enzymes, inhibition. enzymes, catalysts of biological systems 1.enzymes in general 2. development of...
TRANSCRIPT
Enzymes, inhibition
ENZYMES, CATALYSTS OF BIOLOGICAL SYSTEMS
1. Enzymes in general
2. Development of enzymes
3. General mechanisms of enzymes
4. Kinetic characteristics of enzymes
5. Inhibition of enzymes regulation/control of enzymes
1. Enzymes in general
Keywords: catalyst, activation energy, enzyme, substrate, active centre, coenzyme, cofactor, prosthetic group, metalloenzyme, metal ion activated enzyme, inhibition
The rate constant of several biochemical reactions and the half life of the reactants without a catalyst (pH = 7, t = 25 °C)
Reaction Rate constant
(s–1)
The half life of starting
material
CO2 hydration ~ 0.1 ~7 s
Triose phosphate isomerization ~5×10–6 ~2 days
Cytidine deamination ~5×10–10 70-80 years
Hydrolysis of peptides ~5×10–11 700-800 years
Hydrolysis of phosphoric acid
monoesters
~5×10–14 500000 years
DNA hydrolysis ~10–16 ~200 million years
Decarboxylation of Glycine ~10–17 ~ 1 billion years
1. Enzymes in general
Living systems need enzymes for normal functioning because of the following reasons:
(i) The non-catalysed reactions are very slow under conditions (temperature, pressure, concentration, etc.) of life, and thus these rections have to be accelerated in living systems.
(ii) Possibility for coupled reactions – an endothermic reaction may occur only enzymatically, when the necessary energy is covered by a parallel high energy reaction step, and the two reactions together becomes favoured energetically. Most cases the energy is provided by the hydrolysis of a high energy phosphoric acid esters. Among these, hydrolysis of ATP is the most important coupling reaction.
(iii) The controlled function of the biological systems requires high specificity.
(iv) The biochemical processes must proceed without side reactions.
1. Enzymes in general
Names: The systhematic name consists of two parts: the first part relates to the name of the substrate (compound which reacts in the reaction) followed by the type of the reaction in which it reacts with the traditional „ase” ending. E.g. ribonucleotide reductase.
Enzyme clasess:
(i) Oxidoreductases
(ii) Transferases
(iii) Hydrolases
(iv) Liases
(v) Isomerases
(vi) Ligases
1. Enzymes in general
Class Subclass Example
EC 1: Oxido-
reductases
(Oxidation/re
duction
processes)
1. CH-OH donors
2. aldehyde or oxo donors
3. CH-CH donors
4. CH-NH(2) donors
... reactions
alcohol dehydrogenase (EC 1.1.1.1)
CO dehydrogenase (EC 1.2.2.4)
Acil-CoA dehydrogenase (EC 1.3.1.8)
L-amino-acid oxidase (EC 1.4.3.2)
...
1. Enzymes in general
Class Subclass Example
EC 2: Trans-
ferases
(Transfer of atom
sor functional
groups from one
molecule to
another)
1. C1 group
2. aldehyde or keto
group
3. acyl transferases
4. glycosyl transferases
...
Methionine S-methyltransferases (EC
2.1.1.12)
Transaldolase (EC 2.2.1.2)
Histone acetyltransferase (EC 2.3.1.48)
Deoxiuridine phosphorylase (EC
2.4.2.23)
...
1. Enzymes in general
Class Subclass Example
EC 3:
Hydrolases
(Hydrolytic
processes)
1. ester bond cleav.
2. glycosidases
3. ether bond cleav.
4. peptide bond cleav.
...
alkaline phosphatase (EC 3.1.3.1)
2-deoxiglycosidase (EC 3.2.1.112)
colesterol-5,6-oxid hydrolase(EC .3.2.11)
carboxipeptidase A (EC 3.4.17.1)
...
1. Enzymes in general
Class Subclass Example
EC 4: Liases
(Non-hydrolytic
cleavaege of
group or molecule
(e.g. H2O, CO2,
NH3) from the
substrate)
1. C-C liases
2. C-O liases
3. C-N liases
4. C-S liases...
pyruvate decarboxylase (EC 4.1.1.1)
citrate dehydratase (EC 4.2.1.4)
Histidin ammonia-liase (EC 4.3.1.3)
Methionin gamma-liase (EC 4.4.1.11)
...
1. Enzymes in general
Class Subclass Example
EC 5:
Isomerases
(Isomerisation
processes)
1. racemases, epimerases
2. cis-trans-izomerases
3. intramolecular oxido-
reductases
4. Mutases
...
prolin racemase (EC 5.1.1.4)
retinol isomerase (EC 5.2.1.7)
ribose isomerase (EC 5.3.1.20)
methymalonyl-CoA mutase (EC 5.4.99.2)
...
Class Subclass Example
EC 6: Ligases
(Any of a class of enzymes that catalyze the linkage of two molecules, generally utilizing nucleosid triphosphate (such as ATP) as the energy donor)
1. C-O bond
2. C-S bond
3. C-N bond
4. C-C bond
...
alanine-tRNa ligase (EC 6.1.1.7)
acetate-CoA ligáz (EC 6.2.1.1)
glutamine synthetase (EC 6.3.1.2)
pyruvate carboxylase (EC 6.4.1.1)
...
1. Enzymes in general
Several prosthetic group and coenzyme and their role
Prosthetic group (P) /
Coenzyme (C)
Role
hem ring (P) electrontransfer, O2 binding,
catalysis of redox reaction
Biotin (P) CO2 molecule binding
NAD+ (nicotin amide-adenine-
dinucleotide) (C)
providing hidrogen atom + electron
ATP (C) Providing phosphoryl group
Coenzym F430 (C) electron transfer
Methylcobalamin (C) providing methy group
1. Enzymes in general
2. Development of enzymes
Examples for template reactions:
Mo(CN)84-
N
N
NH N
N
NH2
NH
N
HN
NO
HHM2+
4 + 4
a.
b.
The RNA life hypothesis Ribozyme
2. Development of enzymes
Substrate mediated formation of amino acid based biocatalysts.The substrate may serve as a template for the formation of a specific
biocatalyst, which will transfer further and further substrates.The reproduction is provided by the substrate itself.
These hypothesis (RNA and substrate role) might be enough to understand for example the possibility of the prebiotic-biotic „big jump”.
And as a results of these about 3.5 billion years ago the life occurred on the earth.
2. Development of enzymes
3. Mechanism of enzymes
Lock and key model
Induced fit hypothesis
Transition state stabilisation
3. General mechanism of the enzymes
Schematic energy diagram of the enzymatic (full line) and non-catalysed (dashed line) reactions
3. General mechanism of the enzymes
The schematic mechanism of the adenosine-deaminase
3. General mechanism of the enzymes
Dependence of the initial rate of a simple enzymatic reaction on the concentration of the substrate
4. Enzyme kinetics
At the initial part of the reaction:
In steady state:
Michaelis constant
4. Enzyme kinetics
Considering that [E]0 = [E] + [ES],
The above equation can be modified:
Expressing [ES]:
Then substituting this into the V0 = k2[ES] rate equation, the
Michaelis-Menten equation is obtained:
4. Enzyme kinetics
By compairing the above equations the meaning of a and b are obtained.
KM can be considered as the dissociation constant of complex ES, or it equals the substrate concentration where v0 = Vmax/2.
4. Enzyme kinetics
The Lineweawer–Burk plot
4. Enzyme kinetics
5. Enzyme inhibition
As it is an equilibrium system, at very high substrate concentrations the
effect of the inhibitor is negligible, and thus the maximum reaction rate
(Vmax) does not change, while the KM increases with the increasing
inhibitor concentration.
Increasing the substrate concentration, it is not able to displace the
inhibitor and thus Vmax decreases. The substrate binding site remains
the same and thus KM does not depend on the concentration of the
inhibitor.
5. Enzyme inhibition
As the inhibitor does not compete with the substrate but does
decrease the activity of the enzyme Vmax decreases and KM
increases with the increase of the concentration of the inhibitor.
5. Enzyme inhibition