Enzymes & Coenzymes

Question 1

Why are enzymes important?

Answer 1

natures catalysts
carry out all reactions in the cell
inherited diseases caused by mutations in key enzymes
diagnose diseases
food products and detergents
drug synthesis

Question 2

What are the 6 classes of enzymes?

Answer 2

Oxioreductase
Transferase
Hydrolase
Lyase
Isomerase
Ligase

Question 3

What is an oxioreductase?

Answer 3

Catalyses oxidation-reduction in which oxygen and hydrogen are gained or lost

cytochrome oxidase, lactate dehydrogenase

Question 4

What is a transferase?

Answer 4

Catalyses transfer of functional groups
e.g. amino group, acetyl group or phosphate group

acetate kinase, alanine deaminase

Question 5

What is a hydrolase?

Answer 5

Catalyses hydrolysis
addition of water

Lipase, sucrase

Question 6

What is a lyase?

Answer 6

Catalyses removal of groups of atoms within a molecule

oxalate decarboxylase, isocitrate lyase

Question 7

What is an isomerase?

Answer 7

Catalyses rearrangement of atoms within a molecule

Glucose-phosphate isomerase, alanine racemase

Question 8

What is a ligase?

Answer 8

Catalyses joining of two molecules
using energy usually derived from the breakdown of ATP

Acetyl-CoA synthesise, DNA ligase

Question 9

Reaction energetics

Answer 9

For a favourable reaction, delta G is negative
products lower energy than reactants

speed of reaction (kinetics) determined by activation energy
higher activation energy means a slower reaction

Question 10

What is the Arrhenius equation?

Answer 10

Gives relationship between activation energy and reaction rate constant

k = Ae ^-ae/RT

Question 11

Energy diagram

Answer 11

y = energy state
x= reaction coordinate (time)

Equilibrium will lie heavily to R because of products
Higher the graph hump, the higher the activation energy

Question 12

What is a transition state?

Answer 12

A transient high energy species in conversion of substrate to molecule

Question 13

What affect do catalysts have on activation energy?

Answer 13

Lower the ae for reaction, but don’t change the energy of reaction

can’t make a thermodynamically unfavourable reaction become favourable

don’t change equilibrium position

Products and substrates have same energy with to without an enzyme

make an unstable intermediate more stable, lowering the energy barrier to overcome
creating a faster reaction

Question 14

What are the roles of an enzyme as a catalyst?

Answer 14

1. enzyme provides specific environment for substrate where reaction more favourable
2. reaction pocket = active site
3. lowering activation energy
4. not used up in the process
5. enzyme-substrate and enzyme-product are reaction intermediates

Question 15

LOOK AT ENERGETIC PROFILE OF ENZYME CATALYSED REACTION

Answer 15

DIAGRAM

Question 16

What is an enzyme pocket?

Answer 16

Designed to complement reaction transition state
bonds are H bonds, hydrophobic, ionic and VdW
(some transient covalent bond formed)

enzyme complementary to the transition state

Question 17

What is binding energy?

Answer 17

Energy derived from enzyme pocket complex

Question 18

What is a coenzyme?

Answer 18

Non protein organic molecule required for catalysis

biotin, NAD+, FAD and most vitamins

Question 19

What is a cofactor?

Answer 19

Inorganic substances that are required for catalysis

metal ions: Fe2+, Zn2+, Cu2+, Mg2+

Question 20

What is the combination of a coenzyme and cofactor called?

Answer 20

Holoenzyme

Question 21

What is a protein without a coenzyme?

Answer 21

Apoenzyme

Question 22

What is the function of coenzymes and co factors?

Answer 22

allow enzymes to access chemistries that amino acid side chain can’t access

allow for further and different reactions

Question 23

coenzymes

Answer 23

have a catalytic role, not substrates
some don’t finish reaction same way they started

Question 24

common coenzymes

Answer 24

coenzyme A (HSCoA)
adenosine triphosphate (ATP)
S-adenosyl methionine (SAM)
pyridoxal phosphate (PLP)
thiamine diposhphate (TPP)
nicotinamide adenine dinucleotide - oxidised form (NAD+)
lipoate
glutathione
biotin

Question 25

coenzyme disease

Answer 25

arise as result of deficiency in these coenzymes: megaloblastic anaemia - folic acid deficiency beriberi for thiamine deficiency pellagra for nicotinamide deficiency

Question 26

how do enzymes act as general acid-base catalysts?

Answer 26

stabilise unstable (charged) transition states transferring protons to and from them decreasing their free energy

Question 27

what act as weak proton donors or acceptors

Answer 27

amino acid side chains Glu, Asp, Lys, Arg, His, Cis, Tyr

Question 28

Step 1 RNAse mechanism

Answer 28

His12 acts as a general base - takes proton from RNA 2'-OH (accepts as a base) - makes a nucleophile - then attacks the phosphoric group

Question 29

Step 2 RNAse mechanism

Answer 29

His119 acts as a general acid - promotes bond scission ph gains extra bond, breaks the bond and then donate e-

Question 30

Step 3 RNAse mechanism

Answer 30

2',3' cyclic intermediate is hydrolysed through reverse step 1 - water replaces the leaving group

Question 31

interactions between enzyme bound metal and substrate can

Answer 31

anent a substrate for reaction stabilise charged reaction states mediate redox reactions

Question 32

carbonic anhydrase

Answer 32

Zn2+ forms bond with OH- ion in active site Zn is stabilising the hydroxyl

Question 33

Enzyme mechanism

Answer 33

formation of transient covalent bond between enzyme and substrate this complex undergoes a reaction to regenerate free enzyme this formation offers an alternative route to same products that has a lower activation energy

Question 34

Serine Proteases

Answer 34

large family of enzymes include digestive enzymes and blood clotting enzymes end-proteases that hydrolyse the peptide bond have a catalytic trip (3 enzymes in active site) all required for catalysis

Question 35

Protease mechanism

Answer 35

mixture of acid-base catalysis & covalent catalysis serine residue acts as nucleophile and made more nucleophilic by histidine and aspartic acid

Question 36

6 steps of protease mechanism ## Footnote LOOK AT DIAGRAM

Answer 36

1. ES complex - Michaelis complex 2. First transition state - Tehtrahedral intermediate 3. Acyl enzyme intermediate 4. Acyl enzyme water complex 5. Second transition state - tetrahedral intermediate 6. Free enzyme

Question 37

Trypsin in serine protease specificity

Answer 37

Cleaves after Arg & Lys Has an Asp residue in binding pocket

Question 38

Chromotrypsin in serine protease specificity

Answer 38

Cleaves after aromatic residues has serine in bonding pocket

Question 39

Elastase in serine protease specificity

Answer 39

Cleaves after small hydrophobic residues Glycine, alanine and valine