Biochemistry Short Course: Understanding Enzyme Kinetics and Regulation - Prof. Yogarajah , Study notes of Biochemistry

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• (^) Biochemistry: A Short Course
  • (^) First Edition
• (^) Biochemistry: A Short Course
• (^) First Edition Tymoczko • Berg • Stryer © 2010 W. H. Freeman and Company

CHAPTER 6

Kinetics and Regulation

Kinetics and

regulation

Nomenclature Typically add “- ase ” to name of substrate e.g. lactase breaks down lactose (dissacharide of glucose and galactose) based upon the class of organic chemical reaction catalyzed:

1. oxidoreductase - catalyze redox reactions dehydrogenases, oxidases, peroxidases, reductases
2. transferases - catalyze group transfer reactions; often require coenzymes
3. hydrolases - catalyze hydrolysis reactions
4. lyases - lysis of substrate; produce contains double bond
5. isomerases - catalyze structural changes; isomerization
6. ligases - ligation or joining of two substrates with input of energy, usually from ATP hydrolysis; often called synthetases or synthases

Enzyme kinetics: A mathematical and graphical study of the rates of enzyme-catalyzed reactions. k S -----------> P k A + B ---> C The velocity of this reaction can be summarized by the following equation: v = k[S] or v = k[A][B] The rate of the reaction is directly related to the concentration of A s or AB by a proportionality constant, k, called the rate constant

• (^) An enzyme catalyzed reaction approaches a

maximal velocity

• (^) The Michael – Menten model describes the kinetics of many enzymes
• (^) The rate of catalysis , V 0 , which is defined as the number of moles of product formed per second, varies with the substrate concentration, (S), when enzyme concentration is constant.

These same reactions can be described graphically: velocity [S] At low [S], vo increases as [S] increases. At high [S], enzymes become saturated with substrates, and the reaction is independent of [S] --> display saturation kinetics.

• Vmax = kcat[ES] or because the [S] is irrelevant at high [S] Vmax = kcat [E] The graph is a graph of a hyperbola, and the equation for a hyperbola is y = ax b + x where a is the asymptote b is value at a/ E + S -----> ES -----> E + P

Substituting our equation parameters, Vo = Vmax[S] Km + [S] Michaelis-Menten equation Different enzymes reach Vmax at different [S] because enzymes differ in their affinity for the substrate or Km.

• (^) Read clinical insight and K M page 77
• (^) Alcohol cosumption

Enzyme-substrate affinity and reaction kinetics are closely associated

[S] at which v

o

=1/2V

max

= K

m K m is a measure of enzyme affinity K m = k

k 1 reflection of association and dissociation of ES a small K m (high affinity) favors E + S ----> ES a large K m (low affinity) favors ES -----> E + S meaning that the lower the Km, the less substrate is needed to saturate the enzyme.

Alterations in enzyme activity: Enzyme inhibition Molecule that binds to enzyme and interferes with its activity to prevent either:

1. formation of ES complexE + I ---> EI
2. breakdown of ES --> E + P ES + I ---> ESI Used to regulate metabolism. Many drugs act by enzyme inhibition. These molecules can be
3. irreversible - bind to enzymes by covalent means and modify enzyme
4. reversible - noncovalent binding to enzyme

1. competitive Competes with substrate for active site of enzyme. Both substrate and competitive inhibitor bind to active site. These inhibitors are often substrate analogs (similar in structure substrate), but still no product is formed.

Can be overcome by addition of more substrate

(overwhelm inhibitor; a numbers game).

e.g. malonate inhibition of succinate dehydrogenase

succinate ----------------------> fumarate

FAD FADH 2

succinate malonate