Enzyme notes biochemistry Satyanarayan.pdf

enzyme notes

1. Enzymes
Definition, Classification-IUBMB, Factors affecting
Enzyme activity, Enzyme kinetics, Inhibition of
activity, Regulation of activity, Measurement of
Enzyme activity, Isoenzymes, Enzymologyin medicine
MBBSI, 024
ArunPandeya

2. Definition
•biological catalysts that increase the velocity of
chemical reactions
•no change in overall process
•protein in nature. [except-Ribozymes]
•having the suffix –‘ase’(exception-pepsin, trypsin, etc.)
•more than 3000 enzymes

3. Energy of Activation
(E
A)
•Enzymes lower E
A
•amount of energy
required by reacting
molecules to
undergo the
chemical reactions.
Enzyme catalyzed reactions have lower E
A. But, no
difference in net energy between two reactions.

4. Nomenclature
1.Recommendedname:
•Mostoftheenzymesarenamedbyaddingthesuffix-
aseonthesubstrateofthereaction,eg.
•Maltase:changesMaltoseintoGlcandGlc
•Urease:convertsureaintoNH
3&CO
2
•Pyruvatecarboxylase
•Trivialnames:givesnohintsontheenzymicreactions.
–eg.pepsinandtrypsin,etc.
2.Systemicname:sixmajorclasses-

5. •Enzyme binds its substrate on its active site to
form E-S complex and lastly the product.
E + S ⇄ES→E+ P
Mechanism of Enzyme Catalysis

6. Enzyme Substrate Binding
Lock-and-Key Model (Emil Fischer)
Active site of the unbound enzyme is complementary
in shape to the substrate

7. Enzyme Substrate Binding
Induced-Fit Model (Koshland'sInduced Fit Theory)
•enzymechangesshapeonsubstratebinding.
•activesiteformsashapecomplementarytothe
substrateonlyafterthesubstratehasbeenbound.

8. Properties of Enzyme
•Enzymes are biological catalysts and are protein in nature
•Enzyme molecules contain active site, which bind the
substrate to form product.
•Efficiency-Enzyme catalyzed reactions are million times
faster than uncatalyzedreactions.
[turn over number= 10
2
–10
4
s
-1
(substrate transformed/sec]
•Specificity-Enzymes are highly specific catalyzing only one
type of chemical reactions.
•Regulations-Enzyme activity can be regulated, i.e.
Enzymes can be activated or inhibited.

9. Enzyme Classification: Enzymes can be classified into six
major classes.
S.no.Classes of
Enzyme
Examples
1 OxidoreductaseAcyl CoA dehydrogenase,HMG
CoA reductase
2 TransferaseHexokinase,Aminotransferase
3 Hydrolase Digestiveenzymes (Amylase,
Lipase)
4 Lyase HMG CoA Lyase, Aldolase
5 Isomerase PhosphoglucoseIsomerase,Triose
phosphate isomerase
6 Ligase Glutamine synthetase,Pyruvate
carboxylase

10. Enzyme Classification
1.Oxidoreductases:
catalyze the oxidation of
one substrate with
simultaneous reduction of
another substrate.
e.g. AcylCoAdehydrogenase
Glyceraldehyde-3-P
dehydrogenase

11. 2. Transferases:
transfer a functional
group (e.g. a
phosphate) from
one molecule
(donor) to another
(acceptor).

12. 3. Hydrolases: catalyze the hydrolysis of a chemical
bond by adding water.
eg. All digestive enzymes (Amylase, Lipase and
Trypsin) etc.

13. 4. Lyases:
•catalyze the breaking
of various chemical
bonds by means
other than
hydrolysis and
oxidation.
•eg. Aldolase, HMG
CoA Lyase

14. 5. Isomerases:
•catalyze the
interconversionof
isomers.
•e.g. Triosephosphate
Isomerase,
Phosphoglucose
isomerase.

15. 6.Ligases: catalyze the joining of two molecules with the
involvement of ATP (ATP dependent condensation of
molecules.eg. PyruvateCarboxylase, Glutamine
Synthetase).

16. Factors affecting
enzyme activity
The contact
between enzyme
and substrate
determine enzyme
activity

17. The important factors that influence the velocity
of the enzyme reaction are
1.Concentration of enzyme
2.Concentration of substrate
3.Effect of temperature
4.Effect of pH
5.Effect of product concentration
6.Effect of activators

18. 1. Concentration of enzyme:
•Rate or velocity (V) of a
reaction is directly
proportional to the enzyme
concentration, when
sufficient substrate is
present.
•This property is used in determining the level of particular
enzymes in plasma.

19. 2. Effect of concentration of substrate
on increasing the substrate concentration, the velocity
of the enzyme reaction gradually increases within the
limited range of substrate levels.

20. 3. Effect of temperature
•velocity of reaction
increases with increase in
temperature up to a
maximum & then declines
•The temp at which velocity
of enzyme is maximum is
known as optimum
temperature.
Temperature coefficient (Q10): the factor by which the rate of
reaction is increased when temperature rises in 10°C

21. 4. Effect of pH
Each enzyme has an
optimum pH at which the
velocity is maximum.
Below and above this pH,
the enzyme activity is
much lower and at
extreme pH, the enzymes
totally inactive.

22. 5. Effect of activators
•some of the enzymes require certain cofactors
(inorganic ions such as Mg
2+,
Zn
2+
, etc) and some
Co-enzymes (such as vitamins) for their activity.
•eg. Vitamin C (ascorbic acid) is the activator of 7-α-
hydroxylase which leads to increased degradation
of cholesterol forming bile salts.
Thus, vitamin C is the activator of the enzyme.

24. 5. Effect of product concentration
•Accumulation of products generally decreases the
enzyme velocity.
•eg. Accumulation of bile salts inhibits 7-α-
hydroxylasewhich leads to decreased synthesis of
bile salts.

25. Terminologies
•Holoenzyme: functional enzyme having protein part
(Apoenzyme)and non-protein (Cofactor or Coenzyme).
•Coenzyme: small, additional factor which assists enzyme
activity. These are the organic compound and mainly are
derived from B group of vitamins.
•eg. Vitamin C is the coenzyme for 7-α-Hydroxylase
•Cofactor: these assist enzyme activity and are derived
from minerals. These are metal ions such as Zn, Cu etc.
•eg. Cu is the cofactor for Tyrosine hydroxylase

26. Holoenzyme
Small additional factor which assist
enzyme activity, k/a Co-factor
Cofactor
If these are inorganic
metal ions (mineral
derived)
Apoenzyme+
Functional enzyme Protein
Cofactor
Non-Protein
Coenzyme
If these are organic
compound (vitamin
derived)
If the non-protein part is tightly (covalent) bound to
apoenzyme, it is known as prosthetic group

27. Coenzymes from B group of Vitamins
Example of Coenzymes Vitamins
Thiamine Pyrophosphate (TPP) Thiamine (B
1)
Flavinmononucleotide (FMN or FAD) Riboflavin (B
2)
Nicotinamideadenine dinucleotide
(NAD
+
or NADP
+
)
Niacin (B
3)
(Coenzyme A or CoA) Pantothenicacid
Tetrahydrofolate(THF) Folic acid

28. Enzyme kinetics:
Study the rate of enzyme catalyzed reactions
•rate of reaction is assessed by the rate of change of
substrate to product per unit time
•Knowledge of the enzyme catalysis is a prerequisite for
the design of inhibitors (drugs) against a certain enzyme

29. Michaelis-MentenModel
•Enzymereversibly combines with its substrateto
form an ES complex that subsequently yields
product
Where,
E= enzyme; S= substrate; ES= Enzyme substrate complex;
P= product; and k
1k
-1k
2are the rate constants
E + S ES P + E
k
2
k
-1
k
1

30. Michaelis-MentenEquation (simplified form)
v =
v
max[S]
[S] + K
M
if [S] >> K
M then v = v
max
if [S] = K
M,then v =
v
max
2
ThereforeK
M can be viewed as the substrate concentration
with half-maximal velocity.

31. Michaelis-MentenEquation-Conclusion
•describes how reaction velocity varies with
substrate concentration.
•reflects the affinity of the enzyme for that substrate.
•K
Mis numerically equal to the substrate
concentration at which the reaction velocity is
equal to 1⁄2 Vmax.

32. Km does not vary with the [E]
•Large Km: reflects a low affinity of enzyme for
substrate [↑S is needed to half-saturate the
enzyme].
•Small Km: reflects a high affinity of enzyme for
substrate, [↓S is needed to half-saturate the
enzyme].

33. Fig. Effect of substrate concentration
on reaction velocities for two enzymes:
E1 with a small Km &
E2 with a large Km
Small Km (K
m1)= high
affinity. Because a low
concentration of
substrate is needed to
half-saturate the
enzyme-
i.e. to reach a velocity
which is 1⁄2 V
max

34. Relationship of velocity to [S]
•[S] is much less than Km, the velocity of the reaction
is approximately proportional to the substrate
concentration [first order].
•[S] is much greater than Km, the velocity is constant
and equal to Vmax.
[rate of reaction is then independent of substrate
concentration, and is said to be zero order].

35. Michaelis-Menten plot
v
[S]
v
max
K
M
v
max
2
Effect of substrate concentration
on reaction velocity
At Low [S], velocity
of reaction is
proportional to [S]
At high [S], velocity is
independent of [S]

36. Lineweaver-Burk plot
•When v is plotted against [S], it is not always
possible to determine when V
maxhas been achieved
•However, if 1/v is plotted versus 1/[S],a straight line
is obtained.
•This, a double-reciprocal plotcan be used to
calculate K
mand V
max, as well as to determine the
mechanism of action of enzyme inhibitors.

37. Lineweaver-Burke
Plot
Michaelis-MentenEquation
Lineweaver-Burke
Equation

38. Use of Lineweaver–Burk plot
•widely used to determineK
mandV
maxin
enzyme kinetics
•gives a quick, visual impression of the
different forms of enzyme inhibition.
•competitive
•non-competitive

39. Inhibition of Enzyme activity
Inhibitor:
Any substance that can diminish the velocity of
an enzyme-catalyzed reaction.
Two types:
i.Irreversible inhibitors &
ii.reversible inhibitors

40. Irreversible inhibitor
Binds tightly (mostly covalently) at or near the active
site of an enzyme, & form a stable complex
No dissociation of enzyme and I & enzyme is
permanently inactivated. (or slowly reactivated-hrs or
days for reversal)
•eg. Aspirincovalently modifies the enzyme cyclo-
oxygenase, thus, reduces the synthesis of inflammatory
signals
•Penicillincovalently binds at active site of transpeptidase
and modifies it thereby preventing the synthesis of bacterial
cell walls
Inhibitor may or may not resemble the substrate

42. Suicide inhibition
•Irreversible inhibition of enzyme by a substrate
analogue that form reactive species upon enzyme
catalyzed reaction
•eg. Allopurinol, the suicide inhibitor of xanthine
oxidase

44. Reversible inhibitor
•The inhibitor forms a loose, dissociable complex (EI)
with the enzyme
•Catalytic activity of EI complex is lower than that of
the enzyme alone.
•Hence, substrate transformation decreases after
addition of the inhibitor.
•Reversible inhibitor may be:
i.Competitive
ii.Non-competitive
iii.Uncompetetive

45. Competitive inhibition
1.inhibitor resembles
structurally with the actual
substrate.
2.inhibitor binds reversibly
to the substrate binding
site & competes with the
substrate for that site
eg.
•Inhibition of HMG CoA
reductaseby statins
•Inhibition of the succinate
dehydrogenaseby
malonate

46. Role of HMG CoA Reductase
HMG CoA (6C)
Mevalonate(6C)
HMG CoA reductase Rate Limiting
Cholesterol
Statin

47. Competitive inhibition: Effect on V
maxand on K
m
Effect on V
max:
•The effect of a competitive inhibitor is reversed by
increasing [S].
•At a sufficiently high substrate concentration, the
reaction velocity reaches the ‘V
max’
Effect on K
m
•in the presence of a competitive inhibitor, more
substrate is needed to achieve 1⁄2 V
max.

48. V
maxis the same in the
presence of a
competitive inhibitor
Km is increased in
presence of
competitive inhibitor
↑[S]-velocity becomes V
max
↑[S]-required to achieveV
max/2
Km-increased by competitive inhibitor
Competitive inhibition

49. Noncompetitive inhibitor
•A noncompetitive inhibitor can bind
to both free enzymeor ES complex
•Inhibitor binds at site distinct from
active site altering the shape of the
enzyme such that its catalytic activity
is reduced or lost.
non-competitiveinhibitioncanoftenbereversedbyexhaustive
dialysisoftheinhibitedenzyme

50. Noncompetitive inhibitor
•The binding of the heavy metal (Pb) on the enzyme
Ferrochelatase
•Certain insecticidesbind covalently on the
acetylcholinesterase, thus, show the neurotoxic
effect

52. Regulation of Enzyme Activity
•Enzyme activity can be regulated by
i.Allostericeffectors
ii.Covalent modification
iii.Altered rates of enzyme synthesis or
degradation

53. AllostericEffectors
•bind noncovalentlyto the enzyme
•can alter the affinity of the enzymefor its substrate or
modify the catalytic activity of the enzyme, or both.
•Effectors my be-Positive or Negative
•Effectors are of two types:
–Homotropic& heterotropiceffectors
•Act on the committed step of the metabolic pathway.

54. Homotropiceffectors
•the substrate itself serves as an effector
•Presence of a substrate molecule at one site on the
enzyme enhances the catalytic properties of the
substrate-binding sites (co-operativity).
•Activation of Aspartatetranscarbamoylaseby ATP
(pyrimidinebiosynthesis).

55. Heterotropiceffectors
•The effectormay be different
from the substrate
•eg. Inhibition of HMG CoA
Reductaseby Cholesterol
(product inhibition)
•eg. Inhibition of PFK-1 by citrate

56. Regulation of enzymes by
covalent modification
•by the addition or removal of
phosphate groups to/from
the enzyme.
•Phosphorylationand
dephosphorylationis done by
•Protein Kinase
•Protein Phosphatase
•Eg. Glycogen phosphorylase is
active in Phosphorylatedform.
Glycogen synthase is active in
dephosphorylatedform

57. Induction and repression of enzyme synthesis
•cells can also regulate the amount of enzyme
by either increasing (induction) or decreasing
(repression) the enzyme synthesis, leading to
an alteration in the total population of active
sites. eg.

58. Increase in blood Glucose level
Increased release of Insulin from
pancreatic β-cell
increase in the synthesis of enzymes
involved in glucose metabolism

59. Enzymes In Clinical Diagnosis
•Enzymologyin medicine
•Measurement of Enzyme activity
•Isoenzymes

60. Enzymologyin Medicine
•Some enzymes which are present in blood/plasma of
normal individuals at a very low levels, they have no any
known function in plasma are known as non-functional
plasma enzymes.
•Presence of these enzymes in plasma is due to cell
turnover.
•However, increased levels of such enzymes in plasma
suggest an increased rate of tissue destruction, thus can
provide diagnostic information.

61. •Normal level of intracellular enzymes in plasma: Indicates
Normal cell turn over.
•Increased plasma levels of these enzymes: indicate cell
damage, thus provides diagnostic importance.

62. Sources of enzymes
•Enzymes are generally synthesized by cells and are
released into circulation.
•eg. ALT-synthesized by liver cells.
AST-synthesized by cardiac cells.
Amylase-synthesized by pancreas and
salivary gland.
Trypsin and Chymotrypsin-by pancreas.

63. Clinical significance of Enzymes
Enxym
es
Normal
range (U/L)
Tissue source Diagnostic importance
ALT 8-40 Liver, cardiac , skeletal
muscle,
Hepaticdiseases
AST 8-40 Cardiac tissues,
erythrocytes, Liver
Cardiac disease,hemolysis,
hepatic carcinoma
CK 15-100; 10-
80
Muscle, Heart, BrainAMI, Muscular dystrophy
LDH
180-360U/L
Heart,RBC, Muscle AMI
ALP 40-125 Bone, Liver, BiliarycellsBonedisease, Hepato-biliary
obstruction
GGT 6-45; 5-30Liver, Biliarycells Hepato-biliaryobstruction,
alcoholics
Amyla
se
28-100 IU/LPancreas, Parotid glandAcutepancreatitis, parotitis
Lipase<40 U/L Pancreas Acute pancreatitis

64. Isoenzymes
•Different forms of the same enzymes catalyze similar
type of reactions but present on different tissue
locations.
•Differ in amino acid sequence, hence, differ in physical
properties
Example:
•Isoenzymesof CreatineKinase(CK):-CK1, CK2 and CK3
•Isoenzymesof Lactate Dehydrogenase(LDH ):-LDH1-
LDH5

65. Isoenzymes of CK and their normal ranges
1.CK-BB or CK1(brain type)
2.CK-MB or CK2 (hybrid/ cardiac type)
3.CK-MM or CK3 (muscle type)
•Cardiac tissues contain significant quantities of
CK-MB. So injury to cardiac tissues result in
elevation of CK-MB.

66. Iso-enzymeTissue Disorders
LDH-1 (HHHH) Heart, RBC MI
LDH-2 (HHHM) RBC, Heart Hemolytic anemia
LDH-3 (HHMM) Lungs, PancreasPulmonary
embolism,
pancreatitis
LDH-4 (HMMM) Liver Hepatic injury
LDH-5 (MMMM) Skeletal muscleSkeletal muscle
injury