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REVISED: Main Ideas for Biology 1002B February Midterm Test..
REVISED: Main Ideas for Biology 1002B February Midterm Test.docx

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School
Western University
Department
Biology
Course
Biology 1002B
Professor
Denis Maxwell
Semester
Winter

Description
Main Ideas for Biology 1002B February Midterm Test Chalmydomonas  Unicellular autotroph with mitochondria and chloroplast  Chloroplast o Pyernoid is the site of carbon fixation o Orange (carotenoid) eyespot is phototactic (detect light through phototransduction)  Use both flagella to swim toward light and harvest it (not through photosynthesis directly)  Swim away from light  Build up free radicals and reactive oxygen species (ROS)  Natural by product from oxidative phosphorylation that removes e from anything o Outer and inner membrane, stroma and golgi packs and sorts proteins o Thylakoid membrane – photochemistry on thylakoid lumen (ETC)  Derived from common plant and animal ancestor o Genes shared with animals such as flagellum, centriole are lost in many angiosperms o Chlamy and angiosperm genes derived from ancestral green plant genes  Useful model system o Looking at role of light as an energy source and source of information about the environment o Grows in dark on organic carbon source acetate into acetyl coA  No sunlight = no sugar produced and no glucose transporter to extract glucose o Create mutants to see what controls eyespot, phototaxis, flagella, etc. o Evolution of multicellularity  Minimizes photorespiration - o Bicarbonate HCO 3through ATP driven pump into cell)  CO (2iffuse to chloroplast) Photoreceptor Cell  More black and white rods than colour cones  Rods are made of discs with photoreceptor and rhodopsin in bilayer  Rhodopsin = pigment (retinal cofactor) + protein (opsin apoprotein) complex o Post-translational modification required o Beta-carotene + oxygen  2 retinal (vitamin A) ; retinal synthesis not coded by gene  But genes control transcript of enzymes for this pathway  Defects that lower levels of functional photoreceptors (rhodopsin) o Mutated opsin repress protein abundance o No mutation in opsin  Wrong conformation  Not enough retinal or its mutated  Gene turned off (no transcription)  Excess light damage o Mutate into uncoupler  no electrochem  Faster mRNA or protein decay gradient = not hyperpolarized = no signal Visible Light: 400–700 nm suitable range – not too strong to ionize or kill pigments or too little energy for excited state Pigments and Chlorophyll  Conjugated system of alternating double and single bonds o Pi orbital electron will absorb light and give up electron and not bond (retinal exception)  One photon excites one electron  Chromophore: will absorb or reflect colours depending if the energy of photon match electron excited state  Chlorophyll has 2 excited states (blue and red) that it absorbs  Heat loss is so fast that shorter wavelength colours will have same excited state as longer wavelength colours o Back to ground state as heat o Lose as fluorescence as deep red (less energy since some loss as heat) o Energy to do work like photochemistry o Transfer energy to neighbour pigment with minimal energy loss as fluorescence  Isolated chlorophyll has no pathway for energy so will release it as fluorescence Photosynthesis of Chlorophyll Phototransduction (electrical signal) of Retinal  Only energy transfers from most to less  Photoisomerization: 11 cis retinal (same)  absorbent neighbour pigment trans retinal (opp) on disc membrane; not redox o Donor has slightly higher excited state than receiver  Broken π bond removes clef  retinal leave opsin  Transducin attach opsin and phosphodiesterase  Then excite reaction centre by oxidizing and activated to cleave 3’ phosphate of cCMP to 5’ GMP producing an electron for ETC  Chlorophyll stays in chloroplast  Cleaving = cyclic GMP regulated Na channel shuts  Antenna harvest energy in one area for PS off = ↑ voltage difference (↑Na out, ‘-’ inside (anions, amino acids) = hyperpolarize = electric o Retinal harvest light as info (image) current signal inhibit glutamate release Protein Structure  Primary – unique function determining polypeptide sequence of covalently peptide bonded sequence o Dehydration synthesis adding to carboxyl end only; carboxyl + amino group  peptide bond o Nonpolar, uncharged, negatively or positively polar charged (acidic/basic) amino acids  Secondary o Alpha helix cylinder/barrel shape support by top and bottom H bonds o Side by side beta pleated sheet supported by H bonds of N-H and O-C  Tertiary spontaneous 3D folding and interaction of R group o Ionic bond (positive charged amino acid with negatively charged oxygen) o Hydrogen bonding o Hydrophobic interactions where nonpolar cluster away from polar aqueous solution o Disulphide bridges (S-S) (covalent bond) o Structure difference of hyperthermophiles (hot) vs psychrophiles (cold) due to natural selection  Hyperthermophiles have more stronger intramolecular bonds that are harder to break  Regulate membrane fluidity and transcript of desaturase  Too fluid or not flexible enough to shape to fit substrate  Quaternary – many tertiary structures  Protein domain: large subdivision of protein where each domain is structurally, functionally distinct, moveable  Angensen’s Dogma: if you remove denature factor (urea), protein will refold (+ 90% of native) Cofactors/Prosthetic Groups  Organic or inorganic nonprotein bound to protein that is required for some protein to function e.g. vitamins Protein Abundance on Western Blot mRNA Transcript Abundance on Northern Blot  SDSpage gel  incubate antibody on membrane  no staining on gel electrophoresis to bind protein  Eukaryotic bands closer to top (more mRNA)  Stain gel since not a pigment protein complex o Most of RNA is ribosomal (protein noncovalent bond to pigment)  Nylon membrane  radioactive probe (single  Regulate transcription (gene expression kinetics) stranded DNA complementary stick to blot)  Constitutive: actin (housekeeping) no effect exposed to film  Induced: HSP1 accumulate expression  E. Coli not picked up = not similar  Repressed: Expression fall after optimal  Balance rate of transcription rate of mRNA decay  Regulate translation, protease protein breakdown Entropy Enthalpy Gibbs Free Energy  +∆S = ↑ disorder  +∆H = endothermic  +∆G = endergonic, nonspont.  2 law of thermodynamics o potential energy of  -∆G = exergonic, spontaneous o ↑ disorder/higher products > reactants o Exothermic entropy (favoured)  -∆H = exothermic disordered products  Entropy of a system can ↓ as o Potential energy of o Solid  liquid  gas long as universal entropy ↑ products < reactants entropy driven  -∆S = ↓ disorder  ∆G = ∆H - T∆S Enzymes  Catalyst: substance that increases reaction rate without changing itself  Activation energy: increase amount of energy to break bonds at transition state increases reaction rate  Kinetic stability: how fast the actual rate is; most stable with high E e.g. propane A  Thermodynamic stability: -∆G is unstable; does not tell you how fast a reaction is occuring  Active site: where catalysis of substrate induce fit (conformation change to bind)  Catalytic cycle: enzyme recycles back to first reaction  Role in endergonic  Role in exergonic o Increase reaction rate at lower temp o Can’t increase rate of nonspontaneous  Lower E A reach transition easier reaction  Precise orientation of fit o Enzymes do not provide energy, ATP  Charge interaction to bind needed  Catalytic site mimics transition  Conformation strain  Function and growth rate o Optimum temperature = highest collision interaction rate of enzyme and substrate o Enzyme denatures at higher temperature o pH affect ionic interaction by getting rid of protons o Chemicals (urea, detergents) shield groups and prevent interactions to bond Membrane Permeability  Small nonpolar or uncharged easiest to get through e.g. oxygen, carbon dioxide, nitrogen, water  Transmembrane and hydrophobic core of bilayer o 7 alpha helixes o Hydrogen bonding minimizes charges to enable protein to interact with fatty acids o Primary tail to tail sequence (polar charged + inner 17 – 20 nonpolar amino acids) Membrane Fluidity  Adjust saturated ↔ unsaturated fatty acids with desaturase removing 2 H atoms and replace with double bond o Unsaturated fatty acids have double bonds and bends/kinks that make it membrane more fluid  Low Temperature  High Temperature o ↑ unsaturated = ↓ temp turn to semi- o Membrane leakage freely diffuse solid gel o Disruption of ion balance o Inhibit ETC (PQ cannot move) o Inhibit ETC since PQ fall apart  Sterols as membrane buffers o High temperatures help reduce fluidity o Low temperatures help slow transition to gel by occupying space between bilayer Electrochemical Gradient  Attraction of opposite charges of molecule and electrochemical charge stronger than facilitated diffusion Homozygous Recessive Cystic Fibrosis Normal  Brittle and dry mucus lining, gas diffusion prob  CFTR ABC transport synthesized on ER have  CTFR ∆F508 deletion of phenylalanine is still transmembrane and ATP binding domains functiona
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