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Biochemistry 501 > Unit 3 > Flashcards

Unit 3 Flashcards

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1
Q

Oxidation of which of the following bonds result in energy production by candles, cars, mice, and us?

A

C-H and C-C

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2
Q

What characterizes an oxidation reaction in terms of gain/loss?

A

loss of electrons, gain of oxygen, or loss of hydrogen

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3
Q

What characterizes a reduction reaction in terms of gain/loss?

A

gain of electrons, loss of oxygen, or gain of hydrogen

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4
Q

In what direction do reactions go?

A

NET reactions go towards equilibrium; e.g., if equilibrium = 1.8 M of A and 0.2 M of B and we start with 1.9 M of A and 0.1 M of B, reaction will proceed in the forward direction to reach equilibrium

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5
Q

negative deltaG

A

exergonic reaction, meaning if reaction occurs, will proceed in forward direction; energetically favorable

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6
Q

positive deltaG

A

endergonic reaction, meaning if reaction occurs, will proceed in reverse direction; not energetically favorable

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7
Q

0 deltaG

A

reaction is at equilibrium

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8
Q

enthalpy change (deltaH)

A

difference in bond energies between reactants and products; negative deltaH is exothermic (more stable), positive deltaH is endothermic (less stable)

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9
Q

relationship between deltaH and deltaG

A

exothermic (-deltaH) contributes to favorable deltaG (-deltaG)

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10
Q

entropy change (deltaS)

A

change in “randomness;” positive deltaS is favorable

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11
Q

relationship between deltaS and deltaG

A

positive deltaS contributes to favorable deltaG (-deltaG)

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12
Q

relationship between deltaG and Keq

A

as Keq increases, deltaG becomes more favorable (more negativE); large Keq (>1) means forward reaction is favored and thus deltaG is negative, while small Keq (<1) means reverse reaction is favored and thus G is positive

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13
Q

What do the sign and magnitude of deltaG indicate?

A
  1. Sign of deltaG reveals direction
  2. Magnitude of deltaG indicates how far from equilibrium/how much energy will be released as reaction proceeds to equilibrium
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14
Q

Does thermodynamics (deltaG) predict the rate of a reaction?

A

No, thermodynamics does not predict how rapidly equilibrium is approached, but rather how far a reaction is from equilibrium and the direction it will proceed to get there

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15
Q

Do enzymes change deltaG or Keq?

A

No, enzymes only change deltaGDD (double dagger), which is the activation energy of the transition state

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16
Q

How does ATP provide energy to substrates?

A

Going from less stable to more stable releases more energy, and ATP –> ADP is a massive increase in stability (lots of energy released, large -deltaG); subtrate coupling to this ATP breakdown renders amine formation available

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17
Q

yield of glycolysis

A

From one glucose molecule:
2 net ATP (4 total ATP)
2 NADH
2 pyruvate

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18
Q

What is the purpose of the preparatory stage of glycolysis?

A

the generation of two more energetic molecules (G3P) from a single molecule of glucose

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19
Q

Which reactions in glycolysis are coupled to ATP hydrolysis?

A
  1. Glucose + ATP —-> glucose 6-P + ADP via hexokinase and Mg2+
  2. Fru-6-P + ATP —-> Fru-1,6-bisP + ADP via phosphofructokinase (PFK-1)
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20
Q

How does coupling to ATP breakdown affect deltaG?

A

can allow a reaction that would normally not proceed in the forward direction (+deltaGo) garner a -deltaGo and proceed favorably in the forward direction

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21
Q

overview of glycolysis preparatory stage

A

Step 1-Step 5; 2 ATP are consumed in these steps, generating 2 G3P for the payoff stage

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22
Q

overview of glycolysis payoff stage

A

Step 6-Step 10; 4 ATP, 2 NADH, and 2 pyruvate are produced in these steps; remember that 2 net ATP produced because of consumption in prep stage

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23
Q

Which reactions in glycolysis yield NADH?

A

G3P + P + NAD+ <—-> 1,3-Biphosphoglycerate + NADH; this is the only redox reaction in glycolysis, and the energy of oxidation preserved in phosphate bond and NADH

This occurs twice/glucose (2 G3P generated in prep stage)

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24
Q

Where is the energy of oxidation from the dehydrogenase reaction of glycolysis preserved?

A
  1. Phosphate bond
  2. NADH
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25
What is unique about the dehydrogenase reaction in glycolysis?
it is the only redox (oxidation) reaction in glycolysis; is also coupled to the reduction of NAD+
26
dehydrogenation
common redox reaction in which a C-H or C-C bond is oxidized and a cofactor such as NAD+ is reduced (or vice versa)
27
Do all oxidations involve O2?
No, in dehydrogenation, O comes from H2O or a phosphate in dehydrogenase rather than from O2
28
Which reactions in glycolysis yield ATP (payoff steps)?
Both of these occur twice, as glucose has split into two G3P: 1. 1,3-Bisphosphoglycerate + ADP <----> 3-Phosphoglycerate + ATP via a kinase; first payoff, coupled to substrate level phosphorylation 2. Phosphoenolpyruvate + ADP <----> Pyruvate + ATP; second payoff
29
What are inhibitory factors of PFK-1?
high energy molecules such as ATP, fatty acids
30
What are stimulatory factors of PFK-1?
low energy molecules such as AMP, ADP
31
When defines a point of regulation (i.e., when is enzyme regulation necessary)?
any irreversible step such as those which involve a large -deltaG or are very far from Keq are points of regulation; enzymes are highly regulated at these points
32
After glycolysis, what happens to pyruvate?
1. Under aerobic conditions, aerobic respiration involving Acetyl-CoA occurs 2. Under anaerobic conditions, fermentation occurs
33
Pasteur effect
yeast glucose consumption is much greater under anaerobic conditions than aerobic conditions; that is, only 2 ATP/glucose under anaerobic conditions, but 30 ATP/glucose under aerobic conditions
34
What is the primary purpose of fermentations (aside from ATP production)?
ways to anaerobically regenerate NAD+ from NADH to maintain glycolysis
35
2 types of fermentation
1. Pyruvate to lactate via lactate dehydrogenase ("Athletes and Alligators") 2. Pyruvate to ethanol via pyruvate decarboxylase and alcohol DH (yeast)
36
lactate dehydrogenase fermentation
pyruvate + NADH ----> lactate + NAD+ via lactate dehydrogenase enzyme; used in "Athletes and Alligators"
37
ethanol fermentation
2 step reaction; Step 1 catalyzed by pyruvate decarboxylase, Step 2 carried out by alcohol dehydrogenase (in this step NAD+ is regenerated); CO2 byproduct of first step
38
What is the unique byproduct of ethanol fermentation?
CO2
39
How does the energy density of ethanol compare to that of glucose?
ethanol has much greater energy density (7.1kcal/g) despite glucose having more usable bonds; this is because glucose has a higher percentage of oxidized bonds
40
Where does glycolysis occur?
cytoplasm
41
Where does pyruvate oxidation occur?
mitochondrial matrix
42
Where does the Citric Acid Cycle occur?
mitochondrial matrix
43
Where does fatty acid oxidation occur?
mitochondrial matrix
44
Where does ATP synthesis via ATP synthase occur?
inner membrane of mitochondria
45
pyruvate oxidation
pyruvate + CoASH + NAD+ ----> acetyl-CoA + CO2 + NADH via the pyruvate dehydrogenase complex; energy of oxidation preserved in NADH and thiolester bond of acetyl-CoA This step is a preparatory one that is required for entry into the Citric Acid Cycle
46
yield of pyruvate oxidation
NADH, CO2, acetyl-CoA per pyruvate 2 NADH, 2 CO2, 2 acetyl-CoA per glucose
47
Where is energy of pyruvate oxidation preserved?
1. NADH 2. thiolester bond of acetyl-CoA
48
pyruvate dehydrogenase complex
huge regulated enzyme complex with 3 subunits (E1, E2, E3); inhibited by high energy molecules (NADH, ATP, acetyl-CoA) and stimulated by low energy molecules (NAD+, AMP, CoA); TPP and lipoate along with NAD+ and FAD are key cofactors
49
What are the key cofactors of pyruvate dehydrogenase complex?
1. thiamine (TPP) 2. lipoic acid
50
What occurs at E1 in pyruvate DH?
decarboxylation; TPP anion attacks pyruvate; CO2 byproduct
51
What occurs at E2 in pyruvate DH?
oxidation; acetyl-CoA product from step 2 1. TPP-pyruvate complex from E1 attacks oxidized lipoic acid 2. CoASH attacks intermediate (lipoic acid is in acylated form), releasing acetyl-CoA and resulting in reduced form lipoic acid
52
What does the "long arm" of oxidized lipoic acid do?
on E2, this long arm facilitates shuttling of substrate
53
What occurs at E3 in pyruvate DH?
shuttling electrons to NAD+ (carrier), enabling PDH to go another round 1. Reduced form lipoic acid converted to oxidized form, FAD becomes FADH2 2. FADH2 donates its electrons to NAD+, forming FAD and NADH
54
overview of citric acid cycle
Per one molecule of acetyl-CoA (remember there are 2 acetyl-CoA/glucose molecule): Input: Acetate of Acetyl-CoA (2 C and 4 reduced bonds) Output: 3 NADH, FADH2, 2 CO2, and a GTP
55
What drives the first step of the citric acid cycle (oxaloacetate to citrate)?
large -deltaG of hydrolysis of high-energy (CoA-linked) form of acetate; i.e., "cash in" some of saved energy in PDH reaction
56
progressive oxidation
idea of molecules starting in an energy rich, reduced state, and being oxidized through a series of steps until they are energy poor and fully oxidized; dehydrogenases catalyze progressive oxidations in clockwise direction of citric acid cycle
57
How many dehydrogenases are in the Citric Acid Cycle?
4
58
How many reduced cofactors are in the Citric Acid Cycle?
4
59
alpha-ketoglutarate dehydrogenase complex
analogous to PDH; similar E1 and E2, identical E3, energy of oxidation conserved in thiolester bond of Succinyl-CoA and NADH, both thiamine and lipoate are cofactors
60
Which reactions in the citric acid cycle yield FADH2?
desaturation (oxidation) reaction that converts succinate (7 oxidizable bonds) to fumarate (6 oxidazable bonds); FAD serves as an e- acceptor in this reaction, yielding FADH2
61
Why is the fumarase reaction of the citric acid cycle unique?
it is a hydration reaction; simply prepares substrate for final oxidation
62
How many CO2 molecules are produced per glucose in pyruvate oxidation?
2 CO2; one from each pyruvate
63
How many CO2 molecules are produced per glucose in the citric acid cycle?
4 CO2; 2 CO2 per acetyl-CoA, 2 acetyl-CoA from 2 pyruvates
64
What is unique about oxaloacetate concentration in the final step of the citric acid cycle (malate to oxaloacetate)?
concentrations must be kept extremely low due to the fact that deltaGo is very large and positive; deltaG must be very large and negative, and this low concentration allows for that
65
Warburg effect
normal cells produce lactate only when anaerobic, whereas cancer cells produce lactate under both anaerobic and aerobic conditions
66
triacylglycerols vs carbs (energy)
with hydration, triacylgycerols have ~6.75x more energy per gram of fat relative to carbohydrate
67
3 steps of fatty acid oxidation
1. Activation - fatty acid joined to CoA 2. Transport - across inner mitochondrial membrane into matrix 3. Beta-oxidation - conversion of fatty acid into acetyl-CoA units in mitochondrial matrix
68
How are fatty acids activated?
acyl-CoA synthetases react with ATP and CoASH to form fatty acyl-CoA
69
Where does fatty acid activation occur?
cytosol of mitochondria; from here, must be transported into the cell
70
What is the role of carnitine acyltransferase I?
synthesize fatty acyl-CoA-carnitine complex so it can enter the mitochondrial matrix
71
What is the role of carnitine in fatty acid synthesis?
forms a complex with fatty acyl-CoA, allowing it to be transported across the mitochondrial membrane into the matrix
72
What did the Knoop experiment conclude?
that fatty acid oxidation is a step-wise breakdown by 2C units and that oxidation occurs at the beta carbon
73
How many acetyl-CoAs are formed from beta-oxidation?
n+1 acetyl-CoAs formed from n beta-oxidations; e.g., C8 undergoes 3 beta-oxidations, so 4 acetyl-CoAs formed
74
yield of beta-oxidation
A single beta-oxidation yields: 2 acetyl-CoA, 1 FADH2, 1 NADH These 2 acetyl-CoA can go through citric acid cycle to yield an additional 6 NADH, 2 FADH2, and 2 GTP
75
How many beta-oxidations will a fatty acid undergo?
a Cn fatty acid will undergo (n/2)-1 beta-oxidations; e.g., C16 fatty acid will undergo 7 beta-oxidations
76
Why do we subtract 2 ATP from the net yield of beta-oxidation?
the activation of palmitate in fatty acid activation requires the breakage of 2 high energy P bonds
77
Can fatty acids be inhibitory?
Yes, in animals, fatty acids can inhibit PDH in pyruvate oxidation
78
What is the purpose of the urea cycle?
using amino acids for fuel generates toxic NH4+, so we use the urea cycle to eliminate NH4+ in urine as urea
79
detoxification by glutamine synthetase
Glutamate + NH3 + ATP ----> Glutamine + ADP; resulting glutamine delivered to liver, where it can go through urea cycle
80
aminotransferase reactions
transaminations (swapping amino groups); these reactions always involve glutamate and alpha-ketoglutarate
81
How is aspartate generated for the urea cycle?
glutamate reacts with aspartate aminotransferase to form aspartate
82
How is citrulline formed in the urea cycle?
Carbamoyl Phosphate + Ornithine
83
What enzyme releases urea?
arginase
84
glutamine and glutmate urea cycle reaction
Glutamine ----> Glutamate + NH4+ via glutaminase; provides the "first" N for the urea cycle
85
How does NH4+ enter the urea cycle (2 ways)?
1. Glutamine acted on by glutaminase to form glutamate + NH4+. This ammonia reacts with ATP (carbamoyl phosphate synthetase I enzyme) to form carbomoyl phosphate. Carbamoyl phosphate reacts with ornithine to form citrulline 2. ATP is used to energize citrulline, allowing it to react with aspartate to form argininosuccinate
86
ketogenic amino acids
amino acids whose carbons end up in acetate (acetyl-CoA or acetoacetyl-CoA)
87
glucogenic amino acids
amino acids whose carbons end up within citric acid cycle intermediates
88
reduction potential (E)
affinity for electrons; i.e., tendency to become reduced or oxidized
89
Eo
standard reduction potential; more positive Eo in a half-reaction is the reaction that proceeds in the forward direction (i.e., is reduced)
90
path of NADH e- in the electon transport chain
1. Complex I 2. Ubiquinone 3. Complex III 4. cyt C 5. Complex IV 6. O2
91
path of succinate/FADH2 e- in the electron transport chain
1. Complex II 2. Ubiquinone 3. Complex III 4. cyt C 5. Complex IV 5. O2
92
What electrons enter the ETC at complex I?
electrons from NADH
93
What electrons enter the ETC at complex II?
electrons from succinate/FADH2
94
Which molecules are oxidized at complex I in the ETC?
NADH
95
Which molecules are oxidized at complex II in the ETC?
succinate (FADH2 cofactor)
96
Which molecules are oxidized at complex III in the ETC?
ubiquinol (QH2)
97
Which molecules are oxidized at complex IV in the ETC?
cytochrome c
98
Which molecules are reduced at complex I in the ETC?
ubiquinone (Q)
99
Which molecules are reduced at complex II in the ETC?
ubiquinone (Q)
100
Which molecules are reduced at complex III in the ETC?
cytochrome C
101
Which molecules are reduced at complex IV in the ETC?
O2
102
How many protons are pumped at complex I in the ETC?
4 (per NADH, which carries 2 e-)
103
How many protons are pumped at complex II in the ETC?
none, only increases pool of ubiquinol by reducing ubiquinone via succinate dehydrogenase
104
How does ubiquinol arise in the ETC?
Complexes I and II reduce ubiquinone, forming ubiquinol
105
How many protons are pumped at complex III in the ETC?
4 (per 2 e-)
106
How many protons are pumped at complex IV in the ETC?
2 per 2e-, 4 per O2
107
cytochrome c
protein that shuttles electrons between complexes III and IV in the ETC
108
What is the significance of the reaction at complex IV in the ETC?
the reduction of O2 to H2O accounts for greater than 99% of the O2 we use
109
How do we defend against reactive oxygen from ETC?
glutathione peroxidase enzyme reduced peroxide into water
110
electron transport coupling
oxidation/electron transport are coupled to proton pumping; NADH/succinate/FADH2/QH2/cyt c will only be oxidized if proton (H+) pumping can also occur
111
ATP synthesis coupling
ATP production is coupled to H+ flow through ATP synthase; protons will not flow through ATP synthase unless the substrates (ADP + P) are present
112
What would happen if the proton gradient were built up to equilibrium (e.g., when ATP synthase not operating to dissipate H+ gradient)?
there would be no further net oxidations, e- transport or H+ pumping
113
uncouplers
reduce or prevent ATP synthesis, but speed up e- transport
114
DNP and weight loss
if you ingested a non-toxic dose of DNP and did not change your eating habits, you would lose weight because glycolysis and lipid catabolism would increase to "keep up" following disruption of ATP synthesis
115
How do uncouplers (e.g., DNP) affect O2 consumption?
O2 consumption increases, as the electron transport chain increases; more O2 consumed and converted to H2O at complex IV
116
Is ubiquinone membrane soluble?
Yes, ubiquinone is membrane soluble

Biochemistry 501 (4 decks)

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