Enzymes & Coenzymes Flashcards
Why are enzymes important?
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
What are the 6 classes of enzymes?
Oxioreductase
Transferase
Hydrolase
Lyase
Isomerase
Ligase
What is an oxioreductase?
Catalyses oxidation-reduction in which oxygen and hydrogen are gained or lost
cytochrome oxidase, lactate dehydrogenase
What is a transferase?
Catalyses transfer of functional groups
e.g. amino group, acetyl group or phosphate group
acetate kinase, alanine deaminase
What is a hydrolase?
Catalyses hydrolysis
addition of water
Lipase, sucrase
What is a lyase?
Catalyses removal of groups of atoms within a molecule
oxalate decarboxylase, isocitrate lyase
What is an isomerase?
Catalyses rearrangement of atoms within a molecule
Glucose-phosphate isomerase, alanine racemase
What is a ligase?
Catalyses joining of two molecules
using energy usually derived from the breakdown of ATP
Acetyl-CoA synthesise, DNA ligase
Reaction energetics
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
What is the Arrhenius equation?
Gives relationship between activation energy and reaction rate constant
k = Ae ^-ae/RT
Energy diagram
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
What is a transition state?
A transient high energy species in conversion of substrate to molecule
What affect do catalysts have on activation energy?
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
What are the roles of an enzyme as a catalyst?
- enzyme provides specific environment for substrate where reaction more favourable
- reaction pocket = active site
- lowering activation energy
- not used up in the process
- enzyme-substrate and enzyme-product are reaction intermediates
LOOK AT ENERGETIC PROFILE OF ENZYME CATALYSED REACTION
DIAGRAM
What is an enzyme pocket?
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
What is binding energy?
Energy derived from enzyme pocket complex
What is a coenzyme?
Non protein organic molecule required for catalysis
biotin, NAD+, FAD and most vitamins
What is a cofactor?
Inorganic substances that are required for catalysis
metal ions: Fe2+, Zn2+, Cu2+, Mg2+
What is the combination of a coenzyme and cofactor called?
Holoenzyme
What is a protein without a coenzyme?
Apoenzyme
What is the function of coenzymes and co factors?
allow enzymes to access chemistries that amino acid side chain can’t access
allow for further and different reactions
coenzymes
have a catalytic role, not substrates
some don’t finish reaction same way they started
common coenzymes
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
coenzyme disease
arise as result of deficiency in these coenzymes:
megaloblastic anaemia - folic acid deficiency
beriberi for thiamine deficiency
pellagra for nicotinamide deficiency
how do enzymes act as general acid-base catalysts?
stabilise unstable (charged) transition states
transferring protons to and from them
decreasing their free energy
what act as weak proton donors or acceptors
amino acid side chains
Glu, Asp, Lys, Arg, His, Cis, Tyr
Step 1 RNAse mechanism
His12 acts as a general base
- takes proton from RNA 2’-OH (accepts as a base)
- makes a nucleophile
- then attacks the phosphoric group
Step 2 RNAse mechanism
His119 acts as a general acid
- promotes bond scission
ph gains extra bond, breaks the bond and then donate e-
Step 3 RNAse mechanism
2’,3’ cyclic intermediate is hydrolysed through reverse step 1
- water replaces the leaving group
interactions between enzyme bound metal and substrate can
anent a substrate for reaction
stabilise charged reaction states
mediate redox reactions
carbonic anhydrase
Zn2+ forms bond with OH- ion in active site
Zn is stabilising the hydroxyl
Enzyme mechanism
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
Serine Proteases
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
Protease mechanism
mixture of acid-base catalysis & covalent catalysis
serine residue acts as nucleophile and made more nucleophilic by histidine and aspartic acid
6 steps of protease mechanism
LOOK AT DIAGRAM
- ES complex - Michaelis complex
- First transition state - Tehtrahedral intermediate
- Acyl enzyme intermediate
- Acyl enzyme water complex
- Second transition state - tetrahedral intermediate
- Free enzyme
Trypsin in serine protease specificity
Cleaves after Arg & Lys
Has an Asp residue in binding pocket
Chromotrypsin in serine protease specificity
Cleaves after aromatic residues
has serine in bonding pocket
Elastase in serine protease specificity
Cleaves after small hydrophobic residues
Glycine, alanine and valine
