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Year One - Science For Medicine > Enzymes > Flashcards

Enzymes Flashcards

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1
Q

What are enzymes?

A

Enzymes are globular proteins that act as biological catalysts in the body, which means that they are involved in catalysing reactions so that they have a high reaction rate.

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2
Q

What are ribozymes?

A

Ribozymes are catalytic RNA molecules with no protein component.

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3
Q

Why are enzymes highly specific?

A

They have active sites that are complementary to that of their substrate.

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4
Q

What conditions do enzymes work best in?

A

Their optimal pH and temperature

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5
Q

What is a cofactor?

A

Cofactors are non-protein components that bind to enzymes by interacting with the R groups on the amino acids within the protein. They are usually metal ions.

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6
Q

What is a coenzyme?

A

Coenzymes are non-protein components that bind to enzymes by interacting with the R groups on the amino acids within the protein. They are usually organic molecules produced from vitamins.

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7
Q

What is a prosthetic group?

A

Prosthetic groups are cofactors that are covalently bonded to the enzyme and allow the enzyme to carry out an additional function.

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8
Q

What is an apoenzyme?

A

Apoenzyme describes the protein component of an enzyme that doesn’t contain the cofactor.

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9
Q

What is a holoenzyme?

A

Holoenzyme describes the whole enzyme, which is the apoenzyme plus the cofactors

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10
Q

What is a substrate?

A

The substrate of an enzyme is the molecule it acts upon

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11
Q

What is an active site?

A

The active site of an enzyme is the part of the enzyme in which the substrate binds and is acted upon

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12
Q

What do all names of enzymes end in?

A

‘-ase’

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13
Q

What are the six classifications of enzymes?

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
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14
Q

What do oxidoreductases do?

A

They transfer electrons between molecules and therefore carry out redox reactions.

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15
Q

What do transferases do?

A

They transfer groups between molecules.

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16
Q

What do hydrolases do?

A

They are involved in hydrolysis reactions, which means that they are involved in transferring water to one large molecule to break it down into two smaller molecules.

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17
Q

What do lyases do?

A

They form or add groups to double bonds.

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18
Q

What do isomerases do?

A

They transfer groups within a molecule to convert it into its isomeric form.

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19
Q

What do ligases do?

A

They form covalent bonds by cleaving ATP molecules.

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20
Q

What are the role of enzymes?

A

They accelerate the reactions movement towards the reaction equilibria.

They increase the rate of spontaneous reactions.

They lower the activation of energy of reactions, by providing an alternative pathway for the substrate.

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21
Q

Is energy created or destroyed?

A

No, it is simply converted from one form to another.

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22
Q

What is Gibbs Free Energy?

A

Useful energy generated from cellular reactions.

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23
Q

What are spontaneous reactions?

A

Reactions that have a negative charge in free energy value, which means that they release free energy.

They therefore are reactions that decrease in enthalpy and/or increase in entropy.

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24
Q

Are spontaneous reactions instantaneous?

A

No, as there is an energy barrier (activation energy) that they must overcome.

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25
What is the activation energy?
The energy required to form the transition state.
26
What is the transition state?
The complex where chemical bonds within the molecules are partially broken and partially formed.
27
What happens once the transition state has been formed?
The reaction can go either way - we can revert back to the substrate or change to the product.
28
How does the enzyme provide an alternative pathway for the reaction?
It forms intermediates (ES, EP) where the enzyme forms non-covalent bonds with substrate and product molecules. The energy in these bonds is known as the binding energy.
29
How do enzymes lower the activation energy?
1. Entropy reduction. Molecules in free solution will only react when they bump into one another. The enzyme force substrates into the correct orientation by binding them in the formation that need to be in for the reaction to proceed. 2. Desolvation. Weak bonds between the substrate and the enzyme essentially replace most or all of the hydrogen between substrate and aqueous solution. This means that the substrate can now bind to other substrates instead of water. 3. Induced Fit. Conformational changes occur in the protein structure when the substrate binds.
30
What curve is formed when we plot substrate concentration against initial velocity?
Hyperbolic curve.
31
What is Vmax?
The maximum reaction velocity.
32
What does the M-M model state?
The model states that the first part of the reaction where ES is produced is reversibe. It also states that the second part of the reaction, where ES is used to produce E and P is slower and irreversibe. It is threfore the rate limiting step. This means that more ES causes a higher overall reaction rate and less ES causes a slower overall reaction rate.
33
What is Km?
The substrate concentration at half of Vmax, which is half of the maximum reaction rate.
34
What is the problem with gaining these values from a graph?
The graph essentially continues to infinity.
35
How else can we determine Vmax and Km, except from plotting a graph?
Drawing a Lineweaver Burk plot. Vmax is where the line crosses the y-axis and Km is where the line crosses the x-axis.
36
What does Vmax tell you?
Vmax tells you how fast a reaction is proceeding when the enzyme is saturated with substrate. It also measures the enzymatic catalytic rate.
37
What does Km tell you?
Km is the ratio of the rate constant for the breakdown of ES and the formation of ES. Therefore, larger Km values indicate a less ES complex and smaller Km value indicates a more stable ES complex. It tells you the affinity of the enzyme with its substrate.
38
What does it mean if an enzyme has a high Vmax and a high Km value?
It will have a very low affinity but be very fast.
39
What does it mean if an enzyme has a low Vmax and a low Km value?
It will have a very high affinity but be very slow.
40
What are isozymes?
Different enzymes but they catalyse the same reaction. They are sometimes found in different tissues. They are the products of different genes, or the same genes which have been modulated differently Example - glucokinase and hexokinase.
41
What does glucokinase do?
Catalyse the breakdown of glucose and ATP into G-6-P and ADP + Pi. It is found in liver cell.
42
What does hexokinase do?
Catalyse the breakdown of glucose and ATP into G-6-P and ADP + Pi. It is found in all cells of the body but liver cells.
43
What are the properties of glucokinase? What does this mean?
High Vmax, High Km. Fast enzyme but has a low affinity for its substrate
44
What are the properties of hexokinase? What does this mean?
Low Vmax, Low Km. Slow enzyme but has a high affinity for its substrate
45
What do the properties of glucokinase and hexokinase allow?
When blood glucose concentration increases, the glucokinase activity increases as hexokinase activity does not respond as it is already working at full speed. This allows the liver to take up and store glucose through the glucokinase reaction. When blood glucose concentration decreases, gluconeogenesis releases glucose from the liver but glucokinase has a low affinity for glucose so is less likely to take it up compared to other cells within the body.
46
What do enzymes in the wrong place tell us about?
Disease
47
How can we measure enzymatic activity?
Measuring the initial rate, having the substrate in excess and checking that the activity is proportional to enzyme activity.
48
How do we separate enzymes?
Electrophoresis, as this uses charge and size differences between molecules to separate them.
49
What are the three mechanisms that enzymes can use to catalyse two or more substrates in a reaction?
Random order Ordered Double displacement
50
What is involved in the random order mechanism?
The order of binding and release of substrates and products is random. The formation of ternary complex still occurs with substrates and then products of the reaction.
51
What is involved in the ordered mechanism?
The enzyme will bind one specific substrate first and release one specific product first. The enzyme exists in a ternary complex, first with the substrates of the reactions and then after with the products and so on.
52
What is involved in the double displacement mechanism?
The substrate bounce on and off the enzyme as they are catalysed.
53
What is an allosteric enzyme?
Allosteric enzymes are made up of many subunits, which contain many active sites.
54
What does cooperative binding of substrate molecules at allosteric enzymes mean?
One substrate binding to an enzyme can cause changes in other active sites on other subunits.
55
Do allosteric enzymes follow M-M kinetics?
No
56
What will affect an enzyme?
Temperature. Increase number of molecule collisions and internal energy. Denaturation occurs after optimum. pH. Changes the charge of amino acids. Denaturation occurs after optimum Inhibitors.
57
What are competitive inhibitors?
Competitive inhibitors bind to enzymes non-covalently and will always resemble the substrate molecule. This means that they compete with the substrate molecule with the active site.
58
What happens to the Vmax and Km value when competitive inhibitors bind?
Once bound, it leads to a decrease in the affinity between the active site and the substrate. This means that Km increases. Increasing substrate concentration can overcome this inhibition, as this means that the substrate will bind to the enzyme than the inhibitor. Therefore, competitive inhibitors exhibit increased Km values, but the Vmax remains unchanged.
59
What are non-competitive inhibitors?
 Non-competitive inhibitors bind to enzymes non-covalently and will usually attach to a site other than the active site of the enzyme.
60
What happens to the Vmax and Km value when non-competitive inhibitors bind?
The substrate is usually still able to bind to the active site, so the Km of the substrate remains unchanged. Increasing substrate concentration does not change the inhibition so the Vmax will decrease. Therefore, non-competitive inhibitors exhibit unchanged Km values but the Vmax decreases.
61
What are the two main ways regulatory enzymes modulate reactions?
Allosteric enzymes and covalently modified enzymes
62
What is feedback inhibition?
build-up of the end product of a pathway can ultimately slow the entire pathway, as the end product binds to the regulatory pathway and inhibits it. A decreased concentration of the end product can ultimately quicken the entire pathway, as less end product is able to bind to the regulatory enzyme and inhibit it.
63
What are allosteric effectors?
Molecules that bind to a site on the enzyme that is not the active site. When they bind, they change the enzymes structure.
64
What two models explain allosteric enzyme kinetics?
Concerted | Sequential
65
What is the concerted model?
Each subunit can exist in two different conformations. One conformation is able to bind to the substrate well and the other doesn’t. With no substrate the enzyme flips between the two conformations. When one substrate molecule binds to the allosteric enzyme, it locks the other binding sites, stopping them from flipping and allowing other substrates to bind easily.
66
What are allosteric activators?
Allosteric activators will stabilise the open conformation allowing substrate to bind more effectively.
67
What are allosteric inhibitors?
Allosteric inhibitors will stabilise the closed conformation and make it more difficult for substrate to bind effectively.
68
What is the sequential model?
There is no flipping between different conformation states. Substrate binding causes a change in one subunit. This causes a change in another subunit allowing it to bind to the substrate more readily. This continues until all subunits are saturated.
69
What are the three ways that enzymes can be modulated by?
Allosterically Covalent modifications Proteolytic cleavage
70
What is proteolytic cleavage?
Proteolytic cleavage involves proproteins can be cleaved to give active enzymes by proteases.
71
What are proproteins?
Inactive precursor proteins

Year One - Science For Medicine (16 decks)

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