MODULE 7: Chapter 7.5

Question 1

What are the two primary mechanisms of enzyme regulation?

Answer 1

1. Bioavailability 2. Control of catalytic efficiency through protein modification

Bioavailability pertains to the amount of enzyme in different tissues and cellular compartments, while catalytic efficiency is influenced by covalent and noncovalent modifications.

Question 2

What can positive regulatory mechanisms lead to in enzyme activity?

Answer 2

An increase in enzyme activity

This can result from increased enzyme synthesis or enhanced catalytic efficiency due to conformational changes.

Question 3

What are the biochemical processes affecting enzyme bioavailability?

Answer 3

• RNA synthesis (gene transcription)
• RNA processing
• Protein synthesis
• Protein degradation
• Protein targeting

These processes influence the amount of enzyme available for catalytic activity.

Question 4

What are the three primary mechanisms that affect catalytic efficiency?

Answer 4

• Binding of regulatory molecules
• Covalent modification
• Proteolytic processing

These mechanisms help control enzyme activity and responsiveness.

Question 5

What is enzyme inhibition?

Answer 5

A regulatory mechanism to control enzyme activity

Enzyme inhibitors can also be used in research and therapy to affect enzyme function.

Question 6

What are the two types of enzyme inhibition?

Answer 6

• Reversible inhibition
• Irreversible inhibition

Reversible inhibition involves noncovalent binding, while irreversible inhibition involves covalent bonds.

Question 7

How can reversible inhibitors be affected by enzyme dilution?

Answer 7

The effect of reversible inhibitors can be decreased by diluting the enzyme reaction

This is because the noncovalent interactions can be disrupted.

Question 8

What is malonate’s role in enzyme inhibition?

Answer 8

Malonate is a reversible inhibitor of succinate dehydrogenase

It competes with succinate for binding to the active site, inhibiting the enzyme’s function.

Question 9

What characterizes irreversible inhibitors?

Answer 9

They form a tight complex with the enzyme, effectively ‘killing’ it

This occurs through covalent bonds or very strong noncovalent interactions.

Question 10

What is a suicide inhibitor?

Answer 10

A type of irreversible inhibitor that reacts with an enzyme during catalysis but does not complete the reaction

It forms a covalent bond and remains irreversibly bound to the enzyme.

Question 11

What are the three classes of reversible inhibitors?

Answer 11

• Competitive inhibitors
• Uncompetitive inhibitors
• Mixed inhibitors

These classes differ in their binding mechanisms and effects on enzyme kinetics.

Question 12

What defines a competitive inhibitor?

Answer 12

It inhibits substrate binding at the active site

Competitive inhibitors can bind directly to the active site or partially obstruct it.

Question 13

What happens to the apparent Km in the presence of a competitive inhibitor?

Answer 13

The apparent Km increases

This reflects the requirement of higher substrate concentration to reach vmax.

Question 14

What is the effect of uncompetitive inhibitors on Km and vmax?

Answer 14

Both Km and vmax decrease

The net effect is a constant slope of Km/vmax in a Lineweaver–Burk plot.

Question 15

How do mixed inhibitors function?

Answer 15

They bind to both the enzyme and the enzyme–substrate complex

This results in a decreased vmax and forms unproductive EI or ESI complexes.

Question 16

What is the role of structure-based drug design in enzyme inhibition?

Answer 16

It uses knowledge of an enzyme’s structure to create inhibitors that fit the active site

This strategy is employed in the development of drugs targeting specific enzymes.

Question 17

What is the equilibrium dissociation constant KI?

Answer 17

It describes the affinity of an enzyme for an inhibitor

KI specifically refers to the equilibrium dissociation constant for an enzyme–inhibitor complex.

Question 18

How do competitive inhibitors affect enzyme kinetics in a Lineweaver–Burk plot?

Answer 18

Vmax remains unaffected, but the apparent Km increases

This is evident in the shifting of the Lineweaver–Burk plot.

Question 19

What is the effect of increasing substrate concentration in the presence of a competitive inhibitor?

Answer 19

The effects of the inhibitor can be overcome

High substrate concentrations can outcompete the inhibitor for binding to the active site.

Question 20

What is mixed inhibition?

Answer 20

A mixture of competitive and uncompetitive inhibition, where an unproductive EI or ESI complex is formed, decreasing the enzyme’s catalytic activity.

Mixed inhibition results in decreased vmax and may increase or decrease Km depending on the relative KI and KI’ values.

Question 21

What happens to vmax in the presence of a mixed inhibitor?

Answer 21

Decreased.

The effect is due to some enzyme being bound to the inhibitor, making less enzyme available.

Question 22

What is noncompetitive inhibition?

Answer 22

A special case of mixed inhibition where the inhibitor has equal affinity for both the free enzyme and the ES complex (KI = KI’).

Noncompetitive inhibitors bind away from the active site and do not compete with the substrate.

Question 23

What effect does noncompetitive inhibition have on Km?

Answer 23

Unchanged.

Both the free enzyme and the enzyme-inhibitor complex can bind to substrate.

Question 24

How does feedback inhibition work?

Answer 24

The end product of a metabolic pathway inhibits the first enzyme in the pathway when it accumulates.

This mechanism helps regulate metabolic pathways efficiently.

Question 25

What is the role of aspartate transcarbamoylase (ATCase) in metabolic regulation?

Answer 25

It is a key regulated enzyme in the pyrimidine biosynthetic pathway, catalyzing the formation of N-carbamoyl-L-aspartate. ## Footnote ATCase is regulated by feedback inhibition from CTP and activation by ATP.

Question 26

What distinguishes allosteric regulation from standard enzyme kinetics?

Answer 26

Allosteric regulation allows for a higher degree of control and does not follow Michaelis–Menten kinetics. ## Footnote Cooperative binding leads to a sigmoidal activity curve.

Question 27

What are homotropic allosteric activators?

Answer 27

Substrates that affect the binding of the same molecules at other active sites. ## Footnote In the case of ATCase, carbamoyl phosphate and aspartate are homotropic activators.

Question 28

What are heterotropic allosteric regulators?

Answer 28

Molecules that bind to regulatory sites and affect the binding of different substrates at other sites. ## Footnote CTP and ATP are examples of heterotropic regulators for ATCase.

Question 29

What is the impact of phosphorylation on enzyme activity?

Answer 29

Phosphorylation can activate or inactivate enzymes by altering their structure and active site chemistry. ## Footnote This is a common form of covalent modification in enzyme regulation.

Question 30

What is the role of glycogen phosphorylase in glucose metabolism?

Answer 30

It degrades glycogen to generate glucose for energy conversion in glycolysis. ## Footnote The enzyme is active in the phosphorylated R-state and inactive in the unphosphorylated T-state.

Question 31

What is the significance of the regulatory site in glycogen phosphorylase?

Answer 31

It is not directly at the active site but affects activity through structural changes upon phosphorylation. ## Footnote Phosphorylation shifts the equilibrium toward the active R-state.

Question 32

What is adenylylation in the context of enzyme regulation?

Answer 32

A covalent modification that inactivates certain enzymes, such as E. coli glutamine synthetase, by adding nucleoside monophosphate groups. ## Footnote This modification can shift the enzyme between active and inactive states.

Question 33

What is the T-state and R-state conformation in enzymes?

Answer 33

T-state is the inactive form, while R-state is the active form of the enzyme. ## Footnote The transition between these states involves significant conformational changes.

Question 34

What is the role of glutamine synthetase in bacterial nitrogen metabolism?

Answer 34

It catalyzes an ATP-dependent reaction that incorporates free NH4⁺ into the amino acid pool by converting glutamate to glutamine.

Question 35

What conformational states does adenylylated glutamine synthetase exist in?

Answer 35

Inactive T-state conformation and active R-state conformation.

Question 36

What enzyme catalyzes the adenylylation and deadenylylation of glutamine synthetase in E. coli?

Answer 36

Glutamine synthetase adenylyltransferase.

Question 37

How is the activity of glutamine synthetase adenylyltransferase regulated?

Answer 37

Through uridylylation of Tyr51 by uridylyltransferase.

Question 38

Under what conditions is the uridylylation activity of uridylyltransferase stimulated?

Answer 38

Under conditions of high ATP and elevated levels of α-ketoglutarate.

Question 39

What happens when Pi and glutamine levels are elevated in the cell?

Answer 39

The deuridylylation activity of uridylyltransferase is stimulated, activating adenylation activity.

Question 40

What is a zymogen?

Answer 40

An inactive enzyme precursor that is activated by a proteolytic cleavage reaction.

Question 41

What is pepsinogen and how is it activated?

Answer 41

Pepsinogen is a zymogen that catalyzes an autocleavage reaction to generate the active enzyme pepsin.

Question 42

What is the pH environment that stimulates the autocleavage of pepsinogen?

Answer 42

pH 1.5.

Question 43

What is the process by which chymotrypsinogen is converted to its active form?

Answer 43

Proteolytic cleavage events that result in the formation of α-chymotrypsin.

Question 44

Which enzyme initiates the cleavage of chymotrypsinogen?

Answer 44

Trypsin.

Question 45

What type of regulation does proteolytic cleavage represent?

Answer 45

Irreversible regulation.

Question 46

What three primary mechanisms regulate enzyme activity in the cell?

Answer 46

* Competitive inhibition * Allosteric regulation * Reversible covalent modification.

Question 47

What is competitive inhibition?

Answer 47

A mechanism where the product of a reaction competes for substrate binding.

Question 48

What is negative allosteric regulation?

Answer 48

A mechanism where a metabolite acts as an allosteric effector molecule, altering enzyme activity.

Question 49

What are kinases and phosphatases?

Answer 49

* Kinases: Enzymes that phosphorylate * Phosphatases: Enzymes that dephosphorylate.

Question 50

What is feedback inhibition?

Answer 50

An enzyme regulatory mechanism where the end product of a pathway functions as an inhibitor of the first enzyme in the pathway.

Question 51

What is irreversible inhibition?

Answer 51

An enzyme regulatory mechanism in which an inhibitory molecule forms a covalent bond with catalytic groups in the enzyme active site.

Question 52

What is a suicide inhibitor?

Answer 52

An inhibitor that initiates the enzyme reaction mechanism but does not complete it, remaining covalently bound to the active site.

Question 53

What defines a competitive inhibitor?

Answer 53

A molecule that inhibits substrate binding at the active site.

Question 54

What defines an uncompetitive inhibitor?

Answer 54

A molecule that binds to enzyme–substrate complexes and alters the active site conformation.

Question 55

What is a mixed inhibitor?

Answer 55

A molecule that binds to sites distinct from the enzyme active site but can bind to both the enzyme and the enzyme–substrate complex.

Question 56

What is noncompetitive inhibition?

Answer 56

A special case of mixed inhibition where a molecule has equal affinity for both the free enzyme and the enzyme–substrate complex.

Question 57

What is adenylylation?

Answer 57

A covalent modification of an enzyme by addition of AMP that regulates catalytic activity.

Question 58

What is uridylylation?

Answer 58

A process that regulates enzyme activity by controlling adenylylating and deadenylylating activity.