Chemistry 340 Exam 2 Lecture 1 |
|
Introduction to Enzymes
Major concepts:
1. What is the relationship (an equation) of ΔG°′ to Keq?
2. What is the relationship (use a statement) of ΔG† to k for a reaction and, therefore, to rate?
3. What interactions help to promote formation of an ES complex?
Core knowledge:
1. What are the different types of co-factors; what is a distinguishing feature of each type?
2. What are the different classes of enzymes, and how can you identify each type?
3. What is an active site, and what are active site characteristics?
4. What are the mechanisms by which enzymes catalyze reactions, and what is a
distinguishing characteristic of each mechanism?
Enzymes = catalysts in biochemistry – proteins
(ribozymes = catalytic RNA)
Many require co-factors – non-protein components required for activity
Types of co-factors
A. Metals: Mg2+, Fe2+, Zn2+, etc.
B. Organic co-factors = coenzymes (many derived from vitamins)
1. Prosthetic coenzymes – closely associated with the enzyme; remain with it
Frequently participate in the reaction, but must be regenerated by the reaction.
examples = biotin, FAD (flavin adenine dinucleotide), TPP (thiamine pyrophosphate),
PLP (pyridoxal pyrophosphate), and others
2. Co-substrate coenzymes – changed by the reaction, and leave the enzyme
Co-substrate coenzymes go to another enzyme to be regenerated.
examples = ATP, NAD+, CoA-SH
C. Many enzymes require both metals and coenzymes.
Types of enzymes: classification is based upon the reaction catalyzed
A. Oxidoreductases catalyze oxidation-reduction reactions.
common names = dehydrogenase, oxidase
B. Transferases catalyze the transfer of functional groups.
Sub-groups are classified by the groups transferred.
common names = kinase (transfers phosphate from ATP), aminotransferase, mutase
C. Hydrolases catalyze hydrolysis and dehydration synthesis reactions.
Hydrolysis = breaking a bond by adding H2O
Dehydration synthesis = forming a bond by removing H2O
common names = protease, lipase, glycosidase
D. Lyases catalyze addition of groups to double bonds or the reverse.
Frequently difficult to recognize.
E. Isomerases catalyze rearrangement reactions.
common name = isomerase
F. Ligases catalyze bond formation (C–C, C–S, C–N, C–O) reactions that require ATP.
common name = synthetase, ligase
Enzyme nomenclature
Enzyme names:
Most names end in –ase, but some old names (trypsin, chymotrypsin, lysozyme) do not.
Formal EC (Enzyme Commission) number classifies enzyme by type of reaction,
with sub-classes that specify reactant and product
Commonly used names are frequently informative, but not always.
Reaction terms:
Reactant = substrate (S)
Product = product (P)
Part of the enzyme that binds the substrate and catalyzes the reaction = active site
Process of the reaction: S ↔ reaction intermediate (sometimes = transition state) ↔ P
Changes in energy
?G? = change in free energy measured under standard conditions (1 atm, 298 K)
ΔG°′ = ΔG′° = biochemical ΔG, change in free energy measured under standard biochemical
conditions (neutral pH, specified [Mg2+], etc.)
Enzymes do not change ΔG°′ for a reaction.
Reaction coordinate diagram shows
1. Reactant (S) energy level = ground state
2. Transition state energy level
Difference between 1 and 2 = energy of activation = ΔG†
3. Product energy level = product ground state
Difference between 1 and 3 = ΔG°′ for the reaction
4. For enzyme-catalyzed reactions, ΔG† is reduced.
Enzymes catalyze reactions reversibly. Theoretically.
Some reactions have very large negative ΔG°′; reverse reaction does not occur: S → P
For most reactions S ↔ P
Reaction intermediates
For a reaction with only one substrate: E + S ↔ ES ↔ ES† ↔ EP ↔ E + P
Any ↔ step could be a rate-limiting step.
Overall: S ↔ P, and Keq = [P]/[S]
ΔG°′ = – R T ln K′eq
Rate of a reaction (v) is a function of [S]
For a reaction with only one reactant: v = k [S]
The reaction is a first-order reaction, and k is the rate constant (units = s-1).
For a reaction with two reactants: v = k [S1] [S2]
The reaction is a second-order reaction, and k has the units of M-1s-1.
Note that the text skips over the derivation of the equation that relates k, the rate constant,
to ΔG†.
You do not need to memorize this equation. You do need to know that rate of a reaction
is inversely related to ΔG†, and that the relationship is also exponential.
In other words, enzymes have a powerful effect on reaction rate.
Active site definition: the part of an enzyme that binds S and catalyzes the reaction
characteristics
1. usually a cleft or pocket in the enzyme
2. requires enzyme tertiary structure (includes residues that are non-adjacent)
3. provides a specific shape and chemical character
4. complementary to the transition state of the reaction
consequences
1. Enzymes interact with only specific substrates.
An enzyme that catalyzes a redox reaction involving NADH and pyruvate
will not bind a coenzyme or substrate with a different structure.
2. Enzymes catalyze very specific reactions → specific products.
An enzyme that catalyzes a transfer reaction always transfers a specific functional
group, always to a specific carbon.
For example, an enzyme that transfers phosphate to S in – X – X – S – A – E –
will ignore S in – A – X – S – E – X – and Y in – X – X – Y – A – E – –
Energetically, how does this occur?
A. The transition state is more stable in the active site than either S or P.
Binding S is favorable, but binding S† is even more favorable. Fig. 6-5
In other words, the old lock-and-key model isn't really accurate.
B. Formation of a specific ES complex is favorable for several reasons:
1. For reactions with more than one substrate, providing the correct orientation
in the active site favors transition state formation
This reduces entropy of the molecules (is unfavorable), offset by their interactions
with functional groups that are part of the active site.
2. Removal of a solvation (hydration) shell around S is necessary for most reactions.
Also more favorable when the shell is replaced by E – S interactions.
3. Distortion required to create the transition state is offset by E – S† interactions.
4. Enzyme conformation frequently chances when S binds (induced fit).