Download Enzymes - دانشکده پزشکی

TUMS
Azin Nowrouzi, PhD
Tehran University of Medical Sciences
Chemical reaction
A
Catalyst
Product(s)
Reactant(s)
A +B
B
Catalyst
B+C
Catalysts
•Increase the rate of a reaction.
•Are not consumed by the reaction.
•Can act repeatedly.
What are some of the known catalysts?
Heat
Acid
Base
Metals
Enzyme is either a pure protein or
may require a non-protein portion
• Apoenzyme = protein portion
• Apoenzyme + non-protein part = Holoenzyme
According to Holum, the non-protein portion may be:
• A coenzyme - a non-protein organic substance which is
loosely attached to the protein part.
• A prosthetic group - an organic substance which is firmly
attached to the protein or apoenzyme portion.
• A cofactor - these include K+, Fe++, Fe+++, Cu++, Co++,
Zn++, Mn++, Mg++, Ca++, and Mo+++.
Basic enzyme reactions
S+EE+P
S = Substrate P = Product E = Enzyme
Swedish chemist Savante Arrhenius in
1888 proposed:
Substrate and enzyme form some
intermediate substance known as The
Enzyme-Substrate Complex (ES):
S + E  ES Binding step
ES  P + E Catalytic step
There are two models of enzyme substrate interaction
1. Lock and key model Emil Fischer (1890)
2. Induced fit model Daniel Koshland (1958)
The active site:
• Substrate Binding Site
• Catalytic Site
Induced fit in Carboxypeptidase A
Three amino acids are located near the
active site (Arg 145, Tyr 248, and Glu 270)
Enzyme-Substrate complex is transient
S+E
•
•
•
•
S
E
P+E
When the enzyme unites with the
substrate, in most cases the forces that
hold the enzyme and substrate are noncovalent.
Binding forces of substrate are:
Ionic interactions: (+)•••••(-)
Hydrophobic interactions: (h)•••••(h)
H-bonds: O-H ••••• O, N-H ••••• O, etc.
van der Waals interactions
Some important characteristics of enzymes
1.
Potent (high catalytic power) High reaction rates
–
2.
They increase the rate of reaction by a factor of 103-1012
Efficient (high efficiency)
–
catalytic efficiency is represented by Turnover number.
•
3.
moles of substrate converted to product per second per mole of the active
site of the enzyme
Milder reaction conditions Enzymatically catalyzed reactions occur at mild
temperature, pressure, and nearly neutral pH. (i.e physiological conditions)
4.
Specific (specificity)
–
–
–
5.
Substrate specific
Reaction Specific
Stereospecific
Capacity for regulation
Enzymes can be activated or inhibited so that the rate of product formation
responds to the needs of the cell.
6.
Location within the cell
Many enzymes are located in specific organelles within the cell. Such
compartmentization serves
•
•
•
to isolate the reaction substrate from competing reactions,
to provide a favorable environment for the reaction, and
to organize the thousands of enzymes present in the cell into purposeful
pathqways.
Specificity
•
Substrate Specificity
1. Absolute specificity: For example Urease
2. Functional Group specificity: For example OH,
CHO, NH2.
3. Linkage specificity: For example Peptide bond.
•
Reaction specificity
–
–
–
•
Yields are nearly 100%
Lack of production of by-products
Save energy and prevents waste of metabolites
Stereospecificity
–
Enzymes can distinguish between enantiomers and
isomers
Enzymes requiring metal ions as cofactors
Many
vitamins
are
coenzyme
precursors
Many Vitamins are Coenzyme precursors
• Many organism are unable to synthesize parts of the
coenzymes
• These parts must be present in the organism diet and
are called vitamins
Vitamin
Chemical Name
Biochemical Function
Coenzyme Chemistry
B1
Thiamine
Coenzyme
TPP
Decarboxylation of - keto
acids
B2
Riboflavin
Coenzymes FAD, FMN
Redox chemistry
Niacin
Nicotinamide
Coenzyme
NAD
Redox chemistry
B6
Pyridoxal
Coenzyme
PLP
Transamination reactions
B12
Cobalamine
Coenzyme B12
Radical rearrangements (lipid
degradation)
C
Ascorbic Acid
Coenzyme
Redox agent
( collagen formation)
H
Biotin
Coenzyme
Carboxylation
Methods for naming enzymes
(nomenclature)
1. Very old method: Pepsin, Renin, Trypsin
2. Old method: Protease, Lipase, Urease
3. Systematic naming (EC = Enzyme
Commission number ):
The name has two parts:
The first part: name of substrate (s)
The second part: ending in –ase, indicates the type of
reaction.
Additional information can follow in parentheses:
L-malate:NAD+ oxidoreductase (decarboxylating)
Each enzyme has a EC number
= Enzyme Commission number
Enzyme
EC number
Alcohol dehydrogenase
Arginase
1.1.1.1
3.5.3.1
Pepsin
3.4.21.1
• EC number consists of 4 integers
• The 1st designates to which of the six major classes an
enzyme belongs.
• The 2nd integer indicates a sub class, e.g. type of bond
• The 3rd number is a subclassification of the bond type or
the group transferred in the reaction or both (a
susubclass)
• The 4th number is simply a serial number
There are six functional classes of enzymes
Class Names
Functions
1
Oxidoreductases AH + NAD+  A+ + NADH
2
Transferases
A-X + B  A + B-X
3
Hydrolases
A-OX + H2O  A-OH + HOX
4
Lyases
R1R2R3CCR4R5R6 
R1R2C==CR4R5 + R3 + R6
5
Isomerases
trans  cis, L-form D-form, etc.
6
Ligases
Formation of C-C, C-S, C-O, C-N bonds
by condensation reaction
coupled to ATP hydrolysis
EC 3 Hydrolases
Function
EC 3.1
Acting on ester bonds
EC 3.2
Glycosylases
EC 3.3
Acting on ether bonds
EC 3.4
Acting on peptide bonds
(peptidases)
EC 3.5
Acting on carbon-nitrogen bonds,
other than peptide bonds
EC 3.6
Acting on acid anhydrides
EC 3.7
Acting on carbon-carbon bonds
EC 3.8
Acting on halide bonds
EC 3.9
Acting on phosphorus-nitrogen
bonds
EC 3.10 Acting on sulfur-nitrogen bonds
EC 3.11
Acting on carbon-phosphorus
bonds
EC 3.12 Acting on sulfur-sulfur bonds
EC 3.13 Acting on carbon-sulfur bonds
EC5
Isomerases
EC 5.1
Racemases and
epimerases
EC 5.2
cis-trans-Isomerases
EC 5.3
Intramolecular
isomerases
EC 5.4
Intramolecular
transferases (mutases)
EC 5.5
Intramolecular lyases
EC 5.99
Other isomerases
Enzyme Nomenclature and
Classification
EC Classification
Class
Subclass
Sub-subclass
Serial number
Example of Enzyme Nomenclature
• Common name(s)
– Invertase, sucrase
• Systematic name
– -D-fructofuranoside fructohydrolase (E.C. 3.2.1.26)
• Recommended name
– -fructofuranosidase
Kinetic
Energy barrier = Free Energy of Activation
X
T*
Y
T = Transition state
(Ea)
Thermodynamics:
Type (Exergonic or Endergonic)
Kinetics:
How fast the reaction will proceed
Enzyme Stabilizes Transition State
What’s the difference? Many enzymes function
by lowering the activation energy of reactions.
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.166
EA = Activation energy ; a barrier to the reaction
Can be overcome
by adding
energy.......
......or by
catalysis
Enzymes Are Complementary to Transition State
X
If enzyme just binds substrate
then there will be no further
reaction
Enzyme not only recognizes substrate,
but also induces the formation of transition state
Active Site Is a Deep Buried Pocket
Why energy required to reach transition state
is lower in the active site?
+
CoE (1)
(4) (3)
(2)
(1) Stabilizes transition
(2) Expels water
(3) Reactive groups
(4) Coenzyme helps
Juang RH (2004) BCbasics
Active Site Avoids the Influence of Water
+
-
Preventing the influence of water sustains the formation of stable ionic bonds
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.115
Modes of rate enhancement
• Facilitation of Proximity
– Increase the Effective concentration.
– Hold reactants near each other in proper
orientation
• Strain, Molecular Distortion, and Shape
Change
– Put a strain on susceptible bonds
• General Acid –Base Catalysis
– Transfer of a proton in the transition state
• Covalent Catalysis
– Form covalent bond with substrate
of the substrate.
destabilization
Factors affecting rate of enzyme reactions
1.
2.
3.
4.
5.
6.
Temperature
pH
Enzyme concentration [E]
Substrate concentration [S]
Inhibition
Regulation (Effectors)
1- Optimum Temperature
• Little activity at low temperature (low number of collisions)
• Rate increases with temperature (more successful collisions)
– rate doubles for every 10°C increase in temperature
• Most active at optimum temperatures (usually 37 C in humans)
• Enzymes isolated from thermophilic organisms display maxima
around 100°C
• Enzymes isolated from psychrophilic organisms display maxima
around 10°C.
• Activity lost with denaturation at high temperatures
2- Optimum pH
• Effect of pH on ionization of active site.
• Effect of pH on enzyme denaturation.
• Each enzyme has an optimal pH (~ 6 - 8 )
– Exceptions :
digestive enzymes in the stomach( pH 2)
digestive enzymes intestine (pH 8)
3- Enzyme concentration
• The Rate (v) of reaction Increases proportional to
the enzyme concentration [E] ([S] is high).
4- Substrate concentration
• When enzyme concentration is constant, increasing
[S] increases the rate of reaction, BUT
• Maximum activity reaches when all E combines with
S (when all the enzyme is in the ES,
,form).
Enzyme
Velocity
Curve
0
1
2
3
4
5
6
7
8
S
+
E
80
Product (v)
60
P
40
(in a fixed
period of
time)
20
0
0
2
4
6
8
Substrate (mole) [S]
Juang RH (2004) BCbasics
Michaelis-Menten equation
S
k1
E
k-1
maximal velocity, Vmax
5
v, µmol/min
4
3
0.5Vmax
2
Km
1
0
0
10
20
30
[S], mM
40
50
S
E
k2
P
MM equation derivation (steady state)
Practical Summary- Vmax and Km
• Vmax
– How fast the reaction can occur under ideal circumstances.
• Km
– Range of [S] at which a reaction will occur.
– Binding affinity of enzyme for substrate
• LARGER Km  the WEAKER the binding affinity
Enzyme
Substrate
Km (mM)
Catalase
H2O2
1,100
Chymotrypsin
Gly-Tyr-Gly
108
Carbonic anhydrase
CO2
12
Beta-galactosidase
D-lactose
4
Acetylcholinesterase
acetylcholine (ACh)
0.09
• Kcat / Km
– Practical idea of the catalytic efficiency, i.e. how often a
molecule of substrate that is bound reacts to give product.
Order of reaction
1. When [S] << Km
vo = (Vmax / Km )[S]
2. When [S] = Km
vo = Vmax /2
3. When [S] >> Km
vo = Vmax
zero order
Mixed order
2
First order
Importance of Vi
in measurement of Enzyme activity
S
E
k1
k-1
k2
S
E
P
Working with vo minimizes complications with
1. reverse reactions
2. product Inhibition
The rate of the reaction catalyzed by an enzyme
in a sample is expressed in Units.
Units = V = activity = Micromoles (mol; 10-6 mol or ….),
of [S] reacting or [P] produced/min.
It is better to measure it at linear part of the curve
Lineweaver-Burk plot
1
vo
-1
Km
vo
1/2
1
Vmax
1 Km 1
1


v Vmax [S] Vmax
Km Direct plot S
Vmax [S]
v
Km  [S]
Juang RH (2004) BCbasics
Double reciprocal 1/S
Allosteric enzymes
• Why the sigmoid shape?
• Allosteric enzymes are multi-subunit enzymes,
each with an active site.
• They show a cooperative response to substrates
hyperbolic curve
michaelis-menten
kinetics
Sigmoidal curve
 Irreversible Inhibition = Enzyme
stops working permanently
1.
2.
Destruction of enzyme
Irreversible Inhibitor = forms covalent bonds to E
(inactive E)
Examples:
– Diisopropylfluorophosphate
•
•
–
Cyanide and sulfide
•
•
–
Inhibit cytochrome oxidase
bind to the iron atom
Fluorouracil
•
–
inhibits acetylcholine esterase
binds irreversibly to –OH of serine residue
inhibits thymidine synthase (suicide inhibition - metabolic
product is toxic )
Aspirin
•
•
Inhibits prostaglandin synthase
acylates an amino group of the cyclooxygenase
 Reversible Inhibition = Temporary
decrease of enzyme function
•
Three types based on “how increasing [S]
affects degree of inhibition”:
1. Competitive – degree of inhibition decreases
2. Non-competitive – degree of inhibition is
unaffected
3. Anti- or Uncompetitive – degree of inhibition
increases
 The Lineweaver-Burk plot is useful in
determining the mechanisms of actions of
various inhibitors.
The Effects of Enzyme Inhibitors
Example
• When a slice of apple is exposed to air, it quickly
turns brown. This is because the enzyme odiphenyl oxidase catalyzes the oxidation of
phenols in the apple to dark-colored products.
• Catechol can be used as the substrate The
enzyme converts it into o-quinone (A), which is
then further oxidized to dark products.
Experiments
No Inhibitor
Tube A Tube B Tube C Tube D
[S]
4.8 mM 1.2 mM 0.6 mM 0.3 mM
1/[S]
0.21
0.83
1.67
3.33
Δ OD540
(Vi)
0.081
0.048
0.035
0.020
1/Vi
12.3
20.8
31.7
50.0
Effect of para-hydroxybenzoic
acid (PHBA)
Tube Tube Tube Tube
A
B
C
D
Tube A Tube B Tube C Tube D
[S]
1/[S]
4.8 mM 1.2 mM 0.6 mM 0.3 mM
0.21
0.83
1.67
3.33
(
0.040
0.024
0.016
0.010
Vi)
1/Vi
4.8
mM
1.2
mM
0.6
mM
0.3
mM
1/[S]
0.21
0.83
1.67
3.33
0.06
0
0.03
2
0.01
9
0.01
1
16.7
31.3
52.6
90.9
ΔOD
ΔOD54
0
[S]
25
41
62
Effect of phenylthiourea
102
540
(Vi)
1/Vi
I- Competitive Inhibition
EI
S
Competitive
V [S]
v  max
Km  [S]
CI
V [S]
v  max
K m  [S]
Kic
S+E
+
I
E
ES
1 Km 1
1


v Vmax [S] Vmax
5
E+P
1 K m 1
1


v Vmax [S] Vmax
2.5
No I
4
v, µmol/min
µmol/min
v,
0.5Vmax
+CI
0.5V
max
3
2
Km
Kmapp
1
-1/Km
Km
+CI
2
1/v, /µmol/min
/µmol/min
1/v,
 [I] 

  1
 Kic 
1.5
K /Vmax
Kmm
/Vmax
1
1/Vmax
1/V
app
-1/Km
-1/K
m
Kmapp/Vmax
0.5
No I
max
0
0
0
10
20
30
[S], mM
40
50
-0.6 -0.4 -0.2
0 0.2 0.4 0.6 0.8
1/[S], /mM
1
II- Noncompetitive Inhibition
S
Noncompetitive
(mixed-type)
NCI
S
V [S]
v  max
Km  [S]
E
Vmax [S]
v
K m   ' [S]
EI
E
Kic
S+E
+
I
NCI
1 Km 1
1


v Vmax [S] Vmax
E+P
1 K m 1
'


v Vmax [S] Vmax
2.5
55
44
0.5Vmax
33
+ NCImax
0.5V
0.5Vmax
22
11
Km
 [I] 

  1
 Kic 
2
1/v, /µmol/min
/µmol/min
1/v,
No I
v, µmol/min
ESI
Kiu
ES
+
I
 [I] 

'  1
 Kiu 
-1/Km
-1/K
m
Km
1.5
1/Vmaxapp
Km/Vmaxapp
+ NC I
1
0.5
K K/V /V
m mmax
max
1/V
max
1/Vmax
0
00
00
10
10
20
20
30
30
[S],
[S],mM
mM
40
40
50
50
-0.6 -0.4 -0.2
0 0.2 0.4 0.6 0.8
1/[S], /mM
1
No I
III- Uncompetitive Inhibition
Uncompetitive
(catalytic)
Vmax [S]
v
Km  [S]
S
E
Vmax [S]
v
Km   ' [S]
ESI
Kiu
UCI
S+E
ES
E+P
+
I
1 Km 1
1
1 Km 1
'




v Vmax [S] Vmax
v Vmax [S] Vmax
5
2.5
No I
4
v, µmol/min
0.5Vmax
+ UC I
0.5V
max
3
Km
2
0.5Vmax
 [I] 

'  1
 Kiu 
app
Km
1
-1/Km
Km
-1/Km
-1/K
app
m
/µmol/min
1/v, /µmol/min
2
1.5
1/Vmaxapp
Kmapp/Vmaxapp
1
0.5
1/Vmax
Km/Vmax
+ UC I
Km/Vmax
No I
1/Vmax
0
0
0
10
20
30
[S], mM
[S].
40
50
-0.6 -0.4 -0.2
0 0.2 0.4 0.6 0.8
1/[S],
1/[S]. /mM
1
Enzyme inhibitors in medicine
• Many current pharmaceuticals are enzyme inhibitors
(e.g. HIV protease inhibitors for treatment of AIDS)
• An example: Ethanol is used as a competitive
inhibitor to treat methanol poisoning.
 Methanol
Alcohol dehydrogenase
formaldehyde (very toxic)
 Ethanol competes for the same enzyme.
 Administration of ethanol occupies the enzyme
thereby delaying methanol metabolism long enough
for clearance through the kidneys.
Some diagnostically important enzymes
Aminotransferases
Aspartate aminotransferase
(AST or SGOT)
Alanine aminotransferase
(ALT, or SGPT)
Myocardial infarction
Viral hepatitis
Lactate Dehydrogenase (LDH)
myocardial infarction
Creatine Kinase (CK)
Myocardial infarc., brain,
skeletal muscle disorder
Cholinesterase
Liver, erythrocytes
Gamma-glutamyltransferase
Liver damage
Acid phosphatase
Carcinoma of prostate
Alkaline phosphatase (AP)
Bone disease
Lipase
Acute pancreatitis
Ceruloplasmin
Hepatolenticular degeneration
(wilson’s disease)
Alpha-amylase
Intestinal obstruction
Useful enzymes for
early diagnosis of
dental caries and
periodontal disease
Isozymes of lactate dehydrogenase
Isozymes:
– Are catalitically identical (have same catalytic activity) BUT
physically distinct
– Can be detected by gel electrophoresis (different electrical charge)
– Occur in oligomeric enzymes like lactate dehydrogenase (LDH)
In LDH
• Protomers H and M can combine to make five different
tetramers.
Isoenzymes of Creatine kinase
• CK has 3 forms dimer
B and M chains:
• CK1= BB
• CK2= MB
• CK3=MM
• Heart only tissue rich in
CK2, increases 4-8 hr
after chest painspeaks at 24 hr.
• LDH peaks 2-3 days
after MI.
• New markers:
Troponin T, Troponin I
5- Regulation (Effectors)
Effectors can be classified:
According to type:
• Homotropic effector: Substrate itself is the effector
• Heterotropic effector: substance other than substrate is the
effector
According to their effect:
• Activators (positive effectors)
– Increase the rate of enzyme
• Inhibitors (negative effectors)
– Decrease the velocity of reaction
– Stop the enzyme
• Irreversible
• Reversible
– Competitive
– Non-competitive
– Uncompetitive
Increase or decrease
in enzyme reaction
rate is reflected in the
graph of V versus S
Metabolic pathways
• A metabolic pathway is a chain of enzymatic
reactions
– Most pathways have many steps, each having a
different enzyme (E1, E2, E3, E4)
– Step by step, the initial substance used as substrate
by the first enzyme is transformed into a product that
will be the substrate for the next reaction
• Metabolic regulation is necessary to:
– maintain cell components at appropriate levels.
– conserve materials and energy.
Regulation of “Enzyme activity”
A. Regulation at trascription level (slowest)
B. Isozymes: Regulation specific to distinct tissues
and developmental stages
C. Compartmentation of S, E and P
D. Specific Proteolytic Cleavage
E. Covalent Modification
(Reversible phosphorylation or adenylation)
F. In response to metabolic products (fastest)
1.
2.
3.
4.
Substrate level control
Product Inhibition
Feedback control
Allosteric Effectors
A. Regulation at transcription level
1. Regulation of [E] by
•
•
Gene repression
Induction of genetic expression of enzyme
2. There is competition in a cell between
the processes of protein synthesis and
protein destruction.
•
By altering these rates, one can alter the
whole cell catalytic rate.
3. It is rather slow
B. Isoenzymes
• Isozymes Provide a Means of Regulation
Specific to Distinct Tissues and
Developmental Stages
• Differential expression of isozymes
• LDH (for example)
• Preferential substrate affinity
C. Compartmentalization of enzymes
Substrates and cofactors within the cell are also
compartmentalized
Examples:
• Enzymes of glycolysis are located in the cytoplasm
• Enzymes of citric acid cycle are in the mitochondria
• Hydrolytic enzymes are found in the lysosome
but the release of these suicide enzymes during
apoptosis is an on/off switch than a true regulation.
D. Proteolytic activation
Activation of a zymogen.
•
Some enzymes are secreted as inactive
precursors, called zymogens.
•
•
•
•
Pancreatic proteases - trypsin, chymotrypsin,
elastase, carboxypeptidase are all synthesized
as zymogens - trypsinogen, chymotrypsinogen,
proelastase and procarboypeptidase
Clotting factors are also part of a proteolytic
cascade
Hormone peptides (Proinsulin
Insulin)
an on/off switch more than regulation.
E. Covalent modification
Reversible phosphorylation
Phosphorylation is the most common
type of modification
Two important classes of enzymes are:
– Kinases
Add a phosphate group to
another protein/enzyme (phosphorylation)
•
transfer of phosphoryl group from ATP to -OH
group of serine, threonine or tyrosine
– Phosphatases
Remove a phosphate
group from a protein/enzyme
(dephosphorylation)
1- Control of [S]
• Concentration of substrate and product
also control the rate of reaction, providing
a biofeedback mechanism.
• Usually,
0.1Km<[SPhysiology]<10km
Mild changes
in [S]
Change in enzyme
activity
Homotropic effectors – substrate itself
(binding at different site than the active site)
affects enzyme activity on other substrate
molecules. Most often this is a positive effector.
2- Product inhibition
• Enzyme is reversibly inhibited by the product.
Example: hexokinase - first reaction in glycolysis,
hexokinase is inhibited by glucose-6-phosphate (G6P, the product)
glucose + ATP
glucose-6-phosphate + ADP
_
Why?
As v approaches Vmax, the product becomes significant, and can
compete with the substrate for the enzyme
The product becomes a competitive inhibitor and slows down activity
of the enzyme.
3- Negative Feedback control
(End product inhibition)
• Final product of a metabolic sequence feeds-back negatively on
early steps
• In feedback inhibition, there is a second binding site on the enzyme
where the inhibitor binds, so that the inhibitor is not necessarily
similar in structure to the substrate.
Enz 1
A
_
Enz 2
B
Enz 3
C
Enz 4
D
E
What happens?
•
•
•
As the need for product E decreases, E will accumulate
Most efficient to inhibit at first step of the pathway, slow the first
reaction so intermediates do not build up
An increase in the concentration of E, leads to a decrease in its rate
of production of E.
Regulation of the metabolism, feed-back inhibition by
the final product - end product inhibition
1. Simple feed-back inhibition. The final
product (E) inhibits the step from A to B.
2. Co-operative feed-back inhibition.
Both final products (D, E) inhibit the first
step of their own synthesis together.
3. Multivalent feed-back inhibition.
4. Inhibition at a ramification of a
biosynthesis pathway (sequential
inhibition)
4- Positive Feedforward control
• Earlier reactants in a metabolic sequence feedforward positively on later steps.
+
If A is accumulating, it
speeds up downstream
reactions to use it up.
+
Metabolism involves
the complex integration
of many feedback and
feedforward loops.
4- Allosteric control
• Allosteric activator stabilizes active "R" state
– shift the graph to the left
• Allosteric inhibitor stabilizes less active or inactive "T" state
– shift the graph to the right
Multi reactant enzymes reactancy
• Published by W. W. Cleland in1963
• Nomenclature is based on number of
substrates and products in the reaction.
• Reactancy: the number of kinetically
significant substrates or products and
designated by syllables Uni, Bi, Ter, Quad.
AP
Uni Uni
AP+Q
Uni Bi
A+BP+Q
Bi Bi
A+B+CP+Q+R+S
Ter Quad
Multi reactant enzymes mechanism
Sequential - if all S add to E before any P
are released.
– Sequential ordered - if S add in an obligatory
order (two on; two off).
– Sequential random - if S do not add in
obligatory order (two on; two off).
Ping Pong - If one or more S released
before all S bind
• (one on, one off; one on, one off);
• Note: there is some sort of modified enzyme
intermediate (often covalent intermediate).
Random sequential (example)
Ordered sequential (example)
Ping pong or double displacement
mechanism
Double displacement (example)
Other enzymes
• Some ribonucleoprotein enzymes have
been discovered.
– The catalytic activity is in the RNA part.
– They are called Ribozymes
• Catalytic antibodies are called Abzymes.
• In competitive inhibition the inhibitor is similar in structure
to the substrate and binds to the enzyme at the active
site, preventing the substrate from binding. In feedback
inhibition, the inhibitor binds to the enzyme at a site
away from the active site and acts by altering the shape
of the enzyme in such a way that it is incapable of
catalyzing the reaction. Feedback inhibition is a natural
part of the process by which an organism regulates the
chemical reactions that take place in its cells. In that
sense it is done on purpose. Competitive inhibition
usually involves inhibitors, commonly called poisons, that
do not belong in the cell.
•
Enzymes may be regulated by
1..
2.Competitive product inhibition and
allosteric regulation (fastest).
• Many enzymes are inhibited by either their
products, or by other chemicals, often those
from further down a metabolic pathway.
• Such enzymes may be 'gatekeepers' to a
specific branch of metabolism,
Biochemical reaction
When the chemical reaction occurs in a biological
system it is called a biochemical reaction.
Biological system:
Mild conditions
Simultaneous presence of different substances
Specific needs in specific times
Catalyst
A
Reactant
B
Product
What are the biocatalysts ( Enzymes)?
Proteins & RNA ???
Basic enzyme reaction
Catalyst
A
Product
Reactant
Enzyme
S
Substrate
S+E
ES
P
Product
ES (Enzyme-substrate complex)
P+E
k1
S
B
E
k-1
Binding step
S
E
k2
P
Catalytic step