BABS1201 Study Notes

BABS1201 Study NotesLife

Universe = 13.8bya

Solar System = 4.6bya

Life = 3.8bya

1.8million species identified, thousands more each year, with 10-100 million species in total, of which are arthopods

Characteristics of Life: Reproduce

Grow and Develop

Metabolise

Respond to Stimuli/Environmental Changes

Have Cells (organizational units)

Possess the Chemicals of Life

Carbohydrates

most abundant, chemically simple organic molecules

store/transport energy (mostly in plants, animals use lipids), structural components

monosaccharides link to form oligosaccharides (2-6) or polysaccharides

Proteins

Dependent on amino acid sequence, linked by peptide bonds

4 different levels of organisation (shape-dependent)

Lipids

fats, oils, waxes, cholesterol, fat-soluble vitamins (A, D, E, K), monoglycerides, diglycerides, phospholipids

energy storage, structural component of cell membrane

Nucleic Acids

formed by linking nucleotides

store/transfer genetic information DNA, RNA

Prions (proteinaceous infectious particles) are altered proteins that can change other proteins through conformation.

Domains (classification), defined by Carl Woese (compared ribosomal RNA, formed phylogenetic tree):

Eukarya (35 subdivisions) - plantae, fungi, animalia, 50-100 protist kingdoms Bacteria (19 subdivisions)

Archaea (16 subdivisions) - many are extremophiles (halophiles, thermophiles, methanogens - swamps/marshes, anaerobic and produce methane)Prokaryotes = bacteria + archaea; thrive almost anywhere, more in handful of soil than the number of people who have ever lived

Bacteria/ArchaeaEukarya

no-membrane around organellesmembrane-enclosed organelles

no nucleusnucleus (usually largest organelle)

simple, small (1m; 0.5-5m)complex, larger (10-100m)

Viruses - 50-100nm (only seen with electron microscope)

Origin of Life:

1)Abiotic synthesis of small, organic molecules

2)Joining of these into macromolecules

3)Packaging into protobionts (perhaps by membrane, prokaryotic precursors)

4)Origin of Self-Replicating Molecules

Fossil Record - biased for species that existed for a long time, were abundant and widespread, and had hard parts. However it shows macroevolutionary changes (ones youd be able to see, not genetic) in many species. Comparisons in common structures, such as common DNA or the same structure of cilia in Paramecium (protist) and windpipes are evidence for evolution (as with the pentadactyl limb, comparative embryology, comparative biochemistry - comparing proteins like haemoglobin).

Darwins Theory of Natural Selection explained the duality of unity and diversity through two main points:

species showed evidence of descent with modification from common ancestors

natural selection was the mechanism behind this

Cells

Bacteria and Archaea: most numerous cells on the planet

no defined nucleus (DNA in cytoplasm)

very wide range of metabolic diversity

cell wall

10-20 times as many bacteria in/on the ;human body than there are human cells (of which there are 1013)

Cell Membrane has a hydrophilic head and 2 hydrophobic tails (controls what comes in and out of cell).

All cells contain: plasma membrane

cytosol (semifluid)

chromosomes

ribosomes

Bacterial Morphology and Colony FormationBacteria and Archaea undergo binary fission (not mitosis which involves nuclear division, which they do not have, and instead chromosomes simply replicate)BacteriaArchaea

Cell membrane contains ester bondsCell membrane contains ether linkages

Cell wall made of peptidoglycanCell wall lacks peptidoglycan

One RNA polymeraseThree RNS polymerases (like eukaryotes - genes and enzymes are more like this)

Bacterial ribosomes sensitive to some antibioticsArchaea (and Eukarya) are not

UbiquitousTypically extremophiles, also in many marine environments

Whilst archaea are similar to bacteria in size, shape, lack of interior membranes (and hence organelles), no nucleus (DNA in a single loop - plasmid), and they are both usually bound by a cell wall, archaea are more genetically similar to eukaryotes.Cell Theory:

The smallest unit of life is a cell

All life forms are made of cells

Cells only arise from pre-existing cells

Major cellular components of eukaryotes:

cytoplasm - comprised of organelles and cytosol (gelatine-like aqueous fluid containing salts, minerals and organic compounds)

nucleus - contains nucleoplasm in nuclear envelope (double membrane system - two lipid bilayers) which has selectively permeable pores for RNA and ribosome output; a nucleolus/nucleole (no membrane) composed of protein and nucleic acids where ribosomal RNA transcription (ribosome manufacture occurs); also houses chromosomes (DNA+histones), which are condensed together into chromatin ribosomes - (no membrane because in both eukarya and prokarya) converts mRNA sequence into proteins by connecting amino acids to tRNA which then complements the mRNA, catalysing some components of this reaction (e.g. polymerisation of amino acids into polypeptide chain); consists of large and small subunit; biochemically consists of rRNA (ribosomal RNA) and ~50 structural proteins endoplasmic reticulum - the endomembrane system modifies protein chains into their final form, synthesises lipids and packages final proteins and lipids into vesicles for export or use in the cell; continuous with the other membrane of the nuclear envelope, forming a web or mesh of interconnected membranes coming off the nucleus Rough ER - closest to the nucleus, contains ribosomes for translation with mRNA coming out of nucleus, and is used for protein synthesis and transport (through the channels formed) Smooth ER - lacks ribosomes, instead makes lipids (fatty acids, phospholipids and sterols), and is also involved in cholesterol metabolism and membrane synthesis; packages lipids into transport vesicles (small membrane bound sacs) and sent to the Golgi body Golgi body/apparatus - receives transport vesicles on one side of the organelle (the cis face), binding it to the first layer, then modifying, sorting and packaging the protein or lipid as they pass through the various layers, and pushing them out at the trans face; molecular tags are added to the fully modified substances, allowing the substances to be sorted and packaged, and then where they need to be shipped, to be then stored or secreted; pinching off of membrane can produce other membrane-bound organelles like lysosomes and vacuoles lysosomes - small organelles that contain enzymes which breakdown lipids, carbohydrates and proteins into small molecules that can be used by the cell, and also to remove junk and clutter cytoskeleton - network of protein filaments and microtubules, controls cell shape, maintains intracellular organisation, acts as tracks for transport, and is involved in cell movement; three types of fibres Microfilaments - (mostly actin, 7nm thick) maintain cell shape by compression resistance, involved in membrane pinching in division, forming pseudopodia, and in muscle contraction Intermediate Filaments - (keratin, rope-like fibres, 8-12nm, hollow) only in multiceullar organisms for cell structure and shape (resist tension), anchoring of organelles, and may help hold neighbouring cells together Microtubules - (- and -tubulin forming a heterodimer (two different proteins making a polymer), 25nm, hollow) have +ve and -ve end, forming a track for molecular motor proteins to move organelles and other structures, powerhouse of flagella and cilia, pull everything in mitosis, generatored from centrosomes/MTOC (microtubule organising centres) mitochondria - (1-10m) generate most of the cells ATP supply, also used in signalling, cell cycle, growth and death; contain folds called cristae and matrix within chloroplast - found in plant, algae and some bacteria for photosynthesis, contain granum (stacks of thylakoid discs), surrounded by the gelatinous stroma and connected by stroma lamellae membraneEndosymbiosis - symbiosis in which one of the organisms lives inside another (as with mitochondria and chloroplasts from cyanobacteria). Evidence includes:

double membrane (one from original cell, one from new packaging)

contain ribosomes more like prokaryotes

contain circular DNA (plastids), growing and reproducing independent of the cell through binary fission size of bacteria is the same as the organelles

Macromolecules99% of living things are made CHON, with P&S also abundant, which join to form macromolecules: a large molecule formed by the joining of smaller molecules usually by a dehydration reaction. Macromolecules (except for some lipids) are polymers of similar or identical subunits (usually monomers) linked by covalent bonds. Polymer breakdown is hydrolysis as a water molecule is added to break the covalent bond.MacromoleculeSubunitBondExamples

CarbohydrateMonosaccharides (glucose, can form disaccharides like maltose)Glycosidic BondStorage and Structure

Starch (glucose) - stored by plants as granules (accessed by hydrolysis)Glycogen (branched glucose) - stored by animals in liver and muscle cells (cant sustain animal for long period of time)

Cellulose (flipping glucose) - structure, component of plant cell walls

Chitin (glucose with nitrogen groups) - exoskeletons in arthropods (insects, spiders, crustaceans)

LipidFatty Acids(In TAG, three fatty acids each join to a glycerol by an ester bond, varying in length, and number and positions of double bonds)Ester BondHydrophobic (non-polar)Saturated - no double bonds in fatty acids between carbons

Unsaturated - 1+ double bonds in hydrocarbon chain of the fatty acid, causing kinks

Phospholipids are two hydrophobic fatty acid tails connected to glycerol, which is connected to a phosphate group which in turn is connected to a polar group like choline (replacing one of the fatty acids)

Energy Storage and Transport - triacylglycerols or TAGs

Structure - phospholipids, sterols

Chemical Messengers - steroids (cholesterol), glycolipids

Photoreceptors - carotenoids

Coverings - waxes

ProteinAmino Acids(20 different ones that form polypeptides which fold into 3D structure)Peptide BondsAll amino acids consist of:

central () carbon atom amino group (NH3+) carboxyl group (COO-) hydrogen atom (H) a variable side-chain (R) - determines whether they are non-polar, polar or electrically charged (also hydrophilic)

When polymerised they become a backbone with various side-chains that determine how it folds and 3D structure (primary, secondary, tertiary and quaternary levels of folding determine final shape)Used as structure (keratin), storage (casein), transport (haemoglobin), hormones (insulin), movement (actin), enzymes (sucrase)Enzymes - catalytic proteins selectively speed up chemical reactions without being consumed, allowing reactions to be fast enough for a cell to survive

E (enzyme) + S (substrate) ES E + P (product)

Catalysis occurs at the active site

Enzymes lower the activation energy (EA) of a thermodynamically favourable reaction, but do not affect the equilibrium or free energy change (G - the difference in the energy between the reactants and products) and cannot make a thermodynamically unfavourable reaction favourable

Nucleic AcidsNucleotidesPhosphodiester BondsDNA or RNA, store hereditary information, polymers also called polynucleotides

Cell IntegrityThe membrane prevents unwanted nutrients and toxins from entering/leaving, and hence maintains cell integrity. There were two proposed models for the membrane: Davson-Danielli Model (1935) - phospholipid bilayer with proteins above and below

Fluid Mosaic Model (1972 by Singer and Nicholson) - integral membrane proteins sat inside, peripheral proteins above and below, with a cytoskeleton supporting it; had sidedness or asymmetrical distribution of proteins, carbohydrates and lipids (like cholesterol) between each side as many were formed inside the cell but cannot pass to the outside the fluidity refers to the rapid movement of lipids and proteins laterally - shown by:

the fusing of mouse and human cells, and proteins were mixed, not one-side human, the other mouse microscopy with staining

FRAP (fluorescence recovery after photo-bleaching) - altering DNA to produce proteins that lose colour after laser beam exposure to one section of the membrane, and over time colour comes back as this area is filled with non-zapped proteins

Membrane members: Lipids - of which 0-25% is cholesterol; lipid rafts are semi-solid molecules that keeps proteins together or anchors them to the cytoskeleton Proteins - both peripheral and integral that span the membrane and shoot out either side but with different domains on each side Carbohydrates (glycolipids and glycoproteins) - the addition of the sugar groups allow cells to be recognised by other proteins or present different messages through a variety of combinationsSidedness is important for cell recognition and adhesion

Membrane Permeability (selective nature maintains cell integrity): small molecules can pass through (O2, CO2, H2O) hydrophobic molecules will dissolve in the hydrophobic core and diffuse across

ionised, polar and large molecules cannot cross without a protein transporter

Animals prefer isotonic environments, die in hypotonicity (lysis).

Plants prefer hypotonic environments, die in hypertonicity (plamolysis).

Cellular TransportPassive Transport (no energy required): Diffusion - down concentration gradient

Facilitated Diffusion - down concentration gradient with assistance of transporter protein (either for faster transfer or for molecules that could not otherwise cross

Channels/Conduits - allow direct passage from one side to another

corridor for specific molecules or ions to cross

Example: aquaporins are the protein channel for water (water is polar and travels quite slowly otherwise)

may be gated (require another molecule to be bound to a specific site before they function)

Carriers/Transporters

alternates between two shapes, moving the solute across in the process in either direction (dependent on concentration gradient)

binding sites for activation show specificity

slower than channels

Active Transport - with a protein AGAINST the concentration (uses energy from ATP), and hence they are directional/irreversible (depends on protein; multidirectional pass different proteins each way).Concentration gradients are maintained by active transport against the gradient (in addition to chemical reactions).Proton pumps:

electrogenic pumps which ensure H+ is more concentrated in the extracellular fluid, creating a stored energy in the form of a concentration gradient which is used to drive other processes in the plants, fungi and bacteria requires ATP to function (hence active transport), but can be used to drive other processes

Example: indirect active transport of sucrose by having H+ move down its own concentration gradient and bring sucrose with it through the protein

Membrane potential:

potential difference across a membrane, created by differences in cation and anion distribution (cytoplasm more negative, -50 to 200mV)

in animals, created by sodium-potassium pump (Na out, K in, both AGAINST concentration gradient, overall more out than in) favours passive transport of cations into the cell, anions out of the cell

diffusion is influenced by both concentration gradient and electrochemical gradient

changes in membrane potential can also regulate voltage gated channels tracked by attaching non-functioning fluorescent tags to ions that change shape and fluoresce when attached

Large molecules (polysaccharides, proteins) cross the membrane in bulk through vesicles by:

Pinocytosis (cellular drinking) - all outer solutes surrounded by membrane which combines to cell membrane (but doesnt go straight in), then transfer proteins choose which ones go through (no specificity)

Phagocytosis (cellular eating) - wrapping pseudopodia around solutes, packaging in vesicle/vacuole, some absorbed, the rest thrown out (specific)

Receptor-Mediated Endocytosis - like pinocytosis, except receptor proteins on membrane surface recognise and bind to specific molecules in clustered regions called coated pits, and if all molecules are accepted then they are all taken in (specific)

PhotosynthesisThe physico-chemical process is used by plants, algae (oxygenic) and photosynthetic bacteria (anoxygenic; uses bacterial chlorophylls) to produce organic compounds with light as oxygen (only 0.5% of the 21% is produced by NON-biological processes, the main sources being cyanobacteria, plankton and plants), whilst consuming the toxic CO2. Photosynthesis supplies all food, petrol (and natural gas, coal and ethanol), and clothing and building materials. In eukaryotes, photosynthesis occurs in chloroplasts (green + form or entity), which are double membrane-bound flat discs 2-10m in diameter and 1m thick, containing lots of small discs called thylakoid (thylakos = sac) which consist of a thylakoid membrane surrounding a thylakoid lumen, and exist as stacks called grana (Latin for stacks of coins), connected by intergrana or stroma thylakoids. This is placed in a thick fluid called the stroma (the site of light-independent reactions). The pigment chlorophyll is used to absorb light on the thylakoid membrane, and green light is reflected whilst red and blue are mostly absorbed (by chlorophyll a and b and carotenoids).Photosynthesis occurs in two stages:1. Light-Dependent Reactions - light captured, electron and proton transfer reactions to make energy-carrying molecules, produces ATP and NADPH2. Light-Independent Reactions - ATP and NADPH used to convert CO2 into glucose

ATP (adenosine-5-triphosphate) is produced by either redox reactions or photons. If it is done by photons (sunlight) it is called photophosphorylation (phosphorylation simply means adding phosphate group). The light energy is converted into electrical energy and packaged into chemical energy as ATP or NADPH (nicotinamide adenine dinucleotide phosphate; considered energy couriers - provide temporary storage of chemical energy). This process is performed by photosystems (protein complexes that contain chlorophyll) found in thylakoid membranes. The chlorophyll are bound to proteins which act as antennae that absorb photons and transfer the excited electron to the reaction centre.First a photon hits a chlorophyll molecule surrounding the Photosystem II (P680 as it absorbs a wavelength of 680mm - penetrated faster than longer wavelengths, hence first), and the chlorophyll molecules transmit energy from the excited elections in the antenna complex to a reaction centre. Each photosystem has one pair of chlorophyll a molecules, but hundreds of chlorophyll b and carotenoid molecules. Chlorophyll b and carotenoids absorb photons and pass excited electrons to each other until it reaches the chlorophyll a, where the electrons can then be transferred (by an electron transfer chain) to the primary electron acceptor (P.E.A.).

Electrons lost from the P680 are replaced by the splitting of water (2H2O 4H+ + O2 + 4e-), where the protons and oxygen are produced in the thylakoid space (producing a proton gradient across the thylakoid membrane) whilst the electrons continue in the membrane until they reach plastoquinone (Pq), the first mobile carrier, where the electron carrier that holds the electron takes it to the cytochrome complex (consists of several subunits like cytochrome f and cytochrome b6) back into the thylakoid space. The electrons are then transferred to plastocyanin (Pc), until they reach Photosytem I (P700; discovered first). This is another large protein-pigment complex that contains light-absorbing antenna molecules where photons are absorbed and electrons taken to reaction centres, then on to ferredoxin (Fd) outside the thylakoid, which transfer the electron to Ferredocin NADP Reductase (FNR) which catalyses NADP+ + H + 2e- NADPH in the case of non-cyclic photophosphorylation.

In cyclic photophosphorylation ATP is produced (as this is sometimes needed to power other activities in the chloroplast), where the electrons are recycled by being transferred back to the cytochrome b6f complex (via Fd and Pq) to resume the cycle.Light-independent reactions occur in the stroma (outside the thylakoids) in the Calvin cycle. It requires: Ribulose-1,5-biphosphate carboxylase oxygen (RuBisCO) - which catalyses carbon fixation to RuBP, probably most abundant protein on Earth

Ribulose-1,5-biphosphate (RuBP) - 5-carbon sugar chain, CO2 acceptor in first major step of carbon fixation

CO2 - used during fixation ATP and NADPH - used in reduction phase to convert 3-phosphoglycerate to glyceraldehyde-3-phosphate (three carbon precursor to flucose), and ATP is used in regeneration phase where it converts this back into RuBPThe first stage is carbon fixation, where RuBisCO attaches CO2 to RuBP (6-carbons), which breaks into two phosphoglyceric acids (3-PG as they have 3 carbons each). This is phosphorylated (adds phosphate group) by ATP to form 1, 3-biphosphoglycerate, then NADPH reduces this in the reduction phase into glyceraldehyde-3-phosphate (G3P) - the ultimate goal of the Calvin Cycle. This is composed of the simplest sugar known (D-aldotriose), which can be combined to form organic molecules like fructose (which can then be rearranged into glucose, or other molecules like sucrose and starch). In the regeneration phase G3P can be converted back to RuBP by ATP. In total, one glucose molecule requires 6CO2, 18ATP, 12NADPH (1NADPH 3ATP in terms of energy).An Introduction to Metabolism

Metabolism - the totality of an organisms chemical reactions (both catabolic and anabolic pathways) to manage material and energy sources. A metabolic pathway involves a starting molecule/s which undergoes several reactions catalysed by enzymes to produce intermediates and eventually a desired product. Catabolic pathways RELEASE energy (produce ATP) by breaking down complex molecules INTO simpler ones (e.g. cellular respiration - break down of glucose in presence of O2). Anabolic pathways CONSUME energy (use ATP) to build complex molecule FROM simples ones.

All organisms require both an energy and carbon source from the environment:

Phototrophs

energy = lightChemotrophs

energy = chemicals

Autotrophs

carbon = CO2Photo-autotrophs

(photosynthetic bacteria, plants, some protists like algae)Chemo-autotrophs

chemicals are inorganic

(some bacteria)

Heterotrophs

carbon = one or more organic compounds, e.g. glucosePhoto-heterotrophs

(some bacteria)Chemo-heterotrophschemicals are organic(many bacteria and protists, animals, parasitic plants)

ATP is the energy shuttle of a cell, composed of a ribose (sugar), adenine (nitrogenous base) and three phosphate groups. The bonds between the phosphate groups of the ATP tail can be broken down by hydrolysis (addition of water), and the lone inorganic phosphate becomes Pi, producing G=-31kJ/mol of energy and leaving adenosine diphosphate (ADP - note only two phosphate groups now). The ATP cycle allows energy from catabolism (exergonic) to be transported to areas where energy is required and consumed (endergonic). ATP can be generated in two ways: Oxidative Phosphorylation - addition of Pi to ADP to produce ATP powered by redox reactions in the electron transport chain

Substrate-level Phosphorylation - an enzyme transfer a phosphate group from a DIFFERENT substrate (which has a phosphate group) to produce ATPCatabolic processes in higher animals and other organisms require O2 (they are aerobic). For example, respiration: C6H12O6 + 6O2 6CO2 + 6H2O. In many protists and bacteria catabolic processes dont need O2. For example fermentation: C6H12O6 2C2H5OH + 2CO2 OR C6H12O6 C3H5O3- (lactate ion) + 2H+.Fermentation also occurs in eukaryotic cells, as glucose undergoes glycolysis to to form pyruvate, in which either fermentation can occur and only 2ATPs are produce, or respiration can continue into the mitochondria and produce a net energy of 36ATP.Oxidation is the loss of electrons (or H atoms as often e- is attached to a proton), whilst reduction is the gain, however these two reactions are done simultaneously. Catabolism is generally oxidation, whilst anabolism is generally reducation. When a metabolic fuel is oxidised, electrons are collected by a coenzyme/cofactor like NAD+ (nicrotinamide adenine dinucleotide - two nucleotides joined together at their phosphate groups) which becomes NADH with the enzyme dehydrogenase.Metabolism can be regulated by feedback inhibition, where a product of the pathway inhibits an enzyme earlier in the pathway, and hence when enough product is formed the enzyme stops and no more is produced until there isnt enough product. Enzymes with allosteric properties (activity that changes through binding an effector molecule at an allosteric site - different to the active site) are commonly involved in control of metabolic processes. Alternatively, allosteric regulation could stimulate enzyme activity instead of inhibiting it. Enzymes will often oscillate between an active and inactive state, so a stabiliser can help it stay either active or inactive.Catabolic pathways are often inhibited by ATP, whilst activated by ADP or AMP (mono-, one phosphate group). Anabolic pathways are inhibited by ADP or AMP, whilst activated by ATP. Generally all metabolic pathways are activated by earlier reactants and inhibited by later products.

Cells are compartmenalised, and cellular structures help bring order to metabolic pathways. In eukaryotes, some enzymes reside in specific organelles, like those for glycolysis (glucose breakdownpyruvate) are located in the cytosol whilst those for the TCA cycle are in the mitochondria.Extracting Energy from FoodCellular respiration - the process by which cells break down organic compounds using various catabolic pathways for the purpose of generating ATP

Glycolysis consists of 10 enzyme-catalysed reactions (found in all organisms), where glucose (6C) is oxidised into 2 pyruvate molecules (3C each). The pathway has to stages - an energy investment and energy payoff - overall yielding 2ATP per glucose and producing the reduce cofactor NADH. The pyruvate could then be fermented anaerobically (and produce wastes) or undergo respiration in which it is converted to acetyl-CoA by pyruvate dehydrogenase that produces CO2, converts NAD+ to NADH and adds Coenzyme A in the mitochondria in preparation for the TCA cycle.The TCA (or citric acid) cycle occurs inside the mitochondria and is where the acetyl- group (from acetyl-CoA) is broken down. The 3C from the pyruvate are broken down to produce 3 more CO2 molecules, 4NADH and 1FADH are produced, and one ATP is formed.Cellular respiration also involves a controlled energy release whilst the reaction 2H2 + O2 2H2O occurs. This is done by the respiration chain, where reduced cofactors transfer their reducing power (H atoms and/or electrons) to oxygen through a series of redox reactions with a G=217kJ/mol. The components of this electron transport chain are all proteins (except Coenzyme Q) located in the inner mitochondrial membrane within or between protein complexes I (proton comes from NADH), II (proton comes from NADH), III (proton comes from I or II) and IV (from III). O2 is the terminal electron acceptor after this protein complex, whilst the proton is transferred out of the mitochondria and eventually back in by ATP synthase to produce an ATP from ADP and Pi.Chemiosmosis (first proposed by Peter Mitchell in 1961) is the theory that the proton gradient created by the respiratory chain (as it pumps protons out of the mitochondria) provides a means of free energy (a proton motive force) that can drive the activity of ATP synthase to generate ATP (oxidative phosphorylation). This can be shown experimentally as mitochondria at pH 8 that are shifted to pH 4 have a burst of ATP synthesis without any respiratory chain activity (no O2 is used, so it is the protons that matter). If the inner membrane is made permeable to protons, no ATP is synthesised as no gradient is produced.ATP synthase includes integral membrane proteins (located in mitrochondrial and chloroplast membranes in eukaryotes, or the plasma membrane in bacteria). ATP synthase has membrane-spanning domains that form a rotor which is driven by the movement of protons down the H+ concentration gradient (think of it as electric charges in a DC motor). Rotating the motor shaft in head piece causes conformational changes in the active sites that bind ADP and Pi, and provides energy for this synthesis.The mitochondrial membrane is important for ATP synthesis as it is: fluid - allows H atoms/electrons/protein components to move and interact asymmetric - monodirectional proton pumps drive ATP synthesis through gradients impermeable to ions - maintains proton gradientIn total 30-32 ATP equivalents (NADH 2.5ATP, FADH2 1.5ATP) are produced from one glucose, which would only produce the initial 2NADH and 2ATP in anaerobic fermentation.

Respiration is controlled by allosteric enzymes. For example, phosphofructokinae (PFK) catalyses the third step in glycolysis, however it is inhibited by citrate (from the citric cycle) and ATP, whilst being stimulated by AMP.Amino acids from proteins are broken down to acetyl-CoA or intermediates within the glycolysis or TCA cycle, whilst carbohydrates and fats are both broken down aerobically into acetyl-CoA (allows for recycling of some materials, which is what occurs when eating food). Ultimately it will form CO2 and H2O (the products of respiration). In cases of low O2 supply, such as intense exercise in skeletal muscle cells and red blood cells, carbohydrate catabolism involves fermentation, and the glucose is converted to lactate (lactic acid), which causes cell death if oxygen supply is interrupted.From Gene to FunctionThe genetic language must be accurately copied and passed on and readily accessed for the information contained. Proteins had greater complexity and 20 building blocks, whilst DNA had a regular structure and only 4 building blocks so it was believed proteins would the means of inheritance, however like binary the simpler language still allowed for complexity. Experimental data in the 1940s-early 50s suggested that DNA may be genetic material. For example, in 1953 Hershey and Chase grew two batches of bacteriophage T2 (virus that infects bacteria, one with radioactive sulfur (present in two amino acids) which labelled proteins, the other with radioactive phosphorus which labelled DNA. Mixing these with bacteria infected the bacteria with the genetic material of the virus, and upon centrifuging to separate the bacteria from the viruses they found it was the DNA inserted into the bacteria.In 1953 Watson and Crick published the structure of DNA using molecular models from X-ray diffraction patterns, proving it was a double helix (they knew it had the nucleotide bases adenine, thymine, cytosine and guanine which stood on sugars, each linked by a phosphate group after an H2O has been taken out). DNA is deoxyribonucleic acid, whilst RNA is ribonucleic as it has an extra O. Combined with a phosphate group and base, it becomes a nucleotide.A & G are double-rings (purines), so an A & G would produce a strand to wide (to be consistent with X-ray data). T & C are single-ringed (pyrimadines - smaller size compensated for by longer name), and would produce a strand too close for DNA. Hence one pyramidine had to be paired with one purine. In addition, A & T have two hydrogen bonds, whilst C & G have three, so they can only match like AT and CG. It forms an alpha helix (follows right-hand grip rule), and being a helix (not spiral) the strands are not evenly distributed but close then far then close then far, which produces almost a spiral shape with the resulting ribbon (but as the two strands are separate it is not a spiral). Each strand is considered antiparallel (running in opposite directions - the phosphates charges face opposite directions and the carbons sit on the opposite sides). The 5 phosphate end (the top) finishes with a phosphate, whilst the 3 hydroxyl end finishes with the OH from the sugar.

Humans have 3.2109 base pairs (2m long, 0.01mm wide), and this is complexed with histones (proteins) to form nucleosomes, solenoids and eventually chromatin. Histones maintain structure of the chromosome and help regulate gene expression/activity. It is folded, coiled and condensed in preparation for cell division.Mitochondria also have their own circular DNA within their matrix (the part inside the folds (cristae), not the tissue itself), which codes for proteins essential for normal mitochondrial function.

DNA ReplicationFirst, at the origin of replication helicase unwinds the strands and forms a small bubble. Multiple origins are needed to ensure replication occurs as quickly as possible (in human cells there are 6 billion base pairs all copied within a few hours). DNA polymerase then catalyses the addition of new nucleotides in opposite directions on each strand (as the two strands are anti-parallel). Incoming nucleotides have 3 phosphate groups, and 2Ps are released to provide energy for the reaction (as those are high-energy bonds). DNA polymerase must have a 3 OH group to add on to, and hence will move along the template strand from 35, producing a new growing strand and elongating it in the 53 direction (as the DNA polymerase can only exist at the 3 end). DNA synthesis cannot initiate unless a primer (short piece of RNA that contains a 3 OH) to continue building off.After a primer has been made in leading strand synthesis DNA polymerase III (which consists of a sliding clamp ring and boxing glove) starts synthesising the leading strand right after the helicase continues to unwind (otherwise it will join back) and forming a replication fork. However in the lagging strand, as it moves in the opposite direction to the helicase (anti-parallel), it must do so in small fragments, called Okazaki fragments. First, primase joins RNA nucleotides into a primer on the template, then DNA polymerase III adds DNA nucleotides to the primer, forming Okazaki fragment 1, then a new primer is added slightly before and the polymerase attaches to this once finishing its fragment, forming a second fragment until it reaches the original primer and detaches. DNA polymerase I replaces the RNA with DNA (by adding to the 3 end of fragment 2), then DNA ligase forms a bond between fragment 2 and fragment 1.Replicating the ends of chromosomes is difficult as there are no 3 OH ends to build off, and hence with every replication the 5 end becomes shorter on the lagging strand (but not on the leading as it runs until the end as thats a 3). To counter this, telomeres are sequences (10, 000 base pairs at each end) produced by telomerase (which also has RNA within the enzyme, not just amino acids, to produce remaining base pair sequence) extending the ends of the sequences. Telomerase in inactivated in post-embryonic cells (and many cancers involve reactivating telomerase).To treat disease, nucleotide analogues can be used. For example, thymidine (the nucleotide with thymine) can be replaced with AZT, which swaps the OH group on the sugar for a triangle of nitrogens, and hence no OH group is present for DNA polymerase to continue constructing off and blocking DNA replication. This is how AIDS (HIV) is treated.

Gene Expression: TranscriptionTo express a gene, it undergoes transcription into mRNA (which is complementary through base pairing - hydrogen bonding; thymine is replaced with uracil), and then each codon (triplet of base pairs) is translated into an amino acid. The reasoning for triplets is that arranging our four base pairs gives 43=64 possibilities, which is enough for 20 amino acids plus stop (42=16 isnt enough), however much of this code is redundant as it doubles up (which provides some protection). To crack this code they synthesised strands of just specific codons (e.g. AAAAAA) then observed the protein in vitro (outside a cell). The code was also found to be genetic, as the gene coding from the firefly luciferase protein (which makes it glow) was inserted into a mouse embryo, and the mouse was able to produce a functional fluorescent protein.Transcription has three stages:1. Initiation - RNA polymerase binds to the promoter region upstream of the gene, DNA strands unwind, RNA synthesis is initiated by the RNA polymerase2. Elongation - the polymerase complementary copy downstream, adding to the 3 in the mRNA (moving away from 5), unwinding the DNA and elongating the mRNA transcript; the mRNA does not stay bound to the DNA, but sits parallel to it, and once the RNA polymerase has been through the DNA reforms a double helix3. Termination - upon reaching a termination point the RNA polymerase transcribes a terminator sequence which signals the end of the gene, and the RNA polymerase and transcript are releasedThis process is vital, shown by the toxin -amanitin produced by the death cap mushroom. The toxin binds to RNA polymerase, preventing transcription and inhibiting protein synthesis, often resulting in kidney and liver failure.

Prokaryotic cells have no nucleus, so the mRNA is immediately translated into a protein. The mRNA is formed as pre-mRNA in the nucleus, and this is extensively modified before being exported to the cytoplasm for protein synthesis by adding a 5 cap and poly(A) tail (to the 3 end) which package it for protection against exonucleases used to kill virus RNA (signals it as eukaryotic) and labels it for correct cellular course. Intervening sequences (introns) are also spliced out leaving just the expressed sequences (exons). Exons can be spliced in different ways to produce different proteins from the same gene sequence. For example, the muscle protein -tropomyosin has 12 exons which can be used to produce striated muscle, smooth muscle, fibroblasts (for connective tissue) or brain cells.

Initiation in eukaryotes begins with transcription factors (proteins) that mediate the initiation of transcription by blocking the promoter sequence.

Gene Expression: TranslationThe ribosome is the protein synthesis factory, and where the tRNA (carrying amino acids) base pairs (hydrogen bonds) with the mRNA, ensuring amino acids are placed in the correct mRNA (and hence DNA) sequence. tRNA (transfer) is single stranded (however intramolecular H-bonds make it fold to look sort of double-stranded). The amino acid attaches to the 3 end of the tRNA, and partway between the 3 and 5 is the anticodon (at the bend) that H-bonds to the codon in the mRNA. Each amino acid has a different tRNA, joined by aminoacyl-tRNA synthetase (this is done by the enzyme first binding ATP and the amino acid by one P and releasing the other two (but adenosine still attached, so AMP), and then the tRNA replaces the AMP).The ribosome has two subunits (small and large), and three sites: A site - aminoacyl-tRNA binding site

P site - peptidyl-tRNA binding site (contains many amino acids, hence peptide chain)

E site - exist site

The stages of translation are:

1. Initiation - the small subunit binds the mRNA, and the initiator tRNA (complement to AUG with methionine) binds to it, then the larger subunit binds to the initiator tRNA in the P site (uses energy from GTPGDP, not A)

2. Elongationa.Codon Recognition - next tRNA binds to A site codon (requires 2GTP2GDP)

b.Peptide Bond Formation - peptide bond forms between amino acids (catalysed by enzymes in the ribosome itself; the peptide chain is joining onto the new amino acid)

c.Translocation - then the mRNA moves along, putting the tRNAs into the E and P site (requiring another GTP) and the tRNA is ejected and recycled at the E site, and then the cycle begins anew3. Termination - a stop codon is recognised in the mRNA by a release factor (protein), allowing the last tRNA and new protein to leave, the ribosome units to separate (for recycling) and mRNA released (to be broken down or reused)Many antibiotics target bacterial transcription and translation (which is sufficiently distinct in prokaryotes from eukaryotes that it is possible to specifically inhibit them). For example, RNA polymerase can be blocked with rifampin, and protein synthesis with 30S inhibitors like tetracycline and streptomycin, or 50S inhibitors like erythromycin and chloramphenicol.In prokaryotes control of gene expression occurs at the level of transcription (whether a gene is transcribed), as once the mRNA is formed it is immediately transcribed (which allows them to respond immediately to their environment). In eukaryotes, the most important stage of gene expression occurs during transcription (initiating), however also occurs at processing, transport and degradation of mRNA. At the protein level, proteins can be modified, transported and degraded.By activating eye genes on a Drosophila larvae leg, the adult grew an eye on its leg. However as no neurons connected it to the brain it was not functional.

The size of a genome varies amongst organisms, a more base pairs generally but doesnt always mean more genes. Organism complexity doesnt necessarily determine how many genes you have (as worms, water fleas and plants have more genes than a human, although most have fewer base pairs). Humans have 20, 000 genes, with each gene having an average of 27, 000 base pairs (ranges from 1000 to 2.4 million). 99.9% of the genome is the same in all people. Genes are not evenly distributed amongst chromosomes (chromosome 1 has 2968, Y has 231). The function of many genes is still unknown.

Cell Division and ReproductionIn prokaryotes, cell reproduction occurs by binary fission, in which DNA replication commences at the origin of replication until each chromosome has been completely replicated, and each origin becomes separately attached to the plasma membrane. Once replication is complete, the plasma membrane grows inwards to produce two daughter cells and a cell wall is deposited.In humans there are 1 billion cells/gram of tissue, all derived from a fertilised egg, so this cycle must be regulated precisely. Most cells replicate between 10-30 hours (whilst E. coli is 20mins). Cell replication has two major phases (basically 2n4n (two of each individual single chromosome)2n):

Interphase - growth and replication of cellular components, gathers materials and ensures enough for replication G1 - growth

S - DNA synthesised (replicated/duplicated)

G2 - cell components replicated (including centrosomes, which have perpendicular centrioles - smaller component) Mitotic Phase - nucleus divides and chromosomes are distributed to daughter cells (mitsosis) and the cytoplasm divides into two daughter cells (cytokinesis)

Mitosis Prophase - chromosomes condense, centrosomes separate and form mitotic spindle Prometaphase - nuclear membrane breaks down, further condensing, centrosomes move to spindle poles where they anchor, microtubules connect to centromeres (centre of duplicated DNA) by binding to kinetochores (also made of microtubule)

Metaphase - each chromosome attaches to a spindle pole (equal pressure each way - if not properly attached one cell will have an extra copy, the other missing one; NOT trisomy, as this isnt meiosis)

Anaphase - protease chews through protein holding sister chromatids together and they are pulled apart causing cell elongation

Telophase - nuclear membrane reforms and chromosomes decondense

Cytokinesis - cleavage furrow (contracting ring of microfilaments in animals, cell plate made of vesicles in plants which becomes part of cell wall) separates the two cellsTo ensure DNA is being replicated correctly, there are multiple checkpoints:

G1 Checkpoint - sufficient nutrients, nucleotides, starts choosing to get ready for mitosis

G2 Checkpoint - checks all DNA for mitosis has been replicated properly

M (metaphase) Checkpoint - ensures all chromosomes are connected to spindles before anaphase commences

Apoptosis is programmed cell death which removes unwanted cells (webbing between digits during embryo development, shedding of leaves provides protection against cold and recycles nutrients, removal of damaged cells, disintegration of tadpoles tail for recycling).

Human somatic cells have 46 chromosomes (2n - diploid) whilst gametes (sperm and ova) have 23 (n - haploid) so when they fuse during fertilisation they make 2n. The process of producing a haploid cell is meiosis, which has two stages, the second of which is near identical to mitosis (2n4n (a tetrad of each chromosome pair)2n2n): Interphase - as with mitosis, however instead of one dyad (duplicating each chromosome) a tetrad (two dyads) is formed Meiosis I Prophase I - homologous chromosomes (as dyads) come together and synapse (closely apply themselves to each other); the chromosomes shorten and thicken, and within the tetrad a ladderlike protein structure (synaptonemal complex) aligns the pair and they cross over to form chiasma (swaps genes, increases genetic diversity); the centrioles move to opposite poles of the nucleus and the nuclear membrane breaks down Metaphase I - chromosomes have untwined (are clearly two dyads) and line up in two rows, with homologous pairs next to each other Anaphase I - homologous chromosomes are pulled to opposite sides by kinetochore microtubulues Telophase I - chromosome homologues are at opposite poles, and begin to reform a nuclear membrane

Cytokinesis (not exactly part of meiosis) - produces two DIPLOID cells (basically back to square one, but with crossing over) Meiosis II Interkinesis (Interphase II) - no DNA replication (however still centrosome replication) Prophase II - as with mitosis (includes prometaphase)

Metaphase II - as with mitosis (except each chromosome is made of one of each homologous pair so splitting changes genetic diversity, rather than a duplication of each single chromosome and splitting doesnt change genetic diversity as already the same) Anaphase II - as with mitosis

Telophase II and Cytokinesis - as with mitosis

PCR and Individual VariationIn 2003, human genome project completed (based on the DNA of several people including James Watson and Venter), and multiple human genomes have now been fully sequenced. A single gene is one-millionth of the DNA, and a virus may inject its own DNA (although in only a few out of millions of cells), so the challenge is to detect the gene or viral DNA in the presence of billions of bases, and this is completed using PCR (polymerase chain reactions). PCR requires: DNA polymerase

single-stranded DNA template - pattern to synthesise from

primers - short pieces of DNA to add on to (one for upstream, different one for downstream) free nucleotides - to add to the growing chain (dNTPs=deoxyribunucleotide triphosphate) heat - separates DNA strands (although can denature enzyme)

Note that arrows without lines within them only cover the exactly length of the gene. Each cycle (production of new copies) resulting in a doubling of molecules (2, 4, 8, 16220). As DNA polymerase is denatured at 90oC, the DNA polymerase from the thermophile Thermus aquaticus (Taq) is used, which is stable at 98oC, but optimal at 70oC, allowing extending to be done at a higher temperature than annealing (now 72oC - diagram shows for normal DNA polymerase).

We now have automated PCR machines that can do 96 samples at once using solid states to rapidly increase and decrease temperature (as common in a molecular lab as a photocopier is in an office). PCR is incredibly sensitive and specific, targeting only certain genes, and the electrophoresis can be applied (as DNA is slightly negative moves to positive electrode, smaller molecules can move through gel mesh more easily and hence move further, only those replicated will be potent enough to see after staining with fluorescent that glows in UV when bound to DNA).

Simple sequence repeats (SSR) are short base pair sequences that repeat many times, with a different number for different people. With around 120, 000 SSRs, and each being unique, it is easy to identify a person by their DNA. PCR is used to amplify each specific SSR being analysed using primers designed for those SSRs and then these bands are compared (only identical twins should have identical patterns). Using this, we can identify people after disasters (as in 9/11, comparing to kin), paternity testing (particularly with celebrity heirs), deduce crime suspects (13 used by FBI), or prove historical truths (Anastasia and the Romanovs). However, this evidence can only be used for EXCLUSION, as you can prove that the SSRs dont line up. If they do line up, inclusion cannot be proved as this may be by happenstance. Mitchondria also have their own DNA which comes entirely from the mother, which was used in cases like identifying if Anastasia was still alive by comparing to another great-grandchild of Queen Victoria. Hair cannot be used (as it is just protein, no DNA), however hair follicles can be.MutationA mutation is a change in the nucleotide sequence of an organisms DNA, ultimately creating genetic diversity. They can also occur in virus DNA or RNA. Mutations lead to diversity which is critical to the survival of life. For example, the British Peppered Moth had a mutation resulting in some light, some dark, which were better at camouflage in either lichen-covered trees or soot-covered industrial areas during the Industrial Revolution of the mid-19th C when pollution was being produced. They will only be inherited in offspring if they occur in gametes.Mutations can occur as:

point mutations (changes single base)

insertions

deletions

duplications of sequences

chromosomal rearrangements (like fusion, fission, inversion and translocation)

Mutations can be caused by:

errors in DNA replication (DNA polymerase makes 1 error in 105 bases, leading to incorrect base-pairing, however DNA repair enzymes reduce this to 1 in 1010)

mutagens chemicals (nicotine, asbestos, free radicals, oxidising agents, nucleotide analogues) which damage DNA

radiation (natural radiation like uranium, nuclear waste/bombs, medical X-rays, UV - 20, 000 pyrimidine dimers (e.g. T-T)/hour/cell are caused at 12pm in Sydneys Summer) which damages DNA

transposable DNA (jumping genes)Damaged DNA (like the thymine dimers caused by UV -adjacent thymines that bend towards each other through H-bonds - which causes DNA to buckle due to their pull towards each other and hence interfere with replication) can be repaired to ensure transcription is not problematic and gene expression occurs correctly. Repair is done using a nuclease enzyme that cuts the damaged DNA at two point around the area of damage, and then this is removed. DNA polymerase then fills in the remaining nucleotides (from the OH of the previous one), and DNA ligase seals this to the following strand.Xeroderma pigmentosum (CP) is an inherited defect in a DNA damage repair enzyme, resulting in individuals that are hypersensitive to sunlight (cant correct thymine dimers), which can result in silencing tumour suppression genes and lead to skin cancer.

Most DNA changes are outside of genes, which often doesnt have any effect on the final result, however there are many regulatory genes outside coding regions and hence they can still have large effects on gene expression. These changes can have three outcomes within exons:

No effect - results in different codon that results in same amino acid

Missense - changes amino acid

Nonsense - changes amino acid to stopFrameshift - insertion/deletion of amino acids not a multiple of three will change all amino acids downstream (may introduce missense or nonsense); if it is a multiple of three, it is simply the gain or loss of amino acids. This could result in changing the tertiary structure of the protein depending on the side chain properties of the amino acid (charge, shape) and how different this is to what it was before; otherwise there may be no change. Those that do change may lose some or all functionality, or could gain a new activity. If the amino acid is where the substrate or cofactor binds it will likely have a greater effect than if elsewhere on the protein.Single base changes are the most common variants (~85%) un the human genome, and two unrelated individuals have ~1 in 1000 base pairs that are difference (for a total of 3.2 million differences). There are over 10, 000 gene defects in humans, most of which are rare but have multiple variants. For example, Phenylketonuria (PKU) results in a defective phenylalanine hydroxylase, making a person unable to convert phenylalanine into tyrosine, which can result in death by 30-40 years of age. To avoid this, avoid foods with phenylalanine in them (people are screened at birth to check for this). Cancer is also the result of genetic mutations, from either overstimulation or a lack of inhibition of the cell cycle due to faulty proteins. The classic Irish/Scottish fair skin and hair (blonde or red) results from a mutation in the Mcr1 gene, which results in sunburning instead of tanning and increasing susceptibility to skin cancer. The most common genetic disorders are haemochromatosis (too much iron absorption, 1 in 200), cystic fibrosis (Cl+ imbalance, 1 in 400), thalassemia (reduced production of haemoglobin, 1 in 25 in some areas) and sickle cell anaemia (haemoglobin variant with one amino acid different (GAAGUA, GluVal), allows haemoglobin to form fibres and changes shape; blocks blood flow but also protects against malaria - regions of high malaria are also regions of high sickle-cell anaemia due to natural selection).DNA viruses can correct mistakes that occur during their own replication, whilst some RNA viruses cannot do so and make DNA copies of their genome using an error-prone polymerase which generates mutants easily. HIV is one such virus, and as such can develop resistance to drugs rapidly.

Whether good or bad, mutations provide genetic variation for natural selection through evolutionary fitness (the ability of an organism to survive to reproduction).

Mendels Laws of HeredityGenetics - study of heredity (inheritance); how biological information (DNA base sequence) is passed onto offspring. A genome is the complete genetic composition of an organism, cell or just organelle. In eukaryotes, genomes are comprised of linear chromosomes, usually with multiple chromosomes per genome. In prokaryotes, their genome consists of circular chromosomes, and often plasmids (circular DNA molecules that self-replicated and carry genes).Locus (loci) - the position on a chromosome a gene/sequence is located

Allele - form/variant of a gene at a given locus

Genotype - the alleles an individual has

Phenotype - the physical traits of an organism

We use superscripts of + and - to show if a particular protein is produced by a gene (e.g. in bacteria, leu+ can synthesis leucine, but leu- cannot and required leucine in the medium to grow). Variation in a gene may also not have an effect, for example single nucleotide polymorphism (SNP) is a region of DNA in the introns.

In asexual reproduction, offspring are identical to parks, mostly in prokaryotes (binary fission), but also some eukaryotes like some plants, aphids (plant lice) and hydra (simple freshwater animals). In sexual reproduction, offspring are a combination of parents. Humans have 22 pairs of autosomes and one pair of sex chromosomes, which halve through meiosis (which introduces variation by independent assortment of chromosomes and crossing over/recombination) and combine into a zygote in fertilisation. In diploids we also have:

Homozygote - genotype with two like alleles at a locusHeterozygote - genotype with two different alleles at a locus

Dominant allele - the allele that determines the phenotype (as opposed to the recessive allele)

In 1865, Mendel made inferences on gene activity before we knew what genes were. His theory of dominance was superior to blended inheritance as that would only lead to identical populations. In his experiments he measured a ratio of 3.15:1 (approximately 3:1), and explained in terms of factors. A test/back cross can be used to determine which allele is dominant and if heterozygous or homozygous organisms.

Mendels First Law: diploid individuals carry two copies (alleles) of a gene, which segregate in the formation of gametes, and individuals inherit one copy from each parent (explains 3:1 ratio)

Mendels Second Law: for two genes on separate chromosomes, the pairs of alleles assort independently into gametes (explained 9:3:3:1 in dihybrid crosses)Mechanisms of Inheritance

Huntingtons disease (neural degeneration) is an example of an autosomal dominant (50% of inheritance if one parent has it, affects both sons and daughters), whilst an X-linked recessive would be haemophilia (which can only occur in XaXa (rare) or XaY, but never anyone with XA). Mitochondria are maternally inherited organelles carrying their own genes, and an example of a disease is Kearns-Sayre syndrome, which causes a short stature and retinal degeneration.Occasionally homologous chromosomes dont separate during meiosis (non-disjunction), resulting in n-1 or n+1 haploids and aneuploidy in the diploids (2n-1 or 2n+1 chromosomes). For example, Down syndrome (trisomy-21), Klinefelter syndrome (XXY generally fairly normal, the second X being turned off as if they were female producing a male), and Turner syndrome (monosomy X severe in humans, not so much in mice).Mendels second law of independent assortment was formulated without the knowledge that genes occur on chromosomes, so if two genes are near each other on the same chromosome, the law breaks down (evidenced by a dihybrid testcross of drosophila producing a phenotypic ratio of 5:5:1:1 instead of 1:1:1:1).

Recombination is just the rearrangement of genetic material, particularly by crossing over or artificial joining of DNA segments.

This ratio occurs because the loci/genes are linked on the same chromosome and the closer the loci, the lower the chance of recombination. We can reverse this (the fewer recombinants in a testcross, the closer the genes), with the percentage of offspring being recombinants being the relative distance (in the above example 17%). The maximum recombination is 50% (after which point it is more likely the genes are on separate chromosomes and the complementary percentage is the percentage of recombination). So a 0% chance of recombination means recombinants are impossible, whilst 25% recombination would be 12.5% of each type of recombinant (as there are two when looking at two genes), and 50% would be 25% (at which point it is as likely as independence). This principle is used to map genes that cause disease in many species. Incomplete dominance is when two alleles both contribute to the phenotype, like codominance in Snapdragon (CR + CW = pink), and often occurs in multiple alleles like blood groups (where IA and IB are codominant over io). However this is still not blended inheritance as they dont all come out the same. In pleiotropy, one gene affects more than one trait (for example a gene may encode a protein that forms part of more than one protein complex, or if homozygous for the recessive sickle-cell allele then during low oxygen content red blood cells crystallise and become sickle-shaped, causing the phenotypes anaemia, brain damage and spleen damage, all from the one gene). Epistasis is the interaction of loci or dependence of one gene upon another (for example, enzyme pathways that require one to happen before the other which can affect mouse colour (cc stay white, cannot become brown, those with C become brown, and if bb stay brown but if they have a B then go black). Environment can also influence phenotype, like hydrangeas that change colour depending on the acidity of the soil (this is the reason monozygotic twins are not entirely identical physically). Polygenic traits are those influence by many genes, each having a smaller effect on the phenotype and producing a continuous scale, like height, weight, skin colour and learning ability. They are called quantitative traits as they are measured on a scale rather than being binary (yes or no). Some traits are called complex/multifactorial as they depend on many factors (like environment, epistasis, polygenesis, etc.) and are difficult to map (like diabetes, heart disease, alcoholism).Genes in PopulationsGenetic variation comes from mutations, sexual reproduction (independent assortment and random pairing) and recombination/crossing over. The gene pool is the collection of genes amongst an entire population. Variation at a locus means there are at least two alleles, which may exist at different allele frequencies (a proportion that can be studied over space (mapping sickle-cell anaemia) and time). The Hardy-Weinberg Law/Principle states that assuming you have an infinite population size, no mutation and no migration, no natural selection and random mating, alleles have an equal chance of survival, and hence will maintain their frequency throughout generations, unless an assumption is not met.

In small populations, chance events lead to fluctuations in allele frequencies, with the smaller the population the larger deviation from the law. This is called genetic drift (the changes in allele frequencies due to chance events in small populations which can lead to the fixation (the only gene left) of a particular gene). A bottlenecking event (drastically reduces size of surviving population limits the gene pool, and hence makes them susceptible to further environmental changes). The founder effect is when there is a high frequency of an allele in a small population that continues that species elsewhere (essentially bottlenecking), such as Clinodactyly on the island of Tristan da Cunha, where a small number of British troops who happened to have curved little fingers led to a high frequency in the population.

In natural selection, some genotypes will have a higher probability of surviving due to their higher fitness, and can lead to fixation in the population for fitter alleles, called adaptation. However there is not always biological perfection, as in the case of the peacock whose long a brightly coloured tailed makes it slower and easier to spot (whilst also being good at scaring predators), however its primary advantage is that it makes it more attractive to mates, and this sexual selection has not necessarily lead to a better fitness. Similarly, natural selection ahs lead to increased levels of sickle-cell anaemia in some African countries as it is resistant to malaria, however also has negative effects upon health. Adaptive evolution is also limited by historical constraints, like the epiglottis which chooses lungs or stomach but can result in choking, or standing up in humans which can cause back problems. Microbes also evolve to escape the immune system (those that arent recognise survive) or antibiotics (by developing resistance). EMBED PBrush

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Oliver Bogdanovski