Enzymes

Question 1

What are the 6 enzyme classes?

Answer 1

1. Oxidoreductases
2. Transferases
3. Hydrolases
4. Lyases
5. Isomerases
6. Ligases

Question 2

Oxidoreductases- Function & Examples

Answer 2

Function: Transfer of electrons. Results in a change in oxidation state
Example: Dehydrogenase

Question 3

Transferases- Function & Examples

Answer 3

Function: Transfer of functional group from one molecule to another
Example: Phosphorylase, Kinase

Question 4

Hydrolases- Function & Examples

Answer 4

Function: Breakdown of a covalent bond using water
Example: Protease, Phosphatase

Question 5

Lyase- Function & Example

Answer 5

Function: Breakdown of a covalent bond without water or oxidation
Example: Decarboxylase

Question 6

Isomerase- Function & Example

Answer 6

Function: Rearrangement/Transfer of bonds within a molecule
Example: Mutase

Question 7

Ligase- Function

Answer 7

Function: Formation (Joining) of a covalent bond between two large molecules

Question 8

What reaction types are each class responsible for and what general schemes for these reactions?

Answer 8

Oxidoreductases: Redox reactions
Transferases: Transfer of group from one molecule to another
Hydrolases: Cleavage of group(s) in a molecule
Lyases: Addition of double bond(s) to a molecule
Isomerases: Several types of isomerization
Ligases: Formation of bonds (synthetases)

Question 9

Isoenzymes

Answer 9

Enzymes carrying out same reactions can differ greatly between species and can have different forms of an enzyme within species

Question 10

Example of Isoenzyme

Answer 10

Lactate dehydrogenase ( Imp for anaerobic respiration in microorganisms and in animal muscle cells).
LDH has 4 subunits, but 2 genes encode slightly different subunit sequences
M & H subunits (predominant in muscle or heart). Can combine in any combo to form active tetramer

Question 11

Globular Proteins

Answer 11

Hydrophobic internal residues
Hydrophilic external Residues

Question 12

Active site composition w/ example

Answer 12

A particular group of amino acids. e.g. Chymotrypsin- critical active site residues His57, Asp102, Ser195

Question 13

Chymotrypsin Features

Answer 13

2x Beta Sheet Barrel, C-terminal Alpha Helix, Substrate binding cleft

Question 14

Coenzymes/Cofactors

Answer 14

Many enzymes require non-protein component in order to function.
Apoenzyme (inactive + Cofactor= Holoenzyme (active)
Co-factors can be organic molecules (coenzymes) or inorganic metal ions such as Zn, Co, Mn, Fe.
Cofactors/Coenzymes that are tightly bound are called prosthetic groups

Question 15

Coenzyme feature

Answer 15

Usually organic molecules derived from vitamins, often weakly bound to enzyme, can act as co-substrates and are converted into products

Question 16

Definitions:
Cofactor
Metal ions
Coenzyme
Vitamin

Answer 16

Cofactor: non-protein component essential for enzyme activity
Metal ions: inorganic cofactors
Coenzyme: An organic non-protein component essential for enzyme activity
Vitamin: Organic compounds essential for normal growth and nutrition that can’t be synthesised by the body (many vit are precursors for enzymes)

Question 17

Niacin is…

Answer 17

Vitamin B3

Question 18

Structure of Vit B3

Answer 18

Shorthand

Question 19

International Units of enzyme activity

Answer 19

One I.U= amount of enzyme required to catalyse the conversion of 1 micromole (1 umol) of substrate (or product) per min at 25*C

Question 20

Whats so special about enzymes

Answer 20

work under mild conditions of temp and pH, highly specific for substrates, immense catalytic power- increase reaction rates up to 10^12 fold, can be regulated

Question 21

Example of enzyme catalysing reaction in physiological environment

Answer 21

N2 fixation: Enzyme nitrogenase- catalyses reaction at 20*C, neutral pH, atmospheric pressure

Question 22

Thermophilic Organisms
Psychrophile
Mesophile

Answer 22

T.O: enzymes v. resistant to denaturation at high temperature
P: Low temp optima <15*C
M: Midrange temp optima

Question 23

Taq polymerase

Answer 23

Can withstand 95C and replicate DNA at 75C

Question 24

Specificity in Serine proteases:
Trypsin, Chymotrypsin, Elastase + Explanation

Answer 24

T: Cleaves after Arg, Lys (Basic)
C: Cleaves after Phe, Tyr, Trp (Large aromatic)
E: Cleaves after Ala, Gly (small hydrophobic)
Explanation: Specificity explained by differences in binding pocket for substrate side-chains

Question 25

Types of Specificity:
Absolute
Group
Linkage
Stereochemical

Answer 25

A.S: Enzyme will catalyse only one reaction (Maltose only acts on maltose)
G.S: Enzyme will only act on molecules that have specific functional groups (Tyrosine kinase)
L.S: Enzyme will act on a particular type of chemical bond regardless of rest of the molecular structure (amylase cleaves alpha 1-4 glyosidic link bonds in starch, dextrin and glycogen
S.S: Enzyme will act on a particular steric or optimal isomer (D-amino acid oxidase acts only on D-amino acids)

Question 26

Enzyme Catalysis

Answer 26

Enzymes increase rate of reaction by lowering activation energy barrier, no change in overall thermodynamics or enzyme

Question 27

How do enzymes achieve rate of reaction enhancement (6 things)

Answer 27

1. Proximity and Orientation effects
2. Acid/Base Catalysis
3. Electrostatic Interactions
4. Covalent Catalysis
5. Transition State Stabilisation
6. Metal Ion Catalysis

Question 28

Proximity and Orientation (Rate of reaction enhancement)

Answer 28

Enzyme acts as a template to bring reactants close together and in a favourable orientation for reaction to occur (loss of entropy)

Question 29

Acid/Base Catalysis (Rate of reaction enhancement)

Answer 29

Side chain groups of some amino acids in active site can act as acids or bases by donating/accepting protons from substrates or intermediates (Glutamic acid in Lysosome acts as general acid)

Question 30

Covalent Catalysis (Rate of Reaction enhancement)

Answer 30

Amino Acid side chains can react with substrate to form a covalent intermediate (usually nucleophilic attack on substrate C- Usually Cys, Ser, His) e.g. serine proteases / chymotrypsin
Covalent Catalysis has very different pathway to uncatalyzed reaction

Question 31

Transition State Binding (Rate of Reaction enhancement)

Answer 31

Enzyme active site promotes formation of transition state intermediates
TS- highly unstable intermediates where bonds are made/broken
TS analogs (stable)- found to bind enzymes tighter than substrates e.g Lysosome