Lecture 1 Bioenergetics and Metabolism

Question 1

Define Metabolism

Answer 1

The sum total of all the enzyme-catalyzed reactions taking place in a cell or organism.

• the process by which your body converts what you eat and drink into energy. During this complex process, calories in food and beverages are combined with oxygen to release the energy your body needs to function

Question 2

What is metabolism responsible for?

Answer 2

• Anabolism → Makes biomolecules
• Catabolism → Breaks down biomolecules

Question 3

What are metabolites?

Answer 3

Reactants, intermediates and products of a metabolic pathway.

Question 4

What is a metabolic pathway?

Answer 4

A sequence of enzyme-catalyzed reactions.

Question 5

What is intermediary metabolism?

Answer 5

The metabolic pathways involving small metabolites (<1,000 Da), such as glucose, fatty acids, and nucleotides.

Question 6

Describe the reversibility of metabolic pathways

Answer 6

• Reversible → reactions proceed spontaneously in both directions
• Irreversible → proceed spontaneously in one direction

Question 7

What is flux?

Answer 7

Flux (J) of metabolites through a reaction is the difference between the rate of the forward reaction (Vf) and the rate of the reverse reaction (Vr).

• Difference between forward reaction and reverse reaction
• The reactions that determine the direction in which metabolites will move

Question 8

How is the flux of a pathway determined?

Answer 8

The flux of a pathway is determined by the flux of the rate-limiting (slowest) step. Often this step is said to be the committed step (subsequent steps are likely to be favourable).

• At equilibrium, J = 0 even though the forward and reverse rates may be large.
• Irreversible reactions are said to occur ‘far from equilibrium’: Vf >> Vr and J≈Vf.

Question 9

When does flux = 0

Answer 9

forward reaction = backward reaction

Question 10

What factors control flux?

Answer 10

• Kinetic properties (Km, Vmax, pH, [substrate]).
• Allosteric control (non-covalent effectors).
• Covalent modification (usually reversible, can be in response to hormones, phosphorylation).
• Substrate cycling (two opposing allosteric enzymes, also called a futile cycle).
• Protein-protein interactions (association of catalytic and regulatory subunits).
• Compartmentation.
• Coenzyme pools.
• Genetic control (long-term response).

Question 11

What are the states of enzyme kinetics?

Answer 11

• pre-steady state
• steady state

Question 12

What is pre-steady state enzyme kinetics?

Answer 12

[S] = [E]

In the first moment after an enzyme is mixed with the substrate, no product has been formed and no intermediates exist. The study of the first few moments of the reaction is called pre-steady-state kinetics.

Question 13

What is steady-state enzyme kinetics?

Answer 13

[S] > [E]

• S is unlimited. Reaction depends on E. Multiple turnovers.
• Michaelis-Menten equation that provides a mathematical means for determining the rate of an enzyme reaction.

Question 14

Two main observations of the Michaelis Menten Kinetics

Answer 14

1. The velocity of a reaction is generally proportional to enzyme concentration.
2. However, velocity usually follows saturation kinetics with respect to the concentration of a substrate.

Question 15

Michaelis-Menten equation

Answer 15

Michaelis–Menten equation is the basis for most single-substrate enzyme kinetics

Question 16

How do allosteric enzymes function?

Answer 16

Allosteric enzymes function through the reversible, noncovalent binding of regulatory compounds called allosteric modulators or allosteric effectors, which are generally small metabolites or cofactors.

• The binding of an allosteric modulator induces a conformation change in the protein. Allosteric proteins have “allos stereos” = “other shapes” or conformations.
• The conformation change induced by modulator binding affects the protein function (e.g., the enzymatic activity).

Question 17

Heteroallostery and homoallostery

Answer 17

• Heteroallostery → The regulation of enzyme activity by molecules other than the substrate.
• Homoallostery → Occurs when the substrate is also an allosteric effector. The substrate has two binding sites.

Question 18

Feedback inhibition

Answer 18

A form of allosteric control in which the final product is a negative allosteric effector of an enzyme occurring earlier in the pathway.

Question 19

Where are allosteric sites found?

Answer 19

Allosteric sites on an enzyme may be on regulatory or on catalytic sites.

Question 20

Kinetics of allosteric enzymes

Answer 20

Allosteric enzymes do not follow Michaelis-Menten kinetics. They display a sigmoidal “S-shaped” relationship between velocity and substrate concentration.