Enzymes. Flashcards
1
Q
What is an apoenzyme?
A
An enzyme protein which is not bound to a cofactor.
2
Q
What is a coenzyme?
A
An organic molecule, that is not a protein.
3
Q
What is a coenzyme also known as?
A
A prosthetic group.
4
Q
What are coenzymes used for?
A
To help enzymes form their product.
5
Q
Most coenzymes are what kind of molecule?
A
Vitamins.
6
Q
What is a cofactor?
A
An inorganic molecule that is used to help some enzymes to produce their product.
7
Q
Many cofactors are made up of that type of element?
A
Metallic elements.
8
Q
What is a holoenzyme?
A
An enzyme that bound to its cofactor.
9
Q
What is the induction of enzymes?
A
An up regulation of enzymes.
This is due to an increase in gene expression which signals for more enzymes to be synthesised.
10
Q
What is kinetics?
A
The study of how quickly reactants are converted to products.
11
Q
What are prosthetic groups?
A
These are organic in nature and not made of protein.
Prosthetic groups are very tightly bound (usually covalently) to the enzyme.
12
Q
What is the repression of enzymes?
A
The down-regulation of enzymes.
It is caused by a decrease in gene expression, leading to fewer enzymes.
13
Q
What is a zymogen?
A
An inactive form of an enzyme.
14
Q
What controls and regulates metabolism?
A
Many different enzymes.
15
Q
What are enzymes?
A
Biological catalysts that lower the activation energy required for a reaction to occur.
16
Q
What is the active site of an enzyme?
A
The site to which the substrate will bind.
17
Q
Can any substrate go into the active site of an enzyme?
A
No.
Enzymes are very specific for a certain substrate and will only work on one particular substrate.
18
Q
What is enzyme specificity?
A
That each class of enzyme will only react with one class of substrate.
19
Q
What is the substrate?
A
The molecule that the enzyme is working on and will eventually change into products.
20
Q
What is the turnover number of an enzyme?
A
The number of substrate molecules that are converted to product, per enzyme per second.
21
Q
Are cofactors organic or inorganic?
A
Inorganic.
22
Q
If an enzyme requires a cofactor, will it be able to work without that cofactor?
A
No.
23
Q
If an enzyme is bound to its cofactor, what is the complex called?
A
A holoenzyme.
24
Q
If an enzyme is not bound to its cofactor, what is the complex called?
A
An apoenzyme.
25
Are coenzymes usually organic or inorganic?
Coenzymes are made from organic material but they are not proteins.
26
Can some enzymes use cofactors and coenzymes?
Yes.
Some can use both.
27
If a cofactor is covalently bound to the enzyme, what can it be called?
A prosthetic group.
28
What is a simple enzyme?
A simple enzyme is made up of only a protein.
They can be composed of single or many polypeptides.
29
Do simple enzymes often need prosthetic groups or cofactors?
No.
30
Do complex enzymes often require need prosthetic groups or cofactors?
Yes, always.
31
Are complex enzymes often composed of subunits?
Yes.
Of which 1 is catalytic and 1 is regulatory.
32
Enzymes are made of what type of organic molecule?
Proteins.
33
What isn enzyme classification based on?
On what an enzyme does or on the type of reaction that they catalyse.
34
What kind of reactions are oxidoreductases involved in?
They will catalyse oxidation and reduction reactions.
Therefore, it will transfer electrons from one atom to another which usually increases the double bonds in the molecule that lost electrons.
35
What is a common metabolic reaction that oxidoreductases are involved in?
A transferase will usually transfer electrons to NAD+ making it NADH + H.
36
Oxidoreductases are often known as what?
Dehydrogenases or oxidases.
37
What kind of reactions are transferases involved in?
They will move or transfer a specific group or functional group from one molecule to another.
38
What are transferases often known as?
As transaminase or as a kinase.
39
What kind of reactions are hydrolases involved in?
They catalyse the cleavage of bonds by the addition of water.
40
What is the name of the reaction that hydrolases use to cleave bonds?
A hydrolysis reaction.
41
What kind of reactions are lyases involved in?
A lyase is similar to a hydrolase as its main function is the cleavage of bonds.
The exception being that lyases do not need water to cleave bonds.
42
What bonds are most often cleaved by lyases?
C-C.
C-S.
C-N.
43
What are lyases often referred to as?
Decarboxylases and aldolases.
44
What kind of reactions are isomerases involved in?
They will change the molecular formula of the substrate to form an optical or a geometric isomer.
45
What are isomerases often referred to as?
Mutases or epimerases.
46
What kind of reactions are ligases involved in?
They will catalyse the formation of bonds between C, O, N and S.
47
What kind of reactions are kinases involved in?
A kinase is a specific type of transferase and will take a phosphate from ATP and will transfer it to an enzyme that has a hydroxyl group.
48
If an enzyme has a phosphate group added to it, it is said to be what?
Phosphorylated.
49
What kind of reactions are phosphatases involved in?
A phosphatase is the opposite of a kinase, as they will break off a phosphate group from a protein.
50
What is proteolytic cleavage
This is when an inactive enzyme (zymogen) is activated by the removal of a short peptide segment from the amino terminus.
51
When proteolytic cleavage occurs, the short peptide is removed from which part of the amino acid?
The amino terminus.
52
Give an example of proteolytic cleavage?
Trypsinogen is the inactive form of trypsin.
When the enzyme enteropeptidase removes the first 6 amino acids from amino end, trypsin is formed in its active state.
53
What is the covalent modification of an enzyme?
When a new covalent bond is added to the enzyme.
54
What is a common form of covalent modification?
The addition of a phosphate group to the enzyme.
55
What enzymes are heavily involved in covalent modification?
Kinases.
56
What are 2 less common forms of covalent modification?
Adenylation.
Methylation.
57
What effect will covalent modification have on enzyme activity?
It will either increase or decrease enzyme activity.
58
Kinases typically modify what localised groups within the R groups?
The hydroxyl groups on the R groups of some amino acids by removing the hydrogen and adding a phosphate group.
59
Which amino acids commonly undergo covalent modification from a kinase?
Serine.
Threonine.
Tyrosine.
60
The addition of a phosphate group will have what affect on an enzyme?
It will either activate or inactivate the enzyme.
61
Do phosphatases add or remove a phosphate group?
The will remove phosphate groups.
62
What is the sequestration of enzymes?
When some enzymes can be found in different forms, within the cell.
When the enzyme is in these different forms, it will be inactive.
63
What is the allosteric regulation of enzymes?
An allosteric molecule can bind to the allosteric site and this can regulate the enzyme or activate it.
64
How many sites do allosteric enzymes have?
Allosteric enzymes have 2 sites, an active site and a 2nd site, which is called an allosteric site.
65
What effect does allosteric modification have on the active site?
When the allosteric modifier binds to the allosteric site, the active site will physically change.
66
If an allosteric enzyme has a catalytic and regulatory subunit, where will the substrate and allosteric modifier bind on the enzyme?
The substrate will bind to the active site in the catalytic subunit.
An allosteric activator or inhibitor will bind to the allosteric site at the regulatory subunit.
67
What effects can allosteric modification have on an enzyme?
Allosteric modification will either increase or decrease enzyme activity.
68
What effect will a positive allosteric modifier have on an allosteric enzyme?
It will increase enzyme activity.
69
What effect will a negative allosteric modifier have on an allosteric enzyme?
It will decrease enzyme activity.
70
What is the process called, by which the body will create more enzymes?
Enzyme induction.
71
What is responsible for initiating an upregulation of enzymes?
Hormones.
72
How does a hormone initiate enzyme induction?
They will cross the plasma membrane.
They will find a specific receptor in the cytoplasm and will bind to it.
The active complex moves into the nucleus and will bind to a region of DNA.
It will then find a specific gene and activate it.
The gene will then make mRNA which is translated into enzymes.
73
What is the composition of specific receptor that hormones find in the cytoplasm?
A protein.
74
What is the structure called when the hormone binds to the receptor in the cytoplasm?
An active complex.
75
What is the region of DNA called that the active complex binds to?
An enhancer region of DNA.
76
When the active complex binds to DNA, what is the region of the gene called that will be activated?
The promoter region.
77
Is up-regulation the activation of proteins?
No.
It is the making of more proteins.
78
What is an isozyme?
They are enzymes that perform the same reaction as a particular enzyme, but have a different molecular structure.
79
Are the proteins that make up an isozyme and its enzyme cousin different?
Yes.
80
Give an example of an enzyme that has isozymes?
Creatine kinase is capable of existing in 3 isomeric forms, each of which does the same job.
81
Describe how each isozyme of creatine kinase differs?
CK1 is made up of 2 identical polypeptides.
CK3 is also made up of 2 identical polypeptides, yet these are different from those that make up CK1.
CK2 is made up of 2 different polypeptides, one the same as the two that make up creatine kinase 1 and one the same as two that make up creatine kinase 3.
82
Where is CK1 found?
In the brain.
83
Where is CK2 found?
In cardiac tissue and skeletal muscle.
84
Where is CK3 found?
CK3 is found in muscular injuries.
85
Do different cellular metabolic pathways take place in the same organelle or within different organelles?
Within different organelles.
86
Are different enzymes likely to be found in different areas of the cell?
Yes, because different parts of the cell are involved in different metabolic pathways.
87
How do enzymes make a reaction more likely to happen?
By lowering activation energy.
88
What is formed when the enzyme and substrate come together?
The enzyme substrate complex.
89
What happens once the enzyme substrate complex is formed?
The complex will then enter a transition state.
Finally, the complex contains the enzyme and the final product.
90
What is the transition state of the enzyme substrate complex?
It is where the substrate is in between its original state and the final product.
91
Is the enzyme damaged or destroyed during the conversion of substrate to product?
No.
Only the substrate is altered in the reaction.
92
Are enzymes large proteins?
Yes, they are very large.
93
What are the 2 sites that the active site is divided into?
The binding site and the catalytic site.
94
What is the binding site?
It is where the enzyme binds to the substrate.
95
The binding site is an example of what kind of protein feature?
It is an example of a domain.
96
The binding site forms what kind of bonds to the substrate?
Non-covalent bonds.
97
How many amino acids make up the binding site?
Around 200.
98
How many acids make up the catalytic site?
Around 12.
99
What happens at the catalytic site?
This is where the reaction takes place.
This is where bond breaking and making occurs.
100
What kind of bonds are formed between the catalytic site and the substrate?
Non-covalent bonds.
101
What effect will an increase in enzyme activity have on product formation?
More product will be formed.
102
What effect will a decrease in enzyme activity have on product formation?
Less product will be formed.
103
What is the lock and key model of enzyme activity?
It describes that the substrate fits into the enzyme like a key into a lock.
The wrong key will not open a door, just like the wrong substrate will not fit into an enzyme.
104
What is the induced fit model?
It states that an enzyme can change its structure to fit the substrate.
105
What are the conditions called that an enzyme likes to work in?
Optimal conditions.
106
What are optimal conditions for an enzyme?
The specific pH and temperature that they like to work at.
107
If an enzymes optimal pH increases or decreases, what will happen to the enzyme?
It will stop working.
108
Most enzymes work best at what temperature range?
Between 25 and 40 degrees C.
109
What happens to enzymes if temperatures increase?
They will lose their tertiary structure.
110
What happens to enzymes if temperatures decrease?
There is not enough energy for the enzyme bump into its product so activity will decrease.
111
What are cofactors?
Small metallic molecules that are used by some enzymes to help catalyse a reaction.
112
What happens to enzyme activity if many cofactors are available?
Activity will increase.
113
Will an enzyme work without a cofactor?
No.
114
What are enzyme effectors?
Small organic molecules that will bind to an enzyme at an allosteric site.
They can increase or decrease enzyme activity.
115
What does enzyme kinetics help us to understand?
How an enzyme will behave under certain conditions.
When enzymes are working at their absolute maximum.
How fast they can change products to reactants.
116
What is enzyme kinetics?
The study of how quickly enzymes change their reactants to products.
117
What is the velocity (v) of an enzymatic reaction?
The change in concentration of reactants to products over a certain time period.
118
What is the rate (k) of an enzymatic reaction?
The change in total quantity of reactant or product over a period of time.
119
What is the initial velocity (V0) of an enzymatic reaction?
A reaction where not much product is formed and not much substrate is consumed.
Therefore, this usually occurs in the linear phase of a reaction.
120
What are the 3 important assumptions of Michaelis Menten kinetics?
That the amount of enzyme substrate complexes remains constant during the initial phase of a reaction.
When the enzyme is saturated, all of the enzymes are in the enzyme substrate complex.
If all the enzymes are in the enzyme substrate complex then the rate of product formation is at its maximum (Vmax).
121
What does the Michaelis Menten equation state?
That you get maximum activity for every enzyme that is saturated with substrate.
122
What is the Y axis of a Michaelis Menten graph?
The velocity of the reaction.
123
What is the X axis of a Michaelis Menten graph?
The amount of substrate.
124
Regular enzymes have what kind of curve on a Michaelis Menten graph?
A hyperbolic curve.
125
Allosteric enzymes have what kind of curve on a Michaelis Menten graph?
A sigmoid (S shaped) curve.
126
Why do allosteric enzymes have a sigmoid curve on a Michaelis Menten graph?
Because allosteric enzymes can be activated or inhibited by an effector.
127
A positive effector will increase what Michaelis Menten aspect of an enzyme?
Its Vmax.
128
A negative effector will decrease what Michaelis Menten aspect of an enzyme?
Its Vmax.
129
Why do positive effectors shift enzyme activity to the left of the graph?
Because, when less substrate is available, the enzyme will still work very efficiently.
130
What direction will positive effectors shift a Michaelis Menten graph when less substrate is available?
To the left.
131
What direction will negative effectors shift a Michaelis Menten graph when less substrate is available?
To the right.
132
What needs to be made available to an enzyme that has shifted to the right of a Michaelis Menten graph?
More of substrate needs to be available before the enzyme will start working efficiently.
133
The Micahelis Menten equation describes the relationship between what 4 enzyme related factors?
The rate of an enzyme catalysed reaction.
The concentration of the substrate.
The Michaelis Menten constant.
The maximum velocity of the enzyme.
134
What is the Michaelis Menten constant (Km)?
The concentration of substrate at half Vmax.
135
What will the Michaelis Menten equation tell you?
The enzyme activity at a certain substrate concentration.
136
On a Michaelis Menten graph, if the substrate concentration is increased, how will this affect enzyme activity?
The enzyme activity should also increase, unless the enzyme is at V max.
137
On a Michaelis Menten graph, if the substrate concentration is decreased, how will this affect enzyme activity?
Enzyme activity should decrease.
138
What does Km describe for a Michaelis Menten graph?
An enzymes affinity for a substrate, when the enzyme is at half Vmax.
139
What does a low Km indicate about an enzymes affinity for its substrate?
A low Km means that the enzyme has a high affinity for the substrate.
140
What does a high Km indicate about an enzymes affinity for its substrate?
A high Km means that the enzyme has a low affinity for the substrate.
141
What is enzyme affinity?
How tightly the enzyme will bind to the substrate.
142
Why does a low Km indicate high enzyme affinity for the substrate?
Because Km represents the concentration of substrate.
If the enzymes affinity is high then it does not require a lot of substrate to start work.
143
Why does a high Km indicate low enzyme affinity for the substrate?
If kM is high, then the enzyme will have low affinity for the substrate and will require a lot of substrate before it can start work.
144
If an enzyme has a high Km, will it be shifted to the right or left of an MM graph?
The right.
145
How can you work out the Km of an enzyme?
By seeing when the enzyme is at 1/2 Vmax and finding the Km.
146
What units is Km represented in?
Concentration units as it represents the amount of substrate.
147
Is Km linked to Vmax?
No.
Vmax is independent of Km.
Some enzymes will have a low Vmax and a high Km.
Others will have a high Km and a low Vmax.
148
What does initial velocity represent on an MM graph?
The velocity of the enzyme, when enzyme activity is low and substrate concentration is low.
149
When does an enzyme reach V max?
When it cannot go any faster.
150
What is said to have happened to the enzyme when it reaches Vmax?
It is said to be saturated.
151
Can substrate concentration increase when the enzyme is at Vmax?
Yes, but enzyme activity will not increase.
152
How does the Lineweaver Burk graph manipulate the MM equation?
It takes the reciprocal of both sides.
1/V0 = 1/(Vmax * S / Km + S).
153
What is the Y axis on a Lineweaver Burk graph?
1/V.
154
What is the X axis on a Lineweaver Burk graph?
1/S.
155
What shape is a Lineweaver Burk graph?
A straight line.
156
What does the Y intercept of the LB graph represent?
1/Vmax.
157
What does the X intercept of the LB graph represent?
-1/Km.
158
The X intercept is always on what side of an LB graph?
The negative side.
159
Which is more accurate, the LB graph or the MM graph?
The LB graph.
160
What are the 4 factors that can lead to enzyme inhibition?
Substrate analogs.
Toxins.
Drugs.
Metal complexes.
161
What are substrate analogs?
They inhibit enzyme activity by mimicking the substrate and blocking the active site.
162
How do toxins lead to enzyme inhibition?
They will covalently modify an enzyme by adding new bonds to the active site.
163
How do drugs lead to enzyme inhibition?
They can covalently modify the active site of the enzyme, meaning that no substrate can enter.
Or they will mimic the substrate and bind tightly to the active site
164
How do heavy metals inhibit enzymes?
Due to their charge, they can bind irreversibly to the active site of the enzyme.
165
What type of enzyme inhibition can be reversed when the inhibitor is removed?
Reversible inhibition.
166
What are the 3 types of reversible inhibition?
Competitive inhibition.
Non-competitive inhibition.
Uncompetitive inhibition.
167
Competitive inhibition is usually done by what kind of inhibitor?
A substrate analog.
168
Why is competitive inhibition competitive?
Because the substrate competes with the inhibitor to enter the active site.
169
How can competitive inhibition be reversed?
By increasing the amount of substrate.
170
How does competitive inhibition affect Km and Vmax?
Km will increase.
Vmax will not change.
171
Why does competitive inhibition increase Km?
Because when the enzymes affinity for the substrate decreases, Km will increase.
172
What is non-competitive enzyme inhibition?
When an inhibitor binds to an allosteric site and will change the conformation of the active site.
173
Will a non competitive inhibitor completely stop enzyme activity?
No.
It will just slow the enzyme down.
174
How does a non competitive inhibitor affect Km and Vmax?
The Vmax will decrease.
Km will be unchanged.
175
What is uncompetitive enzyme inhibition?
It is similar to non competitive inhibition as the inhibitor binds to an allosteric site.
The major difference is that it binds to the allosteric site after the substrate has bound to the active site.
176
Do uncompetitive inhibitors bind to the enzyme or the complex?
They bind to the complex.
177
How does an uncompetitive inhibitor affect Km and Vmax?
Both Km and Vmax will be decreased.
178
How are enzymes irreversibly inhibited?
Irreversible inhibitors will form strong covalent or non covalent bonds to the binding site and cannot be removed.
179
Many irreversible inhibitors are what kind of elements?
Heavy metals.
180
Where do irreversible inhibitors bind to the enzyme?
At the active site.
181
On an MM graph, will a competitively inhibited enzyme or an uninhibited enzyme have a higher Km?
The enzyme that is inhibited will have a higher Km than the same uninhibited enzyme.
182
On an MM graph, will a competitively inhibited enzyme or an uninhibited enzyme have a higher Vmax?
Both will achieve the same Vmax, but the inhibited enzyme will need more substrate to achieve Vmax.
183
How will a competitively inhibited enzyme and an uninhibited enzyme differ on a LB graph?
The Y intercept (V max) is the same for both enzymes.
The X intercept (1/Km) is different for both enzymes.
184
On an MM graph, will a non competitively inhibited enzyme or an uninhibited enzyme have a higher Km?
They will be the same
185
On an MM graph, will a non competitively inhibited enzyme or an uninhibited enzyme have a higher Vmax?
The inhibited enzyme will have a lower Vmax.
186
How will a non competitively inhibited enzyme and an uninhibited enzyme differ on a LB graph?
Both enzymes will start at the same point on the X axis meaning they both have the same 1/Km.
However, their Y intercepts (1/Vmax) will be different indicating a different Vmax.
