Lecture 9: WHY ARE ENZYMES ESSENTIAL FOR LIFE?

Question 1

What are enzymes?

Answer 1

Biological catalysts which increase the rate of reaction by lowering the activation energy

Question 2

What are most enzymes?

Answer 2

Proteins

Question 3

What are exceptions to proteins being enzymes?

Answer 3

Catalytic RNA’s, ribozymes including ribosomes

Question 4

What don’t enzymes change?

Answer 4

The free energy level (equilibrium) of products and reactants

Question 5

What is the relative abundance of products and reactants predicted by?

Answer 5

The Gibbs free energy

Question 6

What happens when Gibbs free energy is less than 0?

Answer 6

There is energy released and the products dominate

Question 7

What happens when the Gibbs free energy is greater than 0?

Answer 7

Energy is required and the reactants dominate

Question 8

What happens when the Gibbs free energy is equal to 0?

Answer 8

The reaction is at equilibrium (reactants and products are of equal concentrations)

Question 9

What does overall Gibbs free energy have components of?

Answer 9

Enthalpy (H) and entropy (S)

Question 10

What is T?

Answer 10

Absolute temperature

Question 11

What must happen to favour the forward reaction?

Answer 11

Either enthalpy must decrease or entropy must increase

Question 12

What does cellular integrity mean?

Answer 12

A decrease in entropy (disorder) in the cell so energy from elsewhere is required

Question 13

What do enzymes control?

Answer 13

Where and when energy is released to maintain the cell

Question 14

What do reactions pass through?

Answer 14

High energy transition states

Question 15

What determines the rate of a reaction?

Answer 15

The activation energy required to reach the transition state

Question 16

What is the activation of the back reaction?

Answer 16

The Gibbs free energy + the activation energy

Question 17

What does free energy do at equilibrium?

Answer 17

Sets the ratio of products to reactants

Question 18

What is the Gibbs free energy for cleavage of DNA phosphodiester backbone?

Answer 18

Negative

Question 19

How long is the DNA phosphodiester backbone stable for uncatalyzed?

Answer 19

Thousands of years

Question 20

What is the speed of ribonuclease A?

Answer 20

Less than a millisecond

Question 21

What does aldolase have?

Answer 21

Very positive Gibbs free energy but a big rate enhancement

Question 22

What does adenylate kinase have?

Answer 22

Gibbs free energy near zero but a big rate enhancement

Question 23

What are isozymes?

Answer 23

Enzymes which differ in amino acid sequence but catalyse the same reaction

Question 24

What are the classes of enzymes?

Answer 24

Oxireductases, transferases. hydrolyses, lyases, isomerases and ligases

Question 25

What are oxireductases involved in?

Answer 25

Redox (transfer of electrons)

Question 26

What are transferases involved in?

Answer 26

Transfer of a functional group

Question 27

What are Hydrolyses involved in?

Answer 27

Hydrolysis reactions (using water)

Question 28

What are lyases involved in?

Answer 28

Non-hydrolytic breaking or making of bonds (not using water)

Question 29

What are isomerases involved in?

Answer 29

Transfer of atoms/groups within a molecule to yield an isomeric form

Question 30

What are ligases involved in?

Answer 30

Joining two molecules together (forming a new bond) which is usually coupled to ATP cleavage

Question 31

What does muscle myosin do?

Answer 31

Use energy from hydrolysis of ATP (general energy store) to drive muscle contraction

Question 32

What does ATP synthase do?

Answer 32

Couple electrochemical gradient across the membrane to synthesise ATP

Question 33

Where does enzyme substrate binding occur?

Answer 33

At a specific site on the enzyme called the active site

Question 34

What does the active site have?

Answer 34

Amino acid side chains projecting into it

Question 35

What does the active site do?

Answer 35

Bind the substrate via several weak interactions

Question 36

What does the active site determine?

Answer 36

The specificity of the reaction

Question 37

What are the types of enzyme substrate bonds?

Answer 37

Ionic bonds/salt bridges, hydrogen bonds, van der Waals interactions and covalent bonds

Question 38

What do ionic bonds do?

Answer 38

Make use of charged side chains (Asp, Glu, Arg, Lys)

Question 39

What happens in hydrogen bonds?

Answer 39

Side chain or backbone O or N atoms can often act as hydrogen bond donors and acceptors (prevalent and give specificity)

Question 40

What are van der Waals interactions?

Answer 40

Between any protein and substrate atoms in close proximity (weakest interactions but abundant)

Question 41

What are covalent bonds?

Answer 41

Relatively rare and much stronger than the other bonds

Question 42

What are the models for enzyme substrate binding?

Answer 42

Lock and key and induced fit

Question 43

What is the lock and key model?

Answer 43

The shape of the substrate and the conformation of the active site are complementary to one another

Question 44

What is the induced fit model?

Answer 44

The enzyme undergoes a conformational change upon binding to substrate. The shapes of the active site becomes complementary to the shape of the substrate only after the substrate binds to the enzyme

Question 45

Are enzymes dynamic or static?

Answer 45

Dynamic

Question 46

What do many weak interactions ensure?

Answer 46

Specificity and reversibility

Question 47

How does enzyme substrate binding show specificity?

Answer 47

Several bonds are required for substrate binding

Question 48

When can weak bonds form?

Answer 48

Only if the relevant atoms are precisely positioned

Question 49

What can weak bonds allow?

Answer 49

reversible binding

Question 50

What is critical?

Answer 50

Molecular complementarity between enzyme and substrate

Question 51

What is optimal binding?

Answer 51

Not too tight

Question 52

How can activation energy be lowered?

Answer 52

By ground state destabilisation, transition state stabilisation and an alternate reaction pathway with a different (lower energy) transition state

Question 53

How can ground state destabilisation and transition state stabilisation occur?

Answer 53

By having an active site that has shape/charge complementarity to the transition state, not the substrate

Question 54

What are coenzymes?

Answer 54

Small organic molecules

Question 55

What type of substrates are coenzymes?

Answer 55

Cosubstrates

Question 56

What are cosubstrates carriers of?

Answer 56

Electrons, atoms or functional groups

Question 57

What are cofactors often derived from?

Answer 57

Vitamins