Biochem exam III

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Biochem exam III
2014-12-15 20:47:25

Biochem Exam III; metabolism (unfinished)
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  1. autotrophs
    • sole C source is CO2 in atmosphere
    • energy source is light (plants, photosynthetic bacteria)
  2. heterotrophs
    • C source is carbs, fats and proteins
    • energy is degredation of biopolymers
    • can be aerobes or anaerobes
  3. aerobes
    require O2 for metabolism
  4. anaerobes
    don't require O2 for metabolism
  5. metabolic pathway
    • an entire series of steps, converting a precursor to product (like glycolysis converts glucose to pyruvate)
    • Can be Linear, cyclic or spiral
  6. metabolites
    • intermediates in the pathway (stable compounds) 
    • most molecules inside living organism
  7. catabolism
    • degrades complex molecules into small, simple molecules
    • exergonic, releases energy (usually ATP)
    • oxidative (uses NAD+ and FAD)
  8. anabolism
    • synthesizes complex molecules from small molecules
    • reductive (uses NADPH)
    • requires energy, endergonic (ATP)
  9. ATP energy cycle
    • catabolism (convergent): energy generating reactions (glucose oxidation) coupled to energy utilizing reactions (ATP synthesis)
    • anabolism (divergent): energy generating reactions (ATP hydrolysis) coupled to energy utilizing reactions (biosynthesis, mechanical work)
  10. 3 stages of metabolism
    • macromolecules
    • monomers
    • acetyl CoA
  11. ΔG
    free energy change for a reaction.  the MAXIMUM AMOUNT of free energy that a reaction can deliver.  G of products - G of reactants
  12. ΔGo definition
    ΔG (free energy change for a reaction) at standard conditions (25 C, 1 atm, 1M solute concentration)
  13. ΔGo' definition
    ΔGo (free energy change for a reaction at 25C, 1atm, 1M solute) at pH 7, H2O 55.5M
  14. ΔGo' equation
    -RT ln K'eq
  15. K'eq equation
    • K'eq =  
    • Can use equilibrium concentrations of rx components to calculate (0.200M, nothing for water)
  16. If K'eq is large, ΔGo' is_______, reaction is ______
    negative, exergonic and spontaneous
  17. If K'eq is less than 1, ΔGo' is ______ and reaction is _________
    positive, endergonic, nonspontaneous
  18. If K'eq is 1, ΔGo' is _______ and reaction is _______
    0, nothing, at equilibrium
  19. Effect of catalyst on ΔGo'
  20. Effect of ΔGo' on reaction rate
  21. ΔGp definition
    • ΔG at physiological conditions, different for each species.  
    • 37C and physiologic solute concentration
    • can be spontaneous even if ΔGo' is not (spon in vivo)
  22. ΔGp equation
    • ΔGp = ΔGo' + RTlnQ
    • Q = mass action expression, same as K'eq at NONEQUILIBRIUM
  23. Mass action expression
    • Q (like K'eq but at NON-EQUILIBRIUM conditions)
  24. entropy
    • the degree of disorder/randomness in a system
    • gas has higher S than liquid
    • mixture has higher S than two separate
    • mix of amino acids has higher S than protein with same aas.  
    • Constantly increasing (NaCl + H2O becomes Na + Cl, increase in S)
  25. Gibbs free energy equation
    • ΔG = ΔH - TΔS
    • free energy = enthalpy (heat content, - for exothermic) - temp (K) x entropy
  26. chemical coupling
    • hydrolysis of high energy compound pays for anabolic rx with -ΔGo'
    • - must be larger than +
  27. def of high energy compounds
    • contain one or more bonds whose ΔGo' of hydrolysis is more negative than -25 kJ/mol.  
    • Hydrolysis is IRREVERSIBLE
    • high activation energy for hydrolysis
    • require enzymes to be broken down
  28. 5 categories of high energy compounds
    • anhydrides (resonance) (ATP, lowest)
    • mixed anhydrides (resonance)
    • enoyl phosphate (PEP, highest)(keto-enol)
    • phosphocreatinine (resonance)
    • thioesters (acetyl CoA) (resonance
  29. Hess' Law
    balance and split equilibrium reaction, add half-reactions from table, add ΔGo' (flip the backwards one)
  30. phosphoryl groups flow spontaneously from _______ to ________ in coupled rx
    more unstable (more negative ΔGo') to less unstable (less negative ΔGo')
  31. coupling efficiency in ATP
    • max # of ATP formed from a catabolic step calculated by ΔGo' for that step
    • always round down to nearest WHOLE NUMBER.
  32. if coupling efficiency is (almost) same for aerobic and anaerobic, why is aerobic better?
    gets more out of glc
  33. oxidation
    • loss of electrons.  Oxidized thing is the reducing agent.  
    • gain of O
    • Loss of H
  34. reduction
    • gain of electrons.  Reduced thing is the oxidizing agent  
    • Loss of O
    • gain of H
  35. NAD+
    • nicotinamide adenine dinucleotide
    • becomes NADPH when P added to 2'OH of ribose
    • from vit B3 (niacin)
    • can follow on assays at 340nm
  36. FAD
    • flavin adenine dinucleotide
    • absorbs light at 450nm
    • derived from B2 (riboflavin)
    • FAD - AMP = FMN (flavin mononucleotide)
  37. When ΔEo' is positive, the reaction
    • is spontaneous
    • the ΔGo' is negative (=-nFΔEo')
  38. Eo' is a measure of
    • reduction potential (electric potential), in volts.  
    • Highest on table = highest Eo'
    • To find oxidizing agents that would be reduced by something, look ABOVE ON TABLE
  39. Equation to calculate ΔGo' from redox potential
    • ΔEo' = -nFΔEo'
    • n = # electrons transferred or # molecules in the rx
    • F is a constant, given
  40. How does oxidative phosphorylation work (general)?
    When potential difference (ΔEo')(V) between two electron carriers in the electron transport chain is large enough to cause a ΔGo' that is MORE NEGATIVE than -30.5kJ/mol, can be chemically coupled to make 1 mole of ATP
  41. glycolysis and net reaction
    • anaerobic oxidation of glucose, 2 steps (investment and payoff)
    • glc + 2 ADP + 2Pi + 2 NAD+ →
    • 2 pyruvate + 2 ATP + 2 NADH + 2 H+ + 2H2O
  42. what can follow glycolysis (3)
    • anaerobic glycolysis (lactic acid fermentation)
    • ethanol fermentation (yeast)
    • citric acid cycle
  43. lactic acid fermentation
    • 2 CH3-C-COO- + 2 NADH + 2 H+ →
    • 2 CH3-C-COO- + 2 NAD+
    • source of muscle ATP during sustained muscle exercise, anaerobic (fast sprint, 10s) 
    • stored ATP, creatine phosphate, then glycogen (slow)
    • helps survive brief hypoxia
    • only ATP in some areas of body (retina, cornea, RBC) b/c no mitochondria
  44. ethanol fermentation (yeast)
    • 2 pyruvate (CH3-C-COO-) + 2 NADH + 4H+ → 2 CO2 + 2 ethanol + 2 NAD+
    • reoxidizes NADH to NAD+
  45. What is the difference between pyruvic acid/pyruvate and lactic acid/lactate?  Which dominates at pH 7.0?
    acid and conjugate base.  Pyrvate and lactate are COO- form, at pH 7.0.
  46. Investment phase of glycolysis
    • ATP phosphorylates sugar
    • glc is destabilized
    • no oxidation/energy release
    • 5 steps.
  47. pay-off steps of glycolysis
    ATP produced.
  48. Step 1 of glycolysis 
    glc + ATP→(hexokinase)→glc 6-P
    • investment step
    • kinase transfers phosphoryl, works on any hexase
    • gatekeeper step, traps glc in cell, commits to metabolism
    • activation step, irreversible, regulatory enzyme
  49. step 2 of glycolysis
    • investment step
    • aldose/ketose isomerization (isomerase), changes carbonyl group position
    • positive ΔGo'
  50. step 3 of glycolysis
    Fru 6-P + ATP→phosphofruktokinase-1 (PFK-1)→ fru 1,6-bisphosphate + ADP
    • investment step
    • kinase catalyzes irreversible, catalyzed by regulatory enzyme
  51. step 4 of glycolysis
                      dihydroxyacetone phosphate
    fru 1,6 bisphosphate⇆aldolase↗↘
                              glyceraldehyde 3-P
    • investment step
    • lyase
    • 6C sugar split into 2 3-C sugars, REVERSE ALDOL CONDENSATION (joining of aldehydes or ketones = alcohols)
    • fru 1,6-bis-P unique to glycolysis
  52. step 5 of glycolysis
    dihydroxyacetone phosphate(DHA-P)⇄ triose phosphate isomerase ⇄glyceraldehyde 3-P

    • investment step
    • prevents glycolysis becoming 2 pathways (inefficent), lets all subsequent steps be x2
    • joining of fork in pathway (triangle)
  53. dehydrogenase (general)
    oxidoreductase that removes H, used in step 6 of glycolysis
  54. step 6 of glycolysis
    glyceraldehyde 3-P + NAD+ + Pi ⇄ glyceraldehyde 3-P dehydrogenase ⇆ 1,3bis-P glycerate + NADH + H+
    • first payoff step
    • not negative ΔG, coupled with step #7.  
    • dehydrogenase = oxidoreductase that removes H
    • energy from oxidation of substrate drives phosphorylation, produces high-energy mixed anhydride + NADH
  55. step 7 of glycolysis
    1,3-bis-P glycerate + ADP ⇄ phosphoglycerate kinase, Mg2+⇆ 3-P glycerate + ATP
    • pay-off step
    • high-energy, gives some energy to previous step (coupled) 
    • Enzyme is only non-regulatory kinase (reversible)
    • SUBSTRATE-LEVEL PHOSPHORYLATION (1,3BPG is higher energy than ATP)
  56. mutase
    isomerase that moves a group between 2 positions on same molecule
  57. step 8 of glycolysis
    3-P glycerate ⇄ phosphoglycerate mutase, Mg 2+ ⇄ 2-P glycerate
    • payoff step
    • mutase, moves Phosphoglycerate to another spot on same molecule
  58. step 9 of glycolysis
    2-P glycerate ⇄ enolase ⇄ PEP + H2O
    • payoff step
    • dehydration, catalyzed by a lyase, removes H2O to make double bond, makes a high-energy compound (highest)
  59. step 10 of glycolysis
    PEP + ADP→ pyruvate kinase, Mg2+  pyruvate + ATP
    • payoff step
    • very exergonic so irreversible/regulatory
    • 2nd substrate-level phosphorylation
    • last step
  60. Energy yield of glycolysis
    • net gain of 2 ATP per glc oxidixed (2 invested, 4 yield)
    • 2 NADH produced from NAD+
    • requires Pi
  61. Pasteur effect
    • rate of glycolysis decreases when muscles switch from anaerobic to aerobic metabolism
    • Don't need to work as hard, so don't. 
    • Feedback inhibition, only make as much ATP as you need.
  62. ATP yield from anaerobic glucose oxidation
    2 ATP/glc
  63. ATP yield from aerobic glucose oxidation
    32 ATP/glc
  64. multienzyme complexes
    enzymes of glycolysis are connected, CHANNEL SUBSTRATE from one step to next, funnel in, faster, eliminates diffusion.
  65. Path of aerobic pyruvate metabolism
    pyruvate = acetyl CoA = citric acid cycle (+ ADP, Pi, NADH, H) = CO2 + NAD+ + ATP + H2O
  66. 2 paths of anaerobic pyruvate metabolism
    • lactate fermentation (anaerobic glycolysis of animal muscle): pyruvate + NADH + H+ ⇄ LDH ⇄ lactate + NAD+
    • alcohol fermentation: pyruvate + H+ → pyruvate decarboxylase, TPP → acetaldehyde + NADH + H+ ⇄ alcohol dehydrogenase ⇄ ethanol + NAD+
  67. Cori cycle
    • recycling of lactate into pyruvate in liver after you catch your breath.  
    • otherwise lactate is dead-end product, lowers pH of cells and causes cramping.  Just regenerates NAD+ to keep glycolysis moving.  REDOX, H+ eventually inhibits PFK-1 to avoid lactic acidosis
  68. LDH always present in myocytes, why is only a small amt of pyruvate converted to lactate when there is O2?
    • shortage of substrate.  Aerobic turns NADH to NAD+, no NADH to run lactate synthesis.  
    • Pyruvate sent into mitochondria so also not available.
  69. alcohol fermentation
    • anaerobic pathway of pyruvate metabolism.  
    • TPP as cofactor, nucleophile cleaves bonds acetyl group carrier, decarboxylates.  
    • irreversible, releases CO2
  70. ethanol metabolism in humans
    • oxidized in liver into acetyl CoA, becomes fat or citric acid cycle.  
    • excessive depletes NAD+ = liver cirrhosis
    • accum of acetaldehyde (when no NAD+) causes hangover.  
    • Inhibits glycolysis and gluconeogenesis, causes hypogylcemia and temp regulation issues
  71. tx of alcoholism
    • duslfiram: accumulates acetaldehyde to increase hangover
    • opioid antagonist: counteracts high, suicide.
  72. fetal alcohol syndrome
    acetaldehyde crosses placenta, fetal liver can't oxidize
  73. methanol poisoning
    • oxidized by ADH to formaldehyde
    • tx with IV ethanol bc ADH is nonspecific ALCOHOL dehydrogenase, so competitive inhibition with higher-affinity substrate
  74. polysaccharide feeder pathway for glycolysis
    • cellular glycogen glycogen phosphorylase PHOSPHOROLYTIC CLEAVAGE
    • only works on 1->4 linkage, enzyme phosphoglucomutase for nonreducing end when hits 1->6
    • isomerization sends into glycolysis
    • glycogen cleavage MOBILIZES stored fuel (regulatory)
  75. dietary glycogen and starch feeder pathway for glycolysis
    • hydolyzed by salivary and pancreatic a-amylases at a1->4
    • isomaltase for a1->6
    • monosacc enter glycolysis
  76. disaccharide feeder pathway for glycolysis
    • cleaved to monosacc by membrane-bound enzymes at brush border (isomaltase, maltase, sucrase, lactase), become glc, fru, gal
    • (____ + H2+ ---> 2____)
    • hexokinase works on any hexose.  Liver uses fructokinase
    • galactokinase on UDP
  77. galactosemia
    • genetic disease, lacks enzyme in galactose pathway
    • hepatomegaly, jaundice, cataracts, mental retardation, vomiting
  78. glycogen phosphorylase
    • enzyme in feeder pathway for glycolysis
    • degrades cellular glycogen (removes 1 glc and phosphorylates)
    • works on a1->4
  79. hexokinase
    • enzyme in glycolysis and feeder pathways
    • phosphorylates any hexose.  Fructose, mannose in feeder pathway, glc in glycolysis
  80. energy charge formula in regulation of carbohydrate metabolism
    energy charge = 

  81. Functions of Carbohydrate metabolism regulation
    Maintain constant blood glucose, ATP, variation of priorities in dif cells, avoid futile cycles, keep metabolic intermediates from accumulating.  Blood glc wins for brain.
  82. mechanism of carbohydrate metabolism regulation
    • allosteric regulation (feedback inhibition, feed-forward activation)
    • covalent modification
    • differential behavior at isozymic forms (myosites vs hepatocytes)
  83. isozymes
    • distinct enzymes that catalyze the same reaction
    • usu oligomeric enzymes, dif in subunit to make dif activities, Vmax, Km, pH optimum.
    • LDH has H and M subunits, work in muscle and heart, etc.  Requires fewer genes to make
  84. spatial regulation
    • isozymes have different Vmax, Km, pH optimum, etc.  Behaves differently based on location.  
    • Other option is temporal regulation, different at different times.
  85. isozyme clinical application
    • diagnose tissue damage
    • usu intracellular, so if in blood, tissue damage
    • electrophoresis vs ELISA
  86. Overview of regulation of glycogen phosphorylase
    • allosteric or covalent
    • makes/uses ATP in muscle, breaks down glycogen to maintain blood sugar in liver
  87. allosteric regulation of glycogen phosphorylase
    muscle activated by AMP, inhibited by ATP.  Liver inactivated by glc
  88. covalent regulation of glycogen phosphorylase
    • activated by cascade (adenylyl cyclase → ATP-cAMP activates PKA, activates phosphorylase b (conformational), glc becomes glc 1-P.  
    • Signal amplification
    • Off by phosphorylase a phosphatase and phosphodiesterase
    • diff purposes in dif tissues
  89. function of glycogen phosphorylase activation
    • mycyte: produce ATP in response to epinephrine, break down glycogen
    • hepatocyte: maintain blood glc levels by breakdown of glycogen
  90. regulation of hexokinase
    • allosteric
    • feedback inhibition by glc 6-P (intermediates)
    • If PFK-1 decreases glc 6-P will build up too high, but need glc 6-P for glycogen so ISOZYMES.  Only active if high blood glc.  Weak inhibition, just higher K0.5
  91. Regulation of phosphofructokinase
    • major regulatory enzyme in glycolysis after glycogen synthesis branch.  
    • fru 1,6 bis-P UNIQUE to glycolysis
    • allosteric, inhibited by products of glycolysis (ATP, citrate, H+)
    • activated by AMP, ADP, fru-2,6-bis-P (increases affinity in liver to slow glycolysis when blood glc is low)
  92. Regulation of pyruvate kinase
    • allosteric: inhibited by ATP, acetyl CoA and alanine (like pyruvate, feedback inhibition)
    • activated by fru 1,6-bisP (synch with PFK-1)
    • covalent: liver isozyme inactivated with low blood glc
    • Break even point in glycolysis
    • most dramatic effect on flux through glycolysis (rest are stronger regulators)
  93. If ATP is low in muscle and AMP is high, what happens to glycogen, AMP, glycolysis
    • glycogen becomes glc 1-P, AMP allosteric activator of phosphorylase b
    • glycolysis makes ATP, AMP allosteric activator of PFK-1
  94. If ATP is high, what happens to phosphorylase, PFK-1, pyruvate kinase and glycolysis
    • all decrease.  In muscle glc 6-P increases, inhibits hexokinase
    • in liver glc 6-P increases but does not inhibit glucokinase, glycogen is made
  95. If ATP is high AND blood glc is low, what happens to glucagon, glc 6-P, glucokinase and glycogen phosphorylase
    • glucagon decreases PFK-1 and pyruvate kinase
    • glc 6-P dephosphorylates to increase glc in blood
    • glucokinase decreases (high Km)
    • glcyogen phosphorylase increases, glycogen broken down
  96. Pentose phosphate pathway
    • alternate use of glc, provides ribose 5-P, NADPH, uses ATP
    • NADPH reduces tripeptide glutathione, which protects erythrocytes from oxidative damage
    • glucose 6-P dehydrogenase deficiency: genetic X-linked dz, protects against malaria
  97. Pyruvate dehydrogenase complex (PDH complex)
    • multienzyme complex of mitochondrial matrix
    • receives pyruvate from cytosol, converts to acetyl CoA, uses NAD+ (reduced) and pyruvate (oxidized by oxidative decarboxylation)
    • gatekeeper (aerobic oxidation), activation, regulatory
    • 5 steps, 3 enzymes, 5 coenzymes
  98. 5 steps of Pyruvate dehydrogenase complex (PDH complex)
    • 1. decarboxylation of pyruvate (TPP - acyl carry)
    • 2. oxidation of activated aldehyde to thioester (lipoyllysine - acyl carry and oxidize)
    • 3. transfer of acetyl group from lipo to CoA (acyl carrier and activator--trans, GOAL ACCOMPLISHED)
    • 4. oxidation of lipoyllysine by FAD (recycle cofactors)
    • 5. oxidation of FADH2 by NAD+ (recycle cofactors)
  99. coenzymes of pyruvate dehydrogenase complex (PDH Complex)
    • CoA and NAD+ used as substrates (one in, one out)
    • TPP, lipoyllysine and FAD used and regenerated
  100. multienzyme complex
    multiple copies of each component packed into a specific geometry that allows substrate channelling
  101. How many turns of citric acid cycle are needed to completely oxidize 1 glc to CO2?
    2.  2 pyruvate enter cycle from glycolysis, 2 acetyl CoA, 2 CO2 exit.
  102. step 1 of citric acid cycle
    oxaloacetate + acetyl-CoA + H2O→citrate synthasecitrate + CoA + H+
    • aldol condensation and hydrolysis
    • reaction driven by hydrolysis of acetyl CoA
    • irreversible, regulatory
  103. step 2 of citric acid cycle
    citrate ⇄ aconitase ⇄ isocitrate
    • OH is tertiary, moves to oxidizable position
    • 2 steps vial dehydration-rehydration
    • aconitase is a LYASE (not a mutase)
  104. step 3 of citric acid cycle
    isocitrate + NAD+→ isocitrate dehydrogenase α-ketoglutarate + CO2 + NADH + H+
    • oxidative decarboxylation
    • regulatory/irreversible
  105. step 4 of citric acid cycle
    α-ketoglutarate + NAD+ + CoA → α-KG dehydrogenase COMPLEX, TPP, lipollysine, FAD → succinyl-CoA + NADH + H+ + CO2
    • oxidative decarboxylation
    • like PDH complex
    • Irreversible, regulatory
    • GOAL ACCOMPLISHED, have thioester CoA, now regerate oxaloacetate
  106. step 5 of citric acid cycle
    succinyl CoA + GDP ⇄ succinyl CoA synthetase ⇄ succinate + CoA + GTP/ATP
    • substrate-level phosphorylation
    • hydrolysis of high-energy "pays" for ATP/GTP (which depends on enzyme)
  107. step 6 of citric acid cycle
    succinate + FAD ⇄ succinyl dehydrogenase ⇄ fumarate +FADH2
    • ONLY redox that produces C=C
    • stereospecific - TRANS only
    • ONLY FAD in cycle
    • ONLY membrane-bound enzyme in cycle
    • part of electron transport chain, feeds FADH into it
  108. step 7 of citric acid cycle
    fumarate + H2O ⇄ fumarase ⇄ L-malate
    • hydration, from lyase
    • only L-isomer formed (stereospecific enzyme)
  109. step 8 of citric acid cycle
    L-malate + NAD+ ⇄ malate dehydrogenase ⇄ oxaloacetate + NADH + H+
    • redox with oxidoreductase
    • regenerates starting compound
  110. energy yield from citric acid cycle
    • 1 GTP, 3 NADH, 1 FADH2 per acetyl CoA
    • 2 acetyl CoA/glc
    • 10 ATP per acetyl CoA
    • 20 ATP per glc 
    • doesn't include PDH or glycolysis
  111. key regulatory step of citric acid cycle
    PDH complex, feeds acetyl CoA into cycle
  112. Inhibition of PDH complex
    • high ratio  of ATP/ADP, NADH/NAD+, acetyl CoA/CoA
  113. Mechanism of PDH complex regulation
    • allosterism
    • covalent by reversible phosphorylation
  114. Regulation/activation/inhibition of citric acid cycle enzymes
    • allosteric
    • inhibited by high energy charge (ATP, NADH)
    • activated by low energy charge (ADP, NAD+) (Not FAD)
    • coordinates with glycolysis, citrate inhibits PFK-1