Enzymes

Question 1

Symbol for transition state

Answer 1

double dagger ‡

Question 2

Activation energy

Answer 2

the rate of a reaction reflects the activation energy

a higher activation energy corresponds to a slower reaction

lowering the activation energy increases the rate of reaction

Question 3

Reaction coordinate

Answer 3

progress along a reaction pathway

Question 4

Why does sugar not spontaneously combust?

Answer 4

due to kinetics

event though combustion of sugar is thermodynamically downhill, it is kinetically blocked
- because activation energy is high

• and a room temp sugar molecules don’t have enough energy to reach the transition state

-therefore the reaction rate is zero

Question 5

Axis on a free energy profile of a chemical reaction

Answer 5

Y axis- free energy (G)
X axis- reaction progress

Question 6

Free energy (G)

Answer 6

Gibbs free energy is the amount of energy in a system that is available to do useful work at constant temperature and pressure.

Question 7

Transition state

Answer 7

this is the peak of the curve (the highest energy, most unstable configuration)

to reach it, the system must absorb energy

that required energy is the activation energy

this means the free energy needed to go from substrate to the transition state on the way to product

Question 8

What is activation energy

Answer 8

the barrier that must be overcome for the reaction to proceed

even if the product is lower in energy, the reaction cannot start unless molecules reach the transition state

this is why reactions with high activation energies are slow without catalysts

Question 9

What is an enzyme

Answer 9

• a catalyst that lowers reaction energy (free energy of activation)
• but is not used up in the reaction (otherwise reactant)

Question 10

Enzymes and equilibria

Answer 10

catalysts do not affect reaction equilibria

any enzyme that catalyses the reaction S–>P will also catalyst the reaction P–>S, the role of enzymes is to accelerate the interconversion of S and P

the enzyme is not used up in the process and the equilibrium point is unaffected

however the reaction reaches equilibrium much faster

Question 11

What is one way to speed up a reaction by lowering entropy?

Answer 11

Restrict the freedom of movement (rotation/translation) of reacting groups so they collide more easily.

Question 12

Why does restricting rotation increase reaction rate?

Answer 12

It reduces entropy, meaning the reacting groups are already aligned and require less random motion to meet.

Question 13

What is the rate enhancement when the reacting groups are linked but still flexible?

Answer 13

Approximately 10⁵‑fold enhancement

Question 14

What is the rate enhancement when the reacting groups are locked in a rigid cyclic structure?

Answer 14

Approximately 10⁸‑fold enhancement.

Question 15

What is meant by “rate enhancement by entropy reduction”?

Answer 15

Speeding up a reaction by decreasing the randomness of the system so reactants are pre‑organized for reaction.

Question 16

How do enzymes use entropy reduction to speed up reactions?

Answer 16

They bind substrates in specific orientations, reducing their freedom and increasing reaction probability.

Question 17

Naming enzymes

Answer 17

usually named by either:

adding the suffix -ase to the name of the substrate that they modify

or the type of reaction they catalyst

but some have arbitrary names (e.g trypsin)

Question 18

what is a Zymogen

Answer 18

inactive form of enzym e

Question 19

what is a Holoenzyme

Answer 19

apoenzyme +cofactor

Question 20

What are enzyme cofactors

Answer 20

Enzyme cofactors are non‑protein molecules or ions that an enzyme requires in order to function properly.

Question 21

Oxidoreductases

Answer 21

transfer electrons via oxidation or reduction

A + B: –> A: + B

Question 22

Transferase enzymes

Answer 22

transfer of chemical groups from one molecule to another

A + BX –> AX + B

Question 23

Hydrolases

Answer 23

cleavage of a substrate using water (hydrolysis)

A + H20 –> B + C

Question 24

Lyases

Answer 24

addition of groups to double bonds or formation of double bond following removal of a group

A –> B + C

Question 25

Isomerases

Answer 25

rearrangement of a single substrate, generating isoforms ABC -->ACB

Question 26

Ligases

Answer 26

joining of two substrates, often by eliminating water A + B --> AB +H2O

Question 27

Three types of reactions

Answer 27

anabolic- smaller to larger A +B --> C catabolic- larger to smaller X--> Y+Z interconversions D + E <--> F +G

Question 28

Breaking bonds

Answer 28

hydrolase enzymes the breaking of single bonds through the addition of water turning into a H+ and OH-

Question 29

Mechanisms of enzyme action

Answer 29

lock and key (fisher) induced fit (koshland)

Question 30

Lock-and-key enzyme model

Answer 30

active site of unbound enzyme is complementary to shape of substrate

Question 31

Induced fit enzyme model

Answer 31

enzyme changes shape when substrate binds- active site complementary to shape of substrate only after substrate binds

Question 32

Enzyme active sites

Answer 32

is a 3D arrangement of specific amino acids usually has two functional zones- usually adjacent pockets (recognition and reaction) bonding and catalytic residues

Question 33

Binding residues on enzymes active site

Answer 33

(recognition pocket) these amino acids hold the substrate in place they recognise specific chemical groups on the substrate they determine which substrates can bind

Question 34

Catalytic residues on active site

Answer 34

(reaction pocket) these amino acids perform the chemistry they may: donate/accept protons, form temporary covalent bonds or stabilise the transition state

Question 35

source of substrate and reaction specificity

Answer 35

usually only a small part of the substrate enters the active site (e.g a chemical group) - a range of substrates which all have this group substrates held by specific interactions

Question 36

Factors affecting enzyme activity

Answer 36

pH temperature [substrate] presence of inhibitors

Question 37

Factors affecting enzyme activity: pH

Answer 37

optimal pH range for normal conformation outside this range: ionisation of amino acid side chains leads to change in conformation may denature enzymes

Question 38

Factors affecting enzyme activity: temperature

Answer 38

affects kinetic energy of substrate and enzyme determines frequency of S + E interaction rate of reaction increases until enzyme is saturated or becomes denatured

Question 39

Factors affecting enzyme activity: [substrate]

Answer 39

determines frequency of substrate and enzyme interaction rate of reaction increases until E saturated

Question 40

enzyme definition

Answer 40

biological catalyst that speeds up reactions by lowering activation energy

Question 41

△G definition

Answer 41

change in Gibbs free energy between substrate and product: determines spontaneity

Question 42

Free energy of activation definition

Answer 42

energy required to reach the transition state: controls reaction rate

Question 43

Coenzyme definition

Answer 43

organic cofactor that carries chemical groups or electrons

Question 44

V0 definition

Answer 44

initial reaction speed measured before substrate depletion (Start of reaction)

Question 45

Vmax definition

Answer 45

maximum reaction speed when enzyme is saturated with substrate

Question 46

Km definition

Answer 46

substrate concentration at 1/2Vmax reflects enzyme affinity

Question 47

Hyperbolic plot

Answer 47

Michaelis-Menten curve showing V0 vs [S]