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Enzymes Cheat Sheet (DRAFT) by

Enzymes enzymes enzymes

This is a draft cheat sheet. It is a work in progress and is not finished yet.

General Properties of Enzymes

How enzymes differ from ordinary chemical catalysts
faster, milder condit­ions, specific, regula­table
Class 1: Oxidor­edu­ctase
Catalyze Redox Reactions
Class 2: Transf­erases
Transfer of functional groups
Class 3: Hydrolases
Hydrolysis Reactions
Class 4: Lyases
Group elimin­ation to form double bonds
Class 5: Isomerases
Isomer­ization
Class 6: Ligases
Bond formation using ATP hydrolysis
Cofactors
Can be metal ions or coenzymes. Substances that increase the rate of enzymes in their reactions.
Coenzymes
Are chemically changed, organic, must be regene­rated. Can be cosubs­trates or prosthetic groups.
Cosubs­trates
dissociate from enzyme
Prosthetic groups
perman­ently associated with enzyme
Free energy of activation ΔG⁺⁺
free energy of transition state minus free energy of reactants. When this variable is larger, the reaction is slower.

Enzyme Inhibition

Compet­itive Inhibitor
Binds at substrate binding site. Reduces concen­tration of free enzyme available for substrate. Ex: Aspartic Protease
Uncomp­etitive Inhibitor
The inhibitor binds to the enzyme­-su­bstrate complex but not to the free enzyme. Distorts SUBSTRATE OCCUPIED active site.
Mixed/­Non­com­pet­itive
Compounds that bind to the free enzyme AND to the enzyme­-su­bstrate complex
 

Catalytic Mechanisms

1. Acid Base Catalysis
Ex: RNase, activity is affected by pH
Acid Catalysis
enzyme gives substrate a proton
Base Catalysis
enzyme takes proton from substrate
Amino acids that act as acids
Asp, Glu
Amino acids that act as bases
Arg, Lys, His
2. Covalent Catalysis
Nucleo­philic attack on substrate by enzyme, resulting in temporary covalent bond formation
Nucleo­philic groups
Have electrons, want proton
Electr­ophilic groups
Have protons, want electrons
3. Catalysis through proximity and orient­ation
bring substrates into contact, freeze out relative rotational and transl­ational motions in transition state
4. Catalysis through binding transition state
strained version of substrate fits in enzyme better than unstrained substrate
 
This implies that you can inhibit with a transition state analog
5 Metal ion catalysis
the unique electronic properties of the metal ion facilitate the reaction.
Serine Proteases
catalyze peptide bond hydrolysis (breakage) in target proteins.
 
proximity and orient­ation effects, acid–base catalysis, covalent catalysis, electr­ostatic catalysis, and transition state stabil­iza­tion.
Chymot­rypsin
Binds Bulky hydrop­hobic side chain, cleaved by trypsin
Trypsin
Binds positively charged side chain, cleaved by entero­pep­tidase
Elastase
Binds neutral, small side chains, cleaved by trypsin
 

Reaction Kinetics

To find the mechanism of an enzyme
measure kinetics, use X-ray crysta­log­raphy
K, rate constant
the rate of an elementary reaction is propor­tional to the frequency by which the reacting molecules come together. The propor­tio­nality constant is k
V, Reaction Velocity
the instan­taneous rate of appearance of product (or disapp­earance of substr­ate).
Order
the molecu­larity of a reaction, i.e. the number of molecules that must simult­ane­ously collide to generate a product.
First Order
A -> P, linear
Second Order
A + A -> P
Third Order
A + B -> P
KS
measure of enzyme affinity for its substrate
Km
the concen­tration of substrate which permits the enzyme to achieve half Vmax
Bisubs­trate reactiona
usually group transfer reactions
Sequential reactions
All substrates must combine with the enzyme before reaction can take place and products released.
Ordered
order matters
Random
order does not matter
Ping Pong Reaction
One or more products are released before all substrates have been added. • The two substrates do not encounter one another on the enzyme surface.