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Biochem 501 > Catabolism and Bioenergetics > Flashcards

Catabolism and Bioenergetics Flashcards

1
Q

Cells obtain most of their energy by ____________ reactions of C-C and C-H bonds.

A

cells obtain most of their energy by oxidation reactions of C-C and C-H bonds

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2
Q

Keq

A

Keq=[C][D]/[A][B]
Keq=concentration of products / concentration of reactants.

  • If forward rxn favored, Keq greater than 1 and deltaG(naught) is negative.
  • If reverse rxn favored, Keq less than 1 and deltaG(naught) is positive.
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3
Q

The sign (+ or -) of delta G reveals…

A

direction of reaction toward reactants or products.
delta G negative (exergonic) = product-favored
delta G positive (endergonic) = reactant-favored

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4
Q

Magnitude of delta G indicates…

A

how far from equilibrium the reaction is; how much energy will be released as it proceeds to EQM.

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5
Q

Note, there are two deltaG’s…

A

the change in energy needed for a rxn to proceed to the transition state, and the difference in energy between reactants and products.

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6
Q

Cells store energy through

A

Adenosine triphosphate (ATP)

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7
Q

Basis of large free energy change (neg delta G) associated with ATP hydrolysis

A
  • electrostatic repulsion between O- on phosphate groups
  • resonance stabilization of products
  • ionization stabilization and solvation with H2O
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8
Q

Value and significance of -deltaG associated with ATP hydrolysis in a cell

A
  • 50 kJ/mol in a cell (-30.5kJ/mol under standard conditions)
  • Important because this value is “in the middle”–can donate AND receive phosphate groups
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9
Q

glycolysis pathway overview

A

Goal is for cell to derive energy.
Glucose (6-C sugar)&raquo_space;> 2 Pyruvate (3-C sugars),
Net gain of 2 ATP and 2 NADH

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10
Q

preparatory vs. payoff phase of glycolysis

A

Preparatory phase is when cell needs to put energy into system.
Payoff phase is when energy is stored for a net gain.

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11
Q

ATP’s role in glycolysis

A

ATP is the phosphate donor in glycolysis; drives reaction toward the products

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12
Q

A particularly large negative free energy change in a mechanism is an indicator of ________.

A

A particularly large negative free energy (exergenic) change in a rxn mechanism is an indicator of enzyme regulation that favors the products.

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13
Q

why are steps 1, 3 and 10 of glycolysis irreversible?

A

1,3- These are typically irreversible steps because the enzyme is a catalyst in the forward direction; the cellular conditions don’t allow reverse. Excess of reactants activates the enzyme.
10- product going into citric acid cycle, so irreversible

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14
Q

Regulation of phosphofructokinase in glycolosis

A

Presence of ADP represents a low energy concentration in cell and stimulates PFK-1 to carry out glycolysis and produce more ATP.
Large enzyme.
Step 3 of glycolysis.
Major control point, regulated by energy balance and use of fats as fuel.
Phosphorylates a substrate.
Regulated by an ATP substrate.

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15
Q

what are 2 major products of the (after glycolysis) pyruvate dehydrogenase complex that store energy?

A

NADH and bond between S and CoA

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16
Q

2 fates of pyruvate (after glycolysis)

A
  1. fermentation, anaerobic conditions (without oxygen)

2. aerobic respiration (with oxygen)

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17
Q

Pasteur Effect demonstrated

A

yeast cells consumed much more glucose under ANaerobic conditions. They were getting a much smaller yield of ATP per glucose molecule, therefore needing to increase glycolysis.

Much greater yield of ATP under aerobic conditions

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18
Q

Goal of fermentation

A

anaerobically regenerate NAD+ form NADH to maintain glycolysis.

If NAD+ is used up, there is no electron acceptor for oxidation, and glycolysis stops.

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19
Q

how do muscles recover from lactate build-up?

A

lactate can diffuse out of muscle cells and be converted to glucose and glycogen in liver.

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20
Q

what makes a molecule more energy rich?

A

C-C and C-H bonds store energy that can be oxidized to provide energy
ex. ethanol releases more energy when oxidized than pyruvate

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21
Q

energy density of a molecule

A

how much energy is stored per atom; molecules with fewer oxidized bonds have higher energy density

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22
Q

role of mitochondria in oxidations

A

Contains double membrane system, a soluble matrix, and ATP Synthase.
Lots of chemistry occurs in mitochondria:
-pyruvate oxidation
-citric acid cycle
-fatty acid oxidation

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23
Q

pyruvate dehydration (DH) complex (enzyme) subunits

A

Huge regulated enzyme complex. 3 subunits (E1, E2, and E3).

-E1=Decarboxylation
Anion attack, covalent intermediate releases CO2, C-C becomes C-H making a 2 carbon unit. Thyamine required.

-E2=Oxidation
Lipoic acid enters. 2 carbon unit oxidized to C=O. C=O displaced by CoA-SH. Now carrying electron pair.

-E3=shuttling electrons to NAD+ carrier so PDH can go “another round”.
NADH released storing energy.

Plus electron energy stored in S complex.

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24
Q

pyruvate dehydration (DH) complex (enzyme) regulation

A

INHIBITED by indicators of high energy (NADH, ATP) plus Acetlyl-CoA product.

STIMULATED by indicators of low energy (NAD+, AMP, and CoA).

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25
Q

2 roles of Coupling

A
  1. Drive unfavorable reactions forward via energy of ATP breakdown
  2. Preserve energy of highly favorable reactions by coupling to high energy compound (ATP, NADH, acetyl CoA, 1,3 BPG, etc.)
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26
Q

catabolism

A

the breakdown of complex molecules in living organisms to form simpler ones, together with the release of energy; destructive metabolism.

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27
Q

metabolism

A

the set of life-sustaining chemical reactions in organisms.
The three main purposes of metabolism are
1) the conversion of the energy in food to energy available to run cellular processes;
2) the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and
3) the elimination of metabolic wastes.

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28
Q

Citric Acid Cycle Inputs and Outputs

A

INPUTS: acetate of acetyl-CoA (2 C and 4 reduced bonds)

OUTPUTS: 3 NADH, FADH2, 2 CO2, and a GTP

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29
Q

If given 16 C fatty acid, how many acetyl CoA, FADH2, and NADH will result from beta oxidation?

A

16 C chain produces:
8 acetyl-CoA
7 NADH
7 FADH2

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30
Q

If given 16 C fatty acid, how many acetyl CoA, FADH2, and NADH will result from beta oxidation?

A 
16 C chain produces:
8 acetyl-CoA
7 NADH
7 FADH2
(After citric acid cycle, net 106 ATP!
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31
Q

Do fatty acids inhibit or promote the pyruvate dehydrogenase complex?

A

presence of fatty acids INHIBITS pyruvate dehydrogenase enzyme.
Fatty acids produce a great energy yield, so if they are present, the cells will use those for energy

32
Q

Role of fatty acid camaltine

A

transports fatty acid CoA from the cytosol across the inner membrane of the mitochondria to the mitochondria matrix for conversion back to fatty acid CoA and beta oxidation.

33
Q

What was concluded from the Knoop experiement?

A

fatty acids are oxidized 2 carbon units at a time.

34
Q

Enthalpy change

A

delta H
difference in bond energies between reactants and products.
exothermic = neg delta H; heat released as more stable bonds form.
endothermic = pos delta H; heat absorbed as less stable bonds form.

35
Q

entropy

A

change in randomness.
delta S.
increase in randomness is POS delta S by convention, which contributes to negative (favorable delta G).
delta G = delta H - TdeltaS

36
Q

Math relating delta G and Keq

A

deltaG = -6 * log Keq
(assumes standard conditions–naught)

deltaG / -6 = log Keq
10^(deltaG/-6) = Keq

  • If forward rxn favored, Keq greater than 1 and deltaG(naught) is negative.
  • If reverse rxn favored, Keq less than 1 and deltaG(naught) is positive.
37
Q

allosteric

A

non covalent bonding

38
Q 
2 fermentation (anaerobic) pathways
(there are others)
A

1) Pyruvate reduced to lactate,
NADH oxidized to NAD+

2) Pyruvate to ethanol (ex: yeast)
Ethanol provides higher energy density because it releases CO2, resulting in more C-C and C-H bonds.
(drinking alcohol is the reverse pathway, detoxing)

39
Q

Lactate diffuses out of muscle cells and can be converted to

A

glucose and glycogen in the liver

40
Q

site of oxidations

A

mitochondria!
oxidations for the citric acid cycle
fatty acid oxidation
pyruvate oxidation

41
Q

pyruvate oxidation to acetal-CoA

A

happens in the pyruvate dehydrogenase complex in the mitochondria

Inhibited by indicators of high energy,
Stimulated by indicators of low energy

IN: CoASH + NAD+
OUT: NADH + CO2

42
Q

Indicators of high energy in cell

A

NADH, ATP, FADH2

43
Q

Indicators of low energy in cell

A

NAD+, AMP, ADP, CoA

44
Q

Citric Acid Cycle forms ___ CO2 per ___acetyl CoA.

A

Citric Acid Cycle forms 2 CO2 per 1 acetyl CoA.

45
Q

How many reduced bonds does acetate bring in to the Citric Acid Cycle?

A

Acetate has 4 reduced bonds

46
Q

Lipid

A

general term which includes membrane components, hormones, vitamins, etc.

47
Q

triacylglycerols (aka triglycerides)

A

Triacylglycerol is a type of lipid used for energy storage.
Fatty acid joined to glycerol (otherwise would be soap and degrade organic molecules in our body!)
With hydration, 6.75x more energy per gram of fat relative to carbohydrate.
Very efficient way to store energy.

48
Q

Lipases

A

Lipases: enzyme that does a hydrolysis reaction with triacylglycerols to move fatty acids across membranes.

49
Q

The beta oxidation step of fatty acid oxidation breakdowns __ carbons at a time.

A

2

50
Q

If you have a 16 C chain go through the beta oxidation step of the citric acid cycle, it will result in ___ acetyl-CoA; plus reducing power in the form of ___NADH, and ___FADH2.

A

16 C chain in…
8 acetyl CoA
7 NADH
7 FADH2

51
Q

kinase

A

category of enzymes that add or remove phosphate

52
Q

isomerase (and mutase)

A

category of enzymes that isomerize molecules

Sets up a more favorable substrate. Generally used in next step of mechanisms, so the small concentration of product drives the reaction forward.

53
Q

dehydrogenase

A

category of enzymes that oxidize and reduce

steps that involve NADH or FADH2.

54
Q

role of glutamine synthetase

A

Detoxifies NH4+ generated by tissues other than the liver; results in gln to liver via bloodstream

55
Q

In liver cytoplasm, Nitrogen flows to urea cycle via amino acids. Goes to _______ and ________ in mitochondrial matrix, then to NH4 and aspartate.

A

In liver cytoplasm, Nitrogen flows to urea cycle via amino acids. Goes to glutamine and glutamate in mitochondrial matrix, then to NH4 and aspartate.

56
Q

role of aminotransferase enzyme

A

in using amino acids as fuel, aminotransferase converts glutamine and glutamate to aspartate.

57
Q

The two Nitrogen sources for the urea cycle are…

A

Aspartate and glutamate (from glutamine)

58
Q

E tells us

A

E = reduction potential in a redox reaction.

Delta E is the difference in reduction potentials, sometimes called the electron motive force.

By convention, positive delta E = spontaneous.

Calculate by comparing at half-cell reactions; greater E value gets the electrons (reduced) and lower E value is oxidized. Delta E is the spread between the two.

59
Q

Ubiquinol (QH2)

A

Ubiquinol is a membrane-soluble mobile carrier in the electron transport chain.

Used to make ATP in the mitochondria of cells.

Also called coenzyme Q or ubiquinone in oxidized form. QH2 is the reduced form.

60
Q

ATP synthesis is driven by ________.

A

ATP Synthase.

Protons flow through ATP synthase when the substrates ADP and Pi are present.

Rotary-like operation in mitochondria.

61
Q

Proton matrix force

A

Conformational change in subunits of ATP synthase that RELEASES ATP. The energy for this critical conformational change requires the energy of the PROTON GRADIENT (for subunit rotation).

On the other side of EQM, ATP can be used to make the proton gradient.

62
Q

Why do we get hot and winded running?

A

Use lots of ATP to run.
To replenish, you need lots of reducing power, so the citric acid cycle runs more rapidly.
This means greater NADH and FADH2 production, and more electron transport.
So, you need more OXYGEN to accept electrons.
This is not 100% efficient, so delta G released as heat.

63
Q

The Calvin Cycle converts…

A

in Photosynthesis, the Calvin Cycle converts (NADPH, ATP) + CO2 > sugars.

64
Q

Why does fermentation have to happen?

A

to regenerate NAD+

65
Q

Why do we need to get rid of NH4?

A

Ammonia can cross blood-brain barrier

66
Q

decarboxylation enzyme

A

makes a CO2 leaving group

67
Q

Purpose of enzymes

A

lower the activation energy for reactions

68
Q

How many redox reactions in the citric acid cycle?

A

4.

4 oxidations, 4 reduction

69
Q

ATP yield from reduction of NADH, FADH2, GTP

A

NADH gives 2.5 ADP
FADH2 gives 1.5 ADP
GTP gives 1.0 ADP

70
Q

Energy storage for both pyruvate dehydrogenase complex and the alpha ketoglutarate dehydrogenase complex

A

some of the energy from the substrate oxidation is preserved in a thiolester bond to coenzyme A

71
Q

Number of molecules of CO2 produced in one turn of the citric acid cycle?

A

2

72
Q

ATP’s role in urea production

A

In the series of reactions that result in the formation of urea from ammonia (NH4+) and aspartate, the energy of ATP is used to create a high energy intermediate from bicarbonate (aq CO2) so that adding ammonia to bicarbonate is a favorable reaction.

73
Q

light-activated electron carriers of photosynthesis

A

ATP and NADPH

74
Q

In photosynthesis, the source of electrons that flow through electron carriers in the chloroplast membrane is:

A

H20

75
Q

Role of uncoupler 2,4 dinitrophenol (DNP) and Oligomycin

A

Within ATP synthesis, DNP uncouples ATP production from electron transport chain and stops the protein gradient from pumping.

ATP production decreases. If not pumping H+, ATP synthase can’t spin as well.

Electron transport continues, leading to heat.
Oxidation of NADH continues, increases.
O2 still final electron acceptor so O2 consumption continues.

76
Q

Key points of Citric Acid Cycle

A

1) acetate from acetyl CoA comes in; 2C, 4 bonds that will be oxidized.
2) 4 bonds to be oxidized = 4 RedOX steps with the dehydrogenase enzyme for each turn of the cycle.
3) 2 CO2 released

Biochem 501 (2 decks)

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