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BIOC4331: Biochemistry I > Quiz 5 (Lectures 13-15) > Flashcards

Quiz 5 (Lectures 13-15) Flashcards

1
Q

In reality, forms of P are observed with [completely/partially] filled L binding sites.

A

partially

(n-1, n-2, etc. ligands bound)

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2
Q

In Hill plots, experimentally, the slope of the line is always ___.

A

< n (Total number of binding sites on P)

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3
Q

What is the variable that represents the slope for Hill plots?

A

nH (Hill coefficient)

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4
Q

What’s the x-intercept value for Hill plots?

A

(log Kd) / nH

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5
Q

What’s the y-intercept value for Hill plots?

A

-log Kd

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6
Q

If the binding affinity change is the same as each subsequent ligand binds, then the plot will be a ______ line.

A

straight

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7
Q

Hill plot curves are usually what shape?

A

Sigmoidal

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8
Q

nH is the measure of the degree of _______.

A

cooperativity

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9
Q
  1. If nH = 1, there’s ___ cooperativity.
  2. If nH > 1, there’s ___ cooperativity.
  3. If nH < 1, there’s ___ cooperativity.
A
  1. no
  2. positive
  3. negative
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10
Q

Experimentally, nH is always ____ than the actual number of binding sites.

A

less

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11
Q

As [L] is raised to a power, this produces a _____ curve.

A

sigmoidal

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12
Q

Kd encompasses all bind sites. True or false?

A

True

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13
Q

What’s the variable P50?

A

The average dissociation for each site

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14
Q

What does the Hill plot for myoglobin (Mb) look like?

A

It’s linear wih a slope of 1.

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15
Q

What does the Hill plot for hemoglobin (Hb) look like?

A

It’s sigmoidal with two asymptotes.

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16
Q

What is the lower asymptote/P50 for the first O2 bound on hemoglobin?

A

100 kPa

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17
Q

What is the upper asymptote/P50 for the last O2 bound on hemoglobin?

A

0.7 kPa

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18
Q

What’s the Hill constant for the Hb Hill plot?

A

~3

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19
Q

CO is produced at low levels during _______.

A

metabolism

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20
Q

Free heme binds CO with _______ higher affinity than O2.

When heme is bound to Mb or Hb, the affinity for CO is only ___ (Mb) or ___ (Hb) folder higher than O2.

A

20,000

200; 250

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21
Q

Why doesn’t CO bind to Mb or Hb as strongly as it does with free heme?

A

There’s a weaker binding mode for CO with Fe2+.

CO can’t form its optimal linear conformation due to the steric presence of a His (E7).

His additionally stabilizes the preferred bent binding mode of O2 to Fe2+ through the formation of a hydrogen bond.

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22
Q

Who’s more susceptible to CO poisoning?

A

Smokers, individuals with heart/lung conditions or blood diseases that reduce availability of O2 to tissues, and fetuses (Fetal Hb has a higher affinity for CO than adult Hb)

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23
Q

Why doesn’t CO/O2Hb release much O2?

A

CO bound to 1-2 subunits of the Hb tetramer increases the affinity for O2 at the remaining subunits.

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24
Q

Describe the effect of pH (Bohr effect):
1. CO2 is converted to carbonic acid (H2CO3) via __________ in the _____.
2. Carbonic acid dissociates to yield ______, _______ the pH of the blood.
3. This causes _______ of some of the _______ involved in ionic interactions at the subunit interface in Hb.
4. This also causes a conformational change that facilitates __ release.

A
  1. carbonic anhydrase; erythrocytes
  2. protons; lowering
  3. protonation; amino acids
  4. O2
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25
Q

How does His (HC3) of the beta subunit play a major role in the Bohr effect?

A

When protonated His can form the ion pair with Asp, that stabilizes deoxyHb in the T state (low oxygen affinity).

The ion pair stabilizes the protonated form of His, giving it an abnormally high pKa.

In the R state, the ion pair is not present and the pKa drops back to 6.0. The residue is largely unprotonated in oxyHb at pH 7.6, the pH of blood at the lungs.

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26
Q

The high pO2 at the lungs causes O2 to [bind/dissociate] from Hb.

A

bind

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27
Q

As the conformation of Hb alters towards the R state (at the lungs), this causes what?

A

The release of protons picked up by the Hb amino acids at the tissues

These recombine with bicarbonate (HCO3-) to give a carbonic acid (H2CO3), which is then catalyzed by carbonic anhydrase back to CO2.

CO2 is then exhaled.

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28
Q

H+ binding to Hb stabilizes the __ state and is antagonisitic to ___ binding, stabilizing the __ state.

A

T; O2; R

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29
Q

At pH 7.6, Hb has a ____ affinity for O2.

A

higher

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30
Q

As the pH drops, the __ state is more favored.

A

T

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31
Q

Most of the metabolic CO2 is transported to lung as soluble _______. How does this compound contribute to the Bohr effect?

A

bicarbonate

About 15% of this reacts with the N-termini of Hb subunits and is transported as a covalent adduct. This releases protons that contribute to the Bohr effect.

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32
Q

What’s 2,3-bisphosphoglycerate (BPG)? What does it do?

A

It’s a heterotrophic allosteric modulator of Hb.

A single BPG molecule binds in a positively charged cavity between the subunits of Hb in the T state, making the transition to R state more difficult and lowering Hb affinity for O2.

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33
Q

What would happen without BPG under normoxic conditions?

A

Little O2 would be released from Hb at the tissues.

34
Q

BPG binding helps O2 transport under what conditions?

A

Hypoxic conditions

35
Q

If a person is quickly transported to high altitudes, BPG levels will _____, leading to a _____ in Hb O2 affinity.

A

increase; decrease

36
Q

BPG has a substantial effect on the amount of O2 picked up at the lungs. True or false?

A

False.

It has a substantial effect on its release at the tissues, restoring O2 delivery back to 40% of maximum.

37
Q

Fetal Hb has a ____ affinity for BPG than adult Hb, and thus a ____ afffinity for O2.

A

lower; higher

38
Q

What are cofactors?

A

Additional atoms or molecules essential for protein function

39
Q

What are metal cofactors? What are they involved in?

A

The simplest cofactors are metal ions that bind directly to the protein.

They can be involved in catalysis, binding ligands, electron transfer, and structural roles, and neutralizing highly charged biomolecules.

40
Q

Different metals have preferred protein ligands, such as…

A

N, O, or S donor atoms

41
Q

What’s a prosthetic group?

A

Permanently associated chemical component beyond the amino acids of the protein

42
Q

Metals involved in catalysis and electron transfer are generally ones that can easily change their _____/_____ state.

The most common ones are what?

A

charge/oxidation

Iron (Fe2+ and Fe3+)
Copper (Cu2+ and Cu+)

43
Q

Zn2+ can’t change its charge state, but it is a good _____.

A

Lewis acid (accepts electron pair)

44
Q

Hemes are cofactors in many different proteins. Most importantly, which three?

A

Hemoglobin, myoglobin, and cytochromes

45
Q

The ring that surrounds the iron ion in heme is called…

A

porphyrin

(May be attached to protein backbone)

46
Q

How is heme synthesized?

A
  1. CoA activates and solubilizes acyl groups.
  2. 8 molecules each of succinyl CoA and Gly are required to produce one molecule of heme.

(First step requires an enzyme, δ- ALA synthase, that requires an organic cofactor, pyridoxal phosphate (PLP), synthesized from Vitamin B6.)

47
Q

What’s a coenzyme?

A

Low molecular weight compound required for catalytic activity

Acts as a transient carrier of specific functional groups

48
Q

All water-soluble vitamins are…

A

coenzymes or the raw material to make coenzymes.

49
Q

Following a complete reaction cycle, what happens to the catalyst?

A

It returns to its orginal chemical and electronic state.

50
Q

What’s catalytic power?

A

The rate of the catalyzed reaction over the rate of the uncatalyzed reaction

51
Q

Most enzymes are proteins, but a few are what?

A

RNA

52
Q

What are prosthetic groups?

A

Cofactors or coenzymes that are tightly bound to the enzyme

(Ex. FAD)

53
Q
  1. What are holoenzymes?
  2. What are the protein parts called?
A
  1. Catalytically active enzymes that contain cofactors and/or coenzymes
  2. Apoenzyme or apoprotein
54
Q

What are the six classes of enzymes? What do they do?

A
  1. Oxidoreductases: Transfer of electrons
  2. Transferases: Group transfer reactions
  3. Hydrolases: Hydrolysis reactions
  4. Lyases: Addition of groups to double bonds or formation of double bonds
  5. Isomerases: Transfer of groups within molecules to yield isomers
  6. Ligases: Formation of C-C, C-S, C-O, and C-N bonds via condensation reactions
55
Q

What’s the active site?

A

The pocket on the enzyme in which a reaction takes place

56
Q

What’s a substrate?

A

The molecule that binds and is acted upon by the enzyme

57
Q

The complementarity of the binding surfaces means that enzymes have a _________ for their substrate.

A

high specificity

58
Q

Enzymes are often ________ in the reactions they catalyze.

A

stereospecific

59
Q

Simple chemical catalysts usually lead to a ______ of products.

A

racemic mixture

60
Q

Enzymes alter the ____ of chemical reactions.

A

rates

61
Q

Enzymes have no effect on what two things?

A

Free energy (∆G’º) and equilibrium position (K’eq)

62
Q

Enzymes speed up the forward and backward reactions equally. True or false?

A

True

63
Q

Reaction: X -> Y -> Z

The second reaction favors the final product (Z). It’s very energetically favorable in the forward reaction, so how can we deplete the initial substrate (X)?

A

By coupling the second reaction with a less favorable reaction

64
Q

Why are enzymes dependent on pH?

A

Because of the ionization state of active site residues and substrate, but also the stability of the protein fold

65
Q

The substrate on the way to product forms various distinct __________ with the enzyme.

A

reaction intermediates

66
Q

What’s the transition state complex? What does it represent?

A

The most strained structure between intermediates that has the highest energy

This represents the highest energy barrier that must be crossed to reach product (activation energy).

67
Q

The transition state represents a point at which decay to substrate or product is _______.

A

equally likely

68
Q

How do enzymes work to increase the rate of reaction/attainment of equilibrium?

A

They lower the activation energy.

69
Q

What are reaction intermediates?

A

Any species on the reaction pathway that has a finite chemical lifetime

(Longer than a molecular vibration 10^-13 s)

70
Q

What is ‡?

A

The transition state

71
Q

The stabilization of a certain transition state also controls the path of the reaction if multiple chemical side-products are possible. True or false?

A

True

72
Q

Reaction rates are determined by what two things?

A

The concentration of the reactants(s) and the rate constant (k)

73
Q

How is the activation energy lowered by enzymes?

A

The enzyme may form a transient covalent bond with the substrate to activate it, or a functional group from the substrate may be transiently transferred to the enzyme.

74
Q

In enzyme-catalyzed reactions, what’s the major source of free energy that lowers activation energies?

A

The contribution of non-covalent interactions in enzyme-substrate interactions

75
Q

Enzyme active sites are most complementary to the ________.

A

transition state

76
Q

Name four thermodynamic/physical barriers that contribute to the activation energy.

A
  1. Reduction in entropy required to orient 2 molecules correctly to react
  2. The removal of the solvation shell from reactants for them to react
  3. The distortion/strain that must occur in molecules in many reactions
  4. The need to properly align catalytic groups
77
Q

As [S] is increased while maintaining the total concentration of enzyme, a point will be reached where all the enzyme sites are occupied by S. What’s this point represented by?

A

Maximum velocity (Vmax)

78
Q

What’s kcat?

A

The turnover number of the enzyme (The rate of product formation per enzyme molecule)

79
Q

What’s Km (Michaelis constant)?

A

The [S] at which the initial velocity = 0.5 Vmax

The dissociation constant of ES
(E + S -> ES)

A measure of the affinity of the enzyme for the substrate

80
Q

As Km decreases, the affinity of the enzyme for the substrate ______.

A

increases

81
Q

When [ES] is constant, that’s called…

A

steady state.

82
Q

What’s the specificity constant equivalent to?

A

The rate constant for the reaction between free enzyme and free substrate

BIOC4331: Biochemistry I (9 decks)

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