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Biology 1002 Midterm 1 notes!!!.pdf

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Biology 1002B
Tom Haffie

BIO 1002 Midterm 1 Chlammy Structure Pyrenoid: is in the chloroplast. It is the site where carbon fixation takes place and also where starch is formed Quantitative Relationship Between When an electron absorbs a photon, the energy it gains can cause it to change orbitals. The result is ionization. The electron can then emit a photon in the process of "falling back" into its original orbit. Note that electrons won't absorb a photon that cannot give them enough energy to reach a higher orbital. There are no "half measures" in this aspect of quantum mechanics as electrons cannot be shifted "half way" to the next higher orbital. So, a photon gives the electron energy to jump from its stable orbit. This has an important connection: • this relationship is vital to photosystem 1 and 2 as they split water to gain electrons for electron transport Similarities between phototransduction and photosynthesis • both need to absorb a photon to start their photochemical processes Differences • Photosynthesis needs light to split H2O to gain electrons that power the electron transport chain which is eventually given to NADPH. This energy is then used in carbon fixation • Phototransduction uses the light to react with retinal which starts the isomerisation process How does an excited antenna pigments organized to provide energy to the reaction center? The vast majority of the pigments in a photosynthetic organism are not chemically active, but function primarily as an antenna (1,4). The photosynthetic antenna system is organized to collect and deliver excited state energy by means of excitation transfer to the reaction center complexes where photochemistry takes place. The antenna system increases the effective cross section of photon absorption by increasing the number of pigments associated with each photochemical complex. The intensity of sunlight is sufficiently dilute so that any given chlorophyll molecule only absorbs at most a few photons per second. By incorporating many pigments into a single unit, the biosynthetically expensive reaction center and electron transport chain can be used to maximum efficiency. BIO 1002 Midterm 1 ABC Transporter The shuttling of substrates across a cellular membrane frequently requires a specialized ATP-binding cassette (ABC) transporter, which couples the energy of ATP binding and hydrolysis to substrate transport. Due to its importance in immunity, the ABC transporter associated with antigen processing (TAP) has been studied extensively and is an excellent model for other ABC transporters. The TAP protein pumps cytosolic peptides into the endoplasmic reticulum for loading onto class I major histocompatibility complex (MHC) for subsequent immune surveillance. Here, we outline a potential mechanism for the TAP protein with supporting evidence from bacterial transporter structures. The similarities and differences between TAP and other transporters support the notion that ABC transporters in general have adapted around a universal transport mechanism Lecture 2 • the energy of the light is inversely proportionate to its wavelength visible spectrum 400-700 • • pigments absorb light • conjugated system is the alternation between double and single bond •indicates non bonding electrons (pi orbital electrons) its these electrons that react with light •retinal a pigment does involve bonding electrons • pigment arent free they are bound to proteins • isolate protein carefully you get the pigment which shows colours • called pigment protein complexs pigment is bond non covalently to the protein • BIO 1002 Midterm 1 mitochondrial proteins dont have pigments • • pigments mean you dont have to stain during gel electrophersis but you must be careful • PIGMENTS ARENT FREE Light Absorbtion • pigment absorbs light which allows electron to jump from ground state to higher excited state • also lose some energy as heat higher state decays (loses heat) and drops to lower excited state • Lose excited state: 1. heat (not too much or cell blows up) 2. Flourescence (light, slightly lower energy and longer wavelength) 3. (trapping energy to do work) PHOTOCHEMISTRY 4. transfer energy to neighbouring pigment Why is chlorophyll green? • there is no green excited state or chlorophyll would be able to absorb it but there is no green excited state and therefore it is reflected • one photon can excite one electron • 1:1 and energies must match • for the energy to absorb, the energy in the photon must match the amount of energy that it takes for a electron to jump from the ground state to the excited state this is needed for light absorption • Phototransduction vs Photosynthesis • Photochemistry happens in the photoreceptor (molecule within the membrane) • isomerization of retinal • photosystem is more about light capture • purple antenna (protein) and chlorophylls bounds to it, which surrounds reaction center • in atenna there is no photochemistry, its just energy transfer, excites electron and passes excited state from neighbouring pigment to other neighbouring pigments until the energy reacts the reaction center where PHOTOCHEMISTRY TAKES PLACE • which is the oxidation of chlorophyll (Takes electron off) • which drives electron transport in the thylakoid membrane of the chloroplast Photochemistry: changing molecules BIO 1002 Midterm 1 • rhodopsin=retinal (red pigment) +opsin (protein surrounding retinal) • manypigments use non bonding electrons not in this case • trans: H on opposite sides • Cis: on same side • different molecules • double bond prevents rotation • this transition is exactly what happens when a molecule of retinal absorbs a photon of light.... Cis to trans @ carbon 11 • photon of light breaks the double bond excites electron and the a new bond is formed in the trans configuration • this is the photochemical event in the eye • photoisomerization • can happen about once every 1000 years without light Retinal Isomerization linked to opsin change • transducin interacts with rhodopsin • transducin must interact(bind in cleft) with opsin to create reaction process • in the dark there is no cleft to bind too • retinal shifts to trans that form of the pigment detaches from the opsin • in a photosystem the chlorophylls always stay put • photoreceptor the retinal shifts to trans and is lost and then opsin cannot absorb light anymore • opsin is recycled and new retinal is attached Cis to trans changes the shape of the protein opsin opening up a cleft so the • transducin can interact and once it interacts it activates phosphodiesterase What’s so special about visible light? The visible light is so dominant in our atmosphere and at the surface of the earth. Its also energetically perfect. UV and gamma would just destroy chloroplasts. Not enough energy to excite electron in microwaves. Lecture 3 • photochemistry takes place in the reaction center and the photoreceptor Why is there no anetenna around the photoreceptor like in the photosystem? if your a photosystem (chlammy) you want to harvest as much light as possible in a photoreceptor rods and cones are trying to use the photons for information, where they come from gives information (image) BIO 1002 Midterm 1 Protein structure and Function • biological function is based on proteins • biochem: isolate protein • genetics: genes molecular biology is a combo of both • Protein Abundance • What controls protein abundance? • is to control transcription ( the conversion of DNA to RNA) • control translation (MRNA to protein) • What controls abundance? • depends on transcription • MRNA decay or MRNA turnover (some stay a while or not), this is controlled!!!! How do we measure transcript abundance of one species of MRNA example Hexocinase? isolate RNA from cell or tissue samples • • same amount of RNA in each lane of gel phoresis so you can quantify it • Don’t see any MRNA on the gel, total percent of RNA is rRNA (97%)which are the bands you see • however, MRNA is very limited (3%) • RNA is transfered to a membrane (can fold and move) and probe it for the specific MRNA • label radioactive gene specific probe • can make a single stranded DNA probe that would hybridize to the MRNA corresponding to the MRNA • radioactive probe will stick to the very spot where the MRNA is Measuring Protein Abundance • stain gel transfer gel to membrane and probe it for specific protein using an antibody that • detects specific protein • antibody=western blot • single stranded DNA=northern blotting BIO 1002 Midterm 1 Chlammy Heat Shock Response 3 types of kinetics • Constitutive: doesn’t respond to heat/change in temperature induced : increases • • Repressed: Decreases Photoreceptor Abundance • A defect makes mice almost blind...what biochemical process could account for the mutation? • could be a defect in opsin in the translation or transcription • MRNA decay could go be going nuts • mutation in transcription factor • there is a mutation to the opsin gene • absorb to much light so it damages the photoreceptor • opsin could be perfectly fine, rhodopsin requries retinal if there is a defect in retinal • RETINAL IS NOT CODED BY A GENE! Post-translational Modification • opsin must integrate with retinal to product functional rhodopsin Apoprotein:protein before its combined into functional protein (opsin) Protein Folding • For a protein to be functional... •it has to fold, it must acquire the correct three dimensional shape (primary to secondary) •native conformation is the correct 3D shape Anfensen’s dogma: if you have an enzyme that has the correct shape you can • measure the product of the reaction (change in colour) • Native changes colour a lot, 100% active • adding urea disrupts bonding arrangements, unwravels (no colour) • take out urea and it refolded and the native was more than >90% active • protein folding is very fast • spontaneous • depends on primary sequence BIO 1002 Midterm 1 Lecture 4-Energy and Enzymes 2nd law of thermodynamics - disorder of system+surroundings increases • life is ordered but they give off disorder (heat, motion) which increases the universes disorder • a cell is an open system which allows for exchange of energy and matter • living things maintain low levels of disorder by using huge amounts of energy Free Energy • delta G=delta H- Tdelta S • free energy is G • endergonic reaction (+) • exergonic reaction (-) reactions tend to be spontaneous when delta G is negative • • when products have less potential energy than the reactants • tends to happen when the products are more disordered than the reactants (entropy is higher in products than in reactants) • S entropy (more or less disorder) • H is enthalpy (overall potential energy that molecules have) • endothermic (+) • exothermic (-) Contributions of Enthalpy and Entropy • whenever you go a phase change (solid---> liquid--->gas) the disorder will always increase • melting of ice is a spontaneous reaction, delta G is exergonic (-) and endothermic • why is it then exergonic? because of the massive increase in disorder, delta S, entropy • Enzymes • biological catalysts that increase the rate of a spontaneous reaction, must have a delta G • OMP from 78 million years to 20 milliseconds • rate increases from 10E12 to 10E20 • Why does life need enzymes? • we need these reactions to happen at a process that we can utilize it (speed) • and to maintain low temperature and pressure because biological molecules cannot handle high temp and pressure BIO 1002 Midterm 1 What enzymes do and don’t do? • enzymes can only catalyse exergonic reactions • they cannot convert a reaction from positive G to negative G • to get a positive reaction to react you must add energy Exergonic Reaction Energy Profile • products have more free energy then the reactants • must acquire transition state where the electrons are in excited state and the bonds are ready to break • Activation energy (Ea) is the energy it takes to get the reactants to the transition state this is why some reactions happen slowly • Ea is a barrier • if you need a lot it might b a million or a billion years breakdown in glucose is spontaneous still takes a while • • ENZYMES LOWER ACTIVATION ENERGY • MANY MORE MOLECULES CAN REACH THE TRANSITION STAGE But how do enzymes lower Ea? • substrate molecules must obtain the precise orientation of the active site to reach the transition state • the enzyme forces the substrate into the right orientation the enzyme provides the charge needed for the interaction • • the enzyme can conformationally strain the substrate • the catalytic site mimics the transition state, it provides the mircro environment for the reaction to occur Enzyme Structure and Catalysis • enzymes are huge and substrate small • when the substrate nears the enzyme, the enzyme changes shape this is called induced fit • enzyme needs exact tertiary structure • this 3D structure must be flexible due to its structural change when a substrate nears • unknown enzyme, its not obvious where the active site from the primary structure it must fold into its tertiary structure E+S----> E-----------> E+P (catalytic cycle) •
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