Structure and Functions of Enzymes

Question 1

Proteins that use the energy of BINDING to increase RATES of chemical reactions

Answer 1

Enzymes

Question 2

Substrate binds to what part of the enzyme?

Answer 2

Active site

Question 3

How many different classes of enzymes are there?

Answer 3

6

Question 4

What are the different classes of enzymes?

Answer 4

Oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases

Question 5

Catalyzes reaction that has the transfer of electrons (hydride ions or H atoms)

Answer 5

Oxidoreductases

Question 6

Catalyzes reaction that are group transfers

Answer 6

Transferases

Question 7

Catalyzes hydrolysis reactions (transfer of functional groups to water)

Answer 7

Hydrolases

Question 8

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

Answer 8

Lyases

Question 9

Catalyzes transfer of groups within molecules to yield isomeric forms

Answer 9

Isomerases

Question 10

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

Answer 10

Ligases

Question 11

Examples of enzymes that don’t end in “-ase”

Answer 11

Lysozyme, Pepsin, Trypsin, Chymotrypsin

Question 12

Many enzymes rely on some “help” from specific cofactors. What are examples of these cofactors?

Answer 12

Metals (Cu2+, Mg2+, Fe2+/Fe3+, etc) and coenzymes (prosthetic groups like FAD), NAD, Coenzyme A

Question 13

What is the speed of uncatalyzed reactions?

Answer 13

They are slow. Biomolecules are stable

Question 14

How do enzymes work?

Answer 14

They speed up reactions, break substrate down, build it up, and move it around

Question 15

A special environment where the reaction will occur more rapidly - separate from the extracellular milieu

Answer 15

Active site

Question 16

How do enzymes enhance the rate of catalysis?

Answer 16

They lower the activation energy

Question 17

How do enzymes lower the activation energy?

Answer 17

They stabilize the transition state

Question 18

How do enzymes stabilize the transition state of a substrate?

Answer 18

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.

Question 19

When using an enzyme, does delta G change or stay the same?

Answer 19

Because the energy of the products and the reactants stays the same, the free energy (delta G) also stays the same

Question 20

Why aren’t we shown endergonic reactions?

Answer 20

Endergonic reactions are non-spontaneous and slow. Exergonic reactions are faster and will happen spontaneously so we focus on those.

Question 21

Describes difference in free energy between S and P ground states. It is not affected by catalysis

Answer 21

Equilibrium

Question 22

How do enzymes drive catalysis?

Answer 22

They overcome the energy barriers that prevent non-spontaneous chemical reactions.

Question 23

Does favorable equilibrium imply an appreciable rate?

Answer 23

No

Question 24

Transient state. Where the decay of S or P is equally probable

Answer 24

Transition state

Question 25

What are some energy barriers that can arise from S and P?

Answer 25

alignment of the reacting groups, forming unstable charge distributions, bond rearrangements, etc.

Question 26

Chemical species involved in the steps of a catalyzed reaction. The bottom hump

Answer 26

Reaction intermediates

Question 27

Reactions with several steps are limited by what?

Answer 27

Rate-limiting steps

Question 28

Why does the enzyme bind most strongly to the transition state of the substrate rather than the original substrate?

Answer 28

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.

Question 29

Do enzymes bind to any substrate they find?

Answer 29

No, enzymes are specific. They often discriminate between very similar substrates.

Question 30

How do enzymes lower the activation energy barrier?

Answer 30

Non-covalent interactions (binding energy), and rearrangement of covalent bonds during the reaction. Both involve specific interaction between enzyme and substrate

Question 31

deltaGB. Major component of catalysis. Has complementarity to the transition state

Answer 31

Binding energy

Question 32

Binding energy is a major source of free energy. When is the free energy released?

Answer 32

When forming many weak bonds.

Question 33

What are factors that contribute to the binding energy?

Answer 33

Specificity, transition state affinity

Question 34

the many weak interactions that define the “fit” between substrate and the binding site that release free energy

Answer 34

Specificity

Question 35

The catalytic site actually has a tighter association with the transition state than with the S or P alone

Answer 35

transition state affinity

Question 36

Weak binding interactions between E and S provide what?

Answer 36

They provide the main driving force of catalysis. These weak binding interactions work best with “size” so enzymes tend to be very large

Question 37

Binding energy helps enzymes overcome what barriers?

Answer 37

Entropy, Desolvation, Distortion, and Proper Alignment

Question 38

Entropy

Answer 38

Binding energy holds the substrates in the proper orientations

Question 39

Desolvation

Answer 39

Takes place in water. ES interactions replace the substrate-H2O interactions which promotes catalysis

Question 40

Distortion

Answer 40

Binding energy from weak interactions compensates for distorting (bending) the molecules into the transition state

Question 41

Proper alignment

Answer 41

Induced fir capability of enzymes allows them to breathe when the substrate binds - bringing everything into proper alignment

Question 42

Additional contributors to catalytic mechanisms include transient covalent interactions.

Answer 42

General acid-base catalysis (Chymotrypsin), covalent catalysis (lysozyme), and metal ion catalysis (enolase)