complementary sequences are built, DNA polymerase I and III act as control checkers by proofreading the new strand. They can function as exonuclease- an enzyme that cuts out nucleotides at the end of a DNA strand They must work immediately to avoid the mistake of being copied in subsequent replications

3.3 The Central Dogma DNA is too valuable to exit the nucleus if damaged or distorted, it would lead to lethal or harmful effects of the cell DNA is transcribed into a complementary RNA message that is capable of encoding genetic information. Transcription. The ribosomes translate the message into polypeptide chains (sequences of amino acids), which are processed into proteins. Translation. 3.4 Protein Synthesis 3.4.1 Transcription 1. Initiation RNA polymerase binds the DNA molecule upstream of the gene to be transcribed at the region known as the promoter Promoter region is high in adenine and thymine due to low H bonding, resulting in less energy expended by RNA polymerase 2. Elongation RNA polymerase begins building the mRNA in the direction of 5 to 3 without the need of a primer The promoter region itself is NOT transcribed Only 1 DNA strand is used as the template strand (3-5). The strand not used for transcription is known as the coding strand (5-3) 3. Termination RNA polymerase recognizes the end of a gene when it comes to a terminator sequence The newly synthesized mRNA dissociates from the DNA template strand and is known as the primary transcript RNA polymerase is free to bin another promoter region and transcribe another gene

Post Transcriptional modifications (eukaryotic cells): o 5 cap added to primary transcript to protect mRNA from digestion by nucleases and phosphatases. Also used to initiate translation o Poly-A-tail- added to 3 end of the primary transcript to protect it from degradation later on o Introns (noncoding regions) are cut out by splicosomes leaving behind exons (coding regions), allows the protein to fold properly mRNA is now known as mRNA transcript

3.4.2 Translation (See Appendix 6.3) 3.5 Control Mechanisms 3.5.1 Control mechanisms in Eukaryotes Gene regulation: turning specific genes on or off depending on the requirements of an organism. It may occur at different times during protein synthesis. 3.5.2 Control mechanisms in Prokaryotes Operon: cluster of genes under the control of one promoter and one operator exclusive to prokaryotes o Promoter: Regulating sequence of DNA. Does not code for structural proteins. o Operator: Regulating sequences of DNA that binds repressor proteins. Does not code for structural proteins. o Structural genes: Genes coding for particular proteins. 3.5.3 LAC Operon Genes code for proteins involved in the metabolism of lactose Lac Z-codes for B-galactosoidase, breaks down lactose Lac Y-codes for B-galactosoidase permease, increase permeability Lac A-codes for transacetylase Lac I Protein: repressor protein blocking the transcription of the B galactosidase binding to the operation and covering part of the promoter hence preventing RNA polymerase from binding. No B-galactosidase is transcribed or translated Occurs when there is low level of lactose If lactose is introduced in the cells environment the repressor protein is removed (Lac I) Lactose acts as a Signal Molecule/inducer Lactose binds to LacI protein and changes its conformation so that it cannot stay bound the operation region RNA polymerase can now read the genes responsible for breaking down lactose (See appendix 6.3.2) 3.5.4 TRP Operon genes code for enzymes required to synthesize the amine acid trypophan trp operon is repressed when high levels of tryptophan are present tryptophan binds to the tryp repressor proteins and alters the shape of the repressor protein allowing the repressortryptophan complex to bind the trip operator o tryptophan is known as a corepressor When the level of a tryptophan decreases the repressor- tryptophan complex dissociates and the RNA polymerase is free to transicribe the trp operon genes

3.6 Mutations Mutations: errors made in the DNA sequence. Can be negative or positive side-effects. 3.6.1 Types of Mutations Silent Mutation: Does not change the amino acid code and will therefore cause no phenotype change Missense mutation: Signaled substitution of an amino acid in the resulting polypeptide Nonsense mutation: a mutation that converts a codon for an amino acid into a termination coon o Missense and nonsense mutation can arise from substitution deletions or insertions of nucleotides Point mutations: happen at a specific base pair in the genome o Substitution: replacement of one base in a DNA sequence for another base o Deletion: elimination of a base pair or group of base pairs from a DNA sequence o Insertion: the placement of an extra nucleotide in a DNA sequence Frame shift: When a mutation changes the reading frame for codons. Results in different amino acids being incorporated in the polypeptide. Chromosomal Mutation: When a segment of DNA gets transferred/relocated to another part of the genome. Usually happens during crossing over non-homologous chromosomes. Inversions are caused by the reversal of information of a segment of DNA. 3.7 Important Scientists 3.7.1

3.7.2 Meelson and Stahl Semi-conservative: process of replication in which each DNA molecule is composed of one parent strand and one newly synthesized strand Two Nitrogen isotopes, density gradients were analyzed to determine the nature of DNA The first generation (a), the second generation (b), and the third generation (c) shows the intermediate layer of DNA always present after replication

4. Evolution
4.1 Contribution of Charles Darwin Observations 1) Organism produce more offspring than can survive 2) Variation exists in the population and it is hereditary 3) These individuals that are better suited to the local conditions survive and produce offspring. 4) Process of change is slow and gradual. Interferences/ Conclusions 1) Competition: members of the same species compete for resources 2) Survival of the fittest: offspring with favorable variations are more likely to survive and pass on their traits. Survival is not random. 3) Survivors: reproduce more and in turn pass on more favorable variations to their offspring and successive generations; therefore the favorable variations will become more common. 4.2 Evidence for evolution 1) Radiometric dating proved the earth is at least 3.5 billion years old 2) More fossil records have filled the gaps from ancient to modern species 3) Anatomy a. Homologous Structures i. Structures that have the same origin but different functions b. Analogous Structures i. Structures that have different origins but the same function (bat and insect wings) c. Vestigial structures i. Structures that were functional in the organisms ancestors but have no current function 4) Embryology: when examining the embryos of various organisms similar stages of development are observed 5) Industrial Melanism of the peppered moth illustrated survival of the fittest 6) Molecular biology: can determine how closely related organisms are by comparing their DNA 4.3 Random Change Genetic Drift: a change in the genetic makeup of a population resulting from chance Bottleneck Effect: dramatic reduction in population size usually resulting in genetic drift Founder effect: when a small number of individuals separate from their original population an find a new population resulting in genetic drift. 4.4. Types of Selection Directional Selection: Selections that favors an increase or decrease in the value of a trait from the current population average Environment favours individuals with average variations of a trait; does not favor one of the extremes. Stabilizing Selection- Selection against individuals exhibiting variation in a trait that deviates from the current population average Environment favors the most common phenotypes in the population Disruptive Selection-Selection that favors two or more variations or forms of a trait that differ from the current population average Environment favors individuals with variations at opposite extremes of a trait over individuals with intermediate variations. Sexual selection: differential reproduction success that results from variations in the ability to obtain mates. Environment favors any trait that influences the matting success of an individual

4.5 Reproductive Isolating Mechanisms

4.6 Hardy-Weinberg Equilibrium The Following must be true for the Hardy-Weinberg Equilibrium: The population is very large Mating opportunities are equal No mutations Allele Frequencies p = frequency of allele A (dominant) q = frequency of allele a (recessive)

No migrations No natural selection

Calculating allele frequencies p+q=1

Genotype frequencies p2= frequency of AA genotype (homozygous dominant) 2pq= frequency of Aa genotype (heterozygous) q2= frequency of aa genotype (homozygous recessive)

Calculating for genotype frequency p2+2pq+ q2=1 4.7 Speciation Speciation Evolutionary formation of a new species Allopatric speciation: the evolution of populations into separate species as a result of geographic isolation Sympatric speciation: the evolution of populations within the same geographic area into spate species

5. Population Density
5.1 Definitions Crude Density: Population density in terms of number of organisms of the same species within the total area of the entire habitat. Ecological density: Population density in terms of the number of organisms of the same species per unit area or volume actually used. Carrying capacity: The maximum number of organisms that can be sustained by available resources over a given period of time. Indicator species: A species sensitive to small changes in environmental conditions; monitoring the health of their population is used to indirectly monitor the health of the environment which they live. Resource partitioning: avoidance of, or reduction in, competition for similar resources by individuals of different species occupying different non-overlapping ecological niches i.e. a means to overcome interspecific competition. 5.2 Mark and Recapture Problems Sampling technique used for estimating population size and density by comparing the proportion of marked and unmarked animals capture in a given area # () # ( )

()

()

5.3 Population Density Problems Quadrat: Sampling frame used for estimating population size. Frames can be real or virtual. Average sampling density =
#

5.4 Changes in Population Size

Population change:

x 100 Open population: influenced by natality, mortality, immigration and emigration Closed population: influenced by natality and morality Biotic potential: maximum rate a population can survive under ideal conditions
5.5 Population Growth Models Survivorship Curves:

+ ( + )

5.6 Factors Effecting Population Change

Density Dependent Factors o Factors influencing population regulation, having a greater impact as population density increases, or decreases, i.e. intraspecific competition, predation, allele effect, etc. o Minimum viable population size: Smallest number of individuals that ensures a population can persist for a defined interval of time Density Independent Factors o Factors that influence population regulation regardless of population density i.e. extreme temperatures, insecticide application, etc. o Limiting factor: any essential resource that is in short supply or unavailable. Inhibits populations from reaching Biotic Potential. 5.7 Interaction within A Community o Interspecific competition: competition between individuals of different populations i.e. interference competition, exploitative competition, etc. o Intraspecific competition: competition between individuals of the same population o Symbiosis: relationship in which individuals of two different species live in close, usually physical contact

Predation: an ecological relationship in which a member of 1 species catches, kills, and eats a member of another species.

6. Appendix
6.1.1 Protein Formation

6.1.2 Glycolysis

6.1.3 Krebs Cycle

6.2.1 Overview

6.2.2 Neuron

6.2.3 Urine Formation

6.2.5 Stress Response

6.2.6 Reflex Arc

6.2.7 Spinal Cord

6.3
6.3.1 Translation

6.3.2 LacI Operon

6.3.3 Trp Operon

6.4 Reproductive System