Chapter 6

What do we mean when we say that enzymes are catalysts?

They increase reaction rates without being used up. 

What kind of proteins are enzymes?

Globular.

Other than globular proteins, what can also catalyze reactions?

RNA (ribozymes and ribosomal RNA)

What is the oldest field of biochemistry?

Study of enzymatic processes (late 1700s)

Enzyme History: Buchner

Enzyme History: Sumner

Enzyme History: Haldane

1930’s suggested weak bonding interactions between the enzyme and substrate might be used to catalyze a reaction

catalytic activity depends on the

catalytic activity depends on the

Molecular weight of enzymes = 

ranges from 12,000 to >1 million

cofactor =

1+ inorganic ions, such as Fe2+, Mg2+ , Mn2+, or Zn2+

coenzyme =

complex organic or metalloorganic molecule that act as transient carriers of specific functional groups

Structure essential to

catalytic activity

Inorganic ions:

Inorganic ions:

Coenzyme: Organic or organometallic • Prosthetic group: tightly bound • HOLOENZYME = Enzyme + Cofactor • Apoenzyme: missing cofactor

What is a cofactor?

An inorganic ion or coenzyme required for enzyme activity.

What is a prosthetic group on an enzyme?

A coenzyme or metal ion tightly or covalently bound to it’s protein

What is a holoenzyme?

Complete catalytically active enzyme together with its bound coenzyme and/or metal ions

What is an apoenzyme?

The protein part of a holoenzyme.

How are enzymes classified?

By reaction type. with subclasses and formal systematic name vs. common name.

In classifications of enzymes, each has a ….

four part Enzyme Commission number (EC number) and a systematic name.

Give Reaction Type and Class

1. Oxidoreductase. 

Alcohol dehydrogenase (oxidation with NAD⁺)

Give Reaction Type and Class

2. Transferases

Hexokinase (phosphorylation

Give Reaction Type and Class

3. Hydrolases

Carboxypeptidase A (peptide bond cleavage)

Give Reaction Type and Class

4. Lyases

Pyruvate decarboxylase (decarboxylation)

Give Reaction Type and Class

5. Isomerases

Maleate isomerase (cis-trans isomerization)

Give Reaction Type and Class

6. Ligases

Pyrucate carboxylase (carboxylation)

Enzymatic reactions occur in ______.

Specialized pockets called active sites.

What occurs at active sites?

A reaction - the conversion of a substrate to a product. W

What is a substrate?

A molecule acted on by an enzyme.

By how much do enzymes enhance rate?

By 10⁵ to 10¹⁷

Enzymes are characterized by the formation of which complex?

Enzyme-substrate

Do enzymes lower the activation barrier?

Yes

Do enzymes affect the equilibrium?

No

What are five reasons why biocatalysis is better than inorganic catalysis?

What is Phenylalanine Hydroxylase?

an enzyme that catalyzes the hydroxylation of the aromatic side-chain of phenylalanine to generate tyrosine

Enzymatic Substrate Selectivity of PAH

What is an active site?

provides a specific environment in which a given reaction can occur more rapidly

What is a substrate?

the molecule that is bound to the active site and acted upon by the enzyme

simple enzymatic reactions can be written as

where E, S, and P represent the enzyme, substrate, and product and ES and EP are transient complexes of the enzyme

Can enzymes affect the free energy of the reaction?

No

Slow reactions face what to occur?

Activation barriers.

How do enzymes overcome high activation barriers?

Label this Reaction Coordinate Diagram.

biochemical standard free energy change =

activation energy (∆G‡) =

difference between the ground state energy level and the transition state energy level

any enzyme that catalyzes the reaction S → P also catalyzes the reaction _____.

P → S

enzymes ________the interconversion of S and P

Accelerate

reaction intermediate =

any species on the reaction pathway that has a finite chemical lifetime – example: ES and EP complexes

rate-limiting step =

= the step in a reaction with the highest activation energy that determines the overall rate of the reaction

Enzymes exhibit a very high degree of _______

Specificity

Each enzyme catalyzes____ chemical reaction, or sometimes________ reactions

Only one; a few closely related

Reaction activation barriers are thus _____ selectively.

lowered

reaction equilibria are linked to the

standard free-energy change for the reaction, ∆G′°

reaction rates are linked to the

activation energy, ∆G‡

under standard conditions: K′ _eq =

from thermodynamics: ∆G′° =

The Relationship between K′ eq and ∆G′ °

Inverse.

the rate of any reaction is determined by the _______________ and the _________

concentration of reactant(s) and the rate constant, k

for the unimolar reaction S → P, a ___________ expresses the rate of the reaction

rate equation

first-order reaction =

rate depends only on the concentration of S

k has units of

reciprocal time, such as s–1

Equation for Relatioinship b/n Rate Constants and Activation Energy

The relationship between the rate constant k and the activation energy ∆G‡ is _______ and ______

inverse and exponential

Boltzmann constant

k_B=1.3806 × 10^-23 J/K

Planck’s Constant used in the formula for The Relationship between Rate Constants and Activation Energy

h = 6.626 × 10^-34 d ^. s

R for The Relationship between Rate Constants and Activation Energy

R = 8.314 J/ (mol ^. K)

Enzymes enhance rates in the range of __ to __ orders of magnitude

5 to 17

Rate enhancement =

Carboxypeptidase

What two concepts explain the catalytic power of enzymes?

1. Enzymes bind most tightly to the T_s of cat. rxn, using binding E to lower the activation barrier

2. Enzyme active sites are organized by evo to facilitate multiple mech of chem cat simultaneously.

Define Binding Energy

∆G_B = energy derived from noncovalent enzyme-substrate interaction

What interactions mediate binding energy?

H bonds, ionic interactions, and the hydrophobic effect.

What is the major source of free E used by enzymes to lower the activation energy?

Binding Energy

What can covalent interactions bwetween the enzyme and substrate do to the activation energy?

Lower it. 

When are noncov int b/n E and S optimized?

In the transition state.

What is the lock and key hypothesis

enzymes are structurally complementary to their substrates – would make for a poor enzyme

What do enzymes bind best? Who proposed this idea?

Transition states. Linus Pauling in 1946

Enzyme active sites are___________ to the transition state of the reaction. Enzymes bind transition states______ than substrates

Complimentary; better

Stronger/additional interactions with the_____ state as compared to the _____ state _____ the activation barrier. Largely___effect

transitional; ground; lower ;ΔH‡

the full complement of interactions between substrate and enzyme is formed only when___________________.

the substrate reaches the transition state

Stickase

Enzymes must________ the transition state to achieve rate enhancement

preferentially stabilize

the sum of the _____________ and the _____________ results in a lower net activation energy

unfavorable activation energy ∆G‡; favorable binding energy ∆GB

_______________between the enzyme and the substrate drive enzymatic catalysis

weak binding interactions

optimized binding energy in the transition state is accomplished by _____________ (the _______), removed from ___

positioning a substrate in a cavity; active site; H2O

Define specificity. What is it given by?

= ability to discriminate between a substrate and a competing molecule – given by binding energy

barrier to reaction , ∆G‡ includes what four things?

– the entropy of molecules in solution

– the solvation shell of hydrogen-bonded water that surrounds and stabilizes most biomolecules in aqueous solution

– the distortion of substrates that must occur in many reactions

– the need for proper alignment of catalytic functional groups on the enzyme

Enzymes organize reactive groups into _______ and _________

Close proximity and proper orientation

Uncatalyzed bimolecular reactions

two free reactants → single restricted transition state conversion is entropically unfavorable

Uncatalyzed unimolecular reactions

flexible reactant → rigid transition state conversion is entropically unfavorable for flexible reactants

Catalyzed reactions

Enzyme uses the binding energy of substrates to organize the reactants to a fairly rigid ES complex

Entropy cost is paid during binding

Rigid reactant complex → transition state conversion is entropically OK

Entropy Reduction

large restriction in the relative motions of two substrates that are to react

binding energy constrains substrates in the _______ to reaction

proper orientation

Desolvation

replacement of the solvation shell of structured water around the substrate with weak bonds between substrate and enzyme