Enzymes

Question 1

In the absence of enzymes, digesting a meal could take

Answer 1

50 years

Question 2

How can a reaction be accelerated

Answer 2

Adding heat or adding a catalyst which increases reaction rates, not consumed in the reaction

Question 3

Are enzymes proteins

Answer 3

With few exceptions, enzymes are proteins. Primary structure, secondary structure, tertiary structure, and quaternary structures. Typically, globular proteins. Structure is governed/determined by the same forces.

Question 4

Are enzymes catalysts

Answer 4

Accelerate reaction rates. Regenerated at the end of the reaction. 10^6 to 10^20-fold increase in reaction rates Highly specific, A + B → C + D, No side reactions

Question 5

How do we name Enzymes

Answer 5

Typically end in -ase, Name often describes the process: Substrate name (or the product name) or Chemical Reaction.

Question 6

How are enzymes regulated

Answer 6

Distinguishes enzymes from non-biological catalysts. As proteins, enzyme structures are (to an extent) flexible. Changing the shape of an enzyme changes its function.

Question 7

How will reactions proceed

Answer 7

In all systems, biological or otherwise, a reaction will proceed only if the free energy of the products is less than the free energy of the reactants.

Question 8

What is an exergonic reaction

Answer 8

When delta G is negative: Reaction is exergonic and “thermodynamically favourable” (spontaneous). Thermodynamically favorable reactions DO NOT NECESSARILY proceed at measurable rates

Question 9

What state as the highest free energy

Answer 9

Transition state

Question 10

What determines the rate of reaction

Answer 10

Activation energy determines the rate of reaction

Question 11

Do enzymes affect the free-energy change, reactants, transition state or products?

Answer 11

Enzymes do not affect the free-energy change (delta G) of the reaction! Enzymes are with reactants and the products, and the transition state complex.

Question 12

How do enzymes reduce the free energy of the transition state

Answer 12

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 13

What are active sites

Answer 13

Region of enzyme where catalysis occurs. Usually only a small portion of the protein. Key amino acids are in the active site: Binding and Catalysis Determines affinity, specificity, and rate. Complementary to substrate/transition state: Shape, hydrophobic interaction, hydrogen bonds and ion pairs.

Question 14

What is the Active Site of Lysozyme

Answer 14

The active site is a 3-D cleft/crevice within the 3-D shape of the protein

Question 15

What is the complementarity in substrate binding

Answer 15

Interactions between substrate and enzymes? Groups that are hydrophobic, hydrogen bond donors, hydrogen acceptors and ion pairs, these are paired with their complement in the binding site. Design of the active site contributes to: Affinity andSpecificity

Question 16

What is Desolvation

Answer 16

Exclusion of water provides three advantages: Removal of water shell accelerates reactions, Enhances polar interactions (hydrogen bonds, ion pairs), Prevents side reactions. “Induced Fit.”

Question 17

What is “Induced Fit”

Answer 17

Some enzymes change shape when substrate binds. Closes off active sites (excludes more water) and brings catalytic groups together.

Question 18

What is Induced Fit

Answer 18

Some enzymes show a pronounced conformation change upon binding of substrate

Question 19

What is the Induced Fit Model

Answer 19

Active site changes as substrate(s) bind

Question 20

How does proximity and orientation play a role in binding sites

Answer 20

Chemical reactions only occur if substrates come together in the right orientation to react. Active sites bind substrates close to each other (proximity) and in the correct geometry (orientation). May account for a thousand-fold increase in reaction rates. All enzymes do this.

Question 21

What are Participation Reactions

Answer 21

Some enzymes participate in the reactions by positioning functional groups near the substrates in the active site.

Question 22

What are examples of participation reactions

Answer 22

Acid/base catalysts, Covalent catalysis and Metal ion catalysis

Question 23

Which amino acid side chains can act as acid-base catalysis

Answer 23

Asparate (Asp), Glutamate (Glu), Histidine (His), Lysine (Lys), Cysteine (Cys) and Tryptophan (Tyr)

Question 24

What amino acid side chains can act in nucleophilic catalysis

Answer 24

Serine (Ser), Tryptophan (Tyr), Cysteine (Cys), Lysine (Lys) and Histidine (His)

Question 25

What are holoenzymes

Answer 25

When the polypeptide is combined with the prosthetic group to form the functional tertiary structure it can be referred to as the holoenzymes.

Question 26

What are apoenzymes

Answer 26

Without the prosthetic group, the polypeptide can be referred to as the apoenzyme.

Question 27

What are holoproteins and apoproteins

Answer 27

Holoprotein and apoprotein can be used respectively to refer to non-enzymatic proteins with or without prosthetic groups (ex: apomyoglobin is the myoglobin polypeptide chain without heme associated).

Question 28

What is Transition State Stabilization

Answer 28

Binding the transition state will aid in lowering delta G. Parts of the protein interact with the unstable transition state. Enzyme active sites bind the transition better than they bind the substrate.

Question 29

How does tightness of an enzyme bind relate to catalytic activity

Answer 29

The more tightly an enzyme binds the transition state relative to the substrate the greater the catalytic activity of the enzyme.

Question 30

What are transition state analogs

Answer 30

Transition state analogs are POTENT inhibitors of many enzymes. Bind to enzyme with higher affinity compared to substrate.

Question 31

What is V0 in enzyme kinetics

Answer 31

Initial velocity (rate of production formation)

Question 32

What is Vmax in enzyme kinectics

Answer 32

Maximum rate or product form

Question 33

What are the mechanisms can affect the intrinsic activity of the enzyme

Answer 33

Competitive inhibition, allostery, reversible covalent modification and ionic signals (such as Ca2+ ions)

Question 34

What are the mechanisms do not affect the intrinsic activity of the enzyme

Answer 34

Regulation of gene expression and changes in subcellular localization

Question 35

What are competitive inhibitors

Answer 35

Substances that bind reversibly in the active site. Resemble the substrate or transition state but do not react. Physically blocks active site

Question 36

What does it mean when a competitive inhibitors blocks the active site

Answer 36

Fewer active sites available. Lower reaction rates (inhibited, curve shifts right) and and Apparent increase in Km.

Question 37

How does the Vmax change when the substrate concentration overcomes inhibition

Answer 37

No change in Vmax

Question 38

What are inhibitors

Answer 38

Inhibitors are similar to the substrate in shape and size but differ chemically in such a way that they cannot react

Question 39

How do competitive inhibitors affect the apparent affinity for enzyme and substrate

Answer 39

Competitive inhibitors decrease the apparent affinity (increase Km) for enzyme and substrate

Question 40

What are allosteric enzymes

Answer 40

Many enzymes are oligomeric (multi subunit). Like hemoglobin, enzyme activity may be cooperative. Sigmoidal relationship between substrate and reaction velocity. Reflects different states (geometries) and active site. Change between low activity (T) and high activity (R) states. Compounds besides the substrate may affect the equilibrium between T and R states. Allosteric effectors (positive/negative; activators/inhibitors). Quite common in regulation.

Question 41

What is a positive homoallostery

Answer 41

Active site is available and it leads to product formation

Question 42

What is a negative heteroallostery

Answer 42

One of the active sites is taken up by an inhibitor so it leads to no product formation or reduced product formation

Question 43

Do allosteric enzymes have different states

Answer 43

They have two states, a T state (low activity) and R state (high activity)

Question 44

What state does the allosteric activators favour

Answer 44

Favours the R state

Question 45

What is Reversible Covalent Modification

Answer 45

Covalent modification of an amino acid residue changes the tertiary structure. Phosphorylation is the most common type of reversible covalent modification. (Ser/Thr/Tyr – OH becomes phosphorylated. Increases size, polarity, and charge significantly.) May increase or decrease activity of the target enzyme

Question 46

What is the reversible phosphorylation of enzymes

Answer 46

Protein kinases catalyze the phosphorylation of proteins. Protein phosphates catalyze the dephosphorylation of proteins by hydrolysis. These are enzymes, often regulated themselves.