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Main Ideas for Biology 1002B February Midterm Test.docx

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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)  Use both flagella to swim toward light and harvest it (not through photosynthesis directly)  Swim away from light  Wrong intensity (UV dimers), colour/wavelength  Build up free radicals and reactive oxygen species (ROS) o ↑natural byproduct of metabolism of oxygen damages cell structures 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 use glucose from PS 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 2diffuse 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 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  Faster mRNA or protein decay Visible Light  400-700nm 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  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 side) absorbent neighbour pigment  trans retinal (opposite); not redox  Then excite reaction centre by oxidizing and  Retinal leaves opsin; broken π bond removes clef producing an electron for ETC  Transduction attach trans retinal and activate  Chlorophyll stays in chloroplast phosphodiester to cleave 3’ phosphate to 5’ GMP  Antenna harvest energy in one area for PS o Retinal harvest light as info (image)  Cleaving = cyclic GMP regulated Na channel shuts off = ↑ voltage difference (↑Na out, ‘-’ inside (anions, amino acids) = hyperpolarize = electric 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) o Structure difference of hyperthermophiles (hot) vs psychrophiles (cold) due to natural selection  Hyperthermophiles have stronger intramolecular forces so harder to break bonds  Regulate membrane fluidity and transcript of desaturase  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  membrane  blot probed  No staining of gel electrophoresis of RNA  Incubate antibody on membrane to bind protein  Eukaryotic bands closer to top (more RNA)  Stain gel (not Pigment protein complex: protein o Most of RNA is ribosomal bound noncovalently to pigment)  Nylon membrane  radioactive gene-specific  Regulate transcription (gene expression kinetics) probe exposed to film  Constitutive: actin gene no effect o Hybridization: single stranded DNA  Induced: HSP1 accumulate expression complementary stick on blot  E. Coli not picked up = not similar  Repressed: Expression fall after optimal  Regulate translation, protease protein breakdown  Balance rate of transcription rate of mRNA decay Entropy Enthalpy Gibbs Free Energy  +∆nd= ↑ 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 = ↓ disorder disordered products o Entropy of a system o Potential energy of o Solid  liquid  gas can ↓ as long as products < reactants entropy driven universal entropy ↑  ∆G = ∆H - T∆S  -∆S = ↓ disorder 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: if you throw it, won’t explode e.g. propane  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 o Can’t increase rate of nonspontaneous  Lower EA- reach transition easier reaction  Precise orientation of fit o Enzymes do not provide energy, ATP  Charge interaction to bind needed  Catalytic site mimics transition o Reaction proceed at lower temperature  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
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