Study Guides (238,353)
Canada (115,095)
York University (9,811)
BCHM 2020 (9)

Biochemistry Post Mid Term II.doc

18 Pages
Unlock Document

York University
BCHM 2020
Mark Bayfield

Biochemistry Post Mid-Term II Material Lecture 1: Metabolism Metabolism is how cells store, process, and regulate energy usage • • Catabolism: degradation of biopolymers (complex to simple, creates ATP) •Overall chemical oxidation that leads to formation of reduced cofac- tors •NADH, NADPH, FADH2 •Convergence of pathways • Anabolism: synthesis of biopolymers (simple to complex, requires ATP) •Overall is a reduction that leads to formation of oxidized cofactors •NAD+, NADP+, FAD •Divergence of pathways • Energy is taken up in form of proteins, carbohydrates, or lipids in animal cells • Intermediate metabolism: synthesis of biological compounds occurs in a se- ries of organized steps, with many intermediates (metabolites) •Sum of all steps in the synthesis or breakdown of a product is referred to as a metabolic pathway • Energy stored in ATP in the form of high energy phosphoanhydride bonds (between phosphate groups) •Phosphate ester bond between alpha phosphate and ribose •30.5 kJ/mol released when ATP hydrolyzed to ADP •34.3 kJ/mol released when ADP hydrolyzed to AMP •14 kJ/mol released when adenosine-phosphate bond is hydrolyzed (rarely occurs) • Oxidation-reduction reductions •A lot of energy acquired in cells comes from oxidation of high energy electrons into less and less reduced forms •Most reduced carbon is CH4, least reduced carbon is CO2 General rule: more bonds of oxygen to carbon=more oxidized, more • hydrogens to carbon=more reduced •Standard redox reaction carried out by dehydrogenates •AH2+B-------------> A + BH2; where A is electron donor (reducing agent) B is electron acceptor (oxidizing agent) Major electron acceptor during oxidation of metabolites is NAD+ • (nicotinamide adenine dinucleotide) •Ethanol + NAD+ ------->acetaldehyde + H+ and NADH •Major donor of electrons during reduction of metabolites is NADPH • FAD (flavin adenine dinucleotide) is reduced in a similar reaction • Group Transfer reactions •Most common & important groups transferred during metabolism=phosphoryl group from ATP •Transfer of acyl group during catabolism from carboxylic acid deriva- tive to SH group of coenzyme A •Creates a thioester •Most important carboxylic acid derivative transferred to coen- zyme A is an acetyl group •Creates acetyl-CoA •Coenzyme A + acetic acid---->Acetyl-CoA and water Hydrolysis reactions • •Opposite of condensation reactions •Includes glycosidic bond hydrolysis (breaks polysaccharides) • All chemical reactions occur to minimize G using : G= H-T S <0 • G must be negative for reaction to be spontaneous • If G =0 then the process is reversible and at equilibrium • If G is positive, process is thermodynamically unfavorable and reverse process is favored • S (entropy) increases with volume: more volume, more disorder • Volume for a finite amount of substance dictates concentration, concentra- tion dictates entropy • Change in free energy depends on concentration of substrates and prod- ucts in a reaction •If substrates are too dilute, reaction won’t happen •A large Keq means that at equilibrium, the products will be in excess •A small Keq means that at equilibrium, the reactants will be in excess G= -RT ln Keq; where R is the gas constant (8.314472 J/Kmol) and T • is in Kelvin • Coupled reactions require taking the sum of the G values • Why is ATP so energetic? •There are more resonance structures available for ADP and Pi than for ATP and H2O •Therefore, ADP and Pi are more stable, and have less energy than ATP Large number of negative charges on the nucleotide form cause • charge repulsion • Relieving this repulsion gives off a lot of energy • Phosphoenolpyruvate hydrolysis to pyruvate also gives off a great amount of energy • ATP can be generated in one reaction to be used in another reaction Lecture 2: Glucose Metabolism • Glycolysis=glucose into pyruvate • Gluconeogenesis= generation of glucose from pyruvate, largely occurs in the livers in animals • Muscles, the brain, testes,kidney medulla, red blood cells, and nervous tis- sues use glucose as their primary energy source • Kidneys and liver synthesize glucose • Reaction 1: glucose to glucose-6-phosphate • Consumption of 1 ATP • Enzyme: hexokinase • Reaction 2: glucose-6-phosphate to fructose-6-phosphate • Isomerization reaction • Enzyme: glucose-6-phosphate isomerase • Changing an aldose to a ketose (making C2 the anomeric carbon) • This is slightly unfavorable under standard conditions, more favorable under cellular conditions G=+1.7kJ/mol; means at equilibrium, you will have more reactant than • product • However, F-6-P is constantly being consumed, so G-6-P is con- stantly being converted to products to keep equilibrium • Reaction 3: F-6-P to F-1,6-bisphosphate • Requires another ATP Enzyme: phosphofructokinase • • PFK levels change depending on whether ATP levels are high or low • F6P---(enzyme PFK1)-->F1,6P • F6P---(enzyme PFK2)(enzyme FBPase)---->F2,6P (this binds to PFK1 to turn on glycolysis) • Reaction 4: breakdown of F-1,6-bisphosphate to dyhydroxyacetone phos- phate and glyceraldehyde 3-phosphate • Highly endergonic, but will proceed due to energy coupling in cells • Enzyme: aldolase Reaction 5: conversion of dihydroxyacetone phosphate to glyceraldehyde 3- • phosphate • Enzyme: triose phosphate isomerase • Constant depletion of G3P forces reaction to the right • SO FAR, OVERALL: GLUCOSE +2ATP---->2G3P + 2ADP • Reaction 6: oxidation of G3P into 1,3 bisphosphoglycerate (x2) • Enzyme: glyceraldehyde-3-phosphate dehydrogenase • Requires 2 NAD+ and 2 Pi • Produces 2 NADH (electron carrier) and two protons • Reaction 7: phosphoryl transfer from 1,3-bisphosphoglycerate to ADP, mak- ing 3-phosphoglycerate and ATP • Enzyme: phosphyglycerate kinase • This is substrate level phosphorylation • 2 ATP produced Reaction 8: 3-phosphoglycerate to 2-phosphyglycerate • • Enzyme: phosphoglycerate mutase • Contains a phosphorylated His residue that catalyzes the reaction through a bis-phosphate intermediate • Rapid conversion of 2-phosphoglycerate moves the reaction to the right • Reaction 9: dehydration of 2-phosphoglycerate to phosphoenolpyruvate • Enzyme: enolase • Produces a water molecule • Reaction 10: transfer of phosphoryl group of phosphoenolpyruvate to ADP, making pyruvate and ATP • Enzyme: pyruvate kinase • Produces 2 ATP, 2 pyruvate molecules • At the end of glycolysis: 2 ATP, 2 NADH, and 2 pyruvate molecules gained • Aerobic metabolism: uses oxygen as final electron acceptor • If oxygen is not present, other molecules must be used to accept electrons • Fermentation • 2 NADHs produced during glycolysis are used to reduce pyruvate into lactate • This occurs in animal muscles when oxygen is depleted • Also important in making alcohol, yogurt, and “muscle burn” • Homolactic fermentation: •Glucose----> f-1,6-bisphosphate (using 2 ATP)----> 2 G-3-P molecules •to 2 phosphoglycerate molecules---->2 pyruvate molecules which then reduce 2NADH to 2 NAD+ and 2 lactate molecules • Alcoholic fermentation: •Glucose----->f-1,6-bisphosphate(using 2 ATP)---->2 G-3-P molecules •To 2 phosphoglycerate molecules--->2 pyruvate molecules (releases 2 ATP) •2 pyruvate--->2 acetaldehyde + 2 CO2----> recuces 2 NADH to NAD+ and 2 ethanol • GLYCOLYSIS IS VERY ENERGETICALLY FAVORABLE Therefore, the process is spontaneous, even under standard condi- • tions •We could make glucose from pyruvate if we can get over 3 major steps: the rxns catalyzed by HK, PFK, and PK • Reactions of gluconeogenesis are simply the reverse of the reactions in gly- colysis, but there are several irreversible steps in glycolysis that must be by- passed • Bypass #1: Making phosphoenolpyruvate (PEP) from pyruvae or lactate •Pyruvate is imported into mitochondria and converted to oxaloac- etate by pyruvate carboxylase and ATP •Oxaloacetate must be converted to malate in order to leave the mito- chondria •Malate enters cytosol and is then converted back to oxaloacetate, then converted to PEP by PEP carboxykinase (PEPCK + GTP) •This moves one NADH from mitochondria to cytoplasm, which we will need to move BPG back to GAP •If you’re starting from lactate, you can get this NADH by making pyrite from lactate (skip malate part and just make PEP from oxaloac- etate in the mitochondria via mitochondrial PEPCK + GTP) • Bypass #2: F-1,6-bisphosphate + H2O----->F-6-Phosphate + Pi • Exergonic, hydrolysis of phosphoryl groups • Enzyme: fructose-1,6-bisphosphatase Bypass #3: G-6-Phosphate-----> glucose • • Enzyme: glucose-6-phosphatase • Summary of glucogneogenesis: 2 pyruvate + 4 ATP + 2 GTP + 2 NADH + 2H+ + 4 H2O-----> GLUCOSE + 4 ADP + 2 GDP + 6 Pi + 2 NAD+ • Phosphofructokinase (PRK-1) and F-1,6-biphosphatase is a major point of regulation for glycolysis vs. Glucogenesis •High ATP= favors gluconeogenesis •High AMP=need energy, favor glycolysis • F-2,6-biphosphate mediates glucose metabolism It is a signaling molecule that is made AND degraded by PFK-2/FBPase • enzyme •Phosphorylation turns OFF PRK-2 and turns ON FBPase •Phosphorylation controlled by glucagon and cAMP levels • High glucagon & high cAMP (low glucose)=high phosphorylation • High insulin (high glucose)=low phosphorylation •Low glucose=high glucagon=phosphorylated PFK-2/FBPase=low F 2,6, BP •High glucose=high insulin=dephosphorylated PFK-2/FBPase=high F 2,6, BP •F 2,6 BP activates PFK= activation of glycolysis • PFK inhibited by ATP binding to allosteric site • When glucose levels are high, PFK-2/FBPase is dephosphorylated, which activates the PFK-2 subunit--> deactivates the FBPase sub- unit--->more F 2,6 BP is made • This leads to stimulation of PFK-1 and results in activation of gly- colysis (use up the high glucose) The Citric Acid Cycle Purpose: the extract energy from 2 pyruvate molecules • • Aerobic metabolism of pyruvate occurs in the mitochondria (matrix and in- ner mitochondrial membrane) • Pyruvate, O2, NAD, FAD, ADP are the substrates • Co2, NADH, FADH2, ATP are products • Enzymes involved are associated in functional units: metabolons and allow for substrate channelling • Pyruvate is imported across inner mitochondrial membrane by pyruvate translocase • Oxidation of pyruvate to acetyl-coA • Enzyme: pyruvate dehydrogenase (multi-enzyme complex) Cofactors: • • Thiamine pyrophosphate (TTP) {vitamin B1}: bound to E1, decar- boxylates pyruvate, yielding hydroxyethyl-TPP • Lipoic acid (lipoamide): bound to E2, via lysine “swinging arm”, ac- cepts hydroxyethyl carbanion from TPP as acetyl group • Coenzyme A (CoA): dissociable substrate for E2, accepts acetyl group from lipoamide • Flavin adenine dinucleotide (FAD): tightly bound to E3, accepts electron pair from reduced lipoamide • Nicotinamide adenine dinucleotide (NAD+): dissociable substrate for E3, accepts pair of electrons from reduced FADH2 • Sum of rxn: decarboxylation, oxidation of C2, and activation via thioester bond to enzyme CoA • Very energetically favorable (-33.5 kJ/mol) • Pyruvate dehydrogenase cycle: • Step 1: pyruvate I decarboxylated by E1 enzyme that requires thiamine pyrophosphate (TPP) •Remaining hydroxyehyl remains bound to TPP • Step 2: the C2 of hydroxyethyl is oxidized into an acetyl group by reduc- ing a disulphide bond of the lipoamide group on the E2 enzyme •This transfers acetyl group to the E2 enzyme via a new thioester bond to the lipoamide prosthetic group • Step 3: acetyl CoA is formed by the transfer of the acetyl group to the thiol group of the pantothenic acid (vitamin B5) containing coenzyme A • Coenzyme A acts as a carrier for the acetyl group, which maintains the high energy of the thioester bond (-31.4 kJ/mol) • Step 4: lipoamide must be reoxidized •FAD attached to E3 is reduced to FADH2 Step 5: to regenerate the FAD, the FADH2 reduces a molecule of NAD+ • to NADH • We have not generated a high energy NADH and are ready to further oxi- dize the acetyl group bound in a high energy thioester bond to CoA • NAD+ picks up two electrons and one proton, releasing one proton to sol- vent • FAD picks up two electrons and two protons • FAD is a stronger oxidizing agent (greater pull for e-) • Step 1: acetyl group of acetyl-CoA is joined to oxaloacetate to make Citrate •Enzyme: citrate synthase •Regenerates Coenzyme A and consumes 1 H2O Step 2: Citrate (tertiary alcohol) isomerized to Isocitrate (secondary • alcohol) • Enzyme: aconitase • Involves a dehydration and subsequent rehydration • Tertiary alcohols cannot be oxidized without breaking a C-C bond, so there is an isomerization first • Step 3: oxidation of isocitrate to a-Ketogluterate • Enzyme: isocitrate dehydrogenase • Results in loss of CO2 and reduction of NAD+ to NADH Step 4: a-ketogluterate is oxidized to Succinyl-CoA • • Enzyme: a-ketogluterate dehydrogenase complex (similar to pyruvate dehydrogenase complex, uses same cofactors) • Loss of CO2 and reduction of NAD+ to NADH • Step 5: succinyl-CoA converted to succinate • Enzyme: succinyl-CoA syntheses • Regenerating Coenzyme A and forming a molecule of ATP (substrate lev- el phosphorylation) • Step 6: oxidation of succinate to fumarate Enzyme: succinate dehydrogenase • • Reduces one FAD to FADH2 • Coenzyme Q is part of the electron transport chain so succinate dehy- drogenase is bound tightly to inner mitochondrial membrane • Step 7: hydration of fumarate to malate • Enzyme: fumarase • Requires H2O molecule • Step 8: oxidation of malate into oxaloacetate • Enzyme: malate dehydrogenase • Converts NAD+ into NADH • Very energetically unfavored, but proceeds because the next step (step 1 of citric acid cycle) is so energetically favored • For every 1 glucose= 2 turns of citric acid cycle One acetyl group transferred to Co-A generates 2CO2, 1 ATP, 3 NADH and • one FADH2 • When Calcium ion is high, muscles contract, therefore: more ATP is required •Ca+ is a positive effector • Mg+ is coordinated by free floating ATP • ATP coordinates more Mg+ than ADP • As free floating ATP increases, Mg+ concentration is low (because it is bound to ATP) Lecture 3: Oxidative Phosphorylation • High energy electrons in NADH and FADH2 are passed along electron trans- port chain to make ATP • This only takes place AEROBICALLY, as oxygen is needed to accept elec- trons at the end of the chain • This takes place in complexes found in the innermitochondrial membrane • As electrons are passed down the chain, they lose energy (in volts) • There is an amount of energy associated with each electron on a given electron carrier • Oxygen’s standard reduction potential E, is + therefore, it is very happy to accept electrons • Standard potential to accept electrons of each carrier, become more and more positive until they reach oxygen • NADH and FADH2 enter the chain at different branches, but converge at CoQ • Electrons travel from smaller E (V) to higher E (V) • Standard reduction potential is related to standard free energy: • G’= -nF E’ •N= number of e- •F= Faraday constant • E= E(acceptor)-(donor) [in volts] •The electron acceptor is the one with the higher (more positive) E val- ue Complex I : NADH dehydrogenase • • NADH is ox
More Less

Related notes for BCHM 2020

Log In


Don't have an account?

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.