Structure and Functions of Enzymes Flashcards
Proteins that use the energy of BINDING to increase RATES of chemical reactions
Enzymes
Substrate binds to what part of the enzyme?
Active site
How many different classes of enzymes are there?
6
What are the different classes of enzymes?
Oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases
Catalyzes reaction that has the transfer of electrons (hydride ions or H atoms)
Oxidoreductases
Catalyzes reaction that are group transfers
Transferases
Catalyzes hydrolysis reactions (transfer of functional groups to water)
Hydrolases
Catalyzes the cleavage of C-C, C-O, C-N, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds
Lyases
Catalyzes transfer of groups within molecules to yield isomeric forms
Isomerases
Catalyzes the formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor
Ligases
Examples of enzymes that don’t end in “-ase”
Lysozyme, Pepsin, Trypsin, Chymotrypsin
Many enzymes rely on some “help” from specific cofactors. What are examples of these cofactors?
Metals (Cu2+, Mg2+, Fe2+/Fe3+, etc) and coenzymes (prosthetic groups like FAD), NAD, Coenzyme A
What is the speed of uncatalyzed reactions?
They are slow. Biomolecules are stable
How do enzymes work?
They speed up reactions, break substrate down, build it up, and move it around
A special environment where the reaction will occur more rapidly - separate from the extracellular milieu
Active site
How do enzymes enhance the rate of catalysis?
They lower the activation energy
How do enzymes lower the activation energy?
They stabilize the transition state
How do enzymes stabilize the transition state of a substrate?
The active site of the enzyme is most complementary to the transition state. The transition state then binds to the active site maximizing the interaction of the two. This stabilizes the transition state and lowers the energy of the transition state.
When using an enzyme, does delta G change or stay the same?
Because the energy of the products and the reactants stays the same, the free energy (delta G) also stays the same
Why aren’t we shown endergonic reactions?
Endergonic reactions are non-spontaneous and slow. Exergonic reactions are faster and will happen spontaneously so we focus on those.
Describes difference in free energy between S and P ground states. It is not affected by catalysis
Equilibrium
How do enzymes drive catalysis?
They overcome the energy barriers that prevent non-spontaneous chemical reactions.
Does favorable equilibrium imply an appreciable rate?
No
Transient state. Where the decay of S or P is equally probable
Transition state
What are some energy barriers that can arise from S and P?
alignment of the reacting groups, forming unstable charge distributions, bond rearrangements, etc.
Chemical species involved in the steps of a catalyzed reaction. The bottom hump
Reaction intermediates
Reactions with several steps are limited by what?
Rate-limiting steps
Why does the enzyme bind most strongly to the transition state of the substrate rather than the original substrate?
If it were to bind to the original substrate the free energy would lower which would increase the activation energy of the enzyme. Catalysis would be impeded.
Do enzymes bind to any substrate they find?
No, enzymes are specific. They often discriminate between very similar substrates.
How do enzymes lower the activation energy barrier?
Non-covalent interactions (binding energy), and rearrangement of covalent bonds during the reaction. Both involve specific interaction between enzyme and substrate
deltaGB. Major component of catalysis. Has complementarity to the transition state
Binding energy
Binding energy is a major source of free energy. When is the free energy released?
When forming many weak bonds.
What are factors that contribute to the binding energy?
Specificity, transition state affinity
the many weak interactions that define the “fit” between substrate and the binding site that release free energy
Specificity
The catalytic site actually has a tighter association with the transition state than with the S or P alone
transition state affinity
Weak binding interactions between E and S provide what?
They provide the main driving force of catalysis. These weak binding interactions work best with “size” so enzymes tend to be very large
Binding energy helps enzymes overcome what barriers?
Entropy, Desolvation, Distortion, and Proper Alignment
Entropy
Binding energy holds the substrates in the proper orientations
Desolvation
Takes place in water. ES interactions replace the substrate-H2O interactions which promotes catalysis
Distortion
Binding energy from weak interactions compensates for distorting (bending) the molecules into the transition state
Proper alignment
Induced fir capability of enzymes allows them to breathe when the substrate binds - bringing everything into proper alignment
Additional contributors to catalytic mechanisms include transient covalent interactions.
General acid-base catalysis (Chymotrypsin), covalent catalysis (lysozyme), and metal ion catalysis (enolase)