BABS1201 Study NotesLife Universe = 13.8bya Solar System = 4.6bya Life = 3.8bya 1.8million species identified, thousands more each year, with 10100 million species in total, ¾ 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 o Carbohydrates most abundant, chemically simple organic molecules store/transport energy (mostly in plants, animals use lipids), structural components monosaccharides link to form oligosaccharides (26) or polysaccharides o Proteins Dependent on amino acid sequence, linked by peptide bonds 4 different levels of organisation (shapedependent) o Lipids fats, oils, waxes, cholesterol, fat-soluble vitamins (A, D, E, K), monoglycerides, diglycerides, phospholipids energy storage, structural component of cell membrane o 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, 50100 protist kingdoms Bacteria (19 subdivisions) Archaea (16 subdivisions) - many are extremophiles (halophiles, thermophiles, methanogens swamps/marshes, anaerobic and produce methane) Page 1 Oliver Bogdanovski Prokaryotes = bacteria + archaea; thrive almost anywhere, more in handful of soil than the number of people who have ever lived Bacteria/Archaea Eukarya no-membrane around organelles membrane-enclosed organelles nucleus (usually largest no nucleus organelle) simple, small (1μm; 0.5-5μm) complex, larger (10-100μm) 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 (one’s you’d 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). Darwin’s 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 Page 2 Oliver Bogdanovski Bacterial Morphology and Colony Formation Bacteria and Archaea undergo binary fission (not mitosis which involves nuclear division, which they do not have, and instead chromosomes simply replicate) Bacteria Cell membrane contains ester bonds Cell wall made of peptidoglycan One RNA polymerase Bacterial ribosomes sensitive to some antibiotics Ubiquitous Archaea Cell membrane contains ether linkages Cell wall lacks peptidoglycan Three RNS polymerases (like eukaryotes - genes and enzymes are more like this) Archaea (and Eukarya) are not Typically 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: Page 3 Oliver Bogdanovski lacks 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. and is used for protein synthesis and transport (through the channels formed) o Smooth ER . forming a web or mesh of interconnected membranes coming off the nucleus o Rough ER . synthesises lipids and packages final proteins and lipids into vesicles for export or use in the cell. catalysing some components of this reaction (e. pinching off of Oliver Bogdanovski . and pushing them out at the trans face. phospholipids and sterols). molecular tags are added to the fully modified substances. which are condensed together into chromatin ribosomes .receives transport vesicles on one side of the organelle (the cis face). contains ribosomes for translation with mRNA coming out of nucleus. consists of large and small subunit. minerals and organic compounds) nucleus .g. also houses chromosomes (DNA+histones). a nucleolus/nucleole (no membrane) composed of protein and nucleic acids where ribosomal RNA transcription (ribosome manufacture occurs). polymerisation of amino acids into polypeptide chain).closest to the nucleus. sorting and packaging the protein or lipid as they pass through the various layers.comprised of organelles and cytosol (gelatine-like aqueous fluid containing salts. Page 4 cytoplasm . and then where they need to be shipped. binding it to the first layer.two lipid bilayers) which has selectively permeable pores for RNA and ribosome output. 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 . to be then stored or secreted. continuous with the other membrane of the nuclear envelope. then modifying. biochemically consists of rRNA (ribosomal RNA) and ~50 structural proteins endoplasmic reticulum . allowing the substances to be sorted and packaged.the endomembrane system modifies protein chains into their final form. instead makes lipids (fatty acids.contains nucleoplasm in nuclear envelope (double membrane system . 25nm. surrounded by the gelatinous stroma and connected by stroma lamellae membrane Endosymbiosis . powerhouse of flagella and cilia. also used in signalling.small organelles that contain enzymes which breakdown lipids. involved in membrane pinching in division. Evidence includes: double membrane (one from original cell. controls cell shape.(1-10μm) generate most of the cell’s ATP supply.and β-tubulin forming a heterodimer (two different proteins making a polymer). acts as tracks for transport. one from new packaging) contain ribosomes more like prokaryotes contain circular DNA (plastids). and may help hold neighbouring cells together o Microtubules . growth and death. maintains intracellular organisation. three types of fibres o Microfilaments . contain folds called cristae and matrix within chloroplast .(α.membrane can produce other membrane-bound organelles like lysosomes and vacuoles lysosomes . algae and some bacteria for photosynthesis. pull everything in mitosis. rope-like fibres. cell cycle.found in plant. and in muscle contraction o Intermediate Filaments . hollow) only in multiceullar organisms for cell structure and shape (resist tension). contain granum (stacks of thylakoid discs). carbohydrates and proteins into small molecules that can be used by the cell.symbiosis in which one of the organisms lives inside another (as with mitochondria and chloroplasts from cyanobacteria). with P&S also abundant. growing and reproducing independent of the cell through binary fission size of bacteria is the same as the organelles Macromolecules 99% of living things are made CHON. anchoring of organelles. and also to remove junk and clutter cytoskeleton . and is involved in cell movement.network of protein filaments and microtubules. forming a track for molecular motor proteins to move organelles and other structures. forming pseudopodia. 7nm thick) maintain cell shape by compression resistance. which join to form macromolecules: a large molecule formed by the Page 5 Oliver Bogdanovski .(mostly actin.(keratin. 8-12nm. hollow) have +ve and -ve end. generatored from centrosomes/MTOC (microtubule organising centres) mitochondria . Macromolecules (except for some lipids) are polymers of similar or identical subunits (usually monomers) linked by covalent bonds. Page 6 Oliver Bogdanovski . Polymer breakdown is hydrolysis as a water molecule is added to break the covalent bond.joining of smaller molecules usually by a dehydration reaction. waxes Oliver . varying in length. three fatty acids each join to a glycerol by an ester bond. glycolipids Photoreceptors .1+ double bonds in hydrocarbon chain of the fatty acid. can form disaccharides like maltose) Lipid Fatty Acids (In TAG.stored by animals in liver and muscle cells (can’t sustain animal for long period of time) Cellulose (flipping glucose) .carotenoids Coverings .stored by plants as granules (accessed by hydrolysis) Glycogen (branched glucose) .steroids (cholesterol).structure. component of plant cell walls Chitin (glucose with nitrogen groups) .exoskeletons in arthropods (insects.Macromole cule Subunit Bond Examples Storage and Structure Carbohydr ate Monosaccharid es (glucose. spiders. causing kinks Phospholipids are two hydrophobic fatty acid tails connected to glycerol. and number and positions of double bonds) Page 7 Bogdanovski Glycosidic Bond Ester Bond Starch (glucose) .no double bonds in fatty acids between carbons Unsaturated . sterols Chemical Messengers . crustaceans) Hydrophobic (non-polar) Saturated . 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 .phospholipids.triacylglycerols or TAGs Structure . enzymes (sucrase) Enzymes .determines whether they are nonpolar. polar or electrically charged (also hydrophilic) Protein Amino Acids (20 different ones that form polypeptides which fold into 3D structure) Peptide Bonds Nucleic Nucleotides Phosphodies Page 8 Bogdanovski When polymerised they become a backbone with various sidechains that determine how it folds and 3D structure (primary. but do not affect the equilibrium or free energy change (ΔG . hormones (insulin). tertiary and quaternary levels of folding determine final shape) Used as structure (keratin).All amino acids consist of: central (α) carbon atom amino group (NH3+) carboxyl group (COO-) hydrogen atom (H) a variable side-chain (R) . transport (haemoglobin). movement (actin). store hereditary information. 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. polymers also called Oliver . storage (casein).catalytic proteins selectively speed up chemical reactions without being consumed. secondary.the difference in the energy between the reactants and products) and cannot make a thermodynamically unfavourable reaction favourable DNA or RNA. Acids Page 9 Bogdanovski ter Bonds polynucleotides Oliver . and proteins were mixed.shown by: the fusing of mouse and human cells. not one-side human.Cell Integrity The membrane prevents unwanted nutrients and toxins from entering/leaving. and hence maintains cell integrity.altering DNA to produce proteins that lose colour after laser beam exposure to one section of the membrane. carbohydrates and lipids (like cholesterol) between each side as many were formed inside the cell but cannot pass to the outside o the fluidity refers to the rapid movement of lipids and proteins laterally .both peripheral and integral that span the membrane and shoot out either side but with different domains on each side Carbohydrates (glycolipids and glycoproteins) . had sidedness or asymmetrical distribution of proteins. the other mouse microscopy with staining FRAP (fluorescence recovery after photobleaching) . lipid rafts are semi-solid molecules that keeps proteins together or anchors them to the cytoskeleton Proteins . There were two proposed models for the membrane: Davson-Danielli Model (1935) . with a cytoskeleton supporting it. peripheral proteins above and below.phospholipid bilayer with proteins above and below Fluid Mosaic Model (1972 by Singer and Nicholson) integral membrane proteins sat inside.the addition of the sugar groups allow cells to be recognised by other proteins or present different messages through a variety of combinations Sidedness is important for cell recognition and adhesion Page 10 Oliver Bogdanovski . and over time colour comes back as this area is filled with non-zapped proteins Membrane members: Lipids .of which 0-25% is cholesterol. but can be used to drive other processes o Example: indirect active transport of sucrose by having H+ move down its own concentration Page 11 Oliver Bogdanovski . creating a stored energy in the form of a concentration gradient which is used to drive other processes in the plants. Proton pumps: electrogenic pumps which ensure H+ is more concentrated in the extracellular fluid.down concentration gradient Facilitated Diffusion . Cellular Transport Passive Transport (no energy required): Diffusion . Plants prefer hypotonic environments. CO2.down concentration gradient with assistance of transporter protein (either for faster transfer or for molecules that could not otherwise cross o Channels/Conduits . and hence they are directional/irreversible (depends on protein. die in hypertonicity (plamolysis). H2O) hydrophobic molecules will dissolve in the hydrophobic core and diffuse across ionised. 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 .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) o Carriers/Transporters alternates between two shapes. fungi and bacteria requires ATP to function (hence active transport). multidirectional pass different proteins each way). polar and large molecules cannot cross without a protein transporter Animals prefer isotonic environments. Concentration gradients are maintained by active transport against the gradient (in addition to chemical reactions).with a protein AGAINST the concentration (uses energy from ATP). die in hypotonicity (lysis).Membrane Permeability (selective nature maintains cell integrity): small molecules can pass through (O2. 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 o tracked by attaching non-functioning fluorescent tags to ions that change shape and fluoresce when attached Large molecules (polysaccharides. created by differences in cation and anion distribution (cytoplasm more negative. K in. both AGAINST concentration gradient. except receptor proteins on membrane surface recognise and bind to specific molecules in clustered regions called “coated pits”. created by sodium-potassium pump (Na out.gradient and bring sucrose with it through the protein Membrane potential: potential difference across a membrane. -50 to 200mV) in animals. packaging in vesicle/vacuole. overall more out than in) favours passive transport of cations into the cell. the rest thrown out (specific) Receptor-Mediated Endocytosis .all outer solutes surrounded by membrane which combines to cell membrane (but doesn’t go straight in).wrapping pseudopodia around solutes. then transfer proteins choose which ones go through (no specificity) Phagocytosis (cellular eating) . and if all molecules are accepted then they are all taken in (specific) Page 12 Oliver Bogdanovski .like pinocytosis. some absorbed. proteins) cross the membrane in bulk through vesicles by: Pinocytosis (cellular drinking) . Light-Independent Reactions . and green light is reflected whilst red and blue are mostly absorbed (by chlorophyll a and b and carotenoids).Photosynthesis The physico-chemical process is used by plants. and clothing and building materials. electron and proton transfer reactions to make energy-carrying molecules.provide temporary storage of chemical energy). This is placed in a thick fluid called the stroma (the site of light-independent reactions). petrol (and natural gas. The chlorophyll are bound to proteins which act as antennae that absorb photons and transfer the excited electron to the reaction centre. connected by intergrana or stroma thylakoids. uses bacterial chlorophylls) to produce organic compounds with light as oxygen (only 0. Light-Dependent Reactions . If it is done by photons (sunlight) it is called photophosphorylation (phosphorylation simply means adding phosphate group).ATP and NADPH used to convert CO2 into glucose ATP (adenosine-5’-triphosphate) is produced by either redox reactions or photons.5% of the 21% is produced by NONbiological processes. The pigment chlorophyll is used to absorb light on the thylakoid membrane.light captured. Photosynthesis occurs in two stages: 1. The light energy is converted into electrical energy and packaged into chemical energy as ATP or NADPH (nicotinamide adenine dinucleotide phosphate. hence first). coal and ethanol). containing lots of small discs called thylakoid (thylakos = sac) which consist of a thylakoid membrane surrounding a thylakoid lumen. First a photon hits a chlorophyll molecule surrounding the Photosystem II (P680 as it absorbs a wavelength of 680mm penetrated faster than longer wavelengths. considered energy couriers . produces ATP and NADPH 2. photosynthesis occurs in chloroplasts (“green” + “form or entity”). the main sources being cyanobacteria. plankton and plants). Photosynthesis supplies all food. and exist as stacks called grana (Latin for “stacks of coins). In eukaryotes. which are double membrane-bound flat discs 2-10μm in diameter and 1μm thick. This process is performed by photosystems (protein complexes that contain chlorophyll) found in thylakoid membranes. algae (oxygenic) and photosynthetic bacteria (anoxygenic. and the chlorophyll molecules transmit energy from the excited elections in the antenna complex to a reaction centre. Each photosystem has Page 13 Oliver Bogdanovski . whilst consuming the toxic CO2. discovered first). where the electrons can then be transferred (by an electron transfer chain) to the primary electron acceptor (P. but hundreds of chlorophyll b and carotenoid molecules.A. until they reach Photosytem I (P700.E.one pair of chlorophyll a molecules. then on to ferredoxin (Fd) outside the thylakoid. 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. It requires: Page 14 Oliver Bogdanovski . The electrons are then transferred to plastocyanin (Pc).→ NADPH in the case of non-cyclic photophosphorylation. Light-independent reactions occur in the stroma (outside the thylakoids) in the Calvin cycle. where the electrons are recycled by being transferred back to the cytochrome b6f complex (via Fd and Pq) to resume the cycle.). This is another large proteinpigment complex that contains light-absorbing antenna molecules where photons are absorbed and electrons taken to reaction centres. 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). Chlorophyll b and carotenoids absorb photons and pass excited electrons to each other until it reaches the chlorophyll a. which transfer the electron to Ferredocin NADP Reductase (FNR) which catalyses NADP+ + H + 2e. In cyclic photophosphorylation ATP is produced (as this is sometimes needed to power other activities in the chloroplast). the first mobile carrier. Electrons lost from the P680 are replaced by the splitting of water (2H2O → 4H+ + O2 + 4e-). 5-carbon sugar chain.5-biphosphate carboxylase oxygen (RuBisCO) which catalyses carbon fixation to RuBP. 18ATP. which breaks into two phosphoglyceric acids (3-PG as they have 3 carbons each). CO 2 acceptor in first major step of carbon fixation CO2 .used in reduction phase to convert 3phosphoglycerate to glyceraldehyde-3-phosphate (three carbon precursor to flucose). or other molecules like sucrose and starch). This is phosphorylated (adds phosphate group) by ATP to form 1. where RuBisCO attaches CO2 to RuBP (6-carbons).the ultimate goal of the Calvin Cycle. then NADPH reduces this in the reduction phase into glyceraldehyde-3-phosphate (G3P) . In the regeneration phase G3P can be converted back to RuBP by ATP.5-biphosphate (RuBP) . 3-biphosphoglycerate.used during fixation ATP and NADPH . 12NADPH (1NADPH ≈ 3ATP in terms of energy). which can be combined to form organic molecules like fructose (which can then be rearranged into glucose. one glucose molecule requires 6CO2. An Introduction to Metabolism Page 15 Oliver Bogdanovski . probably most abundant protein on Earth Ribulose-1. This is composed of the simplest sugar known (D-aldotriose). and ATP is used in regeneration phase where it converts this back into RuBP The first stage is carbon fixation. In total. Ribulose-1. producing ΔG=31kJ/mol of energy and leaving adenosine diphosphate (ADP . A metabolic pathway involves a starting molecule/s which undergoes several reactions catalysed by enzymes to produce intermediates and eventually a desired product. chemicals are inorganic carbon = CO2 plants. animals.break down of glucose in presence of O 2).Metabolism . glucose ATP is the energy shuttle of a cell. Catabolic pathways RELEASE energy (produce ATP) by breaking down complex molecules INTO simpler ones (e.the totality of an organism’s chemical reactions (both catabolic and anabolic pathways) to manage material and energy sources. parasitic plants) e. The ATP cycle allows energy from catabolism (exergonic) to be transported to areas where energy is required and consumed (endergonic). compounds. and the lone inorganic phosphate becomes Pi.addition of Pi to ADP to produce ATP powered by redox reactions in the electron transport chain Substrate-level Phosphorylation . Anabolic pathways CONSUME energy (use ATP) to build complex molecule FROM simples ones. adenine (nitrogenous base) and three phosphate groups.g.g.note only two phosphate groups now). The bonds between the phosphate groups of the ATP tail can be broken down by hydrolysis (addition of water). ATP can be generated in two ways: Oxidative Phosphorylation . cellular respiration . All organisms require both an energy and carbon source from the environment: Phototrophs Chemotrophs energy = light energy = chemicals Photo-autotrophs Chemo-autotrophs Autotrophs (photosynthetic bacteria.an enzyme transfer a phosphate group from a DIFFERENT substrate (which has a phosphate group) to produce ATP Page 16 Oliver Bogdanovski . some protists like (some bacteria) algae) Heterotroph s Chemo-heterotrophs carbon = one chemicals are organic Photo-heterotrophs or more (many bacteria and (some bacteria) organic protists. composed of a ribose (sugar). or respiration can continue into the mitochondria and produce a net energy of 36ATP. In many protists and bacteria catabolic processes don’t need O2. For example. Generally all Page 17 Oliver Bogdanovski .different to the active site) are commonly involved in control of metabolic processes. Oxidation is the loss of electrons (or H atoms as often e.is attached to a proton). allosteric regulation could stimulate enzyme activity instead of inhibiting it. respiration: C 6H12O6 + 6O2 → 6CO2 + 6H2O. whilst activated by ATP. Fermentation also occurs in eukaryotic cells. whilst activated by ADP or AMP (mono-. Metabolism can be regulated by feedback inhibition.Catabolic processes in higher animals and other organisms require O2 (they are aerobic). whilst reduction is the gain. Alternatively.two nucleotides joined together at their phosphate groups) which becomes NADH with the enzyme dehydrogenase. For example fermentation: C6H12O6 → 2C2H5OH + 2CO2 OR C6H12O6 → C3H5O3. Enzymes with allosteric properties (activity that changes through binding an effector molecule at an allosteric site . in which either fermentation can occur and only 2ATPs are produce. and hence when enough product is formed the enzyme stops and no more is produced until there isn’t enough product. as glucose undergoes glycolysis to to form pyruvate. whilst anabolism is generally reducation. Catabolic pathways are often inhibited by ATP. where a product of the pathway inhibits an enzyme earlier in the pathway.(lactate ion) + 2H+. Catabolism is generally oxidation. Enzymes will often oscillate between an active and inactive state. however these two reactions are done simultaneously. When a metabolic fuel is oxidised. so a stabiliser can help it stay either active or inactive. electrons are collected by a coenzyme/cofactor like NAD+ (nicrotinamide adenine dinucleotide . one phosphate group). Anabolic pathways are inhibited by ADP or AMP. Extracting Energy from Food Cellular respiration . some enzymes reside in specific organelles.metabolic pathways are activated by earlier reactants and inhibited by later products. Cells are compartmenalised. 4NADH and 1FADH are produced. where reduced cofactors transfer their reducing power (H atoms and/or electrons) to oxygen through a series of redox reactions with a ΔG=217kJ/mol. O2 is the terminal electron acceptor after this protein complex.overall yielding 2ATP per glucose and producing the reduce cofactor NADH. The 3C from the pyruvate are broken down to produce 3 more CO 2 molecules. The pathway has to stages . converts NAD+ to NADH and adds Coenzyme A in the mitochondria in preparation for the TCA cycle. 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. Cellular respiration also involves a controlled energy release whilst the reaction 2H2 + O2 → 2H2O occurs. This is done by the respiration chain. like those for glycolysis (glucose breakdown→pyruvate) are located in the cytosol whilst those for the TCA cycle are in the mitochondria.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). II (proton comes from NADH). 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). and one ATP is formed. III (proton comes from I or II) and IV (from III). where glucose (6C) is oxidised into 2 pyruvate molecules (3C each). and cellular structures help bring order to metabolic pathways.an energy investment and energy payoff . In eukaryotes.group (from acetyl-CoA) is broken down. The TCA (or citric acid) cycle occurs inside the mitochondria and is where the acetyl. whilst the proton is transferred out of the mitochondria Page 18 Oliver Bogdanovski . ATP synthase includes integral membrane proteins (located in mitrochondrial and chloroplast membranes in eukaryotes.5ATP. (becomes part of 6) Page 19 Oliver Bogdanovski . 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).allows H atoms/electrons/protein components to move and interact asymmetric . FADH 2 ≈ 1.maintains proton gradient In total 30-32 ATP equivalents (NADH ≈ 2. Rotating the motor shaft in “head piece” causes conformational changes in the active sites that bind ADP and Pi. no ATP is synthesised as no gradient is produced. 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.and eventually back in by ATP synthase to produce an ATP from ADP and Pi.monodirectional proton pumps drive ATP synthesis through gradients impermeable to ions . or the plasma membrane in bacteria). which would only produce the initial 2NADH and 2ATP in anaerobic fermentation. 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).5ATP) are produced from one glucose. and provides energy for this synthesis. so it is the protons that matter). The mitochondrial membrane is important for ATP synthesis as it is: fluid . If the inner membrane is made permeable to protons. DNA is deoxyribonucleic acid. A & G are double-rings (purines). Amino acids from proteins are broken down to acetyl-CoA or intermediates within the glycolysis or TCA cycle. whilst DNA had a regular structure and only 4 building blocks so it was believed proteins would the means of inheritance. phosphofructokinae (PFK) catalyses the third step in glycolysis. Experimental data in the 1940s-early 50s suggested that DNA may be genetic material. so an A & G would produce a strand to wide (to be consistent with X-ray data). however it is inhibited by citrate (from the citric cycle) and ATP. each linked by a phosphate group after an H2O has been taken out). and the glucose is converted to lactate (lactic acid). which is what occurs when eating food). such as intense exercise in skeletal muscle cells and red blood cells. however like binary the simpler language still allowed for complexity. Proteins had greater complexity and 20 building blocks.smaller Page 20 Oliver Bogdanovski . whilst being stimulated by AMP. in 1953 Hershey and Chase grew two batches of bacteriophage T2 (virus that infects bacteria. carbohydrate catabolism involves fermentation. In cases of low O 2 supply. T & C are single-ringed (pyrimadines . From Gene to Function The genetic language must be accurately copied and passed on and readily accessed for the information contained.Respiration is controlled by allosteric enzymes. Combined with a phosphate group and base. proving it was a double helix (they knew it had the nucleotide bases adenine. whilst RNA is ribonucleic as it has an extra O. one with radioactive sulfur (present in two amino acids) which labelled proteins. In 1953 Watson and Crick published the structure of DNA using molecular models from X-ray diffraction patterns. thymine. whilst carbohydrates and fats are both broken down aerobically into acetyl-CoA (allows for recycling of some materials. cytosine and guanine which stood on sugars. and upon centrifuging to separate the bacteria from the viruses they found it was the DNA inserted into the bacteria. Ultimately it will form CO 2 and H2O (the products of respiration). For example. Mixing these with bacteria infected the bacteria with the genetic material of the virus. For example. the other with radioactive phosphorus which labelled DNA. it becomes a nucleotide. which causes cell death if oxygen supply is interrupted. producing a new growing strand and elongating it in the 5’→3’ direction (as the DNA polymerase can only exist at the 3’ end). and this is complexed with histones (proteins) to form nucleosomes. Incoming nucleotides have 3 phosphate groups.2×109 base pairs (2m long. Histones maintain structure of the chromosome and help regulate gene expression/activity. which codes for proteins essential for normal mitochondrial function. In addition. Each strand is considered antiparallel (running in opposite directions . not the tissue itself). The 5’ phosphate end (the top) finishes with a phosphate. DNA Replication First. whilst C & G have three.01mm wide). 0. Humans have 3. whilst the 3’ hydroxyl end finishes with the OH from the sugar. and 2Ps are released to provide energy for the reaction (as those are highenergy bonds).size compensated for by longer name). and being a helix (not spiral) the strands are not evenly distributed but close then far then close then far. A & T have two hydrogen bonds. DNA polymerase then catalyses the addition of new nucleotides in opposite directions on each strand (as the two strands are antiparallel). Mitochondria also have their own circular DNA within their matrix (the part inside the folds (cristae). coiled and condensed in preparation for cell division. and hence will move along the template strand from 3’→5’. DNA polymerase must have a 3’ OH group to add on to. at the origin of replication helicase unwinds the strands and forms a small bubble. It is folded. so they can only match like AT and CG. solenoids and eventually chromatin. which produces almost a spiral shape with the resulting ribbon (but as the two strands are separate it is not a spiral). DNA synthesis cannot initiate unless a primer (short piece of RNA that contains a 3’ OH) to continue building off. 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). and would produce a strand too close for DNA.the phosphate’s charges face opposite directions and the carbons sit on the opposite sides). 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 Page 21 Oliver Bogdanovski . It forms an alpha helix (follows right-hand grip rule). Hence one pyramidine had to be paired with one purine. then DNA polymerase III adds DNA nucleotides to the primer. Elongation . To crack this code they synthesised strands of just specific codons (e. which is enough for 20 amino acids plus stop (4 2=16 isn’t enough). it undergoes transcription into mRNA (which is complementary through base pairing . which swaps the OH group on the sugar for a triangle of nitrogens. To counter this. However in the lagging strand. nucleotide analogues can be used. First.the polymerase complementary copy downstream. Transcription has three stages: 1. The reasoning for triplets is that arranging our four base pairs gives 43=64 possibilities. 000 base pairs at each end) produced by telomerase (which also has RNA within the enzyme. Gene Expression: Transcription To express a gene. as the gene coding from the firefly luciferase protein (which makes it glow) was inserted into a mouse embryo. the mRNA does not stay bound to the Page 22 Oliver Bogdanovski . DNA strands unwind. and the mouse was able to produce a functional fluorescent protein. then DNA ligase forms a bond between fragment 2 and fragment 1. called Okazaki fragments. 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 that’s a 3’). RNA synthesis is initiated by the RNA polymerase 2. however much of this code is redundant as it doubles up (which provides some protection). telomeres are sequences (10. Initiation .hydrogen bonding. To treat disease. Replicating the ends of chromosomes is difficult as there are no 3’ OH ends to build off. and hence no OH group is present for DNA polymerase to continue constructing off and blocking DNA replication. it must do so in small fragments. to produce remaining base pair sequence) extending the ends of the sequences. DNA polymerase I replaces the RNA with DNA (by adding to the 3’ end of fragment 2).g. primase joins RNA nucleotides into a primer on the template. forming a second fragment until it reaches the original primer and detaches. Telomerase in inactivated in post-embryonic cells (and many cancers involve reactivating telomerase). thymine is replaced with uracil). AAAAAA…) then observed the protein in vitro (outside a cell). then a new primer is added slightly before and the polymerase attaches to this once finishing its fragment. as it moves in the opposite direction to the helicase (anti-parallel). unwinding the DNA and elongating the mRNA transcript. adding to the 3’ in the mRNA (moving away from 5’). The code was also found to be genetic. This is how AIDS (HIV) is treated. not just amino acids. forming Okazaki fragment 1. thymidine (the nucleotide with thymine) can be replaced with AZT.fork. and then each codon (triplet of base pairs) is translated into an amino acid. For example.RNA polymerase binds to the promoter region upstream of the gene. 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. Initiation in eukaryotes begins with transcription factors (proteins) that mediate the initiation of transcription by blocking the promoter sequence. Termination .upon reaching a termination point the RNA polymerase transcribes a terminator sequence which signals the end of the gene. The ribosome has two subunits (small and large). smooth muscle. the muscle protein αtropomyosin has 12 exons which can be used to produce striated muscle. often resulting in kidney and liver failure. and then the tRNA replaces the AMP). Gene Expression: Translation The ribosome is the protein synthesis factory. preventing transcription and inhibiting protein synthesis. Intervening sequences (introns) are also spliced out leaving just the expressed sequences (exons).DNA. Exons can be spliced in different ways to produce different proteins from the same gene sequence. and partway between the 3’ and 5’ is the anticodon (at the bend) that Hbonds to the codon in the mRNA.peptidyl-tRNA binding site (contains many amino acids. and the RNA polymerase and transcript are released This process is vital. so AMP). and three sites: A site . hence peptide chain) E site . tRNA (transfer) is single stranded (however intramolecular H-bonds make it fold to look sort of double-stranded). so the mRNA is immediately translated into a protein.exist site Page 23 Oliver Bogdanovski . The mRNA is formed as pre-mRNA in the nucleus. The amino acid attaches to the 3’ end of the tRNA. but sits parallel to it. 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. 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. For example. The toxin binds to RNA polymerase. and once the RNA polymerase has been through the DNA reforms a double helix 3. fibroblasts (for connective tissue) or brain cells. Prokaryotic cells have no nucleus.aminoacyl-tRNA binding site P site . shown by the toxin α-amanitin produced by the death cap mushroom. Each amino acid has a different tRNA. then the larger subunit binds to the initiator tRNA in the P site (uses energy from GTP→GDP. transported and degraded. In eukaryotes.a stop codon is recognised in the mRNA by a release factor (protein). and protein synthesis with 30S inhibitors like tetracycline and streptomycin. the most important stage of gene expression occurs during transcription (initiating). Page 24 Oliver Bogdanovski .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.The stages of translation are: 1. For example. as once the mRNA is formed it is immediately transcribed (which allows them to respond immediately to their environment).next tRNA binds to A site codon (requires 2GTP→2GDP) b. In prokaryotes control of gene expression occurs at the level of transcription (whether a gene is transcribed). Termination .peptide bond forms between amino acids (catalysed by enzymes in the ribosome itself. Elongation a. the adult grew an eye on its leg. transport and degradation of mRNA. Codon Recognition . By activating eye genes on a Drosophila larvae leg. or 50S inhibitors like erythromycin and chloramphenicol. the peptide chain is joining onto the new amino acid) c.the small subunit binds the mRNA. However as no neurons connected it to the brain it was not functional. proteins can be modified. not A) 2. however also occurs at processing. Initiation . Peptide Bond Formation . allowing the last tRNA and new protein to leave. Translocation . and then the cycle begins anew 3. At the protein level. 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). and the initiator tRNA (complement to AUG with methionine) binds to it. RNA polymerase can be blocked with rifampin. the plasma membrane grows inwards to produce two daughter cells and a cell wall is deposited. centrosomes separate and form mitotic spindle Prometaphase . The function of many genes is still unknown. which have perpendicular centrioles .each chromosome attaches to a spindle pole (equal pressure each way .growth o S . 99. coli is 20mins).cell components replicated (including centrosomes. 000 genes.The size of a genome varies amongst organisms.smaller component) Mitotic Phase . 000 base pairs (ranges from 1000 to 2.nuclear membrane breaks down. although most have fewer base pairs). centrosomes move to spindle poles where they anchor.growth and replication of cellular components. so this cycle must be regulated precisely. Most cells replicate between 10-30 hours (whilst E. water fleas and plants have more genes than a human. in which DNA replication commences at the origin of replication until each chromosome has been completely replicated. microtubules connect to centromeres (centre of duplicated DNA) by binding to kinetochores (also made of microtubule) Metaphase .4 million). In humans there are 1 billion cells/gram of tissue. further condensing.DNA synthesised (replicated/duplicated) o G2 . cell reproduction occurs by binary fission. Genes are not evenly distributed amongst chromosomes (chromosome 1 has 2968.if not properly attached one cell will have an Page 25 Oliver Bogdanovski . and each origin becomes separately attached to the plasma membrane. Organism complexity doesn’t necessarily determine how many genes you have (as worms. Humans have 20.9% of the genome is the same in all people. with each gene having an average of 27.nucleus divides and chromosomes are distributed to daughter cells (mitsosis) and the cytoplasm divides into two daughter cells (cytokinesis) o Mitosis Prophase chromosomes condense. Cell Division and Reproduction In prokaryotes. gathers materials and ensures enough for replication o G1 . all derived from a fertilised egg. Cell replication has two major phases (basically 2n→4n (two of each individual single chromosome)→2n): Interphase . Y has 231). Once replication is complete. a more base pairs generally but doesn’t always mean more genes. homologous chromosomes (as dyads) come together and synapse (closely apply themselves to each other).protease chews through protein holding sister chromatids together and they are pulled apart causing cell elongation Telophase . The process of producing a haploid cell is meiosis. removal of damaged cells. Human somatic cells have 46 chromosomes (2n . cell plate made of vesicles in plants which becomes part of cell wall) separates the two cells To ensure DNA is being replicated correctly. nucleotides. as this isn’t meiosis) Anaphase .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. the other missing one.sufficient nutrients.checks all DNA for mitosis has been replicated properly M (metaphase) Checkpoint . shedding of leaves provides protection against cold and recycles nutrients.haploid) so when they fuse during fertilisation they make 2n. however instead of one dyad (duplicating each chromosome) a tetrad (two dyads) is formed Meiosis I o Prophase I . and within the tetrad a ladderlike protein structure (synaptonemal complex) aligns the pair and they cross over to Page 26 Oliver Bogdanovski . the second of which is near identical to mitosis (2n→4n (a tetrad of each chromosome pair)→2n→2n): Interphase . disintegration of tadpole’s tail for recycling). starts choosing to get ready for mitosis G2 Checkpoint . the chromosomes shorten and thicken. which has two stages.as with mitosis.cleavage furrow (contracting ring of microfilaments in animals. there are multiple checkpoints: G1 Checkpoint .extra copy.nuclear membrane reforms and chromosomes decondense o Cytokinesis . NOT trisomy.diploid) whilst gametes (sperm and ova) have 23 (n . and multiple Page 27 Oliver Bogdanovski . but with crossing over) Meiosis II o Interkinesis (Interphase II) .chromosome homologues are at opposite poles. increases genetic diversity).as with mitosis (includes prometaphase) o Metaphase II . the centrioles move to opposite poles of the nucleus and the nuclear membrane breaks down o Metaphase I .chromosomes have untwined (are clearly two dyads) and line up in two rows. rather than a duplication of each single chromosome and splitting doesn’t change genetic diversity as already the same) o Anaphase II .as with mitosis o Telophase II and Cytokinesis . and begin to reform a nuclear membrane o Cytokinesis (not exactly part of meiosis) produces two DIPLOID cells (basically back to square one.homologous chromosomes are pulled to opposite sides by kinetochore microtubulues o Telophase I .no DNA replication (however still centrosome replication) o Prophase II . form chiasma (swaps genes. human genome project completed (based on the DNA of several people including James Watson and Venter).as with mitosis PCR and Individual Variation In 2003.as with mitosis (except each chromosome is made of one of each homologous pair so splitting changes genetic diversity. with homologous pairs next to each other o Anaphase I . it is easy to identify a person by their DNA.short pieces of DNA to add on to (one for upstream. A single gene is one-millionth of the DNA. Each cycle (production of new copies) resulting in a doubling of molecules (2. allowing extending to be done at a higher temperature than annealing (now 72oC . 4. which is stable at 98 oC.human genomes have now been fully sequenced. 16…220…). Simple sequence repeats (SSR) are short base pair sequences that repeat many times. targeting only certain genes. and each being unique. but optimal at 70oC. only those replicated will be potent enough to see after staining with fluorescent that glows in UV when bound to DNA).to add to the growing chain (dNTPs=deoxyribunucleotide triphosphate) heat . PCR is incredibly sensitive and specific. and a virus may inject its own DNA (although in only a few out of millions of cells). 000 SSRs. 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). smaller molecules can move through gel mesh more easily and hence move further. As DNA polymerase is denatured at 90 oC. and this is completed using PCR (polymerase chain reactions). the DNA polymerase from the thermophile Thermus aquaticus (Taq) is used. different one for downstream) free nucleotides .separates DNA strands (although can denature enzyme) Note that arrows without lines within them only cover the exactly length of the gene. so the challenge is to detect the gene or viral DNA in the presence of billions of bases. PCR is used to amplify each specific Page 28 Oliver Bogdanovski .pattern to synthesise from primers . With around 120. and the electrophoresis can be applied (as DNA is slightly negative moves to positive electrode.diagram shows for normal DNA polymerase). 8. PCR requires: DNA polymerase single-stranded DNA template . with a different number for different people. medical X-rays. Mutations can occur as: point mutations (changes single base) insertions deletions duplications of sequences chromosomal rearrangements (like fusion. which were better at camouflage in either lichen-covered trees or soot-covered industrial areas during the Industrial Revolution of the mid-19 th C when pollution was being produced. as you can prove that the SSRs don’t line up. Mutation A mutation is a change in the nucleotide sequence of an organism’s DNA. comparing to kin). Mitchondria also have their own DNA which comes entirely from the mother. however DNA repair enzymes reduce this to 1 in 1010) mutagens o chemicals (nicotine. the British Peppered Moth had a mutation resulting in some light. T-T)/hour/cell are caused at 12pm in Sydney’s 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 Page 29 Oliver Bogdanovski . paternity testing (particularly with celebrity heirs). UV . Hair cannot be used (as it is just protein. They can also occur in virus DNA or RNA. 000 pyrimidine dimers (e. deduce crime suspects (13 used by FBI).g.20. fission. oxidising agents. nucleotide analogues) which damage DNA o radiation (natural radiation like uranium. no DNA). we can identify people after disasters (as in 9/11. leading to incorrect base-pairing. which was used in cases like identifying if Anastasia was still alive by comparing to another greatgrandchild of Queen Victoria.SSR being analysed using primers designed for those SSRs and then these bands are compared (only identical twins should have identical patterns). Using this. However. free radicals. inclusion cannot be proved as this may be by happenstance. Mutations lead to diversity which is critical to the survival of life. ultimately creating genetic diversity. some dark. inversion and translocation) Mutations can be caused by: errors in DNA replication (DNA polymerase makes 1 error in 105 bases. They will only be inherited in offspring if they occur in gametes. asbestos. however hair follicles can be. For example. nuclear waste/bombs. this evidence can only be used for EXCLUSION. or prove historical truths (Anastasia and the Romanovs). If they do line up. changes amino acid to stop Frameshift . avoid foods with phenylalanine in them (people are screened at birth to check for this). For example. thalassemia (reduced production of haemoglobin. Phenylketonuria (PKU) results in a defective phenylalanine hydroxylase.and hence interfere with replication) can be repaired to ensure transcription is not problematic and gene expression occurs correctly. which results in sunburning instead of tanning and increasing susceptibility to skin cancer. and DNA ligase seals this to the following strand. Single base changes are the most common variants (~85%) un the human genome. cystic fibrosis (Cl+ imbalance. 1 in 400). Repair is done using a nuclease enzyme that cuts the damaged DNA at two point around the area of damage. Xeroderma pigmentosum (CP) is an inherited defect in a DNA damage repair enzyme. There are over 10. Most DNA changes are outside of genes. This could result in changing the tertiary structure of the protein depending on the side chain properties of the amino acid (charge.2 million differences).changes amino acid Nonsense . making a person unable to convert phenylalanine into tyrosine. DNA polymerase then fills in the remaining nucleotides (from the OH of the previous one). and then this is removed. which can result in silencing tumour suppression genes and lead to skin cancer. shape) and how different this is to what it was before. The most common genetic disorders are haemochromatosis (too much iron absorption. most of which are rare but have multiple variants. To avoid this. however there are many regulatory genes outside coding regions and hence they can still have large effects on gene expression. Cancer is also the result of genetic mutations. 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.results in different codon that results in same amino acid Missense . The classic Irish/Scottish fair skin and hair (blonde or red) results from a mutation in the Mcr1 gene. if it is a multiple of three. which can result in death by 30-40 years of age.insertion/deletion of amino acids not a multiple of three will change all amino acids downstream (may introduce missense or nonsense). resulting in individuals that are hypersensitive to sunlight (can’t correct thymine dimers). 000 gene defects in humans. 1 in 200). it is simply the gain or loss of amino acids. Those that do change may lose some or all functionality. otherwise there may be no change. 1 in 25 in some areas) and sickle cell anaemia Page 30 Oliver Bogdanovski . These changes can have three outcomes within exons: No effect . which often doesn’t have any effect on the final result. from either overstimulation or a lack of inhibition of the cell cycle due to faulty proteins. and two unrelated individuals have ~1 in 1000 base pairs that are difference (for a total of 3. Locus (loci) . offspring are identical to parks. mutations provide genetic variation for natural selection through evolutionary fitness (the ability of an organism to survive to reproduction). and as such can develop resistance to drugs rapidly. In eukaryotes. mostly in prokaryotes (binary fission). In sexual reproduction.g. In prokaryotes. Variation in a gene may also not have an effect. Mendel made inferences on gene activity before we knew what genes were. and often plasmids (circular DNA molecules that self-replicated and carry genes). Mendel’s Laws of Heredity Genetics .(haemoglobin variant with one amino acid different (GAA→GUA.regions of high malaria are also regions of high sickle-cell anaemia due to natural selection). offspring are a combination of parents. Glu→Val). Page 31 Oliver Bogdanovski . which halve through meiosis (which introduces variation by independent assortment of chromosomes and crossing over/recombination) and combine into a zygote in fertilisation. in bacteria.the position on a chromosome a gene/sequence is located Allele . His theory of dominance was superior to blended inheritance as that would only lead to identical populations. allows haemoglobin to form fibres and changes shape. Whether good or bad. leu+ can synthesis leucine.genotype with two different alleles at a locus Dominant allele .form/variant of a gene at a given locus Genotype . whilst some RNA viruses cannot do so and make DNA copies of their genome using an error-prone polymerase which generates mutants easily. for example single nucleotide polymorphism (SNP) is a region of DNA in the introns. A genome is the complete genetic composition of an organism.to show if a particular protein is produced by a gene (e. cell or just organelle.cannot and required leucine in the medium to grow). genomes are comprised of linear chromosomes. DNA viruses can correct mistakes that occur during their own replication. In asexual reproduction.genotype with two like alleles at a locus Heterozygote .the allele that determines the phenotype (as opposed to the recessive allele) In 1865. Humans have 22 pairs of autosomes and one pair of sex chromosomes. HIV is one such virus. but leu.study of heredity (inheritance).the alleles an individual has Phenotype . usually with multiple chromosomes per genome. aphids (plant lice) and hydra (simple freshwater animals). their genome consists of circular chromosomes. how biological information (DNA base sequence) is passed onto offspring. In diploids we also have: Homozygote . blocks blood flow but also protects against malaria .the physical traits of an organism We use superscripts of + and . but also some eukaryotes like some plants. the pairs of alleles assort independently into gametes (explained 9:3:3:1 in dihybrid crosses) Mechanisms of Inheritance Huntington’s disease (neural degeneration) is an example of an autosomal dominant (50% of inheritance if one parent has it. Occasionally homologous chromosomes don’t separate during meiosis (non-disjunction). Klinefelter syndrome (XXY → generally fairly normal. For example. but never anyone with XA). and explained in terms of factors. and Turner syndrome (monosomy X → severe in humans. the second X being turned off as if they were female producing a male). Mitochondria are maternally inherited organelles carrying their own genes. so if two genes are near each other on the same chromosome. We can reverse this Page 32 Oliver Bogdanovski .15:1 (approximately 3:1). 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).In his experiments he measured a ratio of 3. and individuals inherit one copy from each parent (explains 3:1 ratio) Mendel’s Second Law: for two genes on separate chromosomes. which segregate in the formation of gametes. Mendel’s second law of independent assortment was formulated without the knowledge that genes occur on chromosomes. affects both sons and daughters). the lower the chance of recombination. A test/back cross can be used to determine which allele is dominant and if heterozygous or homozygous organisms. Mendel’s First Law: diploid individuals carry two copies (alleles) of a gene. This ratio occurs because the loci/genes are linked on the same chromosome and the closer the loci. Down syndrome (trisomy-21). particularly by crossing over or artificial joining of DNA segments. Recombination is just the rearrangement of genetic material. resulting in n-1 or n+1 haploids and aneuploidy in the diploids (2n-1 or 2n+1 chromosomes). whilst an X-linked recessive would be haemophilia (which can only occur in XaXa (rare) or XaY. not so much in mice). and an example of a disease is KearnsSayre syndrome. which causes a short stature and retinal degeneration. whilst 25% recombination would be 12. Incomplete dominance is when two alleles both contribute to the phenotype. those with C become brown.(the fewer recombinants in a testcross. The gene pool is the collection of genes amongst an entire population.5% of each type of recombinant (as there are two when looking at two genes). skin colour and learning ability. etc.) and are difficult to map (like diabetes. epistasis. Polygenic traits are those influence by many genes. alcoholism). no mutation and no migration. The Hardy-Weinberg Law/Principle states that assuming you have an infinite population size. like hydrangeas that change colour depending on the acidity of the soil (this is the reason monozygotic twins are not entirely identical physically). So a 0% chance of recombination means recombinants are impossible. the closer the genes). Genes in Populations Genetic variation comes from mutations. or if homozygous for the recessive sickle-cell allele then during low oxygen content red blood cells crystallise and become sickleshaped. They are called quantitative traits as they are measured on a scale rather than being binary (yes or no). Environment can also influence phenotype. heart disease. one gene affects more than one trait (for example a gene may encode a protein that forms part of more than one protein complex. enzyme pathways that require one to happen before the other which can affect mouse colour (cc stay white. This principle is used to map genes that cause disease in many species. Epistasis is the interaction of loci or dependence of one gene upon another (for example. all from the one gene). and if bb stay brown but if they have a B then go black). 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). each having a smaller effect on the phenotype and producing a continuous scale. with the percentage of offspring being recombinants being the relative distance (in the above example 17%). causing the phenotypes anaemia. which may exist at different allele frequencies (a proportion that can be studied over space (mapping sickle-cell anaemia) and time). Some traits are called complex/multifactorial as they depend on many factors (like environment. brain damage and spleen damage. sexual reproduction (independent assortment and random pairing) and recombination/crossing over. like height. However this is still not blended inheritance as they don’t all come out the same. and 50% would be 25% (at which point it is as likely as independence). polygenesis. and often occurs in multiple alleles like blood groups (where IA and IB are codominant over io). alleles have an equal Page 33 Oliver Bogdanovski . weight. like codominance in Snapdragon (CR + CW = pink). Variation at a locus means there are at least two alleles. cannot become brown. no natural selection and random mating. In pleiotropy. Adaptive evolution is also limited by historical constraints. In small populations. however its primary advantage is that it makes it more attractive to mates. natural selection ahs lead to increased levels of sickle-cell anaemia in some African countries as it is resistant to malaria. and this sexual selection has not necessarily lead to a better fitness. Similarly. chance events lead to fluctuations in allele frequencies. 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). such as Clinodactyly on the island of Tristan da Cunha. Page 34 Oliver Bogdanovski . some genotypes will have a higher probability of surviving due to their higher fitness. In natural selection. The founder effect is when there is a high frequency of an allele in a small population that continues that species elsewhere (essentially bottlenecking). Microbes also evolve to escape the immune system (those that aren’t recognise survive) or antibiotics (by developing resistance).chance of survival. A bottlenecking event (drastically reduces size of surviving population limits the gene pool. where a small number of British troops who happened to have curved little fingers led to a high frequency in the population. 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). and hence will maintain their frequency throughout generations. however also has negative effects upon health. with the smaller the population the larger deviation from the law. like the epiglottis which chooses lungs or stomach but can result in choking. and hence makes them susceptible to further environmental changes). However there is not always biological perfection. called adaptation. or standing up in humans which can cause back problems. unless an assumption is not met. and can lead to fixation in the population for fitter alleles.