enzymes and co-enzymes and their mechanisms

Question 1

importance of enzymes

Answer 1

• natures catalyst and carry out all reactions of a cell
• many inherited diseases are caused by mutations in key enzymes
• -used commercially in food products and detergents
• used in drug synthesis to produce single isomer drugs

Question 2

what can be used to diagnose disease

Answer 2

measurement of certain enzymes in the blood

Question 3

catalysts..

Answer 3

reduce activation energy–> however they do not change the energy of a reaction

Question 4

catalysts cannot..

Answer 4

make a thermodynamically unstable reaction become favourable i.e. they do not change the position of the equilibrium by they do speed up how quickly the reaction reaches equilibrium

Question 5

for a reaction to be favourable

Answer 5

the pro cuts must be of lower energy than the reactants

Question 6

speed of a reaction is determined by

Answer 6

activation energy

Question 7

role of enzymes as catalysts

Answer 7

1. provide a specific environment for the substrate where the reaction is more favourable
2. the pocket on the enzyme where this occurs is called the active site
3. enzymes lowers the energy needed to carry out the reaction
4. enzyme is not used up in this process
5. accelerates the conversion of s–> p (also p–>s)
6. ES and EP are reaction intermediates

Question 8

breakdown of enzymes catalysing s–>p

Answer 8

E+S ES ES(Transition state)EPE+P

Question 9

what is bad for catalysis

Answer 9

tight binding to either the substrate or product is bad for catalysis - it is the transition state that enzymes bind tightly to

Question 10

what are enzymes pockets or active sister designed to complement

Answer 10

the reaction transition state

Question 11

what forces stabilise ES, ES (TS) and EP complexes?

Answer 11

the same as those forces that stabilise proteins e.g. H bond Hydrophobic, ionic, van der waaal.

Question 12

enzyme is complimentary to..

Answer 12

transition state

Question 13

in some enzymes..

Answer 13

a transient covalent bond is formed during the reaction

Question 14

the energy derived from complex format is..

Answer 14

binding energy

Question 15

co -enzyme

Answer 15

non-protein organic molecules required for catalysis eg. biotin, NAD+, FAD

Question 16

co-factors

Answer 16

inorganic substances that are required for catalysis e.g. metal ions

Question 17

what is a combination protein and coenzyme/cofactor called

Answer 17

holoenzyme

Question 18

holoenzyme

Answer 18

what is a combination protein and coenzyme/cofactor called

Question 19

the protein alone without the co-enzyme/cofactor

Answer 19

apoenzyme

Question 20

apoenzyme

Answer 20

the protein alone without the co-enzyme/cofactor

Question 21

who to coenzymes and cofactors help catalysis

Answer 21

they allows enzymes to access chemistries that are unavailable to amino acid side chains

Question 22

what can occur if there are deficiencies in certain co-enzymes

Answer 22

disease

Question 23

e.g. what co-enzymes and cofactors are deficient in megaloblastic aneomia

Answer 23

folic acid

Question 24

what co-enzymes and cofactors are deficient in Beriberi

Answer 24

thiamine deficiency

Question 25

what co-enzymes and cofactors are deficient in pellagra

Answer 25

nicotinamide deficiency/ nicotinic acid

Question 26

6 main enzyme groups

Answer 26

1. oxidoreductase
2. transferase
3. hydrolase
4. lyase
5. isomerase
6. ligase

Question 27

oxidoreductase

Answer 27

oxidation/redution reaction in which oxygen and hydrogen are gained or lost

Question 28

transferase

Answer 28

transfer of functional groups such as amin groups, acetyl groups or phosphate group

Question 29

hydrolase

Answer 29

hydrolysis

Question 30

lyase

Answer 30

removal of groups of atoms without hydrolysis

Question 31

isomerase

Answer 31

rearrangement of atoms within a molecule

Question 32

ligase

Answer 32

joining of two molecules- using the energy derived from the break down of ATP

Question 33

enzyme mechanism x3

Answer 33

• general acid-base catalyst
• metal ion catalysis
• covalent catalysis

Question 34

general ace-base catalysts

Answer 34

enzymes stabilise unstable charged intermediates by transferring protons to and from the intermediate - therefore decreasing free energy of the transition state
e.g. amino acid side chains act as week proton donor and acceptors e.g. Gaul, lys (acids and bases)

Question 35

Metal ion catalysis

Answer 35

ionic interactions between the enzyme bund metal and substrate can:
1_ orient a substrate for reaction
2_ stables charged reaction states
3_ mediate oxidation- reduction reactions

1/3rd of all known enzymes require a metal for catalytic activity

Question 36

covalent catalysis

Answer 36

formation of transient covalent bods between enzymes and substrate- covalent complex undergoes a reaction to generate free enzymes.
- in comparison with the uncatalysed reaction, the formation of the covalent bond with the enzyme alter the pathway of the reaction and offers an alternative route to the same product that has a lower activation energy

Question 37

what are serine proteases

Answer 37

a large family of enzymes that include digestive enzymes like trypsin and chymotrypsin, and the blood clotting enzyme thrombin.

These are ENDOPROTEASES WHICH HYDROLYSE PEPTIDE BONDS (AMIDE)

Question 38

What catalytic triad to serine proteases have in their active sites

Answer 38

histidine, aspartate, serine

Question 39

examples of serine proteases

Answer 39

trypsin
chymotrypsin
thrombin (blood clotting)

Question 40

what sort of enzyme mechanisms to protease ue

Answer 40

a mixture of acid-base and covalent catalysis

-serine residue acts as a the nucleophile and is made more nucleophilic by histidine and aseptic acid

Question 41

6 steps of protease mechanism

Answer 41

1) ES complex (michaelis)
2) first TS- tetrahedral intermediate
3) acyl enzyme intermediate
4) acyl enzyme water complex
5) second TS- tetrahedral intermediate
6) free enzyme

Question 42

serine protease specificity

Answer 42

each enzyme has a different specificity pocket

Question 43

specificity of trypsin

Answer 43

cleaves after Arg and Lys residues and has an Asp residue at the bottom of the binding pocket

Question 44

specificity of chymotrypsin

Answer 44

cleaves after aromatic residues and has a neutral charged serine at the binding pocket

Question 45

specificity of elastase

Answer 45

cleaves small hydroponic residues eg. glycine, alanine and valine

Question 46

Metal ion catalysis

Answer 46

metal atoms are utilised by enzymes as co-factors.
-metals have the ability to lose electrons very easily.

Therefore this allows them to:

1) stabilise transient and intermediate structures in the AS
2) assist in forming strong nucleophile species
3) hold substrate in place

Question 47

covalent catalysis explained

Answer 47

• many enzymes contain catalytic residues–> responsible for forming a temporary covalent bond with the substrate
• this keeps the substrate molecule inside the AS
• at the end of the reaction this covalent bond is broken to regenerate the free enzyme

Question 48

acid base catalysis

Answer 48

• transfer of protons
• there are specific residues in the active site which will be involved e.g. Histidine used t transfer protons

By transferring H+ ion:

1) activate strong nucleophile required in catalysis
2) stabilise charged groups
3) increase electric interaction that may stabilise the transition state