Malaysia Chinese Independent School Senior 1 Biology (English)

1. 3.2 Enzymes

2. Enzyme 酶
• from Greek en- ‘within’ + zumē ‘leaven’ 酵.
• Name of a protein generally ends with –ase, e.g. amylase, ATPase etc.
• Most enzymes are proteins.
• Enzymes accelerate, or catalyze 催化, chemical reactions.
• As a catalyst, the quantities
and the qualities of the
enzymes do not change after
reaction.
• Reactions that are catalyzed by
enzymes are called the
enzyme-catalyzed reactions.

3. Enzyme as a catalyst

4. 3.2.1 Properties
of enzymes

5. Properties of enzymes
1. Enzyme as biological catalyst
2. Enzymes can be used repeatedly
3. A small amount of enzyme is required
4. Enzyme is a kind of protein
• affected by temperature and pH value of
the environment.
• Each enzyme contain a optimum
temperature and pH value which its activity
is the highest.
5. Enzymes possess specificity
• Enzyme contains specific subtrate 底物
• Determined by the amino acid sequence of
the enzyme (different type of R-groups)
The enzyme glucosidase converts sugar maltose to
two glucose sugars. Active site residues in red,
maltose substrate in black, and NAD cofactor in
yellow.

6. Enzyme speficifity example: a glycolytic
enzyme, fructose-1,6-bisphosphate aldolase
A B C

7. Top S. lycopersicum ‘Moneyberg’ (red tomato) and S.
chmielewskii IL1b (pink tomato).
Left Colour diversity in kiwi fruits.
Presence or absence of chlorophyll, carotenoid and
anthocyanin compounds in different fruit tissues determines
the colour of the fruits. Those pigments were synthesized with
the help of multiple enzymes.

8. Quiz
• An enzyme or any other catalyst essentially works by
A) making a reaction more endergonic.
B) making a reaction more exergonic.
C) lowering the activation energy of a reaction.
D) increasing the net energy yield form a reaction.

9. Quiz
• An enzyme has all of the following properties except
A) it increases the rate of a chemical reaction.
B) it is not permanently changed by the reaction it catalyzes.
C) it increases the energy yield from a chemical reaction.
D) it does not change what the products of a chemical reaction will
be.

10. 3.2.2
Mechanism of
enzyme
catalysis

11. Structure of enzyme
• Enzyme contains an active site 活性部位, which usually a cleft or
depression, to which its substrate 底物 can bind.
• E.g. the active site of lactase binds to lactose, and lactase cleaves
lactose into glucose and galactose.

12. Quiz
• On the image, which letters
represent the enzyme, the
subtrate and the products to the
reaction?

13. Enzyme-substrate complex
• When a subtrate binds to the active site of an enzyme, temporary
bonds, are formed between the subtrate and the enzyme.
• Temporary bonds a generally ionic bonds or van der Waals forces
(hydrogen bonds, London dispersion forces, and dipole-dipole
interactions).
• This combined intermediate structure is termed the enzyme-
substrate complex.

14. Examples of enzyme activity:
protease and lipase

15. Mechanism of enzyme-substrate complex
• There are few of hypotheses for the mechanism of enzyme-substrate
complex, including

16. "Lock and key" model
• Proposed by Emil Fischer in 1894.
• The active site on the surface of the
enzymes, with its shape
complementary to that of the
substrate.
• The enzyme acts as a key, while
substrate act as the lock.
• This hypothesis explains:
• Specificity of enzyme.
• The structure of enzyme remains
unchanged after reaction.
• A change in the structure of the enzyme
will lead to the subtrate not be able to
fit into the enzyme.
• This model, however, fails to explain
the stabilization of the transition state
that enzymes achieve.

17. Induced fit model
• Daniel Koshland suggested this model in 1958, as a modification to
the lock and key model.
• When an enzyme combines with a substrate, its active site undergoes
certain conformation change 构象改变 in the structure to make the
fit more precise.

18. Quiz
• The three-dimensional shape of an enzyme molecule is critically
important to its ability to catalyze chemical reactions. This
characteristic three-dimensional shape is called its
A) primary structure.
B) conformation.
C) substrate.
D) confirmation.

19. Conclusion
• Enzyme is a biological catalyst that can be used repeatedly.
• All small amount of enzyme is required for each metabolism process.
• Enzyme is a kind of protein that is affected by temperature and pH value of
the environment.
• Enzyme contain specificity, which each enzyme only catalyzes a reaction.
• When a subtrate binds to the active site of an enzyme to form an enzyme-
subtrate complex.
• In the ‘lock and key’ model, the active site on
the surface of the enzymes, with its shape
complementary to that of the substrate.
• In the induced-fit model, when an enzyme
combines with a substrate, the active site of
an enzyme undergoes certain conformation
change in the structure to make the fit more
precise.

21. Hyperthermophilic enzymes are enzymes synthesized by hyperthermophiles
(bacteria and archaea with optimum growth temperatures of >80°C) are typically
thermostable. Thermus aquaticus produce the heat-resistant enzyme Taq DNA
polymerase, which is used in the polymerase chain reaction (PCR) DNA
amplification technique.
Jelly made from collagen,
which is a type of protein.
Pineapple contains
bromelain, a type of
proteases that break down
protein molecules. Here it
shows that a small
amount of fresh pineapple
is enough to stop the jelly
solidification process.
Tinned pineapple was
cooked before tinning,
hence the bromelain,
along with other enzymes
inside the pineapple, was
denatured. Hence, tinned
pineapple cannot stop the
solidification process of
jelly.

22. Quiz
• In the previous slide, only a small amount of pineapple is enough to
stop the solidification of the jelly. Which properties of the enzyme is
application to this observation?
a. Enzyme as biological catalyst
b. Enzymes can be used repeatedly
c. Only a small amount of enzyme is required
d. Enzyme is a kind of protein
e. Enzymes possess specificity

23. 3.2.3
Factor affecting
the catalytic
action of
enzymes

24. Factor affecting the catalytic action of
enzymes
• The catalytic rate of an enzyme
will also be affected by the
concentration of the enzyme
and the concentration of the
substrate.
• Enzyme is a protein. Therefore
the effectiveness of the enzyme
can be influence by
environment factor such as pH,
temperature, presence of other
molecules etc.
• Functions of enzymes may be
restrained by inhibitors.
A. primary structure; B. C. secondary structure; D. tertiary
structure; E. quaternary structure.

25. Concentration 浓度 of the enzyme
• When other factor remain
constant, and there is an
abundant of subtrate, the rate
of reaction is directly
proportional 正比 to the
amount of enzyme.

26. Quiz
• Which is the slowest
way to produce a
certain amount of
product?
a. With 2X enzyme
b. With 1X enzyme
c. With no enzyme

27. Concentration of the substrate
• When other factor remain constant, for
a given amount of enzyme, the rate of
reaction increases with increasing
substrate concentration up to a point,
called the point of saturation 饱和.
• Above the point, any further increase
in substrate concentration produces no
significant change in reaction rate, i.e.
the rate of reaction reaches a plateau
平稳时期，稳定水平； 停滞期.
• This is because the active sites of the
enzyme molecules at any given
moment are virtually saturated with
substrate, i.e. they are all in use.
• The enzyme/substrate complex has to
dissociate before the active sites are
free to accommodate more substrate.

28. Quiz
• Substrate concentration increases the rate of an enzymatic reaction
up to a certain point, but then has no further effect and the reaction
rate levels off. This is because
A) excess product is not released from the active site.
B) accumulation of end product shuts down the reaction.
C) excess substrate makes the enzymes change conformation.
D) all the active sites are saturated with substrate molecules.

29. pH value
• Each type of enzyme has a particular pH
value at which its catalytic action is the
highest.
• This pH value is the optimum pH of the
enzyme.
• Most enzyme has an optimum pH
around pH 7.

30. Why pH 7?
• The optimum pH of an enzyme is
correlate with the location of its
activity.
• Mammalian cytoplasm and nucleus
has a pH ~7.3.
• The optimum pH varies for each
enzyme.
• maltase 麦芽糖酶 – pH 7.0
(in the small intestine pH 6 - 8)
• pepsin 胃蛋白酶 – pH 1.8
(in the stomach pH 1.5 - 3.5)
• trypsin 胰蛋白酶 – pH 8.5
(in the pancrease pH 8.6)
• Animal amylase 淀粉酶 – pH 6.2 - 7.0
(in the saliva pH5 - 8)

31. How pH value affects the function of enzyme
• Several amino acids contain side chains with
functional groups that can readily gain or lose a
proton.
• Changes in pH would lead to a change in the
charge of the amino acids, leading to formation
and breakage of bonds and interactions among
amino acids.
• Hence, a change in pH value may change the
shape of an enzyme and its effectiveness.
变性

32. Quiz
• What is the optimal pH for the enzyme
Salivary Amylase?
A. 2
B. 7
C. 9
D. 5
E. 11

33. Temperature
• As temperature increase, the enzyme
catalytic rate increase until the optimum
temperature is reached.
• Then the enzyme catalytic rate decreases
as the structure of the enzyme starts to
break down under high temperature.
• optimum temperature for human enzyme
is usually around human body
temperature 37.5 oC.
• The activity of enzyme is generally
inhibited at 50 oC.

34. Denaturation
• The process of protein loses its structure
is called denaturation.
• Denaturation is (generally) permanent.
(Top) The protein albumin in the egg white
undergoes denaturation and loss of solubility
when the egg is cooked.
(Bottom) Paperclips provide a visual analogy
to help with the conceptualization of the
denaturation process.

35. Quiz
• The rate of an enzymatic reaction increases as the temperature rises,
up to a point. Above 40°C or so, however, the reaction rate begins to
decline because the
A) enzyme changes shape at higher temperatures.
B) substrate changes shape at higher temperatures.
C) enzyme gets used up faster at temperature above 40°C.
D) substrate gets used up faster at temperatures above 40°C.

36. Twofold effects of
temperature
• As the temperature rises, molecules
have more and more kinetic energy.
This increases the chances of a
successful collision and so the rate of
reaction increases
• Above a certain temperature the
enzyme structure begins to denature
as the intra- and intermolecular bonds
are broken as the enzyme molecules
gain even more kinetic energy.

37. Quiz
• What is the optimal temperature
for Enzyme GlenKappie?
A. 0 degrees
B. 43 degrees
C. 60 degrees
D. 73 degrees
E. 88 degrees

38. Conclusion
• Factors that affects the catalytic rate of enzymes includes the
concentration of the enzyme, the concentration of the substrate,
pH, temperature etc.
• The rate of reaction is directly proportional to the amount of enzyme.
• The rate of reaction increases with increasing substrate concentration until it
reaches a plateau after the point of saturation (of the active site).
• Each type of enzyme has a particular pH value (the optimum pH) at which its
catalytic action is the highest.
• The enzyme catalytic rate increase with increasing temperature until the
optimum temperature is reached, then the enzyme catalytic rate decreases
as the enzyme starts to denature.
• Functions of enzymes may be restrained by inhibitors.

39. zymase
C2H5OH
diastase
Carbon dioxide produced from the
fermentation process rises the dough,
while the ethanol gives the bread flavor.
When the yeast cells die, they release high
quantities of a protease which snip protein
strands, and in large die-offs result in soft,
sticky dough, less baked volume and a
coarse crumb, but in smaller die-offs,
increase dough extensibility and baked
volume.
Salt inhibit the yeast, so less CO2 is
produced and the volume of the bread
stayed low.
How did salt inhibit the yeast?

41. 3.2.3.1
Inhibition of
enzymatic
activity

42. Inhibition 仰制作用 and inhibitors 仰制剂
• Enzyme can be inhibited, or restrained
by unflavourable environmental
conditions or by the presence of other
molecules.
• Inhibitors are substances which alter
the catalytic action of the enzyme and
consequently slow down or stop
catalysis.
• There are two types of inhibitors:
• Competitive inhibitor 竞争性仰制剂
• Non-competitive inhibitor 非竞争性仰制
剂

43. Competitive inhibition 竞争性仰制作用
• The competitive inhibitor
closely resembles the
structure and geometry of
the substrate.
• Binding 粘合 of the
competitive inhibitor to the
active site on the enzyme
prevents binding of the
substrate.
• The amount of enzyme
inhibition depends upon the
inhibitor concentration,
substrate concentration, and
the relative affinities of the
inhibitor and substrate for
the active site.

44. Example: Sildenafil – compete with cGMP
• Nitric oxide binds to receptors
on smooth muscle cells to signal
for an increase in cyclic
guanosine monophosphate
(cGMP), leading to vasodilation
血管扩张.
• An enzyme, phosphodiesterase
type 5 (PDE5) degrades cGMP,
stopping vasodilation.
• Sildinafil binds to the active sit
of PDE5, and cause cGMP to
accumulate.
Sildenafil
cGMP

45. Example: Cyanide – compete with oxygen
• A mitochondria produce ATP with an
electron transport chain, which moves
electron around the thylakoid membrane
to create electrochemical proton gradient
to drive the synthesis of ATP.
• The last enzymes involves in this process
is called cytochrome c oxidase (COX). It
transfers electrons to oxygen molecules,
converting a molecular oxygen to two
molecules of water.
• Cyanide has a higher affinity than oxygen
to the active site of the COX, thus rapidly
binds to COX, and inhibits the reduction
of oxygen.
cytochrome c oxidase

46. Non-competitive inhibition 非竞争性仰制作用
• A.k.a allosteric inhibition
• A noncompetitive inhibitor interacts
with the enzyme, but usually not at the
active site.
• A non competitive inhibitor changes
the shape of the enzyme and thus the
active site, so that the substrate can no
longer interact with the enzyme.
• Non competitive inhibitors are not
influenced by concentrations of the
substrate.

47. Example: penicillin
• Bacteria cell wall is formed by cross-linked
peptidoglycan using DD-transpeptidase (D-alanyl-
D-alanine carboxypeptidase).
• Penicillin binds to the bacterial enzyme DD-
transpeptidase.
• Without this enzyme bacteria can no longer make
new cross-links, all the while continuing to make
enzymes that hydrolyze (break-down) these links.
• This will cause holes in the cell wall to form and
eventually force the bacteria to shed most if not all
of its wall.
• The environment is generally hypotonic to the
bacteria, hence water will move into the bacteria
and the bacteria will lyse without a cell wall.
"R" is the variable group

48. Irreversible Inhibitors
不可逆仰制剂
• Irreversible Inhibitors form strong and
irreversible covalent bonds with an enzyme
and modify the basic structure of the enzyme
to the degree that it ceases to work or
denatured.
• Poisonous compounds (e.g. cyanide 氰化
物)and heavy metal ions (e.g. arsenic 砷,
lead 铅, mercury 汞) may kill an organism
when ingested.
Top: Lead paint was commonly used through the 1940's, and to some extent in
the 1950's.
Bottom: Human managed to reduce the arsenic concentration in cassava
through cultivation.

49. Conclusion
• Enzyme can be inhibited can inhibitors such as unflavourable conditions or
other molecules.
• Inhibitors are substances which alter the catalytic action of the enzyme and
consequently slow down or stop catalysis.
• The competitive inhibitor binds to the active site on the enzyme prevents
binding of the correct substrate.
• A non competitive inhibitor changes the conformation of the enzyme and
thus the active site, so that the substrate can no longer interact with the
enzyme.
• Irreversible Inhibitors such as poisonous compounds (e.g. cyanide) and
heavy metal ions (e.g. arsenic, lead, mercury) cause enzyme to ceases to
work or permanently denatured.

50. Quiz
• Why does the body need enzyme inhibitors?
A. To slow down or turn off reactions in the body
B. To make the body sleep
C. To speed up reactions in the body
D. To help digest food

51. Quiz
• Which type of inhibitor binds at the active site?
A. Competitive
B. Uncompetitive
C. Non-competitive
D. All of the answers are correct
E. None of the answers are correct

52. 3.2.4
Cofactors for
the enzyme-
controlled
reactions

53. Cofactor
• Some enzyme required non-protein
cofactors to function.
• Cofactors can be inorganic or organic.
• Inorganic cofactors are metal ions such as
magnesium 镁, zinc 锌, copper 铜, iron 铁
etc.
• Organic cofactors includes vitamins such
as vitamins B1, B2, B6, B12 and other
complex organic molecules called
coenzymes.

54. Example of cofactor
Iron in the Heme group as metal ion
cofactor
Coenzyme Q10 (ubiquinone) as a
component of the electron transport chain

55. Quiz
• Which of the following is a coenzyme?
A) Flavin adenine dinucleotide (FAD)
B) Amylase
C) Ca2+
D) Mg2+

56. 3.2.5 Proenzyme

57. Precursor of enzyme 酶原
• Proenzyme, a.k.a. zymogen, is the inactive
precursor of enzyme.
• Other enzymes, acids, or other small
molecules activate proenzyme by modifying
the configuration of the proenzyme to
reveal the active site.
• Proenzyme exists so that enzymatic
activities only occurs in suitable location or
conditions.
• Pepsinogen activated by hydrochloric acid in
the stomach to become pepsin that can
breakdown protein so the secretory cells
themselves will not be digested

58. Quiz
• Which of the following is the reason that trypsin is synthesized as
trypsinogen?
A. it is simpler to synthesize trypsinogen
B. trypsinogen is a more active enzyme than trypsin
C. trypsin would attack the body's natural proteins
D. trypsin is a larger molecule than trypsinoge

59. Conclusion
• Some enzyme required non-protein cofactors to function.
• Inorganic cofactors are metal ions such as magnesium, zinc, copper ,
iron etc.
• Organic cofactors includes vitamins and other complex organic
molecules called coenzymes.
• Proenzyme is the inactive precursor of enzyme, which has to be
activated by other enzymes, acids, or other small molecules to be a
functioning catalyst.