1
Q
What is a molecule bound reversibly by a protein called?
A
A ligand.
2
Q
What is the structural adaptation that occurs between protein and ligand called?
A
Induced fit.
3
Q
What transition metal is commonly incorporated into heme to bind oxygen?
A
Iron.
4
Q
In what oxidation state must heme iron be to bind oxygen reversibly?
A
The ferrous (Fe2+) state.
5
Q
How many coordination bonds does the iron atom in heme have?
A
Six coordination bonds.
6
Q
What amino acid residue occupies one of the perpendicular coordination bonds in heme?
A
The proximal His.
7
Q
What highly toxic gas coordinates to heme iron with greater affinity than oxygen?
A
Carbon monoxide (CO).
8
Q
What structural motif is made up of eight alpha-helical segments connected by bends?
A
The globin fold.
9
Q
What monomeric protein facilitates oxygen diffusion in muscle tissue?
A
Myoglobin.
10
Q
What tetrameric protein is responsible for oxygen transport in the bloodstream?
A
Hemoglobin.
11
Q
How many amino acid residues make up a single myoglobin polypeptide?
A
153 amino acid residues.
12
Q
What term describes the equilibrium constant that measures the affinity of a ligand for a protein?
A
The association constant, Ka.
13
Q
What are the units for the association rate constant, ka, in a second-order reaction?
A
M^-1 s^-1.
14
Q
What term is equivalent to the molar concentration of ligand at which half of the available binding sites are occupied?
A
The dissociation constant, Kd.
15
Q
A lower value of Kd corresponds to what level of ligand affinity?
A
A higher affinity of ligand for the protein.
16
Q
What is the P50 of oxygen binding to myoglobin?
A
0.26 kPa.
17
Q
What amino acid residue selectively increases myoglobin’s affinity for oxygen by forming a hydrogen bond?
A
The distal His (His64 or His E7).
18
Q
How much better does carbon monoxide bind to free heme compared to oxygen?
A
More than 20,000 times better.
19
Q
How much better does carbon monoxide bind to heme when it is embedded in myoglobin?
A
Approximately 40-fold better.
20
Q
What causes the transient cavities in myoglobin that allow oxygen to enter and leave?
A
Rapid molecular flexing or ‘breathing’ of the amino acid side chains.
21
Q
What cells are mature red blood cells formed from?
A
Hemocytoblasts.
22
Q
How long do human erythrocytes typically survive?
A
About 120 days.
23
Q
What is the approximate oxygen saturation of hemoglobin in arterial blood passing from the lungs?
A
About 96% saturated.
24
Q
What is the approximate oxygen saturation of hemoglobin in venous blood returning to the heart?
A
About 64% saturated.
25
What globin chains make up adult human hemoglobin?
Two alpha chains and two beta chains.
26
How many amino acid residues are identical in the alpha, beta, and myoglobin polypeptide sequences?
Only 27 are identical.
27
What type of interaction primarily stabilizes the alpha-beta interfaces in hemoglobin?
The hydrophobic effect.
28
What are the two major conformations of hemoglobin?
The R state and the T state.
29
Which state of hemoglobin is more stable in the absence of oxygen?
The T state.
30
Which state of hemoglobin has a significantly higher affinity for oxygen?
The R state.
31
What specific bonds stabilize the T state of hemoglobin?
Ion pairs (or salt bridges).
32
What triggers the transition from the T state to the R state in hemoglobin?
The binding of oxygen.
33
What happens to the porphyrin ring when oxygen binds to hemoglobin?
It assumes a more planar conformation.
34
What is the shape of the oxygen binding curve for myoglobin?
Hyperbolic.
35
What is the shape of the oxygen binding curve for hemoglobin?
Sigmoid (or S-shaped).
36
What does a sigmoid binding curve indicate about ligand binding?
It indicates cooperative binding.
37
What is an allosteric protein?
A protein in which the binding of a ligand to one site affects the conformation of the protein either affecting binding properties of another site and/or the protein's function.
38
What are the ligands that induce conformational changes in allosteric proteins called?
Modulators.
39
What is the interaction called when the normal ligand and the modulator are identical?
A homotropic interaction.
40
What is the interaction called when the modulator is a molecule other than the normal ligand?
A heterotropic interaction.
41
What equation is used to study cooperative ligand binding to multisubunit proteins?
The Hill equation.
42
What does a Hill coefficient (nH) greater than 1 indicate?
Positive cooperativity in ligand binding.
43
What does a Hill coefficient (nH) equal to 1 indicate?
Ligand binding is not cooperative.
44
What does a Hill coefficient (nH) of less than 1 indicate?
Negative cooperativity.
45
What model for cooperative binding assumes all subunits undergo the transition from one conformation to the other simultaneously?
The MWC model (or concerted model).
46
What model for cooperative binding proposes that ligand binding can induce a conformational change in an individual subunit?
The sequential model.
47
What enzyme catalyzes the hydration of carbon dioxide to form bicarbonate in erythrocytes?
Carbonic anhydrase.
48
What is the effect of pH and carbon dioxide concentration on the binding and release of oxygen by hemoglobin called?
The Bohr effect.
49
How does the binding of protons and carbon dioxide affect the affinity of hemoglobin for oxygen?
It decreases the affinity for oxygen (inversely related).
50
What amino acid residue makes a major contribution to the Bohr effect by forming an ion pair when protonated?
His HC3 (or His146) of the beta subunits.
51
How does carbon dioxide chemically bind to hemoglobin?
As a carbamate group to the alpha-amino group at the amino-terminal end of each globin chain.
52
What molecule regulates oxygen binding to hemoglobin in relation to the pO2 in the lungs?
2,3-Bisphosphoglycerate (BPG).
53
How does BPG affect hemoglobin's affinity for oxygen?
It greatly reduces the affinity of hemoglobin for oxygen.
54
Which hemoglobin state does BPG stabilize?
The T state.
55
Where does BPG bind on the hemoglobin tetramer?
In the cavity between the beta subunits in the T state.
56
How many molecules of BPG bind to each hemoglobin tetramer?
Only one molecule.
57
What happens to blood BPG concentrations at high altitudes?
The BPG concentration begins to rise.
58
Why must fetal hemoglobin have a greater affinity for oxygen than maternal hemoglobin?
Because a fetus must extract oxygen from its mother's blood.
59
What subunits replace the beta subunits in fetal hemoglobin?
Gamma subunits.
60
Why does fetal hemoglobin have a higher affinity for oxygen?
It has a much lower affinity for BPG than normal adult hemoglobin.
61
What disease demonstrates the importance of amino acid sequence in determining globular protein function?
Sickle cell anemia.
62
What did Eduard Buchner's 1897 experiment demonstrate?
That cell-free yeast extracts could ferment sugar to alcohol, proving biological catalysis could happen outside living cells.
63
Who crystallized the first enzyme (urease) and showed enzymes were proteins?
James Sumner in 1926.
64
What are most enzymes made of?
Proteins.
65
What is an additional chemical component required by some enzymes for activity called?
A cofactor.
66
What is a complex organic or metalloorganic cofactor called?
A coenzyme.
67
What is a coenzyme or metal ion that is very tightly or covalently bound to the enzyme called?
A prosthetic group.
68
What is a complete, catalytically active enzyme together with its bound coenzyme called?
A holoenzyme.
69
What is the protein part of a holoenzyme called?
The apoenzyme or apoprotein.
70
How many classes are enzymes divided into based on the reaction they catalyze?
Seven classes.
71
What suffix is commonly added to the name of a substrate to name an enzyme?
-ase.
72
What specialized pocket on an enzyme does a catalyzed reaction take place in?
The active site.
73
What is the molecule that is bound in the active site and acted upon by the enzyme called?
The substrate.
74
Do catalysts affect reaction equilibria?
No, catalysts do not affect reaction equilibria.
75
What do catalysts do to the rate of a reaction?
They increase the rate of a reaction.
76
What is the starting point for either the forward or reverse reaction in a reaction coordinate diagram called?
The ground state.
77
What is the standard free-energy change at pH 7.0 denoted as?
Delta G nought prime.
78
What fleeting molecular moment exists at the top of the energy hill in a reaction?
The transition state.
79
What is the difference between the energy level of the ground state and the energy level of the transition state called?
The activation energy, Delta G_double_dagger.
80
How does a higher activation energy affect the reaction rate?
It corresponds to a slower reaction.
81
What is any species on the reaction pathway that has a finite chemical lifetime called?
A reaction intermediate.
82
When several steps occur in a reaction, what is the step with the highest activation energy called?
The rate-limiting step.
83
What provides the energy for the dramatic lowering of activation energies by enzymes?
Binding energy, Delta GB, from noncovalent interactions.
84
What hypothesis proposed that enzymes were structurally complementary to their substrates like a puzzle?
The lock and key hypothesis.
85
Why is a 'lock and key' complementary enzyme a poor catalyst?
Because it stabilizes the substrate rather than helping it reach the transition state.
86
To what must an enzyme be complementary in order to catalyze reactions effectively?
The reaction transition state.
87
What is the ability of an enzyme to discriminate between a substrate and a competing molecule called?
Specificity.
88
What does an enzyme do to the solvation shell of structured water surrounding a substrate?
It causes desolvation of the substrate.
89
What catalytic mechanism involves the transfer of a proton from one molecule to another?
General acid-base catalysis.
90
What type of catalysis involves the formation of a transient covalent bond between the enzyme and substrate?
Covalent catalysis.
91
About what fraction of all known enzymes require one or more metal ions for catalytic activity?
Nearly a third.
92
What discipline studies the rate of a reaction and how it changes in response to experimental parameters?
Enzyme kinetics.
93
What is the initial transient period of an enzymatic reaction called?
The pre-steady state.
94
What is the phase where the concentration of the ES complex remains approximately constant called?
The steady state.
95
What term describes the initial rate of an enzyme-catalyzed reaction?
Initial velocity, V0.
96
What is the maximum velocity an enzyme can achieve called?
Vmax.
97
What happens to the reaction rate when the enzyme is saturated with substrate?
Further increases in [S] have no effect on the rate.
98
What equation algebraically expresses the hyperbolic relationship between V0 and [S]?
The Michaelis-Menten equation.
99
What assumption states that the rate of formation of ES is equal to the rate of its breakdown?
The steady-state assumption.
100
What is the Michaelis constant denoted as?
Km.
101
What are the units for the Michaelis constant (Km)?
Units of molar concentration.
102
In practical terms, what substrate concentration is equivalent to Km?
The substrate concentration at which V0 is one-half Vmax.
103
What is the linear transformation of the Michaelis-Menten equation called?
The Lineweaver-Burk equation (or double-reciprocal plot).
104
In a Lineweaver-Burk plot, what does the y-intercept represent?
1/Vmax.
105
In a Lineweaver-Burk plot, what does the x-intercept represent?
-1/Km.
106
In a Lineweaver-Burk plot, what is the slope of the line?
Km/Vmax.
107
Do all enzymes that exhibit a hyperbolic dependence of V0 on [S] have a simple two-step reaction mechanism?
No, many have different mechanisms but still follow Michaelis-Menten kinetics.
108
What enzymes are the most important exceptions to Michaelis-Menten kinetics?
Regulatory enzymes.
109
When k2 is rate-limiting, what does Km approximate?
The dissociation constant, Kd, of the ES complex.
110
What general rate constant describes the limiting rate of any enzyme-catalyzed reaction at saturation?
kcat.
111
What is another name for the rate constant kcat?
The turnover number.
112
What parameter is the best way to compare the catalytic efficiencies of different enzymes?
The ratio kcat/Km (the specificity constant).
113
What is the upper limit to kcat/Km imposed by the rate of diffusion in aqueous solution?
The diffusion-controlled limit (10^8 to 10^9 M^-1 s^-1).
114
Enzymes that have a kcat/Km near the diffusion-controlled limit are said to have achieved what?
Catalytic perfection.
115
How many substrates and products do nearly two-thirds of all enzymatic reactions have?
Two substrates and two products (bisubstrate reactions).
116
What enzyme transfers a phosphoryl group from ATP to glucose?
Hexokinase.
117
In bisubstrate reactions, what is the complex called when both substrates are bound to the enzyme concurrently?
A noncovalent ternary complex.
118
What is the binding mechanism called when the first substrate must bind before the second can bind productively?
Ordered binding.
119
What is the mechanism called when the substrates can bind to the enzyme in any sequence?
Random binding.
120
What is the general relationship between free energy Delta G'o and the equilibrium constant K'eq?
Delta G'o = -RT ln K'eq.
121
What kind of dependence does V0 exhibit on [S] when [S] is very low relative to Km?
A linear dependence.
122
What does the rate equation reduce to when [S] is much less than Km?
V0 = (kcat/Km)[Et][S].
123
In a bisubstrate double-displacement reaction, what is the alternate name for the mechanism?
Ping-Pong mechanism.
124
What disease relies on the administration of 100% oxygen or hyperbaric oxygen to displace a tightly bound toxic ligand?
Carbon monoxide (CO) poisoning.
125
What naturally occurring organic molecule is bound to myoglobin to prevent iron oxidation?
Protoporphyrin IX (part of heme).
126
How many total oxygen molecules can a saturated hemoglobin tetramer bind?
Four.
127
Where is myoglobin particularly abundant?
In the muscles of diving marine mammals (and muscle tissue in general).
128
If a mutation removes the distal His from myoglobin, what is the likely effect on CO affinity relative to oxygen?
CO would bind much more tightly than oxygen (the selective advantage for oxygen would be lost).
129
What happens to the pKa of His146 in hemoglobin during the transition from the R state to the T state?
It increases, allowing it to be protonated and form an ion pair.
130
What term denotes a reaction whose rate is dependent on the concentration of only one reactant?
First-order reaction.
131
What are the units of a first-order rate constant?
Reciprocal time (e.g., s^-1).
132
Which thermodynamic parameter determines the rate of a reaction?
Activation energy (Delta G double_dagger).
133
Which thermodynamic parameter determines the equilibrium of a reaction?
Standard free-energy change (Delta G'o).
134
What principle explains how constraining the motion of two reactants accelerates their reaction?
Entropy reduction.
135
What parameter indicates the fractional saturation of a protein with a ligand?
Y (fraction of binding sites occupied).
136
What does the term [Et] represent in enzyme kinetic equations?
Total enzyme concentration.
137
When solving the Michaelis-Menten equation, what does k2[Et] equal?
Vmax.
138
What model uses magnetic interactions as a paradigm for the binding energy in enzymes?
The 'stickase' model.
139
If V0 = 5 uM/s and Vmax = 10 uM/s, what is the relationship between [S] and Km?
[S] is equal to Km.
140
Why is a transition-state analog a potent enzyme inhibitor?
Because enzymes bind the transition state more tightly than the substrate.
141
What happens to the oxygen binding curve of hemoglobin when the pH drops?
It shifts to the right (lower affinity).
142
In Cleland nomenclature, what denotes a reaction where substrates bind and products release in a specific sequence?
Ordered bi bi.
143
At what physiological location does hemoglobin bind oxygen efficiently due to high pO2?
The lungs.
144
At what physiological location does hemoglobin release oxygen due to lower pO2?
The tissues.
145
What enzyme is famous for a rate enhancement of 10^17 over the uncatalyzed reaction?
Orotidine phosphate decarboxylase.
146
What is the term for a transient chemical species formed during an enzyme reaction step?
Reaction intermediate.
147
If an enzyme has kcat = 600 s^-1 and [Et] = 0.02 uM, what is Vmax?
12 uM s^-1.
BIOMG 3300
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