PH1125 - Enzymes

Question 1

what is an enzyme from a chemical pov?

Answer 1

• well defined sequence of amino acids with well defined 3d structures (proteins)

Question 2

what is an enzyme from a biologial pov?

Answer 2

• macromolecular bio-catalysts

Question 3

what does an enzyme do?

Answer 3

• accelerates a biochemical reaction that would otherwise occur over years instead of seconds

Question 4

are enzymes and proteins changed by the reactions they catalyse?

Answer 4

• no they remain unchanged

Question 5

what are the properties of enzymatic reactions? (3)

Answer 5

• substrate specific
• efficient
• fast

Question 6

what is the lock and key model? (2)

Answer 6

• only a substrate (S) that is complimentary to the enzyme (E) can bind to the active site
• once bound a reaction can occur liberating a product(s) (P)

Question 7

what is the induced fit model? (2)

Answer 7

• in some enzymes the shape of the active site only becomes complimentary after the substrate has bound
• the tertiary structure of the protein change to accommodate the substrate

Question 8

what happens in an induced fit model? (4)

Answer 8

• as a drug approaches an active site complimentary amino acids residues are drawn towards the substrate
• polar attraction and hydrophobic attractions occur
• this pulls the tertiary structure of the protein out of shape to accommodate the substrate through formation of favourable bonding interactions
• while the substrate remains bound, the active site assumes a different shape

Question 9

what is the michaelis menten model?

Answer 9

• it was developed to understnad the kinetics of enzymic reactions

Question 10

what are the assumptions of the michaelis menten model? (3)

Answer 10

• the enzyme binds a single substrate (the model assumes cofactors are already bound)
• there are two distinct steps where the substrate bind reversibly but the product formation is irreversible
• a steady state approximation applies

Question 11

what is the michaelis-menten equation?

Answer 11

• V = (Vmax [S]) / (Km + [S])

Question 12

what is Vmax?

Answer 12

• maximum velocity the reaction can achieve

Question 13

what are the units for Vmax?

Answer 13

• maximum number of moled of substrate than can be processed in a unit of time; mol s-1

Question 14

what is Km? (2)

Answer 14

• [S]; the michaelis constant required to achieve half the maximum velocity
• gives an indication of how tightly the enzyme binds to its substrate

Question 15

what is the Km value for a weak substrate?

Answer 15

• large Km as a high concentration of substrate is needed to achieve Vmax/2

Question 16

what is an inhibitor?

Answer 16

• a compound that binds to an enzyme and interferes with its activity by preventing the formation of the ES complex

Question 17

what two types are reversible inhibitors classified into? (2)

Answer 17

• competitive

- non-competitive

Question 18

what is a competitive inhibitor and how does it work? (3)

Answer 18

• a competitive inhibitor competes directly with the natural substrate for the enzyme active site
• the inhibitor only binds to the free enzyme in the active site (which is the only binding site)
• therefore the amount of free enzyme available for substrate binding is reduced (if the inhibitor binds tightly to the enzyme and remains in the active site)

Question 19

what can competitive inhibitor be overcome by?

Answer 19

• by increasing the substrate concentration

Question 20

what are the kinetics of competitive inhibition? (3)

Answer 20

• the inhibitor (I) and substrate (S) are competing for the active site (E)
• greater the [I] the more (S) needed to achieve saturation
• greater [S] needed to achieve Vmax there Km increase

Question 21

when a competitive inhibitor is added what happens to Vmax and Km on a Lineweaver Burk plot? (3)

Answer 21

• steepness increases
• Vmax remains unchanged
• Km increases as [I] increases

Question 22

what can a non-competitive inhibitor bind to? (2)

Answer 22

• free E

- ES

Question 23

what is a non-competitive inhibitor? (3)

Answer 23

• they generally do not resemble the natural substrate of the target enzyme (as they are bonding at an alternate site)
• inhibition can’t be overcome by increasing the substrate concentration
• acts by decreasing the turnover number of an enzyme

Question 24

what are the kinetics of non-competitive inhibition? (3)

Answer 24

• EI and ESI are inactive forms of the enzyme
• saturation of E with S can occur but is inactivated by I therefore Vmax is reduced
• [S] required to saturate E does not change since the substrate is free to interact with the active site alone

Question 25

when a non-competitive inhibitor is added what happens to Vmax and Km on a Lineweaver Burk plot? (3)

Answer 25

• gradient increases
• Km remains unchanged
• Vmax decreases as [I] increases

Question 26

what is allopurinol? (3)

Answer 26

• competitive inhibitor of xanthine oxidase
• enzyme xanthine oxidase produces gout
• blocking production of uric acid

Question 27

what is captopril? (3)

Answer 27

• competitive inhibitor of angiotensin converting enzyme (ACE)
• an enzyme that controls blood pressure and volume
• enzyme binds to captopril

Question 28

what do kinase enzymes catalyse the transfer of? (2)

Answer 28

• phosphate groups between proteins
• kinase use ATP as a substrate and a source of the phosphate group (cofactor used to transfer phosphate to target molecule)

Question 29

how do irreversible inhibitors form bonds with the enzyme?

Answer 29

• they form strong covalent bond

Question 30

what does penicillin inhibit?

Answer 30

• transpeptidase

Question 31

what is transpeptidase?

Answer 31

• an enzyme involved in the synthesis of bacterial peptidoglycan cell wall synthesis

Question 32

how do penicillins work? (3)

Answer 32

• beta-lactam ring on penicillin molecule is responsible for antibacterial activity
• ring is highly reactive and forms a covalent bons with the enzyme
• bond is irreversibly bound

Question 33

what are prostaglandins? (2)

Answer 33

• hormones that regulate inflammation and pain

- eg aspirin irreversibly inhibits prostaglandin synthesis by the trans-acetylation of a serine in the active site