Enzymes

Question 1

What is an Enzyme

Answer 1

Enzymes are proteins that act as catalysts in biochemical reactions

Question 2

Enzyme Structure

Answer 2

Proteins (can have primary, secondary, tertiary, or quaternary structure)
Typically globular proteins
The structure is determined by the same forces as any other protein

Question 3

Specificity of Enzymes

Answer 3

Enzymes are highly specific because of the shape of their active site

Question 4

How do Enzymes Work as Catalysts

Answer 4

Accelerate reaction rates
Regenerated at the end of the reaction
No side reactions

Question 5

Enzyme Nomenclature

Answer 5

Typically end is -ase

The name often describes the process

Question 6

How are Enzymes Regulated

Answer 6

The body distinguishes enzymes from non-biological catalysts
Enzyme structures are flexible
Changing the shape of an enzyme changes its function

Question 7

The spontaneity of Biological Reactions

Answer 7

When the reaction is exergonic and “thermodynamically favourable”
Does not necessarily proceed at measurable rates though

Question 8

What determines the speed of an uncatalyzed reaction?

Answer 8

It is determined by the size of the activation energy barrier

Question 9

How does temperature increase the speed of an uncatalyzed reaction?

Answer 9

The energy of the molecules involved in the reaction increases and therefore more collisions happen

Question 10

How do enzymes increase the speed of a reaction?

Answer 10

Enzymes reduce the free energy of the transition state

BUT they do not affect the free-energy change of the reaction

Question 11

How do enzymes reduce the free energy of the transition state?

Answer 11

1. Removing substrates from aqueous solution (desolvation)
2. Proximity and orientation effects
3. Taking part in the reaction mechanism
4. Stabilizing the transition state

Question 12

Active Sites

Answer 12

Region of the enzyme where catalysis occurs
Determines affinity, specificity, rate
Complementary to substrate/transition state
Key amino acids are found in the active site

Question 13

Desolvation

Answer 13

Exclusion of water
Advantages:
1. removal of water shell accelerates reactions
2. enhance polar interactions
3. prevents side reactions
Induced fit
-some enzymes change shape when substate binds (excludes more water)

Question 14

Complementarity in Substrate Binding

Answer 14

Lock and key model
design of the active site contributes to affinity and specificity
interactions between substrate and enzymes?

Question 15

Proximity and Orientation

Answer 15

Chemical reactions only occur if substrates come together in the right orientation to react
Active sites bind substrates close to each other and in the correct geometry

Question 16

Amino Acid Side Chains in Acid-Base Catalysis

Answer 16

Asp
Glu
His
Lys
Cys
Tyr

Question 17

Amino Acid Side Chains in Nucleophilic (covalent) Catalysis

Answer 17

Ser
Tyr
Cys
Lys
His

Question 18

Cofactors

Answer 18

Molecules that may enhance the reactive potential of polypeptides by providing new reactive functional groups
Coenzymes (organic) vs metal ions

Question 19

Induced Fit

Answer 19

The binding of a substrate to an enzyme causes the enzyme to change shape

Question 20

Cosubstrate

Answer 20

an organic molecule that binds to the active sites of certain enzymes to assist in the catalysis of a reaction
will be released after a reaction

Question 21

Prosthetic Group

Answer 21

enzyme partner molecules that bind tightly or covalently to the enzyme
a part of the enzyme

Question 22

Holoenzyme

Answer 22

When a polypeptide is combined with the prosthetic group to form the functional tertiary structure

Question 23

Apoenzyme

Answer 23

Without the prosthetic group

Question 24

Transition State Stabilization

Answer 24

Enzyme active sites bind the transition state better than they bind the substrate
The more tightly an enzyme binds the transition state,= relative to the substrate the greater the catalytic activity of the enzyme
-inhibitor of enzymes because they bind to enzymes with higher affinity compared to the substrate

Question 25

Processes by Which Enzymes can be Regulated

Answer 25

Affects the intrinsic activity of the enzyme
-competitive inhibition
allostery
reversible covalent modification
ionic signals

Doesn’t affect the intrinsic activity of the enzyme

• regulation of gene expression
• changes in subcellular localization

Question 26

Competitive Inhibitors

Answer 26

substances that bind reversibly in the active site
resemble the substrate or transition state but do not react
physically block the active site but can be overcome by increasing the substrate concentration to outcompete the inhibitor

Question 27

Allosteric Enzymes

Answer 27

enzyme activity can be cooperative
-sigmoidal relationship b/w substrate and reaction velocity
-reflects different states (T, R) for the active site
compounds besides the substrate may affect the equilibrium between T and R states - allosteric effectors

Question 28

Why are transition state analogs better inhibitors than substrate analogs?

Answer 28

Because the transition state structure would bind more tightly to the active site than the actual substrate

Question 29

Phosphorylation

Answer 29

the most common type of reversible covalent modification
-ser,the,try can be phosphorylated
-increases size, polarity and charge significantly
may increase or decrease activity of the target enzyme