Enzyme Chemistry

Question 1

Define enzyme

Answer 1

a protein molecule that accelerates a specific chemical reaction

Question 2

What do enzymes do?

Answer 2

Enzymes are catalysts
Proteins that facilitate reaction mechanisms
Catalyse specific reactions
Increase rate of reaction

Question 3

Define active site

Answer 3

the region of an enzyme that binds the substrate during a chemical reaction.

Question 4

Define substrate

Answer 4

the reactant(s) in enzyme-catalysed reaction.

Question 5

What are the key features of the active site?

Answer 5

Small relative to the total volume of the enzyme.
Usually occur in clefts and crevices of the protein.
Amino acids and cofactors are held in precise arrangement with respect to the substrate.
Amino acids in the active site define specificity.

Question 6

Why use enzymes as catalysts?

Answer 6

Higher reaction rate.
Milder reaction conditions - neutral pH, atmospheric pressure and close ambient temperature.
Greater specificity (in terms of substrate and products not by-products)
There is capacity for control - they respond to concentration of substances.

Question 7

How do enzymes bind substrates?

Answer 7

Lock and key model
Induced fit
Transition state stabilisation

Question 8

Explain the lock and key model

Answer 8

The structure of the active site is complementary to the substrate (like a lock to it’s key).
The shape of the active site is determined by the tertiary and quaternary structure of the protein.

Question 9

Explain the induced fit mechanism

Answer 9

Certain enzymes can catalyse similar reactions.
The induced fit model suggests that the active site of the enzyme undergoes a conformational change when the substrate binds to be a perfect fit for the substrate.
eg. Hexokinase converts glc to glc-6-p

Question 10

What is substrate specificity determined by?

Answer 10

The active site is complementary to the structure of the substrate (geometric).
The amino acids in the active site interact specifically with the substrate (electronic). If amino acids (AAs) on the substrate are negative then the active site will contain positively charged AAs. If the AAs on the substrate are hydrophobic then the active site will contain hydrophobic AAs.

Question 11

What is stereospecificity in terms of enzyme catalysis?

Answer 11

Enzymes will only bind ONE stereoisomer, eg. only the R form and not the S.
Stereospecificity is due to the active site of the enzyme.

Question 12

Define chiral

Answer 12

Two mirror images that are non-superimposable

Question 13

What are the six classes of enzymes?

Answer 13

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

Question 14

What are cofactors?

Answer 14

Small molecules that some enzymes require during catalysis. They can be metal ions or organic molecules (coenzymes).

Question 15

What is a co-substrates?

Answer 15

Are associated transiently with the enzyme - goes into the active site to facilitate the reaction and then leave the active site to be regenerated. Eg ATP.

Question 16

What is a cofactor know as?

Answer 16

These are known as prosthetic groups and are tightly bound to the enzyme

Question 17

What is a holoenzyme?

Answer 17

A catalytically active enzyme-cofactor complex

Question 18

What is an apoenzyme

Answer 18

An inactive protein due to the absence of a cofactor

Question 19

Can metal ions behave as co-substrates or prosthetic groups?

Answer 19

No only co enzymes (organic molecules) can do this.

Question 20

What is a first order reaction?

Answer 20

One molecule changes to another A -> B v = velocity

v = k[A]

Question 21

What is a second order reaction?

Answer 21

Two molecules react A + B -> P + Q
2A -> P
v = k[A][B]
v = k[A]^2

Question 22

What is the equation that gives the [A]? (first order)

Answer 22

[A] = [A]oe^-kt

Question 23

What do oxidoreductases catalyse? Give an example.

Answer 23

• redox reactions
• transfer hydrogen/oxygen/electrons between substrates
• example is alcohol dehydrogenase

Question 24

What do transferases catalyse? Give an example.

Answer 24

• transfer of functional groups between substrates

- example is hexokinase

Question 25

What do hydrolases catalyse? Give an example.

Answer 25

• hydrolytic cleavage of C-O, C-N, C-C, P-O-P bonds.

- example is carboxypeptidase A which cleaves proteins

Question 26

What do lyases catalyse? Give an example.

Answer 26

• cleavage of C-O, C-N, C-C bonds by elimination
• introduces double bonds/rings or adding groups to double bonds
• example is pyruvate decarboxylase

Question 27

What do isomerases do? Give an example.

Answer 27

• geometric/structural changes within a substrate

- example is malate isomerase which forms the different stereoisomers of malate

Question 28

What do ligases do? Give an example.

Answer 28

• join together two substrates
• coupled to ATP hydrolysis
• use cofactors
• example is pyruvate carboxylase

Question 29

Give an example of an enzyme that relies on stereospecificity.

Answer 29

Yeast alcohol dehydrogenase (YADH)

• converts ethanol to acetaldehyde
• requires NAD
• only transfers pro-R hydrogen of ethanol to the re face of NAD

Question 30

What is the clinical relevance of enzyme activity?

Answer 30

• upregulation of enzymes in cancer cells
• reduced function affects metabolism
• enzymes can be used as disease markers in medical diagnosis e.g. lactate dehydrogenase can be used as a marker for muscle damage.