Enzymes

Question 1

Define enzyme and list some key characteristics

Answer 1

• proteins (typically globular)
• catalysts: accelerate reaction rates & not transformed through reaction (FE = 0)
• highly specific to certain products (specificity)
• flexible to an extent, changing shape = changing function
• regulated

• enzymes release energy more gently
• in the absence of enzymes, digesting a meal could take 50 years

Question 2

Describe the structure of an enzyme and state how it is stabilized

Answer 2

• typically globular proteins
• 1°, 2°, 3°, 4° structures
• stabilized by the same forces as proteins: HP interactions, H bonds, ionic interactions, disulfide bonds

Question 3

State what is meant when we describe enzymes as “specific”

Answer 3

• enzymes are able to selectively catalyze a particular chemical reaction or a specific class of reactions
• this ensures that biochemical reactions proceed efficiently and accurately and contribute to regulation and maintenance of the processes

Question 4

Define the term “substrate”

Answer 4

a reactant in an enzymatic reaction

Question 5

State why the regulation of enzymes is possible

Answer 5

• because enzyme structures are flexible and can change shape in order to change their functions
• enzymes change their shape/function in response to: allosteric regulation, covalent modification, substrate concentration, product/competitive inhibition, pH/temperature, and gene expression

Question 6

State what is meant by the term “spontaneous” when used to describe a biological reaction

Answer 6

• a rxn proceeds if the free energy of the products is less than the free energy of the reactants
  ΔGrxn = GP - GR
• when ΔGrxn is negative, reaction is exergonic and thermodynamically favouable -spontaneous

Question 7

What determines the speed of an uncatalyzed biological reaction?

Answer 7

• the size of the activation energy barrier
• the transition state (TS) is the highest free energy and is associated with the size of the barrier

ΔG (activation energy) = GTS - GR

GTS = transition state energy
GR = energy of reactants/ground state

Question 8

explain how increasing the temperature might increase the speed of an uncatalyzed reaction

Answer 8

• heat adds to the kinetic energy of a reaction therefore may decrease the activation energy barrier

Question 9

State how enzymes increase the speed of a reaction

Answer 9

• enzymes lower the activation energy of a reaction, therefore allowing the reaction to proceed more quickly

enzymes do not affect the free-energy change of the reaction

Question 10

List four mechanisms which contribute to an enzyme’s ability to reduce the activation energy barrier of a reaction

Answer 10

1. Removing substrates from aqueous solution (desolvation)
2. Proximity and orientation effects: brings reactants closer and in proper geometry
3. takes part in the reaction mechanism
4. stabilizes the transition state

Question 11

Define the term “active site”

Answer 11

the region of an enzyme where catalysis occurs

Question 12

how do substrates bind in the active site with specificity and relatively high affinity?

Answer 12

• key amino acids located in the active site ensure proper binding and is involved in catalysis
• the shape, hydrophobic interactions, H-bonds and ion pairs are complementary to the substrate/TS therefore determine the affinity, specificity and rate

lock and key model

Question 13

Induced fit

Answer 13

an interaction between a ligand and a protein that induces a conformational change within the protein that enhance’s the proteins interaction with the ligand
- closes off active site (excludes more water)
- brings catalytic groups together

getting rid of water is necessary if it’s not a reactant

Question 14

what are the 3 advantages of desolvation

Answer 14

1) removal of water shell → accelerates reactions
2) enhances polar interactions (H bonds/ion pairs)
3) prevents side reactions

Question 15

Explain what is meant by the proximity and orientation effect

Answer 15

chemical rxns only occur if substrates come together in the correct orientation
- active sites bind substrates close to each other (proximity) and in the correct geometry (orientation)

may account for a 1000-fold increase in reaction rates, all enzymes do this

Question 16

State two ways in which enzymes may participate in a chemical reaction

Answer 16

some enzymes position functional groups near the active sites
amino acids or cofactors can function in reactions:

1) Amino acid side chains in acid/base catalysis or nucleophilic catalysis (covalent catalysis) - depends on protonation/deprotonation
2) cofactors that provide new reactive FG’s to a reaction

Question 17

Define: 1) cofactor 2) cosubstrate 3) prosthetic group

Answer 17

1. molecules/compounds that may enhance the reactive potential of polypeptides by providing new reactive functional groups (metal ions & coenzymes; prosthetic groups, cosubstrates)
2. a small molecule that is transiently bound to the enzyme during the catalytic cycle but is not covalently attached to the enzyme. (e.g. NAD+)
3. a non-protein component that is essential for its catalytic activity. Unlike cosubstrates they are tightly and often covalently attached to the enzyme. Can include metal ions. (e.g. heme)

Question 18

*why do enzymes need cofactors

Answer 18

they provide the reactive functional groups that facilitate the reactive potential of enzymes

Question 19

what is meant by preferential transition state stabilization

Answer 19

• the TS is often unstable
• enzyme active sites bind the transition state better than they bind the substrate aiding in lower ΔG (transition state)
• the more tightly an enzyme binds the TS relative to the S = ↑ catalytic activity

perfect binding to the substrate wouldn’t allow it to reach the transition state to therefore get to the product

Question 20

6 processes by which enzyme activity can be regulated, in vivo

Answer 20

1. Competitive inhibition
2. Allostery
3. Reversible covalent modification

↑ affect intrinsic activity of enzyme

4. regulation of gene expression
5. changes in subcellular localization

in vivo - process occuring in a living organism

Question 21

explain why competitive inhibition can be overcome by increasing the substrate concentration

Answer 21

• inhibitors are similar to the substrate in shape and size but chemically, do not react
• competitive inhibitors decrease the apparent affinity (increase Km) for enzyme and substrate, Vmax is still unchanged
• if we increase substrate, we increase product and the rate of reaction (Le Chatelier)

Question 22

State why transition state analogs often make better competitive inhibitors than substrate analogs

Answer 22

• TSA bind to enzyme with HIGHER affinity compared to substrate therefore are potent inhibitors of many enzymes

Question 23

Outline the mechanism by which an allosteric effector alters the activity of an allosteric enzyme

Answer 23

heteroallostery: an enzyme’s catalytic activity is modulated by the noncovalent binding of molecules at a site other than the active site, often called the “allosteric site”

• binding of an allosteric ACTIVATOR shifts an enzyme toward the R, high activity state
• binding of an allosteric INHIBITOR shifts an enzyme toward the T, low activity state

slide 45/46

Question 24

Define the term protein phosphorylation

Answer 24

• most common type of reversible covalent modification that changes the 3D tertiary structure of enzymes
• Ser/Thr/Tyr -OH becomes phosphorylated
• increases size, polarity and charge significantly
• may increase/decrease activity of the target enzyme

Question 25

Describe the molecular mechanism by which phosphorylation alters the activity of an enzyme

Answer 25

1. phosphate is transfered from ATP to the target enzyme by protein kinase
2. phosphorylation of specific amino acids modifies the shape and therefore function of the enzyme (↑ or ↓ activity)
3. phosphate is removed/hydrolyzed by protein phosphatase

Question 26

Define: 1) protein kinase 2) protein phosphatase

Answer 26

1) An enzyme that catalyzes the transfer of a phosphoryl group from ATP to the OH group of a protein Ser, Thr, or Tyr residue
2) an enzyme that catalyzes the removal of a phosphate from a protien by hydrolysis