Enzymes Flashcards
What are the 6 enzyme classes?
- Oxidoreductases
- Transferases
- Hydrolases
- Lyases
- Isomerases
- Ligases
Oxidoreductases- Function & Examples
Function: Transfer of electrons. Results in a change in oxidation state
Example: Dehydrogenase
Transferases- Function & Examples
Function: Transfer of functional group from one molecule to another
Example: Phosphorylase, Kinase
Hydrolases- Function & Examples
Function: Breakdown of a covalent bond using water
Example: Protease, Phosphatase
Lyase- Function & Example
Function: Breakdown of a covalent bond without water or oxidation
Example: Decarboxylase
Isomerase- Function & Example
Function: Rearrangement/Transfer of bonds within a molecule
Example: Mutase
Ligase- Function
Function: Formation (Joining) of a covalent bond between two large molecules
What reaction types are each class responsible for and what general schemes for these reactions?
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)
Isoenzymes
Enzymes carrying out same reactions can differ greatly between species and can have different forms of an enzyme within species
Example of Isoenzyme
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
Globular Proteins
Hydrophobic internal residues
Hydrophilic external Residues
Active site composition w/ example
A particular group of amino acids. e.g. Chymotrypsin- critical active site residues His57, Asp102, Ser195
Chymotrypsin Features
2x Beta Sheet Barrel, C-terminal Alpha Helix, Substrate binding cleft
Coenzymes/Cofactors
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
Coenzyme feature
Usually organic molecules derived from vitamins, often weakly bound to enzyme, can act as co-substrates and are converted into products
Definitions:
Cofactor
Metal ions
Coenzyme
Vitamin
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)
Niacin is…
Vitamin B3
Structure of Vit B3
Shorthand
International Units of enzyme activity
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
Whats so special about enzymes
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
Example of enzyme catalysing reaction in physiological environment
N2 fixation: Enzyme nitrogenase- catalyses reaction at 20*C, neutral pH, atmospheric pressure
Thermophilic Organisms
Psychrophile
Mesophile
T.O: enzymes v. resistant to denaturation at high temperature
P: Low temp optima <15*C
M: Midrange temp optima
Taq polymerase
Can withstand 95C and replicate DNA at 75C
Specificity in Serine proteases:
Trypsin, Chymotrypsin, Elastase + Explanation
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
Types of Specificity:
Absolute
Group
Linkage
Stereochemical
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)
Enzyme Catalysis
Enzymes increase rate of reaction by lowering activation energy barrier, no change in overall thermodynamics or enzyme
How do enzymes achieve rate of reaction enhancement (6 things)
- Proximity and Orientation effects
- Acid/Base Catalysis
- Electrostatic Interactions
- Covalent Catalysis
- Transition State Stabilisation
- Metal Ion Catalysis
Proximity and Orientation (Rate of reaction enhancement)
Enzyme acts as a template to bring reactants close together and in a favourable orientation for reaction to occur (loss of entropy)
Acid/Base Catalysis (Rate of reaction enhancement)
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)
Covalent Catalysis (Rate of Reaction enhancement)
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
Transition State Binding (Rate of Reaction enhancement)
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
