Chapter 4: Enzymes Flashcards
1
Q
- effective catalysts for an enormous diversity of chemical reactions
- bring substrates together in an optimal orientation
- catalyze reactions by stabilizing transition states
A
enzymes
2
Q
how do enzymes determine which one of several potential chemical reactios actually takes place
A
selectively stabilizing a transition state
3
Q
- additional chemical component
- one or more inorganic ions
A
cofactor
4
Q
complex organic or metalloorganic molecule
A
coenzyme
5
Q
examples of inorganic ions
A
- Fe2+
- Mg2+
- Mn2+
- Zn2+
6
Q
Coenzyme that transfers CO2
A
biocytin
7
Q
Coenzyme that transfers acyl groups
A
coenzyme A
8
Q
Coenzyme that transfers H atoms and alkyl groups
A
5’-Deoxyadenosylcobalamin (coenzyme B12)
9
Q
Coenzyme that transfers electrons
A
Flavin adenine dinucleotide
10
Q
Coenzyme that transfers electrons and acyl groups
A
Lipoate
11
Q
Coenzyme that transfers hydride ion (:H-)
A
nicotinamide adenine dinucleotide
12
Q
Coenzyme that transfers amino groups
A
pyridoxal phosphate
13
Q
Coenzyme that transfers one-carbon groups
A
tetrahydrofolate
14
Q
Coenzyme that transfers aldehydes
A
thiamine pyrophosphate
15
Q
provide additional chemically reactive functional groups besides those present in the amino acid chains of apoenzymes
A
cofactors
16
Q
are sythesized within the human body using building blocks obtained from other nutrients
A
coenzymes
17
Q
coenzyme or metal ion that is very tightly or even covalently bound to enzyme protein
A
prosthetic group
18
Q
complete, catalytically active enzyme together with its bound coenzyme and/or metal ions
A
holoenzyme
19
Q
protein part of enzyme
A
apoenzyme or apoprotein
20
Q
permanent attachment is __ an absolute requirement for coenzyme to be an active part of enzyme
A
NOT
21
Q
provides an example of coenzyme behavior where it is released after reaction has occured
A
NAD+
22
Q
how are some enzyme protein modified covalently
A
by
- phosphorylation
- glycosylation
- other processes
23
Q
Which of the following statements about conjugated enzyme is correct?
a. it contains only amino acids
b. it always contains a metal atom
c. it always contains a nonprotein part
d. no correct response
A
c. it always contains a nonprotein part
24
Q
Which of the following statements about cofactors is incorrect?
a. all conjugated enzymes contain cofactors
b. metal ions can function as cofactors
c. coenzyme is an alternate name for all cofactors
d. no correct response
A
c. coenzyme is an alternate name for all cofactors
25
Which of the following statements about the interaction of cofactors with apoenzymes is correct?
a. they are always covalently bonded to the apoenzyme
b. they cannot be covalently bonded to the apoenzyme
c. they can, but do not have to be, covalently bonded to the apoenzyme
d. no correct response
c. they can, but do not have to be, covalently bonded to the apoenzyme
26
sugar that can be stored indefinitely on the shelf with no deterioration
glucose
27
what does glucose represent
thermodynamic potentiality
28
suffix that identifies substance as an enzyme
-ase
-in
29
examples of enzymes with -ase
- urease
- sucrase
- lipase
30
examples of enzymes with -in
- trypsin
- chymotrypsin
- pepsin
31
catalyzes an oxidation reaction
oxidase enzyme
32
catalyzes a hydrolysis reaction
hydrolase enzyme
33
catalyzes the oxidation of glucose
glucose oxidase
34
35
catalyzes the carboxylation of pyruvate
pyruvate carboxylase
35
refers to the chemical reaction in which carboxylic acid groups are produced by treating the substrate with carbon dioxide
Carboxylation
35
catalyzes the dehydrogenation of succinate
succinate dehydrogenase
35
catalyzes the hydrolysis of urea
urease
36
catalyzes the hydrolysis of lactose
lactase
37
Predict function of enzyme:
cellulase
catalyzes hydrolysis of cellulose
38
Predict function of enzyme:
sucrase
catalyzes hydrolysis of disaccharide sucrose
39
Predict function of enzyme:
L-Amino acid oxidase
catalyzes the oxidation of L-amino acids
40
Predict function of enzyme:
aspartate aminotransferase
catalyzes transfer of amino group from aspartate to different molecule
41
Six major classes of enzymes on the basis of types of reactions they catalyze
1. oxidoreductase
2. transferase
3. hydrolase
4. lyase
5. isomerase
6. ligase
42
catalyzes an oxidation-reduction reaction
oxidoreductase
43
oxidation reaction
increase C-O
decrease C-H
44
reduction reaction
decreases C-O
increases C-H
45
what do fruits contain that makes it oxidize
phenol derivatives
46
Ways which can prevent or slow down phenolase and enzymatic browning
1. immersion in cold water
2. refrigiration
3. boiling
4. addition of lemon juice
47
catalyzes transfer of functional group from one molecule to another
transferase
48
two major subtypes of transferase
1. transaminase
2. kinases
49
transfer of amino group from one molecule to another
transaminase
50
transfer of phosphate group from adenosine triphosphate (ATP) to give adenosine diphosphate (ADP)
kinases
51
calatyzes reaction between glutamine residue in protein and lysine residue
transglutaminases
52
can be used to make consistent, uniform portions of meat or fish from smaller scraps
meat glue
53
catalyzes hydrolysis reaction in which addition of water molecule causes bond to break
hydrolase
54
what doe pineapply, kiwi, or papaya have that prevents hydrogel from forming
protease (ligase)
55
Protease of fress pineapple
bromelain
56
Protease of fresh kiwi
actinidin
57
Protease of fresh papaya
papain
58
what do the protease of the fresh fruits hydrolyze
hydrolysis of peptide (amide) linkages in gelatin
59
catalyzes the addition of a group to a double bond or the removal of a group to form a double bond in a manner that does not require hydrolysis or oxidation
Lyase
60
example of groups that are removed by Lyase when forming double bonds
- H2O
- CO2
- NH3
61
catalyzes the isomerization of a substrate in a reactio, converting it into a molecule isomeric with itself
isomerase
62
catalyzes the bonding together of two molecules into one wth the participation of ATP
ligase
63
subclasses of oxidoreductase
1. oxidases
2. reductases
3. dehydrogenases
64
oxidation of substrate
oxidase
65
reduction of substrate
reductase
66
introduction of double bond (oxidation) by formal removal of two H atoms from a substrate, with one H being accepted by a coenzyme
dehydrogenases
67
subclasses of transferases
1. transaminase
2. kinase
68
transfer of an amino group between substrates
transaminase
69
transfer of phosphate group between substrates
kinase
70
subclasses of hydrolases
1. lipase
2. protease
3. nuclease
4. carbohydrase
5. phosphatase
71
hydrolysis of ester linkages in lipids
lipase
72
hydrolysis of amide linkages in proteins
protease
73
hydrolysis of sugar-phosphate ester bonds in nucleic acids
nuclease
74
hydrolysis of glycosidic bonds in carbohydrates
carbohydrase
75
hydrolysis of phosphate-ester bonds
phosphatase
76
subclasses of lyase
1. dehydratase
2. decarboxylase
3. deaminase
4. hydratase
77
removal of H20 from substrate
dehydratase
78
removal of CO2 from substrate
decarboxylase
79
removal of NH3 from substrate
deaminase
80
addition of H2O to a substrate
hydratase
81
subclasses of isomerase
1. racemase
2. mutase
82
conversion of D isomer to L isomer or vice versa
racemase
83
transfer of functional group from one position to another in the same molecule
mutase
84
subclasses of ligase
1. synthetase
2. carboxylase
85
formation of new bond between two substrates, with participation of ATP
synthetase
86
formation of new bond between a substrate and CO2 with participatioin of ATP
carboxylase
87
Which of the following paiings of enzyme type and enzyme function is incorrect?
a. lipase - hydrolysis of ester linkages
b. hydratase - addition of water to substrate
c. carboxylase - removal of carbon dioxide from substrate
d. no correct response
c. carboxylase - removal of carbon dioxide from substrate
88
Which of the following pairings of enzyme type and enzyme function is incorrect?
a. kinase - transfer of phosphate group between substrates
b. mutase - introduction of double bond withing a molecule
c. protease - hydrolysis of amide linkages in a protein d. no response
b. mutase - introduction of double bond withing a molecule
89
- thermodynamic property that is a measure of useful energy
- energy that is capable of doing work
Gibbs Free Energy (G)
90
two thermodynamic properties of the reaction in order to understand how enzymes operate
1. free-energy difference (ΔG) between the products and reactants
2. energy required to initiate conversion of reactants into products (Ea)
91
what does the free-energy change provide information about
spontaneity NOT rate of reaction
92
The free-energy change of reaction (ΔG) tells us if reaction can take place spontaneously:
1. ΔG<0 : reaction can take place
2. ΔG=0 : equilibrium, no net change can take place
3. ΔG>0 : reaction cannot take place
4. ΔG of a reaction is independent of molecular mechanism
5. rate of reaction depends on free energy activation (∆G‡)
93
ΔG<0 reactions
exergonic
94
ΔG>0 reactions
endergonic
95
what drives ΔG>0 reactions
input of free energy
96
how do enzymes speed up chemical reactions
- changes path by which reaction occurs
- lowering activation energy
97
∆G
difference in free energy between the products and the reactants
98
what do enzymes alter
reaction rate, not reaction equilibrium
99
denotes the transition state
X‡
100
∆G‡
activation energy
101
X‡ denotes the transition state:
1. transitory molecule no longer substrate but not yet product
2. least-stable, most-seldom occupied species along reaction pathway because it has highest free energy
102
what is the first step in enzymatic catalysis
formation of enzyme-substrate compex
103
why do enzymes bind to and then alter the structure of substrate
promote formation of transition state
104
formula for ∆G‡
X‡ (transition state) - ∆G (free energy)
105
Evidence for existene of enzyme-substrate complex
1. constant concentration of enzyme, reaction rate increases with increasing substrate concentration until maximal velocity is reached
2. spectrosocopic characteristics of many enzymes and substrates change on formation of ES complex
3. x-ray crystallography
106
Common Features of Active Sites of Enzymes
1. 3D cleft formed by groups from different parts of amino acid sequence
2. takes up small part of total volume
3. unique microenvironments
4. substrates are bound to enzyme by multiple weak attractions
5. Specificity of binding depends on precisely defined arrangements of atoms in active site
107
Two types of Mechanism of Enzyme Action
1. Emil-Fischer's Lock-and-Key Mechanism
2. Koshland Induced-fit Mechanism
108
- enzymes and substrates combine due to having complementary geometries
- enzyme is pictured as being conformationally rigid
- explains specificity of enzyme
- not all have specific shapes for lock-and-key
Emil-Fischer's Lock-and-Key Mechanism
109
- substrate induces conformational change resulting in complementary interaction
- protein does not have complementary binding site
Koshland Induced-fit Mechanism
110
intermediate reaction species formed when substance binds to active site of enzyme
Enzyme-substance (ES) complex
111
- free energy released on binding
- free energy released from the formation of large number of weak interactions between complementary enzyme and its substrate
binding energy
112
correct substrate participate in most or all interactions with enzyme
maximize binding energy
113
enzyme facilitates formation of transition state
maximal binding energy
114
formed only when substrate is converted into transition state
full complement of such interactions
115
happens when energy is released by interaction between enzyme and substrate
lowering activation energy
116
state in which substrate is in an energetically unstable form, having features of both substrate and product
transition state
117
Kinds of Transition State Changes
1. enzyme put stress on bond promoting breakage
2. enzyme may facilitate reaction by bringing two reactants close together and in proper orientation
3. active site of enzyme may modify pH of microenvironment
118
Six steps in HIV protease inhibitor and pharmaceutical drug design
1. binding
2. fusion
3. reverse transcription
4. integration
5. replication
6. assembly
119
ability of an enzyme to select a specific substrate from a range of chemically similar compounds
enzyme specificity
120
Types of Enzyme Specificity
1. absolute specificity
2. group specificity
3. linkage specificity
4. stereochemical specificity
121
- enzyme will catalyze only one reaction
- most restrictive
- not common
absolute specificity
122
Ex. of absolute specific enzymes
1. Aminoacyl tRNA synthetase
2. Catalase
123
- selectivity is achieved by binding to a pocket in catalytic site
- correct amino acid has the highest binding affinity for the binding pocket
Aminoacyl tRNA synthetase
124
- catalyzes conversion of hydrogen peroxide and water
- hydrogen peroxide is the only substrate it will accept
catalase
125
enzyme will act only on molecules that have specific functional group, such as hydroxyl, amino, or phosphate groups
group specificity
126
Ex. of group specific enzymes
1. carboxypeptidase
2. hexokinase
127
cleaves amino acids, one at a time, from carboxyl end
carboxypeptidase
128
- catalyzes addition of phosphoryl group to hexose sugar gluose in first step of glycolysis
- can also add phosphoryl group to several other six-carbon sugars
hexokinase
129
enzyme will act on particular type of chemical bond, irrespective of the rest of molecular structure
linkage specificity
130
Ex. of linkage specific enzymes
1. phosphatase
2. protease
131
hydrolyze phosphate-ester bonds in all types of phosphate ester
phosphatase
132
hydrolyze peptide bonds
protease
133
- enzyme act on particular stereoisomer
- chirality is inherent in anenzyme active site
- I-amino acid oxidase will catalyze oxidation of L-form of an amino acid but not D-form of same amino acid
stereochemical specificity
134
QUICK QUIZ:
specificity of enzyme that catalyzes the oxidation of several different alcohols is termed as __
group specificity
135
QUICK QUIZ:
linkage-specific enzymes will act on a particular type of __
chemical bond
136
measure of rate at which an enzyme converts substrate to products in a biochemical reaction
enzyme activity
137
Four factors that affect enzyme activity
1. temperature
2. pH
3. substrate concentration
4. enzyme concentration
138
measure of kinetic energy of molecules
temperature
139
as temperature of enzymatically catalyzed reaction__, so does the __ of reaction
- increases
- rate (velocity)
140
optimum temperature for human enzymes
37C
141
temperature of autoclave
121C
142
when does water starts to boil
atmospheric pressure = vapor pressure
143
- where charge on acidic and basic amino acids
- enzyme exhibit maximum activity in its optimum measurement
pH
144
small changes in __ can result in enzyme denaturation
pH
145
- suicide bags
- degrade large biological molecules into small molecules
lysosomes
146
- new molecule of substrate cannot bind to the enzyme molecule until substrate molecule already held in active site is converted to product and released
- reaction is dependent on amount of enzyme that is available
substrate concentration
147
Two stages of enzyme-catalyzed reaction
1. formation of enzyme-substrate complex
2. conversion of substrate into product and release of product and enzyme
148
formation of enzyme-substrate complex
binding of substrate to active site is rapid
149
conversion of substrate into product and release of product and enzyme
step is slower and limits the rate of overall reaction
150
number of substrate molecules transformed per minute by one molecule of enzyme under optimum conditions
enzyme's turnover number
151
- cell usually keep amount of enzyme low compared to no. of substrate
- concentration of substrate in reaction is higher than enzyme
enzyme concentration
152
why does the cell keep amount of enzyme low compared to substrate
avoid paying energy costs
153
what happens if the no. of enzymes increases while no. of substrate is constant
reaction rate is increased because more substrate are accomodated
154
microorganism that thrives in extreme environments
extremophile
155
microbial enzyme active at conditions that would inactivate enzymes present in other types of higher organisms
extremozymes
156
Ex. of extremophiles
1. acidophile
2. alkaliphile
3. halophile
4. hyperthermophile
5. piezophile
6. xerophile
7. cryophile
157
Industrial Use of Extremozymes Process
1. extremophile samples gathered
2. DNA material extracted and processed
3. macroscopic amounts of DNA produced using polymerase chain reaction
4. produced macroscopic DNA analyzed to find genes present involved in extremozyme production
5. genetic engineering used to insert gene to bacteria to produce extremozyme
6. process commercialized
158
QUICK QUIZ:
number of substrate molecules converted to product per minute is a measure of ____
enzyme activity
159
QUICK QUIZ:
plot of enzyme activity (y-axis) versus pH (x-axis) with other variables constant is a
line with upward slope followed by downward slope
160
QUICK QUIZ:
plot of enzyme activity (y-axis) verus temperature (x-axis) with other variables constant
line with upward slope followed by downward slope
161
energy conservation
regulation of enzyme activity
162
ex. of regulation of enzyme activity
1. cell continually produce large amounts of enzyme, substrate concentration low = production of enzyme turned off
2. product of enzyme-catalyzed reaction present is plentiful (moer than needed) = enzyme needs to be turned off
163
Three Mechanisms by which enzymes within cell can be "turned on"
1. feedback control associated with allosteric enzymes
2. proteolytic enzymes and proenzymes/zymogens
3. covalent modification
164
occurs when a product of the reaction binds to an allosteric site on the enzyme and affects its catalytic activity
feedback control associated with allosteric enzymes
165
enzymes that have an additional binding site for effector molecules other than the active site
Allosteric enzymes
166
structure of Allosteric enzymes
quaternary structure
167
two kinds of binding site of Allosteric enzymes
- for substrate
- for regulator
168
binding sites of Allosteric enzymes
distinct from each other both in location and shape
169
binding of molecule at regulatory site in Allosteric enzymes
changes in overall 3D structure including active site
170
- cell uses feedback inhibitiion to stop producing no longer needed product
- effective metabolic on-off switch
feedback control
171
product can shut off entire pathway for its synthesis
feedback control
172
regulators or particular allosteric enyme may be what?
1. products of entirely different pathways of reaction within cell
2. compounds produced outside cell (hormones)
173
- synthesized as inactive precursors, or "zymogens," to prevent unwanted protein degradation
- enable spatial and temporal regulation of proteolytic activity
Proteolytic enzymes
174
- inactive form of proteolytic enzyme
- converted by proteolysis to the active form when it reached site of its activity
proenzyme or zymogen
175
hydrolysis of protein
proteolysis
176
active form of enzyme
proteolytic enzymes
177
example of proteolytic enzymes
most digestive and blood-clotting enzymes
178
have amino acid serine in the catalytic region of active site that is essential for hydrolysis of peptide bond
serine protease
179
process in which enzyme activity is altered by covalently modifying structure of enzyme through attachement of chemical group
covalent modification
180
most common type of protein modification
1. phosphorylation
2. dephosphorylation
181
QUICK QUIZ:
incorrect information about characterization of allosteric enzyme
substrate and regulator compete for same binding site
182
QUICK QUIZ:
enzyme activity regulation that involves a reaction sequence product inhibiting an enzyme in an earlier step in the reaction sequence
feedback control
183
QUICK QUIZ:
zymogen
inactive precursor of a proteolytic enzyme
184
- either eliminate or drastically reduce their catalytic ability
- chemical that can bind to enzymes
enzyme inhibitors
185
Ex. of enzyme inhibitors
1. arsenic
2. penicillin
186
- binds to thiol groups of cysteine amno acids in proteins
- interfere with formation of disulfide bonds needed to stabilize tertiary structure of protein
arsenic
187
inhibits several enzymes involved in synthesis of bacterial cell wall
penicillin
188
Three modes of inhibition
1. irreversible inhibition
2. reversible competitive inhibition
3. reversible noncompetitive inhibition
189
- generally do not have structures similar to that of enzyme's normal substrate
- bind very tightly, sometimes covalently, to enzyme
- may interfere with catalytic groups of active site
- generally inhibit many different enzymes
irreversible enzyme inhibitors
190
ex. of irreversible enzyme inhibitors
sarin
191
- interferes with process by which nerve cells communicate
- disrupts muscle movement and other processes the nervous system controls
sarin
192
key factors whehter enzyme accepts molecule
- molecular shape
- charge distribution
193
- often refer to as structural analogs
- molecules resemble structure and charge distribution of natural substrate
- inhibitor can occupy enzyme active site
reversible competitive inhibitor
194
reversible competitive inhibitor is often refer to as what
structural analogs
195
Ex. of reversible competitive inhibitor
sulfa drug
196
- binds to active site of bacterial enzyme responsible for producing folic acid
- folic acid production is stopped and bacterial cell will die
sulfa drug
197
vitamin required for the making of DNA and RNA
folic acid
198
- molecule decreases enzyme activity by binding site on enzyme other than active site
- substrate can still bind but presence of inhibitor causes change in structure of enzyme sufficient to prevent proper catalyzing action
- increasing number of substrate do not completely overcome inhibitory effects
reversible noncompetitive inhibitors
199
ex. of reversible noncompetitive inhibitors
heavy metal ions (Pb2+, Ag+, Hg2+)
200
- binding site for these ions are sulfhydryl groups (thiol) located away from active site
- metal sulfide linkages are formed, disrupting secondary and tertiary structure
heavy metal ions (Pb2+, Ag+, Hg2+)
201
PRACTICE:
inhibitor that decreases activity by binding to a site on enzyme other than active site
reversible noncompetitive inhibitor
202
PRACTICE:
inhibitor that inactivates enzymes by forming strong covalent bond at enzyme active site
irreversible inhibitor
203
QUICK QUIZ:
incorrect statement concerning reversible competitive inhibitor
binds at site other than active site
204
QUICK QUIZ:
incorrect statement concerning irreversible enzyme inhibitor
has shape almost identical to that of normal substrate
205
QUICK QUIZ:
binds to an enzyme at a location other than active site
reversible noncompetitive inhibitor
206
PRACTICE:
Determine effect that each of the following changes would have on rate of biochemical reaction that involves substrate urea and liver enzyme urease
increasing urea concentration
enzyme activity will increase untill all enzyme molecules are engaged with urea substrate
207
PRACTICE:
Determine effect that each of the following changes would have on rate of biochemical reaction that involves substrate urea and liver enzyme urease
increasing urease concentration
enzyme activity will increase untill all urea molecules are engaged with urease enzyme
208
PRACTICE:
Determine effect that each of the following changes would have on rate of biochemical reaction that involves substrate urea and liver enzyme urease
increasing temperature from optimum value to 10C higher
enzyme activity will decrease
209
PRACTICE:
Determine effect that each of the following changes would have on rate of biochemical reaction that involves substrate urea and liver enzyme urease
decreasing pH by one unit from optimum value
enzyme activity will decrease
