Enzymes

( Chapter 1)
 Metabolism, Energy and Life
Metabolism:
- sum of the
chemical
reactions that
provide energy
for vital
processes and
synthesizing
new organic
materials in
living cells.
Metabolism, Energy and Life
• Metabolic pathways - chemical
reactions taht take place to create and
use energy.

• Two metabolic pathways:

1. anabolic (anabolism) / endergonic
2. catabolic (catabolism) / exergonic
1. Anabolism Pathway (Endergonic)

• Consume/ abosrb energy to form build more

complex molecules from simple ones.
• None spontaneous reactions.
2. Catabolism Pathway (Exergonic)

• Release energy by breaking down complex

molecules to simpler compounds.
• Spontaneuos reactions.
 Energy Changes:
Exergonic (Anabolism) vs. Endergonic
(Catabolism)
 Energy Coupling
• The energy released from “downhill” reactions of
catabolism can be used in the “uphill” reactions of
anabolism
 Enzyme: Definition
• Enzyme = protein molecule that serves as a
biological catalyst to speed up and regulate
metabolic reactions.
• So ... a enzyme is basically a protein made up of
amino acids.

• Catalyst = a chemical that speeds up the rate of

a reaction without itself being consumed in the
process.
Damm... it just a
protein !!!

Alpha amylase (enzyme)

Enzyme: Characteristics

(Co-factors)
Enzyme: Characteristics
Enzyme: Activation energy (EA)
• Energy needed to start a chemical reactions.
• Different chemical reactions will have different activation
energy.
• Resemble a hill that must be climb if want to reached the
other side.
• Low activation energy, lower hill to be climbed - faster the
reactions.

Conclusion: Enzyme speed

up reactions by lowering the activation energy
(EA).
Enzyme: Activation energy (EA)
Enzyme: Active Site
Enzyme: Active Site
Enzyme: Active Site
 Enzyme: Active Site
• If active site unoccupied and substrates
available =
“the cycle begins (spontaneously)”
• Enzyme substrate complex forms with
hydrogen and ionic bonds
• The substrate is converted to product
• The enzyme releases the product
• The enzyme is available for the next
reaction
Enzyme: Specificity

√ ×
Enzyme: Specificity
 Enzyme: Specificity
• Enzymes are substrate specific (more a
less like the lock and the key)
• Substrate = reactants in an enzyme
catalyzed reaction.
• Each enzyme has a unique 3-D shape and
recognizes and binds only the specific
substrate of a reaction.
• Active site = small portion of enzyme
molecule which actually binds the substrate.
Enzyme: specificity

Two enzyme-subsrate
interaction models
1. The Lock and Key Model
Enzyme are very
specific towards
substrate.

Enzyme active site

(Lock) must be 100%
complementary with
substrate (Key).

Active site shape is

fixed.

Not widely accepted

today.
1. The Lock and Key Model
 2. The Induced fit model
 Induced fit theory widely accepted today.
 Enzyme active site are flexible.
 No need to be 100% complementary with substrate.
 Shape of enzyme, active site and substrate - adjust to
maximize the fit.
 Many substrates (with similar shapes) can react with
one enzyme.
 To begin a reaction, substrate must first
collide with enzyme active site changing the
active site configuration.
 After the reaction, active site return to it's original
conformation (shape) - allowing new reaction to occur.
2. The Induced fit model
Overview: How enzymes
work?

Based on Induced fit model

Overview: How enzymes work?
• Enzymes are proteins.
• Enzymes have either tertiary or quaternary
protein structure.
• Enzymes are substrate-specific.
• Only small amount of enzyme required.
• Substrate only bind to active site of enzyme.
• This will formed enzyme-substrate
complexes.
 Overview: How enzymes work?
• Enzymes active sites can change their shape (flexible -
the induced fit model).
• This will increase the binding opportunities - enzymes are
flexible.
• Enzyme-substrate complex are temporary structure.
• Form by weak non-covalent bonds (e.g. ionic or hydrogen
bonds) between active site and substrate.
• These bonds can be easily break off.
• After reaction, enzyme & active site return to original shape.
• Generally, 1 enzyme can react with few substrates sharing
similar shapes.
 Overview: How enzymes work?
• No substrate; no reactions. No enzyme, no reactions also.
• Enzyme is not destroy during or after the process.
• Enzyme can be recycle again.
• Enzyme not affecting the properties of final products.
• Enzyme speed up a reaction by lowering activation energy
(EA).
• Enzyme reactions are reversible:

A+B C
Enzyme

• Temperature, pH, substrate concentration, enzyme

concentration = factor affecting enzyme efficiency.
 Factors Affecting
Enzyme Activity
• Temperature
• pH
• Enzyme concentration
• Substrate concentration
 Temperature
• Temperature increase, speed of molecular
movement increase, the rate of reaction is increase.
• More substrate will collide with enzymes.
• Tempearture ↑, enzyme activity ↑.

• Too high temperature, the enzymes denature.

• This means that the structure of the enzyme is
altered and the “shape” no longer works with its
specific substrate.
• Too low temperature, enzyme become inactive.
Temperature
Important:
Most enzymes (amylase; lipase etc) in
human body can function at certain range
of temperature (e.g from 25℃to 40℃)

However, enzyme in human body are most

efficient at 37℃,also known as the
optimal temperature.
Factors Affecting Enzyme Activity
pH

• Each enzyme works best at a certain pH - optimal

pH.
• Increasing or reducing pH away from optimal pH
will reduced the rate of enzyme acitivity because H
ions can alter the shape of enzyme and active site;
reducing substrate binding possibility.
• Extreme pH will denature enzyme. This means that
the structure of the enzyme is altered and the
“shape” no longer works with its specific substrate.
Enzyme concentration
Enzyme concentration
Substrate concentration
More substrate the rate increases until optimal
concentration of substrate (point of saturation).
Substrate concentration
After point of saturation - no increase of activity as
number of enzyme does not changed.
 Enzyme Denaturation
• Denaturation = destruction of enzymes structures; the
active sites structures.
• When denature, enzymes cannot work anymore.
• Substrates cannot bind to the active site.
• Higher temperature, extreme pH can denature enzymes.
 Enzyme Inhibition
• There are ways of inhibiting the activity of
enzymes.
• When enzyme activity stop = no more reactions
occur.
• Important to maintain body internal environment.
• Denaturing or destroying the enzyme protein is one
way of doing this irreversibly.
• This can be done by heating, changing the pH, or
by reaction with a variety of chemicals.
• Competitive vs. non-competitive inhibition.
Enzyme Inhibition

Competitive

Irreversible
 1. Competitive Inhibition
• Competitive inhibitor = inhibitor has similar
shape like substrate.
• Compete with substrate for active site,
preventing substrate bind to active site.
• Reversible process = can be corrected.
• Increase substrate concentration and
increase enzyme concentration can correct
the condition.
• Example: Malonate (inhibitor) compete with
succinate (substrate)
This situation is comparable to a lock jammed by a key almost similar to the original one.
Competitive Inhibition
2. Non Competitive Inhibitors
• Not bind to active site of enzyme.
• Bind to allosteric site or other site of
enzyme.
• Can be reversible or irreversible.
• If reversible = still can be corrected.
• If irreversible = cannot be corrected,
enzyme denatured forever.
 2a. Non competitive reversible inhibition
• Inhibitors (e.g. cyanide) formed weak bonding with
enzymes’ allosteric site.
• Not competing with substrates for active site.
• Change enzymes’ shape, enzyme cannot bind to
substrate.
• Enzyme still can be use, but shape changed =
reactions cannot happen.
• Inhibitor ; rate of reaction
• Enzyme ; rate of reaction
• Increase substrates = no effect.
 2b. Non competitive irreversible
inhibition
• Inhibitors bind to active site or allosteric
site of enzyme by strong covalent bond.
• Enzyme will denature.
• Example: mercury (Hg2+), silver (Ag+) and
arsenic (As+)
• Binding is permanent, changing the
structure of enzyme forever.
 Allosteric enzyme and
negative feedback
• Involve allosteric enzymes.
• Allosteric enzymes have two forms:
– Active form vs. inactive form

• Active form: forming enzyme-substrate

complexes.
• Inactive form: active site shape change; no
formation of enzyme-substrate complexes.
Allosteric Enzymes
 Allosteric Enzymes
• Have two site:
– active site vs. allosteric site.
• Allosteric site also known as control site.
• Substrate – active site.
• Allosteric inhibitor – allosteric site.
• Allosteric inhibitor = non competitive inhibitor.

When allosteric inhibitor bind to allosteric

site, enzyme inactive!
Allosteric Enzymes
 Allosteric Enzymes
• Activator can also bind to allosteric
enzyme – increase enzyme activity.

Activator = enzyme more active.

Inhibitor = enzyme inhibited.
 Allosteric Enzymes
Q: Why allosteric site provide fine tuning for
enzyme activity?
A: Allosteric control can increase or decrease enzyme
catalytic efficiency.
 Negative feedback with
allosteric enzyme
• Involve more than one enzyme.
• Product from one enzyme reaction become
substrate for another enzyme reaction.
• The final product produced, can become
allosteric inhibitor.

Why?
Negative feedback - allosteric enzyme

• In reality, not easy to stop enzyme

reactions in body.
• Cannot drink chemical to stop enzyme
from working.
• Some product from enzyme reactions
cannot accumulated in body, too much
can be “poisonous”.
• Need to use allosteric regulation.
Allosteric Regulation
Reaction start from
Enzyme 1 to Enzyme
2 and end with
Enzyme 3.

The product of
Enzyme 1 become
substrate for Enzyme
2 and so on.

The enzyme product

(product of Enzyme
3) is then used as
allosteric inhibitor to
stop the reaction.
Negative feedback - allosteric enzyme

• When too much product, product become

allosteric inhibitor.
• Change the shape of 1st enzyme, stop the
reaction.
• Since 1st enzyme not working, no more
product to be used by next enzyme.
• Finally, all enzyme stop working. Reaction
stop.
Negative feedback - allosteric enzyme

• Allosteric inhibitor is a product that can be use

by body.
• When the product is used up, the allosteric
inhibitor (product) is then used by body also.
• When free from allosteric inhibitor (product),
enzyme active again – reaction continue to
produce more product!
• This is known as negative feedback inhibition
or end product inhibition.
 Enzyme cofactor
• Also known as activator. Activator increase enzyme
activity.
• Most enzymes are protein only.
• Some enzyme has two parts:
– protein parts (apoenzyme)
– non-protein parts (cofactor).
• The cofactor increase enzyme activity,
but remain unchanged after the reaction.
 Enzyme cofactor
Group 1: Inorganic ions
- Enzyme activators.
- Shape up enzyme or substrate to
increase chances forming enzyme-
substrate complex.
- E.g. Zn2+, Mg2+, Cl- , Mn2+, K+, Na+ and
Cu2+.
 Enzyme cofactor
Group 2: Prosthetic group
- Organic non-protein substance.
- Bind tightly to enzyme.
- Highly active part of enzyme.
- Function: take up chemical group from the
protein part.
- E.g. iron (in cytochrome oxidase); FAD+ or
NAD+.
 Enzyme cofactor
Group 3: Coenzymes
- Non-protein organic molecule, like prosthetic group.
- Does not bind tightly to enzyme.
- Do not remain attached to enzyme forever.
- Can be group as transfer agent – transfer
components from one molecule to another.
- Can transfer electron or hydrogen.
- All coenzymes obtained from vitamin
- E.g. NADH, NADPH and FADH2.
Enzyme – 3D Modeling
 Enzyme classification
• Two groups of enzyme:
– Intracellular enzyme = occur inside cells.
– Extracellular enzyme = send out from the cells.

• How to name enzyme?

1. randomly at time of discovery
2. addition of “ase” – urease, amylase, catalase
3. type of reactions – dehydrogenase to remove
hydrogen.
 Enzyme classification
Enzyme Functions

Oxidoreductase Oxidation-reduction; transfer hydrogen, oxygen

or electrons from one molecule to another

alcohol dehydrogenase

ethanal + NADH2 ethanol + NAD

Transferase Transfer chemical group from one substrate to

another

glutamic acid + aminotransferase α-ketoglutaric acid +

pyruvic acid alanine
 Enzyme classification
Enzyme Functions
Hydrolase Splitting of large substrate into smaller
molecules by hydrolysis.

sucrase
sucrose fructose + glucose

Lyase Non-hydrolytic addition or removal of parts in a

substrate

pyruvate decarboxylase
pyruvic acid ethanal + CO 2
 Enzyme classification
Enzyme Functions
Isomerase Isomerisation; involve internal arrangement of

substrate molecules
phosphoglucomutase
glucose-1-phosphate glucose-6-phosphate

Ligase Catalyze joining of tow molecules by

hydrolysis of ATP
amino-acyl-tRNA synthase
amino acid amino acid-tRNA complex
+ specific tRNA + ADP
+ ATP