Chapter 6 + Quiz Questions Flashcards
(159 cards)
1
Q
Life depends on the ability to ..?
A
Efficiently and selectively catalyze chemical reactions
2
Q
True or False: most biomolecules are very stable with rates of uncatalyzed transformations that are too slow to permit life?
A
True
3
Q
Enzymes provide a mechanism for 1., 2., and 3. for reactions
A
- Acceleration
- Regulation
- Coordination
4
Q
The most striking feature about enzymes are their ____ ____ and ______
A
Catalytic power, specificity
5
Q
True or False: enzymes serve only as catalysts?
A
False, they can also be information sensors
6
Q
Define Vitalism
A
The belief that living things are fundamentally different from non-living things; that they contain some non-physical element and are governed by different principles than inanimate objects
7
Q
Which scientist believed in vitalism?
A
Louis Pasteur
8
Q
What as Eduard Buchner’s contribution to Biochemistry?
A
He demstrated that dead yeast still converts sugars into alcohol, indicating the reactions of life were separate from life
9
Q
What are co-factors?
A
Inorganic ions such as Mg2+ and Fe2+
10
Q
What are co-enzymes?
A
Complex organic molecules/vitamins
11
Q
True or False: some enzymes require co-factors or co-enzymes for activity?
A
True
12
Q
What is a prosthetic group?
A
A co-enzymes or co-factor that is tightly associated with the enzyme, the difference is the degree of association
13
Q
Different enzymes that use the same co-enzyme usually perform ___ types of reactions
A
similar
14
Q
Catalysts ___ the amount of energy required for a reaction to proceed
A
lower
15
Q
Do catalysts speed up or slow down the attainment of equilibrium? Do they change equilibrium?
A
Speed up, and they do not influence the difference in
free energy between S and P and therefore do not influence the equilibrium
16
Q
Catalysts are ____ by the reaction; ____ to participate in another reaction
A
unchanged, recycled
17
Q
Which is faster: enzymes or chemical catalysts?
A
Enzymes are often much faster, some approaching catalytic perfection
18
Q
Which of the two require extremes of temperature, pressure and pH: enzymes or chemical catalysts?
A
Chemical catalysts, enzymes function under physiological conditions
19
Q
Which has a higher degree of specificity: enzymes or chemical catalysts?
A
Enzymes, this includes specificity for what they act upon and what they produce, and steroespecificity
20
Q
Which of the two are responsive to the dynamic needs of the cell and organism: enzymes or chemical catalysts?
A
Enzymes
21
Q
True or False: enzyme rates of catalysis can approach the physical limit of rates of diffusion of molecules in solution?
A
True
22
Q
Some enzymes have ___-_____ steps that are roughly as fast as the binding of substrates to the enzymes
A
rate determining
23
Q
Some enzymes are able to catalyze reactions ______ than predicted by diffusion-control limits
A
faster
24
Q
What is the meaning of this relationship? E + S <-> ES <-> E + P
A
Enzymes catalyze the interconversion of substrate and product
25
What is the Active Site?
The portion of enzyme responsible for binding the substrate to formation of an enzyme-substrate (ES) complex
26
The active site is a 3D cleft formed from _______ parts of the _______ chain
different, polypeptide
27
True or False: the active site represents a large part of the enzyme?
False, it represents just a small part
28
Active sites are unique _______
microenvironments
29
Substrates are bound to enzymes by multiple ____ interactions
weak
30
The specificity of substrate binding depends on the ..?
Precisely defined arrangements of atoms in the active site. Enzymes and their active sites can be quite flexible
31
Substrate binding can cause _____ ___ or _______ ______
Induced fit, conformation selection
32
What is the Lock and Key model?
The active site is like a "lock" to which substrate fits like a "key." The enzyme's active site and substrate should fit like lock & key to initiate a reaction
33
What is the Hand-in-a-Glove (induced fit) model?
Binding of substrate induces a conformational change in the active site and both adjust their shapes to provide optimal fit
34
A reaction can only be spontaneous if ΔG ? 0
ΔG < 0
35
Define spontaneous
The reaction will proceed without the input of energy and the reaction releases energy (exergonic)
36
Define Exergonic reaction
The reaction releases energy
37
A reaction is non-spontaneous if ΔG ? 0
ΔG > 0
38
Define Endergonic reaction
An input of free energy is required to drive the reaction
39
In a system at equilibrium, there is no net change in the concentration of the products and reactants, and the ΔG ? 0
ΔG = 0
40
The ΔG of a reaction depends only on ..?
The free energy of the product minus the free energy of the reactants
41
True or False: the ΔG of a reaction is independent of the steps of the transformation?
True
42
True or False: the ΔG provides all the information about the rate of a reaction
False: the ΔG provides no information
43
What determines the rate at which equilibrium is reached?
Activation energy (ΔG‡) between S and P
44
Enzymes provide an alternate, lower-energy pathway between the substrate and product, _____ ΔG‡
lowering
45
The relationship between the rate of a reaction and the activation energy is _____ and _______
inverse, exponential
46
What determines the equilibrium of the reaction
Difference in free energy between S and P
47
Enzymes provide a ____-energy pathway between the substrate and product, ____ the activation energy of the transition state and ____ the rate of reaction
lower, decreasing, increasing
48
Catalytic capabilities of enzymes result from both _____ and ____ effects
chemical, binding
49
What is classified under Binding Effects?
Substrate Binding and Transition-state Stabilization
50
What is classified under Chemical Effects?
Acid/Base Catalysis and Covalent Catalysis
51
Binding of substrate in the active site provides ____ and ____ ____
specificity, catalytic power
52
In this relationship: E + S <-> ES <-> ETS <-> E + P, what is considered Substrate Binding and what is considered Transition State Stabilization?
E + S <-> ES = Substrate Binding
ES <-> ETS = Transition State Stabilization
53
What are the 5 ways Substrate Binding promotes reactions?
1. Reducing entropy
2. Alignment of reactive functional groups of the enzyme with the substrate
3. Desolvation of the substrate to expose reactive groups
4. Distortion of substrates
5. Induced fit of the enzyme in response to substrate binding
54
An increased interaction of the enzyme and substrate occurs in the ____-____
transition-state
55
What is the essence of catalysis?
The stabilization of the transition state
56
The enzyme _____ the substrate, forcing it toward the transition state.
distorts
57
The active site is complementary to the transition-state in _____ and ______ _______
shape, chemical character
58
Active site must be _____ enough to substrate to ensure specificity, ____ enough to promote change
similar, different
59
What are Transition-state analogs (TSAs)?
Stable compounds that resemble unstable transition states
60
True or False: transition-state analogs have potential therapeutic applications as competitive inhibitors
True
61
What are Competitive Inhibitors?
Molecules that bind to the active site of an enzyme,
they tend to resemble the substrate molecule
62
What is the problem with competitive inhibitors and their resemblance to the substrate molecule?
TSAs can bind the active site of a target enzyme active site with high affinity, preventing substrate binding
63
After substrate binding, the enzyme can act upon the substrate to promote ______ of the product
formation
64
The active site often contains ______ ______ side chains
chemically reactive
65
The active site often contains chemically reactive side chains.This includes polar, ionizable side chains (triprotics) such as #1, #2, #3, #4, #5, #6, #7, #8
Asp, Glu, His, Cys, Tyr, Lys, Arg, and Ser
66
In which type of catalysis does the reaction acceleration become achieved by catalytic transfer of a proton
Acid-Base Catalysis
67
In Acid-Base Catalysis, the side chains of some amino acids can acts as either ____(proton acceptors) or ____ (proton donors)
bases, acids
68
In Acid-Base Catalysis, which amino acid, with a pKa near physiological pH, is often involved in acid/base catalysis?
Histidine
69
In Acid-Base Catalysis, the pKa of a functional group is influenced by the ______ ______
chemical microenvironment
70
In Acid-Base Catalysis, functional groups of amino acids can have ______ pKas within the active site which make them more suitable for acid/base catalysis
different
71
In Covalent Catalysis, as a part of the reaction mechanism the substrate is covalently bound to the enzyme to form a _____ _____
reactive intermediate
72
Covalent catalysis often involves two steps..?
1. Forms a covalent linkage to the enzyme
2. Regenerates the free enzyme
73
What is the reaction of Sucrose Phosphorylase? And what are the two steps for covalent catalysis?
Sucrose + Pi <-> Fructose + Glucose-1-P
1. Glucosyl residue is transferred to enzyme
2. Glucose is transferred to phosphate
74
Define Kinetics
The study of the velocity of reactions
75
The velocity of a reaction is quantified as..? And what are the units?
V = Δ[product] ÷ Δtime. Usually mmoles/sec or moles/min
76
As enzymes are proteins, any variable that influences protein structure may ..?
influence enzyme activity
77
True or False: the activity of enzymes is temperature and pH sensitive?
True
78
True or False: Enzymes can have different optimum temperatures and pHs?
True
79
Enzyme velocities are also influenced by ____ and ____ concentration
enzyme, substrate
80
As velocity is defined as the change in product concentration over time, it is necessary to measure ____ ____ before equilibrium is reached
product formation
81
What is Initial velocity (Vo) in terms of kinetics?
The velocity at the beginning of an enzyme catalyzed
reaction, prior to product accumulation
82
In kinetics, K1 and k-1 represent..? And K2 is ..?
Rapid, non-covalent interactions between enzyme and
substrate. The rate constant of formation of product from ES
83
In kinetics, what is the formula for Vo that includes the concentration of ES and K2?
Vo = [ES]k2
84
What is the steady-state assumption?
The rate of formation of the ES complex was equal to the rate of its breakdown
85
Mathematically the steady state assumption states that:
[E][S]k1 = [ES]k-1 + [ES]k2. What is the rate of formation/breakdown of the ES complex?
Rate of formation of the ES complex is [E][S]k1
Rate of breakdown of the ES complex is [ES]k-1 + [ES]k2
86
The Michaelis-Menten equation and plot describe the relationship between..?
Substrate concentration and initial velocity
87
What is the equation used from the Michaelis-Menten plot, and what do the values symbolize?
Vo = (Vmax[S]) ÷ (Km + [S]). Km is the concentration of substrate required for the enzyme to function at
half maximal velocity. Vmax is the maximum velocity of the enzyme
88
For many enzymes, Km provides an accurate approximation of the __ ____ substrate concentration
in vivo
89
When [S] ? Km, enzymes are highly sensitive to changes in substrate concentration but have very little activity
[S] < Km
90
When [S] ? Km, enzymes have high activity but are insensitive to changes in substrate concentration
[S] > Km
91
When [S] ? Km, enzyme has significant activity and is responsive to changes in substrate concentration
[S] = Km
92
What is the velocity of a reaction when substrate concentration is equal to Km?
Vo = 1/2 Vmax
93
What is reaction velocity when substrate concentration is double Km?
Vo = 2/3 Vmax
94
What is the reaction velocity when substrate concentration is a third of Km?
Vo = 1/4 Vmax
95
What are Lineweaver-Burke plots and what are they used for (x4 points)?
1. Describe the relationship between [S] and Vo
2. Are a double-reciprocal plot of 1/Vo vs 1/[S]
3. A more precise method of analysis of kinetic data
4. Used to determine Vmax and Km
96
What is the formula used from Lineweaver-Burke plots?
1/Vo = (Km ÷ (Vmax[S])) + 1/Vmax
97
What is the Enzyme Turnover Number?
1. Kcat
2. Equals the # of molecules of substrate converted to product ÷ time under saturating conditions
3. Calculated by Vmax / [Et]
98
Reversible inhibitors bind to the enzyme by ___-_______ interactions
non-covalent
99
What is a competitive inhibitors ..?
Resemble the substrate and compete with the substrate for binding the active site
100
Competitive inhibitors bind only the ____ ______
free enzyme
101
The effect of competitive inhibitors can be overcome by..?
An excess of substrate (washing out)
102
Uncompetitive inhibitors bind only to the __ ______
ES complex
103
Vmax is decreased by conversion of __ __ ___ which cannot form product in uncompetitive inhibitors
ES to ESI
104
Uncompetitive inhibitors reduce __
[ES]
105
In uncompetitive inhibitors, what causes a decrease in Km?
As E binds S to replenish ES this apparent increase in affinity of the E for S
106
Non-competitive inhibitors binds to _ ___ __
E and ES
107
Vmax is decreased with no change in __
Km
108
Why is there no change in Km in non-competitive inhibitors?
Non-competitive inhibitors don’t influence S
binding
109
Non-competitive inhibitors essentially reduces the number of active _____ _____
enzyme molecules
110
Serine proteases serve as..?
Digestive enzymes that cleave peptide bonds in protein substrates
111
What are some examples are serine proteases?
Trypsin, chymotrypsin, and elastase
112
Members of this family share similar sequences and active site residues. What family is it?
Serine proteases
113
Serine proteases are ______ and _____ in the pancreas as inactive _____ to prevent damage to _____ ______
synthesized, stored, zymogens, cellular proteins
114
Zymogens are activated at the appropriate time by ______ ______
selective proteolysis
115
Catalytic mechanism contains elements of both _____ and ____-____ catalysis
covalent, acid-base
116
Serine proteases have unique _______ that reflect unique ______ _______ ________
specificities, substrate binding pockets
117
Serine Proteases have a conserved catalytic mechanism based on a catalytic triad of residues, what is the triad?
Asp, His, Ser
118
Each residue plays a specific role in the catalytic mechanism, what is the role of His?
Acts to accept and donate a proton at each of the two stages of the reaction mechanism (acid base catalysis)
119
Each residue plays a specific role in the catalytic mechanism, what is the role of Asp?
Stabilizes the positively-charged His to facilitate serine ionization
120
Each residue plays a specific role in the catalytic mechanism, what is the role of Ser?
Attacks the carbonyl group of the peptide bond to be cleaved (covalent catalysis)
121
How many phases are in the chymotrypsin mechanism?
2 Phases
122
Describe the three steps in Phase 1 of the Chymotrypsin mechanism
Step 1: (Acid/Base) Histidine acts as a base to extract proton from hydroxyl of Ser. This activates the oxygen of the hydroxyl group.
Step 2: (Covalent) Formation of a covalent linkage from the hydroxyl group of the Ser to the carbonyl carbon of the peptide bond to be cleaved in the substrate.
Step 3: (Acid/Base) Histidine acts as an acid to donate a proton to the amine group of peptide bond to be cleaved, this cuts the substrate peptide into two pieces
123
Describe the three steps in Phase 2 of the Chymotrypsin mechanism
Step 1: (Acid/Base) Histidine acts as a base to extract a proton from a water molecule, activating the oxygen of this molecule.
Step 2: (Covalent) Activated water molecule attacks the point of covalent linkage between enzyme and substrate.
Step 3: (Acid/Base) Histidine acts as an acid to donate a proton to reform the hydroxyl group of Ser
124
The activity of an enzyme can be regulated by ____________, or by _____________
controlling the amount of the enzyme, adjusting the activity of a constant quantity of the enzyme
125
Which between these two is considered long term, and which is considered short term: controlling the amount of the enzyme, adjusting the activity of a constant quantity of the enzyme?
Controlling - long term, Adjusting - short term
126
What does the regulation of enzyme availability entail?
Location, rates of synthesis and degradation
127
What 2 factors entail the Regulation of enzymes activity, and what are some examples of them?
1. Covalent Modification: phosphorylation, methylation
2. Non-Covalent Modification (allosteric): allosteric regulation
128
What would be the logical point to regulate a reaction pathway? (x3)
1. Enzymatic pathways often controlled through negative feedback inhibition by the final product of the pathway.
2. The final product often inhibits the enzyme catalyzing the first unique and committed step.
3. Regulation at this step conserves material and energy and prevents the accumulation of intermediates.
129
What is the 'formula' for regulation of enzyme activity in points of regulation, and what does each symbol mean?
A -> B -> C -> D -> E -> F, with an arrow going from F back to A with a negative sign. There is also an En over every arrow (E1, E2, ..., E5).
F is the end product is needed in limited amounts and cannot be stored. A is valuable and showed be conserved unless F is needed. B, C, D and E and have no biological roles other except as intermediates in the production of F.
130
Negative feedback in a branched pathway often occurs by..?
The final product of each branch acting to inhibit the enzyme catalyzing the first unique and committed step of the branch
131
Describe the Regulation of enzyme Activity, and where inhibition takes place
Regulation when two pathways cooperate to form a single product. The final product can inhibit the first unique step of each branch. The molecules preceding the merger can inhibit the first step of their branch as well as activating the first step of the opposing branch
132
____ _____ serve as information sensors to coordinate cellular metabolism
Allosteric enzymes
133
Allosteric enzymes are regulated by _________ and by __________.
interaction with metabolic intermediates, allosteric modulators that bind non-covalently at sites other than the active site
134
Allosteric enzymes are usually examples of _____ structure
quaternary
135
Allosteric enzymes often catalyze ____-____ reactions
branch-point
136
Allosteric enzymes are often ____, representing the____ _______ ____ of the pathway
slow, rate limiting step
137
Do allosteric enzymes obey Michaelis-Menten kinetics?
No, they have sigmoidal curves
138
Activities of allosteric regulator enzymes are changed by ____ and _____
inhibitors, activators (modulators)
139
Allosteric modulators bind ___-______ to the enzymes that they regulate
non-covalently
140
Regulatory enzymes often possess ______ structure
quaternary
141
In allosteric enzymes, there is a rapid transition between the ____ and _____ conformations
active (R), inactive(T)
142
Substrates and activators may bind only to the __ state while inhibitors may bind only to the __ state
R, T
143
The binding of the substrate disrupts the __ to __ equilibrium in favor of __. This is the basis of the __-_____ activation of allosteric enzymes.
R, T, R, co-operative
144
Allosteric enzymes transition from a ____ ____ ____ to a ____ ___ ___ within a narrow range of substrate concentration
less active state, more active state
145
The activity of allosteric enzymes is more sensitive to changes in ____ ______ near the Km than Michaelis-Menten enzymes of the same Vmax
substrate concentration
146
Describe the Threshold Effect
Below a certain substrate concentration there is little enzyme activity; after the threshold has been reached the enzyme activity increases rapidly
147
Many enzymes are regulated through the _____ ______ of a modifying group to changes some aspect of the proteins behavior, such as activity
covalent linkage
148
What is the most common post-translation covalent modification?
Through phosphorylation
149
True or False: these modifications are usually reversible with one enzyme catalyzing the addition of the group and another enzyme catalyzing its removal/
True
150
Kinases _____ phosphoryl groups, phosphatases ____ them
add, remove
151
Production and utilization of glycogen is controlled by two enzymes:
1. Glycogen Synthase (anabolic): catalyzes production of glycogen from glucose
2. Glycogen Phosphorylase (catabolic): catalyzes the breakdown of glycogen into glucose
152
In glycogen metabolism, describe the path from glycogen to glucose. (x3)
1. In response to hormones that are released when you are hungry (glucagon) or scared (epinephrine) both enzymes are phosphorylated
2. Phosphorylation activates the catabolic enzyme and inactivates the anabolic enzyme.
3. This situation favors the breakdown of glycogen into glucose.
153
In glycogen metabolism, describe the path from glucose to glycogen. (x3)
1. In response to hormones released in the fed state (insulin) both enzymes are unphosphorylated
2. When unphosphorylated the anabolic enzyme is active and the catabolic enzyme is inactive
3. This situation favors the storage of glucose within glycogen
154
In which of these situations would an enzyme have low activity but be highly sensitive to changes in substrate concentration: [S] < Km, [S] = Km, [S] > Km
[S] < Km
155
The equilibrium between substrate and product is determined by..?
the difference in free energy between the substrate and product
156
True or False: enzymes have equal affinities for their transition states and substrates?
False
157
On a Michaelis-Menten plot, a sigmoidal relationship between velocity and substrate concentration indicates that..?
the enzyme is allosteric
158
Allosteric enzymes are often the _____ enzyme in an enzymatic pathway
slowest
159
Enzymes accelerate reactions by..?
providing a lower energy route between the substrate and product
