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week 6 329

by: Mary-elizabeth Notetaker

week 6 329 Bio 329

Mary-elizabeth Notetaker
U of L

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week 6
Cellular Molecular Biology
Paul Himes
Class Notes
Bio, bio329, Biology, UofL, cellularandmolecularbiology
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This 5 page Class Notes was uploaded by Mary-elizabeth Notetaker on Thursday September 29, 2016. The Class Notes belongs to Bio 329 at University of Louisville taught by Paul Himes in Fall 2016. Since its upload, it has received 6 views. For similar materials see Cellular Molecular Biology in Biology at University of Louisville.


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Date Created: 09/29/16
Week 6 Tuesday, September 27, 2016 3:58 PM  All rxs spontaneously move towards eq ○ Eq does not mean same # P as Rs  Delta G- E absorbed/given off by rx ○ Neg- gives off E, rx goes towards P…. k>1 ○ Pos- takes in E, rx goes towards R.. K<1 ○ Std conds: 25C, 1atm, pH7, all components at 1M expcept water(55.6M) ○ ..making delta G neg may require coupling endergonic and exergonic rxs  Need common intermediate  If favorable rx uses up P of unfavorable rc--> unfavorable one favorable □ 3 Phosphoglycerate to 2 phosphoglycerate (unfavorable.. Would not occur on own spontaneously)… since rx below is favorable, top rx continuous to occur bc P are continually used □ Phosphoenolpyruvate to pyruvate (-delta g)  ATP hydrolysisoften coupled to endergonic rxs in cells □ For coupling, need common intermediate  Product in one is reactant in other  Eq vs steady state metabolism ○ Cellular met is noneq met- if ATP and ADP in eq-> no capacity for work->cell dead ○ Cells are open thermodynamic systems  R & P concentrations are constant but not in eq  New subs enter and P removed  Exceptions: external reg… hormones  Maintaining steady state reqs input of E  To constantly move forward need more than 2x more R than P  Enzymes- special catalysts- speed up chem rxs ○ Usually proteins… ribozymes ○ Can be conjugated w nonprotein components  Cofactors  Coenzymes ○ Req'd in small amts ○ Not permanently altered in rx ○ Highly specific for subs ○ Produce specific products ○ Can be regulated to meet cell needs ○ Cant affect thermodynamics of rxs, just rates  No change in delta G  Ea- small E input needed for chem transformation ○ Slows progress of thermodynamically unstable Rs ○ R mols that reach peak of EA are in transition state, all downhill from there ○ To get more R reaching transition state: add heat( E) or enzyme ○ Active site- region of enzyme where sub binds  Enzyme+sub=ES complex □ Usually noncovalent intxs, sometimes transient covalent bonds form  Sub specificity- result of complementary shapes of active site and sub  Residues of enzyme and sub in close proximity  Mech of enzyme catalysis ○ Sub orientation ○ Change sub reactivity ○ Induce strain in sub- flex/pressure  Enzyme kinetics- how fast Rates inc as sub concentrations inc until enzyme is saturated ○ Rates inc as sub concentrations inc until enzyme is saturated  Saturation= working at max  V at sat= max V  Turnover # K sub mols per min per enzyme mol at Vmax cat  Vmax time rx it takes  K catrxs per unit time per enzyme ○ Michaelis constant(Km)- sub concentration at half of Vmax  In concentration units  Km is constant for given enzyme  Allows comparison of enzymes and effects of inhibitors  Km often related to affinity of enzyme for sub  T and pH affect rx rates ○ Enzymatic Inhibitors- slow rates of enzymatic rxs  Irreversible inhibitors- covalently bind enzyme  Reversible- bind loosely □ Competitive- compete w enzyme for active site- resembles stx of sub  Can be overcome w high sub/inhibitor ratio  Change Km but not Vmax □ Noncompetitive inhibitors- bind allosteric sites (sites other than active sites)--> inactivate enzyme  Changes Vmax but not Km  Have to remove them to reverse their effects  Antibiotics- ex of enzyme inhibitors ○ Target bacterial met w/out harming human ○ Made by one bac to control another ○ Bacteriocidal- kill bac ○ Bacteriostatic- cause bac to stop growing ○ To make new one, look for enzyme bac has that humans don’t  Enzymes involved in synth of bac cell wall  Components of system of duplication, transcription, and translation □ Only 2 new classes in last 50 yrs  Enzymes that catalyze met rxs specific for bac □ Sulfa drugs look like sub needed to make folic acid ○ Misuse- destroy susceptible cells and resistance cells survive and reproduce  Gut commensals killed so bad ones take over  Using when not needed-> inc antibiotic resistant ○ Bac become resistant over time and get genes from other bac  Mut rate for bac lower than virus  Get resistance genes from other bac ○ Combat:  Mult drugs at once  Strong oxidizing agents Have high e- affinity ○ Oxidizer will take e- and become reduced  Catabolic pathways- break down complec subs into simple Ps ○ Gives cell: raw mats, chem E(ATP), reducing power, ion gradients(for work)  Anabolic- make complex end Ps from simple subs ○ Req E ○ Use ATP and NADPH from catabolic pathways …both pathways highly conserved…evolved early on both involve E exchanges thru transfers e-'s  Redox & e- tower ○ As e-s fall from donor at top of tower.. Can be caught by acceptors at any lvl below ○ More sub is reduced, more E can be released  Fats more E dense than carbs bc its more reduced (HCH vs HCOH) ○ Diffs in pot btwn donor and acceptor can be measured in Volts ○ Further e- drops from donor before caught by acceptor=greater amt E released Ox of reduced atoms= E to do work ○ Ox of reduced atoms= E to do work  Intramol redox- w/in org mols, atoms ox/red ○ Across polar bonds:  One atom has more time w e- than other  Partial, not full reductions like when bonds change  More polar bond is, less E stored there  Redox e- carriers ○ In catabolism, e- donor is the E source □ Glucose, succinate, H2S and many others  Electron carriers- Transfer of e- from donor to acceptor thru intermediates  Primary donor --> terminal acceptor □ 2 classes:  Freely diffusible carriers: nicotinaminde-adenine dinucleotides(NAD& NADP) ◊ NAD(oxidizedform), NADP(reduced form) [catabolic] ◊ In anabolic: NADH and NADPH  Attached to proteins- iron sulfur centers, riboflavin(FMN or FAD), hemes(iron containing rings), lipid sol quinones  NAD+/NADH and NADP+/NADPH cycling □ Enzyme 1 rx w sub(e- donor) and oxidized form of coenzyme=NAD+ □ Enzyme 2 rx w sub(e- acceptor) and reduced form of coenzyme, NADH  Reducing power: NADPH and NADH are interconvertible, but have diff met rates □ NADPH is ox in anabolic paths  Supply of NADPH rep's cell's reducing power  Formation of larger mols reqs source of e-s □ NAD+ is reduced in cat paths  Supply of NAD+ reps cells ox power □ Transhydrogenase catalyzes transfer of H atoms from one cofac to another  NADPH is favored when E abundant  NADH used to make ATP when E is scarce ○ E capture and utilization  E released by redox rx --> high E phosphate bonds □ Phosphates linked to org bonds… cleaving gived free E to drive endergonic rxs □ Thioester bonds formed by coenzyme A  Cleaved--> synth of ATP  Used directly--> synth of Fas and other anabolic rxs  ATP present in rel low concentration in cells (2mM)  Glycolysisand ATP formation ○ 2 stages in catabolism of glucose 1. Glycolysis-occurs in soluble portion of cytoplasm Net 2 atp and 4 high E e- per glucose (uses 2 atp, so even tho gross is 4, net is 2) Steps: 1) Glucose phosphorylated to glucose 6-phosphate by using ATP (-delta g) a) E investment.. 1st noneq rx b) Lowers [glucose] so more taken from blood ..kinases- enzymes that transfer phosphate group (type of transferase) 2) Glucose 6-phosphate isomerized to fructose 6-phosphate a) Changes location of -C=O and bond that cyclizes sugar b) Isomerase- enzyme that rearrange atoms in a mol 3) Fructose 6-phosphate phosphorylated to fructose 1,6-biphosphate using another ATP a) Kinase used again b) 2nd non eq rx 4) Fructose 1,6-biphosphate chopped in half by aldolase and forms 2 3C phosphorylated compounds a) Lyase- chops things up (what aldolase is) b) Pos delta g but goes bc constantly making more and breaking c) Dihydroxyacetone makes 2 mols glyceraldehyde 3-phosphate.. So do everything that follows twice twice 5) NAD+ reduced to NADH when glyceraldehyde 3-phosphate and makes 1,3 biphosphoglycerate a) Dehydrogenase- enzymes oxidize and reduce cofacs i) Always redox rx here (same w H transferases) ii) Oxidoreductase 6) 1,3-biophosph converted to 3-phosphoglycerate kinase using ADP..forms ATP too a) Sub lvl phosphorylation.. ATP formed by kinase b) P bonds in ATP are high, but not that high i) Transfer pot tower Higher mols have less affinity for groups being transferred than lower mols Less affinity=better donor Sub lvl phosph- downhill like e- transfer 7) 3-phosphoglycerate converted to pyruvate: 3 sequential rxs a) In 3rd rx kinase phosphorylates ADP to make ATP b) Phosphoglycermutase- change mols..take phosphate group from 3C to 2C c) Enolase- removed water d) Pyruvate kinase convers phosphoenolpyruvate to pyruvate (gives off lots of E) Get net 2 ATP for each glucose Occurs anaerobically Pyruvate(end P) can enter aerobic or anaerobic catabolic pathways Can be turned to acetyl coenzyme A, or acids to AA Has free E More E in e- than ATP, but most E in pyruvate  Anerobic ox of pyruvate: fermentation- restores NAD+ from NADH ○ Glycolysisdec [NAD+], reduces to NADH.. Running out of NAD+ stops process ○ Fermentation: NADH ox to NAD+ by reducing pyruvate  Pyruvate dehydrogenase makes acetyl coA which undergoes aerobic ox in TCA cycle ○ Inefficient… only 8% E of glucose captured as ATP vs. ox phos (2 ATP vs 36) ○ Lots of E left in Ps ○ If make too much ethanol( pyruvate decarboxylase mades acetaldehyde-->ethanol), poisons themselves ○ Benefit: fast  Met regulation- controlling amt/activity of key enzymes of met paths ○ Enzymes controlled by alteration of active site stxs:  Covalent mods of enzymes, phosph by protein kinases (very specific) □ 2 types  Tyrosine  Serine.threonine □ Reversed by phosphatases □ Methylases, acetylases, change other groups  Allosteric modulation- reg'd by compounds binding to allosteric sites □ Binding elsewhere changes shape of proteins (activates or deactivates) □ Noncompetitive inhibition □ Feedback inhibition- product of pathway allosterically inhibits one of the pathways early enzymes  Form of noncomp inhibition  Separating cat/anabolic paths ○ Glycolysis(glucose-->pyruvate)and gluconeogenesis(pyruvate-->glucose)- cat and anabolic paths to met glucose  3 thermodynamically irreversible rxs (large delta g values) □ Going down bond E tower □ Need other enzymes/mechs for reverse  If have lots of atp do glycolysis,if low atp do glucogenesis  Synth of fructose 1,6 biphosp is coupled to hydrolysisof ATP □ Phosphofructokinase is reg'd by feedback inhibition w atp as allosteric inhibiter □ Atp both sub and inhibitor □ 2 diff binding sites w diff affinities Active site pulls more strongly on atp, so if lower amt, all go here  Active site pulls more strongly on atp, so if lower amt, all go here  If lots of atp, will go to both and will bind allosteric site and hide active site to shut it down  Dephosphorylation of fruc 1,6bi by hydrolysis by fructose 1,6 bisphosphatase(onlyactive when kinase phosphorylates it) in gluconeogenesis □ Fuctose 1,6 biphosphatase is reg'd by covalent mod using phosphate binding  Inhibited by AMPK when AMP:ATP ration incs ◊ AMP doesn’t have high E bond, lowest E state ◊ AMPK active when lots of AMP, phosphorylates fructose 1,6 bisphosphatase to allow glucose creation  ATP lvls are highly reg'd 1. TCA(tricarboxylic) cycle- in mitochondria of euk cells  Complete ox of C6H12O6 releases a lot of E (delta G=-686) □ Can make 36 atp/glucose  Of the rxs of glycolysis,only 3 not near eq (delta g=0) under cellular conds □ Driving forces of glycolysis …Coupling works by using products of another rx so constantly moving from eq and driving it forward


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