Lecture 5+ self test 1

Question 1

Binding of a substrate to an enzyme is through:

Answer 1

Noncovalent interactions

Question 2

What is the net direction of a catalysis reaction dependent on?

Answer 2

On delta G0 and the concentrations of substrate and product.

Question 3

What are two main mechanisms (models) of enzymes?

Answer 3

1. Lock-and-key: pre-formed active site for selective binding.
2. Induced fit model: substrate induces a conformational change.

Question 4

How do enzymes lower the activation energy?

Answer 4

1. Proximity and orientation effects.
2. Stabilization of the transition state.
3. Use of specific amino acids in the active site that help to break/form covalent bonds in the substrates.
4. Creation of an optimal reaction site: for example by removing water from the active site.

Question 5

What are the six main classes of enzymes? (Name examples)

Answer 5

1. Oxidoreductases: oxidastion-reduction reactions
2. Transferases: transfer a functional group (example: enzumes in the 1st and 7th step of glycolysis)
3. Hydrolases: hydrolysis reactions.
4. Lyases: example: aldolase and endolase in steps 4 and 5 in glycolysis. Lyases eliminate one group, for the formation of double bonds.
5. Isomerases: Isomerization reactions (arrange things differently)
6. Ligases: bond formation coupled with ATP hydrolysis

Question 6

What is the difference between cosubstrates and prosthetic groups and name examples of these two categories.

Answer 6

• Cosubstrates bind transiently and then dissociate. Examples: NADH, NADPH, ATP and acetyl-CoA.
• Prosthetic groups remain attatched. Examples: heme, chlorophyll.

Question 7

What is a nucleophile? What is an electrophile?

Answer 7

• A nucleophile is an electron-rich atom/chemical group that likes to share its electrons. It seeks an electron-poor atom.
• An electrophile is an electron-poor atom/chemical group that seeks electron-rich atoms.

Question 8

What reaction is catalyzed by chymotrypsin and why is this a good example of a substance that is thermodynamically favourable and not kinetically favourable?

Answer 8

Chymotrypsin catalyzes peptide bond cleavage by water. This reaction is energetically favourable (indicated by a negative delta G), meaning it’s thermodynamically favourable.
It’s activation energy is huge, however, so it’s not kinetically favourable.