1. The Behavior of Proteins: Enzymes
Chapter 6

2. Enzymes are effective biological catalysts
Enzyme: a biological catalyst that can speed up the rate of a chemical reaction
Can increase the rate of a reaction by a factor of up to 1020 over uncatalyzed reactions
RNAs (ribozymes)
Globular proteins
some enzymes are so specific that they catalyze the reaction of only one stereoisomer; others catalyze a family of similar reactions

3. Thermodynamics and Kinetics of Reaction
Thermodynamics – whether a reaction is spontaneous or not
Kinetics – determines how fast a reaction occurs
If a reaction is involving many catalysts/enzymes then it is spontaneous – activation energy is negative. Even if it is negative sometimes, reactions might not happen quickly

4. What is Activation Energy?
The difference between energies of reactants and products – Standard free energy = ΔºG
The rate of a reaction depends on its activation energy = ΔºG+
Speed up reactions
Do not alter free energy change
Lower the activation energy
The difference between energies of reactants (initial state) and energies of the products (final state) of a reaction gives energy change for that reaction – standard free energy change ΔºG

5. What is Activation Energy?
Energy required to initiate a reaction
ΔºG for an uncatalyzed reaction is higher than that of catalyzed reaction
Uncatalyzed reactions requries more energy to get started and is slower in progress than a catalyzed reaction. Enzymes reduce activation energy. The activation energy can be seen as the amount of free energy required to bring the reactants to transition state.

6. Enzyme Catalysis Consider the reaction
Conversion of H2O2 to water and oxygen is an example of effect of catalysis on activation energy. The energy is lowered if the reaction is allowed to proceed on platinum surfaces but is lowered even more by enzyme catalase

7. Temperature dependence of catalysis
Temperature can also catalyze reaction
Increasing temperature will eventually lead to protein denaturation
Temperature can increase rate of reaction

8. Kinetic equations of enzymatic reactions
For any reaction
The rate of reaction is given by rate equation
A and B are reactants and P is the product. The rate of reaction can be expressed as rate of disappearance of one of the reactants or appearance of product. Or the negative signs indicates that A and B are being used up to produce P. K is proportional to product of concentrations of reactants.
raised to appropriate powers. K, f and g should be determined experimentally
Where k is a proportionality constant called the specific rate constant

9. How Enzymes bind to Substrate?
In an enzyme-catalyzed reaction
Substrate, S: a reactant
Active site: the small portion of the enzyme surface where the substrate(s) becomes bound by noncovalent forces, e.g., hydrogen bonding, electrostatic attractions, Van der Waals attractions
The binding of substrate to enzyme occurs because of interactions between substrate and and the side chains and backbone groups of amino acids making up an active site

10. What are the two Binding Models?
Two models have been developed to describe formation of the enzyme-substrate complex
Lock-and-key model: Substrate binds to that portion of the enzyme with a complementary shape
Induced fit model: Binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit

11. 2 Models of E-S Complex Formation

12. Formation of Product – Figure 6.5
Product formed should be released for more substrate to come and bind to the enzyme to form more products

13. Chymostrypsin - An Example of Enzyme Catalysis
Chymotrypsin catalyzes
The selective hydrolysis of peptide bonds where the carboxyl is contributed by Phe and Tyr
It also catalyzes hydrolysis of the ester bonds

14. Non-Allosteric Enzyme Behavior
Point at which the rate of reaction does not change
Enzyme is saturated
Maximum rate of reaction is reached
Hyperbolic

15. Allosteric Enzyme Behavior
Sigmoidal shape- characteristic of allosterism

16. Michaelis-Menten Kinetics
Initial rate of an enzyme-catalyzed reaction versus substrate concentration

17. What is Vmax and KM?
Vmax – describes velocity of an enzyme-catalyzed reaction when there is a saturating level of substrate
Determines the individual rate constant (Kp)
KM is equal to substrate concentration that generates half of Vmax.

18. Lineweaver-Burk Plot
KM is the dissociation constant for ES; the greater the value of KM, the less tightly S is bound to E
Vmax is the turnover number
Reciprocal plot of velocity versus substrate.

19. Turnover Numbers
• Vmax is related to the turnover number of enzyme:also called kcat
• Number of moles of substrate that react to form product per mole of enzyme per unit of time

20. What is an enzyme inhibitor?
A substance that interferes with action of an enzyme and slows rate of reaction – Enzyme inhibitor

21. Reversible Enzyme Inhibition
Reversible inhibitor: a substance that binds to an enzyme to inhibit it, but can be released
Competitive inhibitor: binds to the active (catalytic) site and blocks access to it by substrate

22. Reversible Enzyme Inhibition
Noncompetitive inhibitor: binds to a site other than the active site; inhibits the enzyme by changing its conformation

23. Non-reversible enzyme inhibition
Irreversible inhibitor: a substance that causes inhibition that cannot be reversed
usually involves formation or breaking of covalent bonds to or on the enzyme

24. Other types of Inhibition
Uncompetitive- inhibitor can bind to the ES complex but not to free E. Vmax decreases and KM decreases.
Mixed- Similar to noncompetitively, but binding of I affects binding of S and vice versa

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