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Biochem midterm 2 > Final > Flashcards

Final Flashcards

1
Q

What is the first law of thermodynamics?

A

Energy cannot be created or destroyed, only transformed

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2
Q

What is the second law of thermodynamics?

A

All systems trend towards increasing entropy (increasingly disordered)

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3
Q

Define entropy?

A

entropy is a quantitative expression of the degree of randomness or disorder of the system.

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4
Q

When the delta S is negative what does it mean?

A

the disorder of the system has decreased

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5
Q

When the delta S is positive what does it mean?

A

the disorder of the system has increased.

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6
Q

Define enthalpy?

A

Enthalpy is the heat content of the system. it reflects the number and kinds of chemical bonds in the reactants and products.

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7
Q

When delta H is negative, what does it mean?

A

the chemical reaction produced heat and is exothermic

The heat content of the products is less than the reactants.

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8
Q

When delta H is positive, what does it mean?

A

the reaction system absorbs heat from its surroundings and is endothermic.

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9
Q

Define the Gibbs free energy? and give the equation

A

is equal to the amount of energy capable of doing work during a reaction at constant temperature and pressure.
deltaG= deltaH-T(deltaS)

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10
Q

When delta G is positive, what does it mean?

A

the product contains more free energy than the reactants. non-spontaneous endergonic.

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11
Q

When delta G is negative, what does it mean?

A

the products contain less free energy than the reactants. spontaneous exergonic

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12
Q

What is the chemical equilibrium?

A

the point in a reaction where the rates of the forward and reverse reactions proceed at an equal rate.

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13
Q

How do you calculate the keq?

A

concentration of products/concentration of reactants.

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14
Q

Give the equation for deltaG’

A

DeltaG’= -RT(lnK’eq)

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15
Q

Give the equation for delta G

A

DeltaG= deltaG’+ RT(lnKeq’)

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16
Q

When you have two delta G’ reactions and you want to know the deltaG’ of them both together, what do you do?

A

add both the delta G’ together.

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17
Q

The conversion of ATP to ADP +Pi is exergonic or endergonic?

A

exergonic

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18
Q

Why do the electrons of ATP have high potential energy?

A

Because the four negative charges in its three phosphate groups repel each other.

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19
Q

Why is the hydrolysis of ATP highly favourable under standard conditions?

A
  • better charge separation in products
  • more favourable resonance stabilization of products
  • Better solvation of products.
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20
Q

If you want to know the Keq’ of two reactions knowing their particular Keq’, what do you do?

A

multiply the two Keq’

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21
Q

What are the functions of hexokinases?

A
  • can regulate the rate at which glucose is used in glycolysis
  • can help regulate the amount of glucose-free in the body.
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22
Q

What are the two-steps groups involved in ATP-dependent reactions?

A
  1. a phosphoryl group is transferred from ATP to glutamate

2. The phosphoryl group is displaced by ammonia NH3 and release as Pi.

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23
Q

Where does the ATP come from?

A

Oxidation-reduction reactions

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24
Q

What happens when an atom is oxidized?

A

loses an electron

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25
Q

what happens when an atom is reduced?

A

gains an electron

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26
Q

What is the impact of a reduced compound on free energy?

A

the more reduced a carbon atom is, the more free energy is released upon oxidation.

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27
Q

Which atoms are sharing the bonds with the highest level of energy?

A

C-H and C-C bonds are shared more equally and have higher potential energy

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28
Q

Which bonds are holding less energy?

A

C-O bonds are held more tightly and have low potential energy

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29
Q

What is the mechanism of an electron transport chain?

A

electron transported down a series of acceptors as long as they are attracted by a sufficiently electronegative element.

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30
Q

What is the reduction potential?

A

affinity for electrons–> higher E= higher affinity.

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31
Q

What is the equation of Gibbs free energy based on the reduction potential?

A

deltaG’=-nFdeltaE’
n= number of electron transferred
F= faraday constant

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32
Q

What is the equation to determine the reduction potential?

A

Delta E’= -(RT/nF) *(ln keq)

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33
Q

if you want to combine the reduction potential of 2 reactions what do you do?

A

delta E’= E’(acceptor)- E’(donor)

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34
Q

What are the three redox reactions in which glucose is oxidized?

A
  1. Glycolysis
  2. Tricarboxylic cycle
  3. Electron transport and oxidative phosphorylation
    all part of cellular respiration
35
Q

What are the two electron carriers involved in the oxidation of glucose?

A

NADH

FADH2

36
Q

Give a general description of glycolysis

A

a six carbon glucose is broken down into two three-carbon pyruvate

37
Q

Give a general description of the pyruvate processing?

A

each pyruvate is oxidized to form acetyl CoA

38
Q

Give a general description of the citric acid cycle

A

Each acetyl CoA is oxidized to CO2.

39
Q

Give a general description of the electron transport and oxidative phosphorylation

A

electrons move through a transport chain and their energy is used to set up a proton gradient, which is used to make ATP

40
Q

What happens in cells when oxygen is absent as an electron acceptor?

A

fermentation and anaerobic respiration

41
Q

What are the two fundamental requirements of cells?

A

Energy to generate ATP

A source of carbon to use as raw materials for synthetizing macromolecules

42
Q

What are the four major pathway of glucose utilization?

A

Extracellular matrix and cell wall polysaccharides
Glycogen, starch, sucrose
Oxidation via pentose phosphate pathway –> ribose 5-phosphate
Pyruvate

43
Q

Generally describe the preparatory phase

A

One glucose molecule and two ATP are consumed

Two glycerahdehyde 3-phosphate are produced (both continue to the payoff phase

44
Q

What is the product of the payoff phase?

A

4 ATP + 2 NADH

45
Q

What are the two pathways for creating ATP?

A

Substrate-level phosphorylation, enzyme-catalyzed reaction.

oxidative phosphorylation, electron transport chain

46
Q

How is glycolysis regulated?

A

Regulated by feedback inhibition.

high levels of ATP inhibit the third enzyme phosphofructokinase.

47
Q

Where goes glycolysis occur in the cell?

A

the cytoplasm of the cell

48
Q

Where does the citric acid cycle occur in the cell?

A

mitochondrial matrix

49
Q

Where does oxidative phosphorylation occur in the cell?

A

inner membrane.

50
Q

What are the cristae?

A

extensions of the inner membrane of the mitochondria.
fill the interior of the mitochondria.
the mitochondrial matrix is inside the inner membrane.

51
Q

What are the three fates of pyruvate?

A
  • -> lactate
  • -> ethanol + co2
  • -> acetyl coa
52
Q

What enzyme is catalyzing the pyruvate processing?

A

pyruvate dehydrogenase complex.

53
Q

What are the 5 coenzymes required in pyruvate processing?

A

TPP, lipoyl lysine, FAD, NAD+ and CoA-SH

54
Q

How is pyruvate processing regulated?

A

Feedback inhibition, when products of glycolysis or pyruvate are abundant: PDH is phosphorylated and inhibited through shape change.

55
Q

What is the function of CoA?

A

only to accept and carry acetyl groups. Carrying the remaining carbons from glucose to the citric acid cycle to be further oxidized.

56
Q

What are the two products of pyruvate processing?

A

1 NADH and 1 acetyl-CoA.

57
Q

What do we call a process that involves both catabolism and anabolism? and give an example of such process

A

amphibolic

citric acid cycle.

58
Q

What is the net result of the citric acid cycle?

A

2CO2, 3NADH, FADH2, GTP, CoA, 3H+

59
Q

What is an anaplerotic reaction?

A

replenishment of the intermediates in order for the cycle and central metabolic pathway to continue.

60
Q

Name the 4 anaplerotic reactions for the CAC cycle

A

pyruvate –>(pyruvate caboxylase) Oxaloacetate. liver kidney
phosphoenolpyruvate–> (PEP carboxykinase) Oxaloacetate. heart, skeletal muscle
Phosphoenolpyruvate –> (PEP carboxylase) Oxaloacetate. higher plants, yeast, bacteria
Pyruvate –> (malic enzyme) Malate., eukaryote and bacteria

61
Q

Which compounds are high-energy intermediates in glycolysis?

A

1,3 biphosphoglycerate, phosphoenolpyruvate.

the compounds that produce ATP when transformed.

62
Q

What are the main reducing fuels for the cell?

A

carbohydrates, lipids and amino acids

63
Q

Name the four protein complexes in the electron transport chain

A

complex 1: NADH dehydrogenase
Complex 2: succinate dehydrogenase
complex 3: ubiquinone-cytochrome C oxidoreductace
complex 4: cytochrome C, cytochrome c oxidase, ubiquinone.

64
Q

What happens with the reduction potential as the electron move in the transport chain?

A

reduction potential increases. larger and positive E’ more likely to be reduced.

65
Q

How does O2 enter the mitochondrial matrix?

A

diffusion through inner mitochondrial membrane

66
Q

What is the net reaction of complex 1?

A

NADH + 5H+(matrix) +Q –> NAD+ + QH2 + 4H+ (inner membrane)

67
Q

What is the function of complex 1?

A

2 NADH becomes NAD. (oxidation)

2 H transferred to ubiquinone

68
Q

What is the function of complex 2?

A

Oxidation of FADH –> FAD+
reduction of ubiquinone
no pumping of H+

69
Q

What is the function of complex 3?

A

oxidation of reduced ubiquinone QH2
1 electron transferred to cytochrome C
4H+ are ending up in the intercellular space.

70
Q

What is the function of complex 4?

A

Oxidize the reduce Cyto C.

Oxygen is reduced to water.

71
Q

What is the total net reaction of the electron transport chain?

A

2NADH + 22H+ + O2 –> 2NAD+ + 20H+ +2H2O

72
Q

What provided the energy needed to phosphorylate ADP?

A

the flow of protons down the electrochemical gradient

73
Q

What are the three ways in which the electrochemical proton gradient is formed?

A
  1. actively transporting protons across the membrane with proton pumps.
  2. chemically removing protons from the matrix
  3. releasing protons into the intermembrane space
74
Q

What are the two components of ATP synthase?

A
  • an ATPase knob

- a membrane-bound proton transporting phase (rotor)

75
Q

What is the impact of the rotor F0 on ATP formation?

A

the spinning changes the conformation of the F1 unit so that it phosphorylates ADP to form ATP

76
Q

What is the total yield of ATP per glucose?

A

30-32

77
Q

How can electron carriers be incorporated in the matrix knowing that it is impermeable to them?

A

Incorporating them into malate

transported through malate alpha-ketoglutarate integral membrane transporter.

78
Q

What is the glycerol 3 phosphate shuttle?

A

electrons from the NADH produced during glycolysis instead enter the ECT directly.

  • electron from NADH transferred through glycerol-3-phosphate.
  • FAD –> FADH2
  • electrons are then transferred to ubiquinone within the lipid bilayer. entering the ETC complex 3
79
Q

What primarily regulates oxidative phosphorylation?

A
  • NADH and ADP/Pi

substrate availability

80
Q

What is the inhibitor of F1 and when is it active?

A

IF1

  • prevents hydrolysis of ATP during low oxygen
  • active at lower pH
81
Q

What does the inhibition of oxidative phosphorylation lead to?

A

accumulation of NADH in the cytosol

feedback inhibition up to phosphofructokinase.

82
Q

How can you know that a product is reduced?

A

often gain a H+

83
Q

How can you know that a product is oxidized?

A

often lose a H+

84
Q

What is the function of tautomerization in the last step of glycolysis?

A

lowers the concentration of the products in order to push the reaction toward more ATP formation

Biochem midterm 2 (3 decks)

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