Last section of Biochemistry Flashcards
(97 cards)
1
Q
Which of the following is not an intermediate in the citric acid cycle? A. Acetyl-CoA B.Citrate C. Oxaloacetate D. Succinyl-CoA E. alpha-Ketoglutarate
A
A. Acetyl-CoA
2
Q
Which of the following is not true of the reaction catalyzed by the pyruvate dehydrogenase complex?
A) Biotin participates in the decarboxylation.
B) Both NAD+ and a flavin nucleotide act as electron carriers.
C) The reaction occurs in the mitochondrial matrix.
D) The substrate is held by the lipoyl-lysine “swinging arm.”
E) Two different cofactors containing —SH groups participate.
A
A.) Biotin participates in the decarboxylation
3
Q
How many enzymes make up the Pyruvate dehydrogenase complex? What are the 5 cofactors?
A
- 3 enzymes
- cofactors: Thiamin, lipoate, CoA, FAD, NAD+
4
Q
patients may be given ____ to stimulate PDH by inhibiting the protein kinase that downregulates PDH
A
dichloroacetate
5
Q
Which of the below is not required for the oxidative decarboxylation of pyruvate to form acetyl-CoA?
A) ATP B) CoA-SH C) FAD D) Lipoic acid E) NAD+
A
A) ATP
6
Q
Pyruvate Dehydrogenase Complex: E1 does what?
A
pyruvate dehydrogenase:
- decarboxylates pyruvate via TPP
- oxidizes active acetaldehyde
- transfers 2 electrons and acetyl to lipoic acid on E2
7
Q
Pyruvate Dehydrogenase Complex: E2 does what
A
dihydrolipoyl transacetylase
-transfers acetyl-group to CoA to make acetyl-CoA
8
Q
Pyruvate Dehydrogenase Complex: E3
A
-dihydrolipoyl dehydrogenase
- reduces oxidized lipoic acid on E2
- transfers 2 electrons via FADH2 to NAD+ –> NADH
9
Q
Name the intermediates in the citric acid cycle
A
- oxaloacetate
- citric acid
- isocitrate
- a-ketoglutarate
- succinyl CoA
- succinate
- fumarate
- malate
10
Q
name the enzymes in the citric acid cycle
A
- citrate synthase
- aconitase
- isocitrate dehydrogenase
- a-ketoglutarate dehydrogenase
- succinyl-CoA synthetase
- succinate dehydrogenase
- fumarase
- malate dehydrogenase
11
Q
Pyruvate dehydrogenase and the citric acid cycle occurs in the
A
mitochondrial matrix
12
Q
the citric acid cycle is cyclic so ____ limit the rate of this process
A
-reaction intermediates
13
Q
Name the 4 irreversible reactions in the conversion of pyruvate to citric acid cycle
A
- pyruvate dehydrogenase complex
- citrate synthase
- isocitrate dehydrogenase
- a-ketoglutarate dehydrogenase
14
Q
each turn of the citric acid cycle yields
A
-2 CO2
-1 GTP
-3 NADH
-1FAHD2=1QH2
from each acetyl-CoA
15
Q
Anaplerotic reactions .
A) produce oxaloacetate and malate to maintain constant levels of citric acid cycle intermediates
B) produce biotin needed by pyruvate carboxylase
C) recycle pantothenate used to make CoA
D) produce pyruvate and citrate to maintain constant levels of citric acid cycle intermediates
E) All of the above
A
A) produce oxaloacetate and malate to maintain constant levels of citric acid cycle intermediates
16
Q
Which combination of cofactors is involved in the conversion of pyruvate to acetyl-CoA?
A) Biotin, FAD, and TPP B) Biotin, NAD+, and FAD C) NAD+, biotin, and TPP D) Pyridoxal phosphate, FAD, and lipoic acid E) TPP, lipoic acid, and NAD+
A
E) TPP, lipoic acid, and NAD+
17
Q
plants and some microbes can convert fat into glucose using the ____ cycle
A
-glyoxylate
18
Q
the glyoxylate cycle is confined to
A
-glyoxysomes
19
Q
effects of biotin deficiency
A
- scaly dermatitis
- in pregnant mothers can lead to birth defects
20
Q
synthase
A
condensation reactions occur without NTP
21
Q
synthetase
A
condensation reactions requiring NTP (sometimes called ligases)
22
Q
phosphorylase
A
breaks bonds using phosphate as nucleophile
23
Q
hydrolase
A
-breaks bonds using water as nucleophile
24
Q
kinase
A
-transfers phosphoryl from NTP to acceptor
25
phosphatase
-removes phosphoryl by hydrolysis
26
cytochromes
- always one-electron carriers
| - are proteins that contain iron atoms in hemes
27
Complex 1 of electron transport chain
NADH dehydrogenase: this is the entry point for the NADH electrons
-transfers 2 electrons from NADH and pumps 4 protons
28
complex 2 of ETC
succinate dehydrogenase: entry point for succinate electrons
- no protons pumped
- 2 electrons transferred to Q; 2 protons released from FADH2; 2 protons used for Q--> QH2
29
complex 3 of ETC
- cytochrome bc1 complex: reduces cytochrome c
| - 4 protons per 2 electrons
30
complex 4 of ETC
-cytochrome oxidase- passes electrons to oxygen
31
Give the order of the ETC electron carriers
-NADH--> Q-->cyt b-->cyt c1-->cyt c--> cyt(a+a3)--> O2
32
NADH and succinate are __ electron donors
2
33
FAD and FMN mediate _ or _ electron donations
1 or 2
34
Fe/S, Cu ions, and hemes are all _ electron carriers
1
35
Ubiquinone is a __ electron plus a __ proton carrier
2 and 2
36
electrons from mitochondrial NADH enter ETC through
Complex 1 (NADH dehydrogenase)
37
some electrons from the Citric Acid cycle enter the ETC via Complex
2 (succinate dehydrogenase)
38
other FADH2 using proteins contribute their electrons to QH2 at same level as complex_
2
39
all electrons entering the ETC go through QH2 and then to complex
3
40
which generates more ATP, NADH or QH2?
NADH
41
Consume 1 reduced NADH yields how many protons
2 electrons pump a total of 10 protons
42
1 succinate pumps how many H+?
-6 protons
43
what are the 3 main things the ETC does?
- re-oxidize reduced electron carriers
- translocated H+ from matrix to intermembrane space
- disposes of transported electrons by reducing molecular oxygen to harmless water
44
fermentation
-captures no free energy beyond the 2 ATP from glycolysis and works to regenerate NAD+ from NADH to allow glycolysis to continue
45
anaerobic respiration
-nearly same as oxidative phosphorylation but with a different molecule than oxygen at a complex analogous to complex 4
46
reactive oxygen species
- side products of oxidative phosphorylation
| - full reduction of dioxygen yields water, but partial reduction of oxygen yields toxic, reactive intermediates
47
how does brown fat make heat?
-if proton gradient is dissipated without making ATP, heat can be produced instead of ATP
48
Brown fat has ___, a special uncoupling protein that acts as a hole in then inner mitochondrial membrane
thermogenin
49
memorize figure in lecture 19 second to last slide
dfasdf
50
Antimycin A blocks electron transfer between cytochromes b and c1. If intact mitochondria were incubated with antimycin A, excess NADH, and an adequate supply of O2, which of the following would be found in the oxidized state?
```
A) Coenzyme Q
B) Cytochrome a3
C) Cytochrome b
D) Cytochrome e
E) Cytochrome f
```
B) Cytochrome a3
51
Reduced QH2 is not formed by which of the following?
```
A) Complex I and NADH
B) Complex II and succinate
C) Complex III and cytochrome c
D) Fatty acid oxidation
E) Oxidation of glycerol-3-phosphate
```
C) Complex III and cytochrome c
52
If electron transfer in tightly coupled mitochondria is blocked (with antimycin A) between cytochrome b and cytochrome c1, then:
A) all ATP synthesis will stop.
B) ATP synthesis will continue, but the P/O ratio will drop to one.
C) electron transfer from NADH will cease, but O2 uptake will continue.
D) electron transfer from succinate to O2 will continue unabated.
E) energy diverted from the cytochromes will be used to make ATP, and the P/O ratio will rise.
A) all ATP synthesis will stop.
53
In normal mitochondria, the rate of NADH consumption (oxidation) will:
A) be increased in active muscle, decreased in inactive muscle.
B) be very low if the ATP synthase is inhibited, but increase when an uncoupler is added.
C) decrease if mitochondrial ADP is depleted.
D) decrease when cyanide is used to prevent electron transfer through the cytochrome a + a3 complex.
E) All of the above
E) All of the above
54
Which of the following statements about the chemiosmotic theory is correct?
A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane.
B) It predicts that oxidative phosphorylation can occur, even in the absence of an intact inner mitochondrial membrance.
C) The effect of uncoupling reagents is a consequence of their ability to carry electrons through membranes.
D) The membrane ATP synthase has no significant role in the chemiosmotic theory.
E) All of the above
A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane.
55
Which of the following statements about the chemiosmotic theory is false?
A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane.
B) Energy is conserved as a transmembrane pH gradient.
C) Oxidative phosphorylation cannot occur in membrane-free preparations.
D) The effect of uncoupling reagents is a consequence of their ability to carry protons through membranes.
E) The membrane ATPase, which plays an important role in other hypotheses for energy coupling, has no significant role in the chemiosmotic theory.
E) The membrane ATPase, which plays an important role in other hypotheses for energy coupling, has no significant role in the chemiosmotic theory.
56
2,4-Dinitrophenol and oligomycin inhibit mitochondrial oxidative phosphorylation. 2,4-Dinitrophenol is an uncoupling agent; oligomycin blocks the ATP synthesis reaction itself. Therefore, 2,4-dinitrophenol will:
allow electron transfer in the presence of oligomycin.
57
Upon the addition of 2,4-dinitrophenol (DNP) to a suspension of mitochondria carrying out oxidative phosphorylation linked to the oxidation of malate, all of the following occur except:
A) oxygen consumption decreases.
B) oxygen consumption increases.
C) the P/O ratio drops from a value of approximately 2.5 to 0.
D) the proton gradient dissipates.
E) the rate of transport of electrons from NADH to O2 becomes maximal.
A.
58
Which of the following statements about energy conservation in the mitochondrion is false?
A) Drugs that inhibits the ATP synthase will also inhibit the flow of electrons down the chain of carriers.
B) For oxidative phosphorylation to occur, it is essential to have a closed membranous structure with an inside and an outside.
C) The yield of ATP per mole of oxidizable substrate depends on the substrate.
D) Uncouplers (such as dinitrophenol) have exactly the same effect on electron transfer as inhibitors such as cyanide; both block further electron transfer to oxygen.
E) Uncouplers "short circuit" the proton gradient, thereby dissipating the proton motive force as heat.
D) Uncouplers (such as dinitrophenol) have exactly the same effect on electron transfer as inhibitors such as cyanide; both block further electron transfer to oxygen.
59
When the delta G'° of the ATP synthesis reaction is measured on the surface of the ATP synthase enzyme, it is found to be close to zero. This is thought to be due to:
A) a very low energy of activation.
B) enzyme-induced oxygen exchange.
C) stabilization of ADP relative to ATP by enzyme binding.
D) stabilization of ATP relative to ADP by enzyme binding.
E) None of the above
D) stabilization of ATP relative to ADP by enzyme binding.
60
During oxidative phosphorylation, the proton motive force that is generated by electron transport is used to:
A) create a pore in the inner mitochondrial membrane.
B) generate the substrates (ADP and Pi) for the ATP synthase.
C) induce a conformational change in the ATP synthase.
D) oxidize NADH to NAD+.
E) reduce O2 to H2O
C) induce a conformational change in the ATP synthase.
61
The relative concentrations of ATP and ADP control the cellular rates of:
```
A) glycolysis.
B) oxidative phosphorylation.
C) pyruvate oxidation.
D) the citric acid cycle.
E) All of the above
```
E
62
The rate of oxidative phosphorylation in mitochondria is controlled primarily by:
A) feedback inhibition by CO2.
B) the availability of NADH from the TCA cycle.
C) the concentration of citrate (or) the glycerol-3-phosphate shuttle.
D) the mass-action ratio of the ATD-ADP system.
E) the presence of thermogenin.
D) the mass-action ratio of the ATD-ADP system.
63
Mammals produce heat by using the endogenous uncoupling agent:
```
A) the small molecule 2-4-Dinitrophenol synthesized by the cell.
B) the protein thermogenin.
C) the protein thioredoxin.
D) the protein cytochrome c.
E) a modified form of the FoF1 ATPase.
```
B) the protein thermogenin.
64
Which one of the following best describes the role of mitochondria in apoptosis?
A) Escape of cytochrome c into the cytoplasm
B) Increased rate of fatty acid -oxidation
C) Increase in permeability of outer membrane
D) Uncoupling of oxidative phosphorylation
E) Both A and C are correct.
E) Both A and C are correct.
65
Photosynthesis takes place
in the chloroplasts of
algae and plants, structures enclosed in double
membranes and filled with stacked membranous
discs (thylakoid membranes) containing the
photosynthetic machinery.
66
The light reactions of photosynthesis are those directly dependent on the _____; the
resulting photochemistry takes electrons from ___
and drives them through a series of membrane-
bound carriers, producing ___
- the absorption of light
- H2O
- NADPH and ATP.
67
excited state
A molecule that has absorbed a
photon
-generally unstable
68
The binding site for ___is the point of action of many commercial herbicides that kill plants by blocking electron transfer through ____ and preventing photosynthetic___ production.
- plastoquinone
- the cyto-chrome b6 f complex
- ATP
69
The ultimate source of the electrons passed to NADPH in plant (oxygenic) photosynthesis is ___
water.
70
Who steals an electron from water?
radical P680+
71
oxygen-evolving complex (also called
| the water-splitting complex), passes ______ to P680
passes four electrons one at a time to P680
72
The immediate electron donor to P680 is a ____ (often designated Z or TyrZ) in subunit D1 of the PSII reaction center.
-Tyr residue
73
site of light reactions
thylakoid lamellae
74
in photosynthesis, Protons get concentrated in the
lumen
75
Photosystem 2
– Maximally absorbs light at 680 nm
– High-energy electrons obtained from water via OEC
– Electron transfer used to form a proton gradient via the cytochrome B6F complex ! H+ gradient for ATP production
– Photosynthetic bacteria have related photosystems
76
Photosystem 1
Maximally absorbs light at 700 nm
– High-energy electrons obtained from PSII via plastocyanin
– Excited electrons transferred to NADP+-oxidoreductase
via ferredoxin to reduce NADP+ --> NADPH (usually)
77
Fat digestion occurs in the ___ of the _____
-lumen of the small intestine
78
Bile salts are amphipathic derivatives of ___that can coat ___ in the small intestine
- cholesterol
| - fat particles
79
lipases
- digestive enzymes synthesized in the pancreas as proenzymes
- they are activated in small intestine lumen
80
what are the primary digestion products of Tryacylglycerols?
- Free Fatty acids
| - monoacylglycerols
81
Which of the following answers is not true?
Phospholipase A1 hydrolyzes the fatty acid from the 1-position on the glycerol backbone.
Phospholipase B1 hydrolyzes the fatty acid from the 2-position on the glycerol backbone.
Phospholipase C hydrolyzes the complete phospho-head group from the glycerol backbone.
Phospholipase D hydrolyzes just the head group from the phospho-glycerol backbone.
-Phospholipase B1 hydrolyzes the fatty acid from the 2-position on the glycerol backbone.
82
Eicosanoids
- derived from omega 3 or omega 6 FAs
- made from arichidonic acid
- play important roles in signaling
83
β-oxidation has _steps & parallels _ citric acid cycle steps
4 steps and parallels 3
84
name the 4 enzymes in order of B-oxidation
- acyl-CoA dehydrogenase
- enoyl-CoA hydratase
- B-hydroxyacyl CoA dehydrogenase
- acyl-CoA acetyltransferase
85
How to calculate how many ATPs were produced from B-Oxidation
If each NADH yields 2.5 ATPs and each FADH2 yields 1.5 ATPs, then multiply the number of rounds by 4 and multiply the number of acetyl-CoA molecules by 10.
-Subract two ATP molecules for activation of the fatty acid.
86
how much energy from one turn of CAC ??
Acetyl-SCoA enters the citric acid cycle, where each acetyl-SCoA yields 1 ATP equivalent, 3 NADH, and 1 FADH2
87
mutase
an enzyme of the isomerase class that catalyzes the shifting of a functional group from one position to another within the same molecule. Examples of this are bisphosphoglycerate mutase, which appears in red blood cells and phosphoglycerate mutase, which acts in glycolysis.
88
```
When energy level high (low ADP/AMP)
& citric acid cycle intermediates low:
-Isocitrate dehydrogenase is ____-, BUT
Isocitrate lyase is NOT inhibited
Favors ____
```
- inhibited
| - gluconeogenesis
89
name the 3 essential complexes that participate in photosynthesis
- Cytochrome B6F complex uses electron flow to pump protons (eventually will produces ATP)
- Fd:NADP+ oxidoreductase uses electrons from Fd to reduce NADP+ and make NADPH
- Oxygen evolving complex: extracts electrons from water to replenish the electrons passed from reaction centers into photosystems
90
Glutamine
| synthetase
- major pathway for incorporating ammonia into biomolecules
- make glutamine from glutamate
- regulated by feedback inhibition
91
Feedback inhibition
-by end products of glutamine metabolism allosterically inhibit glutamine synthetase
92
Nitrogen from glutamine (or glutamate) can be transferred to other molecules by two
different routes
- Amidotransferases
| - Aminotransferases
93
Pyridoxal
-is an important cofactor in over a hundred
reactions involving amino acids
-from vitamin B6 carrier of amine groups
94
Excess ammonia moved as
amino acids alanine & glutamine - transported to the liver for disposal
95
```
Urea is made in the
___ in the
____ of ___ cells,
by _____ of
arginine to
ornithine at the end
of the urea cycle
```
- Urea cycle
- cytosol of liver cells
- hydrolysis
- arginine to ornithine
96
the one Urea cycle enzyme to know is
carbamoyl phosphate synthetase 1
97
The Citric acid cycle & the Urea cycle are coupled
through fumarate & α-ketoglutarate -
the asparate-argininosuccinate shunt
-fumarate and a-ketoglutarate
| the asparate-argininosuccinate shunt
