Topic: Enzymes

Specific Learning Objectives:

By the end of the chapter, you should be able to:

Define enzymes as biological catalysts.

Understand that enzyme-catalysed reactions may be either anabolic or catabolic.

Explain that enzymes possess the characteristics:

• All Most are proteins (e.g. ribozymes are made of nucleic acids)

• They increase the rate of a reaction without themselves being used up;

• Their presence does not alter the nature or properties of the end-products of a reaction;

• A very small amount of catalyst effects the change of a large amount of substrate;

• Their activity varies with extreme pH, extreme temperature, substrate and enzyme
concentrations;

• They are specific in action, that is, they generally catalyse only a single reaction.

• Explain that enzymes function as catalysts by reducing activation energy of reaction.

• Explain enzyme action in terms of the ‘lock and key’ hypothesis.

• Explain the mode of action of enzymes in terms of an active site, enzyme-substrate

complex, lowering of activation energy and enzyme specificity

• Explain enzyme action in terms of ‘induced-fit’ hypothesis.

• Investigate, Describe and Explain the effects of

o Enzyme concentration
o Substrate concentration
o Temperature
o pH
▪ on the rate of enzyme catalysed reactions

Follow the time course of an enzyme-catalysed reaction by measuring rates of formation of

products

Page 1 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
 ENZYME example of enzymes
), anolwhatthey
catalase decomposition
do
§
reaction

L
catalase
24202 > 21-1201-02
cmadeof proteins )
to
✗ detoxify,
BIOLOGICAL toxic Harmless produce
enzymes
CATALYST hydrogen 1-120402
¢
peroxide
decomposition make toxins
I spoke ,
made by liver
catalase catalyses the breakdown of toxic vateforbody
✓ Win peroxide into water and oxygen gas
Noun
.

infront
'
of catalyse
-
>
this is catalytic reaction
verb usually
an 012
enzyme
tnisisqnenzyme catalysed reaction
-

Naming Enzymes kinase → Adds ⑤

- -

ASE - e' 9- Amylase , catalase , sucrase phosphatase → Removes ①

sucrase
sucrose >
+ Glucose
enzyme fructose
M Hate
Maltose > Glucose + Glucose
enzyme
lactase
lactose > Glucose 1- Galactose
enzyme
 711101-911
enzymes are Breakdowns
inthesaliva
SALIVARY '

Physical Breakdown ✗ breaking

AMYLASE Breaking down →
bonds
Brought about by force -

large pieces
/
-

→
Breakdown starch to maltose from chewing action Offoodtosmaller
[ carbohydrates ] pieces
chemical Breakdown
Enzymes are biological catalysts
•

• Definition: Enzymes are biological catalysts that are mostly made up of protein. They
speed up the rate of a chemical reaction, while remaining chemically unchanged at the
end of the reaction. ↳ means nobondshovalent )
)
p, exception Ribozyme enzyme
(:
are broken :
intramolecular forces of
• Most enzymes are protein in nature, with the exception of ribozymes, which are made up attraction
of nucleic acids. can hold the 3D structure because of
:

intramolecular forces of attraction

• Enzymes work by lowering the activation energy of a chemical reaction, by providing an
alternative pathway for the chemical reaction to take place.
o Activation energy refers to the energy required to break the existing bonds in the
reactant molecule and begin the reaction. It is the minimum amount of energy required
to start a chemical reaction.
^
o By lowering the activation energy, a larger fraction of the reactant molecules can react
✗
at any one time, causing the reaction to occur more quickly.

n¥ÉFmu energy w/o a V5 b

.

iessenergy required
; union
-

✗
^
enzyme initial ^ Minimal amount
build-up of energy required
reactants takes DIFF b tostdrt looking at
, lotsot reaction
lowered energy

For A. E. take reference

energy v t
b- Difficult K
profile
Did
of

from reactants e. The hump .

Ata
a =
toqonievewp MIHA Vetobeableto
certain enzymes Draw , label
•

energy
level
activation energy

energy
Means reactants ✗
enzymes provide an Possess that
love,

alternative pathway for offing ,

amount of pdt
tiresome chemical reaction to take
.

energy at
place with lower
,
activation energy tnestart
.

•
Enzyme-catalysed reactions may be either anabolic or catabolic.
o anabolic reactions build complex molecules from simpler ones
Metabolic -1
Reactions o catabolic reactions breakdown complex molecules into simpler ones
o metabolism of an organism refers to the sum of all the anabolic and catabolic reactions
that occur within it.

chemical reactions

in the Body outside

body

Metabolic
Reactions

Catabolic Anabolic a
C Breakdown) ( Build )
I Exothermic] [ Endothermic] }
~ ,

CYM/Notes/IP Bio/Biological Molecules (enzymes)

Page 2 of 10
. chan_yu_mun@nygh.edu.sg (email me if you spot errors)

✓
Exothermic
Reaction
The energy level decreases in
an exothermic reaction. This is
because energy is given out
to the surroundings.
Referring
An energy level diagram
Endothermic
fee
shows whether a reaction is
to types exothermic or endothermic.
V5 .
of energy
It shows the energy in the
reactants and products, and
Exothermic profiles
the difference in energy
between them.
why Need A Reaction profile ?
A reaction profile includes the activation energy, which is the
minimum energy needed by particles when they collide for a
reaction to occur. The activation energy is shown as a 'hump' in ^
the line, which:
starts at the energy of the reactants
is equal to the difference in energy between the top of the
'hump' and the reactant ]→ ✓
The overall change in energy in a reaction is the difference
between the energy of the reactants and products.
Endothermic
Reaction
Explaining change in temp
The energy level increases in
an endothermic reaction. This
is because energy is taken in
from the surroundings.
 definition of enzymes

QUESTION

Enzymes are biological catalysts that

are mostly made up of protein. They
speed up the rate of a chemical
reaction, while remaining chemically
unchanged at the end of the reaction.

ANSWER
 Properties of enzymes

• Enzyme activity varies with pH, temperature, substrate and enzyme concentrations.

• Enzymes are required in small amounts

o enzymes increase the rate of a reaction without themselves being used up
o thus small amount of catalyst effects the change of a large amount of substrate

• Enzymes remain chemically unchanged at the end of chemical reactions that they catalyse
o enzymes can be reused, and are only needed in
small amounts
o Their presence does not alter the nature or
properties of the end-products of a reaction;

• Enzymes are substrate specific

o one type of enzyme generally catalyses only a single
reaction
o this is due to the specific 3D conformation of the
active site of the enzyme.

Mode of enzyme action

• The reactant that the enzyme acts on is known as the substrate.

• The conformation of the active site of the enzyme is complementary in shape to the
substrate.
o enzymes are specific in their action

• When the substrate fits to the active site of an enzyme, an enzyme-substrate complex is
formed.

• The catalytic action of the enzyme converts the substrate into product(s).

• The mode of enzyme action can be explained by the lock and key hypothesis or the
induced fit hypothesis.

cqnbelor >1 molecules (ignoreihlocloekeymodel )

( Reactants) ✗

substrate
moving into leave
active site
of the enzyme

snapeottneqctive
Represents siteiswmpiemen -

active site remains

Enzyme tolrytotneshape UNCHANGED
ottneenzyme

To
three -

or dimensional
ES complex
-

shape
-
structure
configuration
-

conformation

Page 3 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
 changes to the hypothesis *

•
various substrates can bind

G. active sitetotnesnolpeof
uanmoyldit
maybe enzyme 's
substrate
Lock and key hypothesis

• The enzyme is the lock, substrate is the key

• The active site on enzymes is where the substrate molecule can fit.

• The conformation of the active site is complementary to the shape of substrate, so only
the specific substrate molecules are able to fit into the active site.
substrate
• One type of enzyme can catalyse only one type of chemical reaction, as it is only able to -

bind to one type of substrate. does NOT react with substrate

✗ enzyme
/ specificity
I
only 't
enzyme can
fit in 't
label
substrate
-

the substrate
the enzyme
•

the Activeside
the products )
'

thees complex
-

show

shape of active
-

site before & • When the substrate binds to the active site of the enzyme, it forms an enzyme-substrate
after [should complex.
be unchanged ] o The substrate fits into the active site of the enzyme, like how a key fits into a lock.
'

shape of substrate
& product b4 • When the substrate is attached at the active site, the reaction is catalysed at the active
and after
site, and the substrate is converted to the products.

• At the end of the reaction, the products leave the active site of the enzyme molecule.

• The enzyme remains unchanged, and is free to catalyse another reaction.

• Not all experimental evidence regarding the mode of enzyme action can be explained by
the lock and key hypothesis (which implies the enzyme is a rigid model).

Page 4 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
 *
Allosteric sites

Induced fit hypothesis

only the
active site
changes ,

not the
whole
some parts enzyme
otthe substrate
makes transient
interaction
substrate
antimatter §
withtheoimino compared
to the enzyme
acid on the
active site

usually
cleft /
crevice

→ Usually
intheqctivesite buried
99s
.no/needn0tbeconsecutiveeXD0seaaotive
sites
• Sometimes the conformation of the active site is not exactly complementary to the shape
of the substrate.

• When the substrate binds to the active site of the enzyme and causes a change in the
conformation of the active site, this is known as induced fit.
o the substrate plays a role in the final shape of the enzyme, and that the enzyme
molecule is slightly flexible

• The proximity and orientation of the substrates in the active site, together with the strains
in their chemical bonds, facilitate the breaking of old bonds and the formation of new ones.
1 I

b. catabolic reactions
• Thus the substrate is converted into the products. a
anabolic reactions
• The enzyme does not change and is free to catalyse the reaction of more substrate
molecules into product molecules.

1- interact with side chains

sidechainl
1. substrates makesomecontactwitnaqsinactivesite
↳ recognise 'the substrate
"
'
g, group → Hora group
-

weak interaction
Rlrgroupl of covalently
bonded atoms
( can be hydrogen bonds) I
(carboxylic
R2 42N C -
COOH
acid )
-

AA Jervetohelp
-

R ,
☐ µ
position substrate I 11 I
(shows that Ñ °O° "
H
3D
4-
the c
HZN
Y
- - -

Amino Acid structure

-

configuration isimpt)
H H
smallest amino acid Glycine :

Iv
H
Peptide
Bond I
HZN -
c- COOH
Page 5 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
H
 How Ehvymes work
www.PBD -1011
compare
activesiteus rest
-

-
subunits of enzymes
citric Acid cycle →
howsnbÑaÑucts ,
f
vii. small
Engine
-
Why close proximity

Affected byptllevehtumpetc
proteins
-

catalysed us
uncataloged enzymes are
Ewhyeasier ? o_0-0-0-0
'

Aconite example § 080

iwneretheactivesiteis,
Hydrogen bonds ? ? ?
active site → consist of
amino vids
\
that are scattered (diff,
bnuotunsewitive) -
but
brought super close
 covalent bonds
D-0-8-01-0 polypeptide
I
peptide
fundergoestoldl.no (dipole
-
dipole, hydrogen bonds)
weak
linkages protein
→ ninth molecular forces of attraction
Effect of temperature on the rate of enzyme catalysed reactions
e. g. at temperatures higher / lower than optimum temperature
Reference pointy

•
peak Of Enzyme
Activity

Definition Of Protein
the
increment
Polypeptide made is
drop is
pretty
ofolminoaoidswvqlently Gradual
sharp
bonded together ing umaybeonlyq Highest
three dimensional tewenzymesqre
catalyst.no reactions
kinetic
Energy
] highest
temp → highest
conformation / configuration
energy
I

• Enzymes are mostly protein in nature, thus are affected by temperature conditions.

• Enzymes are inactive at low temperatures. 10W kinetic energy

o Low temperatures result in low kinetic energy of both enzyme and substrate molecules.
o There is a lower canoes
chance of substrate molecules colliding into an enzyme’s active site
LOtyollisionbetweehenwgmesrsubstrate.no/
in the correct orientation to form the enzyme-substrate easiest
complex.
effective memorise
• As temperature increases, the activity of the enzyme increases.
o Every 10 C increase in temperature causes the enzyme activity to double, until optimal
temperature is reached.
o As temperature increases, the kinetic energy of the substrate and enzyme molecules
increases and collides more frequently with each other.
o There is a higher chance of substrate molecules colliding into an enzyme’s active site
in the correct orientation.
o This increases the formation of the enzyme-substrate complex.

• Every enzyme as an optimal temperature.

o The optimal temperature of an enzyme is the temperature in which the enzyme activity
is the highest.
o It is the temperature in which fastest rate of reaction occurs.

• Beyond the optimal temperature, the activity of the enzyme drops sharply. IRREVERSIBLE
a
o Enzymes molecules are mostly protein in nature and will become denatured at high
temperatures.
3-dimensional
o High temperatures causes the enzyme to lose its 3D conformation, thus the
conformation of the active site will become deformed.
o Substrate molecules can no longer bind to the enzyme at the active site, as their
shapes are no longer complementary.

• At extreme temperatures, enzymes are completely denatured and can no longer speed up
chemical reactions.
o Note: denaturation of enzymes is permanent.

Page 6 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
 Case study 1: heat tolerant bacteria in hot springs

high
-

temperature
liking

• Enzymes have an optimal temperature.

• Most human enzymes have optimal temperatures near human body temperatures
o approximately 35 to 40 °C
o Most organisms will be killed if exposed to high temperatures (even for a short period)
due to the denaturation of their enzymes, and are unable to continue metabolism.

IN VITRO • Certain species of bacteria, those that survive in waters of hot springs with surroundings
test tubes temperatures of almost 100 °C, or bacteria that live in deep-sea vents with temperatures
above boiling water have enzymes with high optimal temperatures.
INVNO
in body • Enzymes with high optimal temperatures are not denatured by its high surrounding
temperatures, allowing these bacteria to survive. Optimum =3 -5°C
-

temperature
2500 still functioning
.am/9ctasestillbWKendown-At550o,m0stenzymesnqve
•

denatured not
: Thus
Effect of pH on the rate of enzyme catalysed reactions all lactase → lactose 1- galactose

HOwdoenzymesdenatureindittptli.mu#
At 7500,911 enzymes denatured
'

I
1

I
,

concentration Ht these charges I

want tointeract "
concentration OH
-
-

withsidechaihsot
-

I
LPHF - amino acids then cannot
. i
1
hold the } -9 Shape of "
tnereaotionstarteawitnatiniteamounts
Mild protein denaturation
otsubstrate
denaturation structure

t ↳ denaturation symmetrical and denaturation

• Enzymes are affected by pH conditions. optimal pH
renomination

• Every enzyme has an optimal pH where the enzyme activity is the highest.

• Deviations from the optimal pH will cause the enzyme activity to decrease.

• Extreme changes in the pH conditions will denature the enzymes.

o Note: denaturation of enzymes is permanent.

Page 7 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
 pepsinogen some enzymes
to would not
function in
pepsin
too acidic / basic
(enzyme)
environment
Case study 2: human digestive enzymes it'sArtintneaotive
sitenasacarboxylioaoid
gwupcneedstobe protonated )

symmetrical
compared
to temperature
curve

• Enzyme activity is very sensitive to pH.

• The temperature of the human body is relatively constant at approximately 37 °C.

• The pH along the alimentary canal (of the digestive system) changes from pH 7 in the
mouth and oesophagus, to pH 2 in the stomach, and pH 8 in the small intestines.

• Digestive enzymes can only function at their appropriate optimal pHs and will be
denatured by changes in the pH of the surroundings.

• Pepsin and trypsin are examples of proteases (enzymes that catalyse the hydrolysis of
proteins), which function at different optimal pH.
o pepsin has an optimal pH of 2, and functions well in acidic conditions in the stomach.
o trypsin has an optimal pH of 8, and functions well in the alkaline conditions in the small
intestine.
o pepsin will become denatured when it enters the alkaline conditions of the small
intestine

Page 8 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
 Denaturation
of enzymes

optimum temperature .PH

Hitman disulfide bridges

Body :

<
hydrogen bonds
37°C
1. the three dimensional conformation '

hydrophobic
'
Ottneactivesiteononges interactions
•

During Denaturation :

otherpartsoftheenzymemayohangesnape intramolecular weak forces of attraction

-
hydrogen bonds break Cohangebaokto linear structure) (between side chains)

> peptide bonds covalent bonds / between aminoacidsDONOI-breaklunlessre.at/yextremetemps)

 Effect of enzyme concentration on the rate of enzyme catalysed reactions

v.
•
There's atimefqopor increasing
Enuyme concentration
When there is an excess of substrate, the rate of reaction is directly proportional to the
enzyme concentration. infinite amount otsubstrate
o this means that as enzyme concentration increases, the rate of reaction also increases.
o under conditions of constant temperature and pH

Effect of substrate concentration on the rate of enzyme catalysed reactions

110
tnerateot reaction

#
/
remains constant
Plateaus ottatgoarbituaryunits
50 -

>
y

500 plateau
nanny, ,
increase saturation
>
cgubuonubeyondpt of
is.no/- limiting
✗ l , in
any further increase
9h4m)
O
envymecono
.

10m01 dm3
• At lower substrate concentrations, the increase in substrate concentration results in a
faster rate of enzyme-catalysed reaction.
o Substrate concentration is limiting at this point of time.

• The more substrate molecules available, the more frequently they have access to the
enzyme’s active site.

• At some point, the substrate concentration is so high that all the active sites of the enzymes
are occupied.
o As soon as the product exits the active site, the active site is free for another a new
substrate to bind to
o At this substrate concentration, the enzyme is saturated.
o The rate of reaction is determined by the speed at which the enzyme’s active site
converts the substrate into products.
o The substrate concentration no longer is the limiting factor of the reaction.

• At enzyme saturation levels, the only way to increase the rate of reaction (product
formation) is to add more enzyme molecules.

Page 9 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
 Case study 3: measuring rates of reaction

enzyme
reactants pdt
looktory
100104 decrease
in Pdt
inrxtants
overtime
overtime
gases
-

colour change
-

precipitation

• Depending the type of chemical reaction catalysed by enzymes, the rate of reaction can
be measured by measuring the rate at which:
o products are formed
o substrates are used up

enzyme activity oahbw modulated

INHIBITION

\
competitive Non-competitive Volume
competitive non-competitive inhibitor
substrate
inhibitor
substrate

enzyme
¥me
Allosteric
site
( position where (hydrogen peroxide and catalase)
noncompetitive
inhibitor binds ) this binding alters the } dimensional shape of active site, substrate cannot bind
• An example of measuring the speed at which the enzyme catalyses the breakdown of
hydrogen peroxide, can be done by measuring the rate of products formed.

• One of the end products of the reaction is oxygen gas.

• The rate at which oxygen gas forms correlates with the rate of the reaction.

• Oxygen gas can be measured easily by measuring the volume of oxygen gas collected in
the gas syringe in an experiment.

Page 10 of 10
CYM/Notes/IP Bio/Biological Molecules (enzymes)
chan_yu_mun@nygh.edu.sg (email me if you spot errors)
 araphotpwduotovertimelenzy.me activity)

conch Enzymatic reaction __

fixed system
of
Pdt fixed number of substrate molecules
j
Plateau
↳ Allsnbslratemoleallesnavebeencovertedtopdts

>
time

FWmthispt.it
saturation substrate
mregionn-iastheamonntotsubstratet.tnerateofrxn
,

rate n
conoisnoiongertne
otrxn limiting factor increases exponentially
:

enzyme who .

mregionB.astneamtofsubstratet.tnerateotrxn

zh9H
:# >
lame
Who .
plateaus off because there are not enough enzymes
oatalysetnerxnoftne substrate .

substrate
substrate concentration istnelimiting

reaction .

n
rate
nocom petition
¥1M itlwantto outcompete inhibitor molecules
tire -

increase substrate wnogreatertrequenuyof collision between

substrate molecules
non-competitive
alter the
> 3D shape of
active site
substrate I 1

enzyme molecules
aremadenon
functional