M3 - Enzymes and Metabolism

Question 1

What are enzymes? What are co-factors?

Answer 1

Enzymes are proteins, but some make use of chemical groups other than those found on amino acids.
Co-factors: small molecules that are not part of the enzyme, but which are required for activity.

Question 2

Describe apoenzyme and holoenzyme.

Answer 2

An enzyme lacking an essential co-factor is known as an apoenzyme.
The complex between an apoenzyme and a co-factor is called a holoenzyme.

Question 3

Describe 3 key points about enzymes.

Answer 3

1. Enzymes increase the rate at which a chemical reaction proceeds
2. Enzymes increase both forward and reverse rates: in other words, they do not change the positions of chemical equilibria.
3. Enzymes do not undergo net change when they participate in reactions as catalysts

Question 4

Describe k(cat).

Answer 4

Catalytic power: the ‘turnover number’ or ‘catalytic constant’ kcat
kcat = the number of molecules of substrate that one enzyme active site can convert into product per second.
e.g. for carbonic anhydrase, kcat = 1,000,000 s-1

Question 5

Describe the specificity of enzymes in specific.

Answer 5

Some enzymes are highly specific: they can discriminate between similar molecules:
- some enzymes can differentiate between optical isomers
- some enzymes can differentiate between positional isomers
- some enzymes can differentiate between presence/absence of functional groups.
This implies a complementarity between the enzyme’s active site and the substrate:
- This implies that the enzyme recognises and binds its substrate in an enzyme: substrate (ES) complex.
- This is the basis of the Michaelis-Menten model for enzyme kinetics.

Question 6

Describe ‘The lock and key’ model.

Answer 6

Emil Fischer (1890) envisaged the active sites of enzymes as a fixed set of chemical groups that fit the substrate exactly: Schlüssel-Schloss-Prinzip, or ‘key-lock-principle’.

Question 7

Describe the ‘induced fit model’.

Answer 7

Daniel Koshland (1958) proposed that substrates cause a change in the 3-D relationship of the active site and these changes bring the catalytic groups into the proper orientation for reaction.

Question 8

Describe the chemistry of the active site.

Answer 8

It is made from different parts of the polypeptide chain, dictated by the ‘fold’ or 3-D structure of the enzyme.
It often forms a cleft or crevice which surrounds the substrate.
When the enzyme:substrate (ES) complex forms, there are multiple weak non-covalent interactions (electrostatic, H bonds, Van der Waals forces) between the substrate and active-site groups.
Formation of these releases energy, which lowers the activation energy.
These interactions facilitate the formation of the transition-state.

Question 9

Describe the 4 basic catalytic principles.

Answer 9

1. Covalent catalysis
   The active site contains a very reactive group that becomes (temporarily) attached to part of the substrate.
2. General acid-base catalysis
   A molecule other than water acts as a proton acceptor or donor e.g. chymotrypsin uses His57 as a base catalyst to enhance the power of Ser195.
3. Catalysis by approximation.
   The enzyme brings together two substrates in order to increase the rate of reaction e.g. carbonic anhydrase brings together CO2 and H2O in adjacent sites.
4. Metal ion catalysis
   Metal ions may facilitate formation of nucleophiles (that donate an electron pair e.g. Zn(II) ion in carbonic anhydrase), of electrophiles (that accept an electron pair.

Question 10

Describe the Michaelis-Menten (1913) equation.

Answer 10

𝑣_0=(𝑉_max [S])/((𝐾_𝑆+[S]) )

Question 11

Describe the equation that links kcat and vmax. Describe what kcat is.

Answer 11

𝑘𝑐𝑎𝑡= 𝑉𝑚𝑎𝑥/[𝐸]
kcat is independent of enzyme concentration, thanks to the term in the denominator.
kcatis thus a constant for an enzyme under given conditions. But if you change conditions, you change kcat.

Question 12

Describe how penicillins inhibit enzyme actions.

Answer 12

Penicillins irreversibly inhibit penicillin binding proteins which enable bacteria to make cell walls. Penicillins fix the ES complex.

Question 13

Describe how salicylic acid inhibit enzyme action.

Answer 13

Salicylic acid (the active metabolite of aspirin) irreversibly inhibits cycloxygenase (COX) that produces prostaglandin, thus blocking inflammation.

Question 14

Describe what organomercurials and nerve gases are.

Answer 14

Organomercurials: often highly toxic – used to be used as drugs
Nerve gases: chemical warfare/assassination agents

Question 15

What is the mode of action of mercuric compounds.

Answer 15

Covalent modification: e.g., the reaction of cys residues with p-hydroxymercurobenzoate leads to permanent irreversible inactivation of some enzymes.
Mercuric compounds are non-specific: they will interact with any available cysteines, not just active site cysteines.
They also interact with selenium, so they also irreversibly inactivate seleno-enzymes such as thioredoxin reductase.