ENT 210 Biochemistry

INTRODUCTION
Lecturers & Teaching Engineer
Dr.Che Wan Sharifah Robiah Mohamad
Prof Dr. Muhamad Iqbal Omar (Director of
Health Centre, Pauh Putra)

PLV/Teaching Engineers
Mrs. Robiyanti Adollah

Engineer Assistant
Mr. Shukri Soid
(1) Kod kursus/ Course code: ENT 210

(2) Tajuk kursus/ Course title: Biokimia/Biochemistry

 
(3) Nilai unit/ Number of unit: 3
 
(4) Jenis kursus/ Course type: Teras/Core
 
(5) Prasyarat/ Prerequisite: Tiada/Nil
 
(6) Sinopsis kursus/ Course synopsis:
The topics covered in this course include the origin of life and structure of prokaryotes and eukaryotes
cells, properties and structure, classification and function of biomolecules such as carbohydrates,
lipids and amino acids. The role of proteins and enzymes in biochemistry, molecular biology and
genetics will be featured in the course. Electron transportation and citric acid cycle in biological
processes will also be briefly highlighted. Laboratory technologies for urine and blood are also
introduced in this course to expose the student to real application of biochemistry knowledge.
 

(7) Senarai eksperimen/ List of experiments:

 
Lab 1: Testing Sugar in Carbohydrate Samples
Lab 2: Protein and amino acid test
Lab 3: Enzyme kinetics based on ‘Michaelis – Menten’equation.
Course Outcome (CO)

CO1:
Ability to differentiate the concepts, structure, classification
and function of biomolecules. C3
 

CO2:
Ability to analyze biomolecule reaction.
C4

CO3:
Ability to propose appropriate measuring principles of
biological system.
C5/c6
Examination: 70%
 
Mid Term Examination = 10%
Final Examination = 60%
 
Continual assessment: 30%

Laboratory reports (2x + 1x) 10%

Assignments (1x + 2x) 10%

Quizzes (2x + 2x) 10%

Tutorial (2x + 2x)
References:
1. Mary K. Campbell, Shawn O. Farrell.
Biochemistry. Cengage Technology Edition,
Asia only.
2. H.R. Horton, L.A. Moran, K.G. Scrimgeour,
M.D. Perry & J.D. Rawn. Principles of
Biochemistry. Pearson International Edition.
3. Others Biochemistry text book
Biochemistry

Biochemistry has become the foundation for

understanding all biological processes.

It has provided explanations for the causes of many

diseases in humans, animals and plants

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Chapter Outline
1-1 Basic Themes
1-2 Chemical Foundations of Biochemistry
1-3 The Beginnings of Biology: Origin of Life
1-4 The Biggest Biological Distinction—Prokaryotes
and Eukaryotes
1-5 Prokaryotic Cells
1-6 Eukaryotic Cells
1-7 How We Classify Eukaryotes and Prokaryotes
1-8 Biochemical Energetics
1-9 Energy and Change
1-10 Spontaneity in Biochemical Reactions
1-11 Life and Thermodynamics
Basic Themes
 Allliving things make use of the same types of
biomolecules, and all use energy.
◦ As a result, all living things can be studied using the
methods of chemistry and physics

 The fundamental similarity of cells of all types

makes it interesting to speculate on the origins of
life
◦ both cells and the biomolecules of which they are made must
have arisen ultimately from very simple molecules, such as
H2O, CH4, CO2, NH3, N2, and H2
• Field of Biochemistry draws many disciplines
• allows us to answer questions related to molecular nature of
life
Levels of
Structural
Organization
in the Human
Body
Chemical Foundations of
Biochemistry
Organicchemistry: the study of the
compounds of carbon
◦ the cellular apparatus of living organisms is made up
of carbon compounds
◦ biomolecules are part of the subject matter of organic
chemistry
◦ the reactions of biomolecules can be described by the
methods of organic chemistry
The experiment of Friedrich Wöhler in 1828
Biomolecules
 Functional
group:
an atom or
group of atoms
that show
characteristic
physical and
chemical
properties
ATP and the Reactions for its
Formation
ATP and the Reactions for its
Formation
ATP and the Reactions for its
Formation
Biomolecules
 Living cells include very large molecules, such as
proteins, nucleic acids, polysaccharides, and lipids
◦ these biomolecules are polymers (Greek: poly +
meros, many + parts)
◦ they are derived from monomers (Greek: mono +
meros, single + part)
--amino acids → proteins
--nucleotides → nucleic acids
--monosaccharides → polysaccharides
--glycerol and 3 fatty acids → lipids

• Proteins and Nucleic Acids play a role in life

processes.
Biomolecules – Structure
Anabolic
 Building block  Macromolecule
 Simple sugar  Polysaccharide
 Amino acid  Protein (peptide)
 Nucleotide  RNA or DNA
 Fatty acid  Lipid

Catabolic

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How did organic complex molecules evolved
from more simple molecules?
• Urea was synthesized by heating the inorganic
compound ammonium cyanate (1828)
• This showed that compounds found exclusively in
living organisms could be synthesized from common
inorganic substances

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The Urey-Miller experiment (1950)

Some amino acids could be produced:

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Many Important Biomolecules
are Polymers

• Biopolymers - macromolecules created by joining

many smaller organic molecules (monomers)

• Condensation reactions (anabolic process) join

monomers
(H2O is removed in the process)

• Residue - each monomer in a chain

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Directionality in Macromolecules
(A) polypeptide
Amino acids - Proteins:
 Amino acids:
• Building blocks of proteins.

• R Group (side chains) determines the

chemical properties of each amino
acids.
• Also determines how the protein folds
and its biological function.

• Functions as transport proteins,

structural proteins, enzymes,
antibodies, cell receptors.

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Proteins as Enzymes
Thousands of different enzymes exist in the body
 Many proteins act as biological catalysts or
enzymes
Enzymes control the rate of chemical reactions by
weakening bonds, thus lowering the amount of
activation energy needed for the reaction ->
Catalysator
-> No not interfere with the equilibrium of
reaction

-> Enzymes are reusable !!!!

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Enzymes:
• Active site - a cleft or groove in an enzyme that binds the
substrates of a reaction

The nature and arrangement of amino acids in the active

site make it specific for only one type of substrate.
(accepts just one enantiomer)

Egg white lysozyme

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Directionality in Macromolecules
(B) polysaccharides
Sugars
 Carbohydrates most abundant organic molecule
found in nature.
 Initially synthesized in plants from a complex series
of reactions involving photosynthesis.
 Basic unit is monosaccharides.
 Monosaccharides can form larger molecules e.g. glycogen,
plant starch or cellulose.

Functions
 Store energy in the form of starch (photosynthesis in plants)
or glycogen (in animals and humans).
 Provide energy through metabolism pathways and cycles.
 Supply carbon for synthesis of other compounds.
 Form structural components in cells and tissues.
 Intercellular communications
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Monosaccharides -Polysaccharides

Glucose - Cellulose

Glycosidic bonds connecting

glucose residues are in red

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Directionality in Macromolecules
(C ) Polynucleotide
Nucleic Acids

Store hereditary information

Contain information for making all the

body’s proteins

Two types exist --- DNA & RNA

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Directionality in Macromolecules
(D ) Lipids and membranes

i) Triglyceride

Glycerol Fatty Acid Chains

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Fatty acids - Lipids
 Are monocarboxylic acid contains even number C atoms

 Two types: saturated (C-C sb) and unsaturated (C-C db)

 Fatty acids are components of several lipid molecules.

 E,g. of lipids are triacylglycerol, steriods (cholestrol, sex

hormones), fat soluble vitamins.

Functions
 Storage of energy in the form of fat
 Membrane structures
 Insulation (thermal blanket)
 Synthesis of hormones

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Structure of a biological membrane

ii) A lipid bilayer with associated

proteins

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Steroids
The carbon skeleton
of steroids is bent to
form 4 fused rings
Cholesterol
Cholesterol is the
“base steroid”
from which your Estrogen
body produces Testosterone
other steroids

Estrogen &
testosterone are
also steroids

Synthetic Anabolic Steroids are variants of testosterone

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Informational Macromolecules
Molecular Organisation of a cell

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Biomolecules
 Enzymes: a class of proteins that display catalytic
activity.
◦ the catalytic effectiveness of a given enzyme depends on its
amino acid sequence
 Genetic code: the relationship between the nucleotide
sequence in nucleic acids and the amino acid sequence
in proteins
◦ theories of the origin of life consider how such a coding
system might have arisen
Molecules to Cells: Biomolecules

 Which came first…the chicken or the

egg?
• catalytic activity associated with
proteins
• coding associated with nucleic acids

• It has been discovered recently that

certain types of RNA have catalytic
activity and are capable of catalyzing
their own further processing RNA is
now considered by many scientists to
have been the original coding material
• it still serves this function in some
viruses
Biochemical Energetics
• All cells require energy to functions
• Light from the sun is the ultimate source of energy
for all life on earth
◦ photosynthetic organisms use light energy to drive the
energy-requiring synthesis of carbohydrates
◦ non-photosynthetic organisms consume these
carbohydrates and use them as energy sources
• The energetics of a chemical reaction
• if the change in free energy is negative (free energy
decreases), the reaction is spontaneous as written
• if the change in positive (free energy increases), the
reaction will not occur as written unless energy is supplied
from an external source
Life needs 3 things:

(1) ENERGY, which it must know how to:

 Extract
 Transform
 Utilize

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How are energy changes
measured?
Thermodynamics- branch of science that answers
questions about processes that are energetically
favorable
The Energetics of Life
• Photosynthetic
organisms capture
sunlight energy and
use it to synthesize
organic compounds
• Organic compounds
provide energy for
all organisms

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Using toxic O2 to generate energy

2 H2O  O2 + 4e- + 4H+ (photosynthesis)

Glucose + 6O2  6CO2 + 6H2O + Energy

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Glycolysis: the preferred way for the
formation of ATP

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Life needs (2) SIMPLE MOLECULES,
which it must know how to:

 Convert
 Polymerize
 Degrade

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Life needs (3) CHEMICAL
MECHANISMS, to:
 Harness energy
 Drive sequential chemical reactions
 Synthesize & degrade macromolecules
 Maintain a dynamic steady state
 Self-assemble complex structures
 Replicate accurately & efficiently
 Maintain biochemical “order” vs outside

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Trick #1: Life uses chemical coupling to drive
otherwise unfavorable reactions

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Trick #2: Life uses enzymes to speed up
otherwise slow reactions

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How does an enzyme do it,
thermodynamically?

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Chemical reaction types encountered in
biochemical processes
1. Nucleophilic Substitution
 One atom of group substituted for another

2. Elimination Reactions
 Double bond is formed when atoms in a molecule is removed

3. Addition Reactions:
 Two molecules combine to form a single product.
 A. Hydration Reactions
 Water added to alkene > alcohol (common addition pathway)

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4. Isomerization Reactions.
 Involve intramolecular shift of atoms or groups

5. Oxidation-Reduction (redox) Reactions

 Occur when there is a transfer of e- from a
donor to an electron acceptor

6. Hydrolysis reactions
 Cleavage of double bond by water.

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 THERMODYNAMICS
 DEFINITION: The investigation of energy
transformations that accompany physical and chemical
changes in matter is called thermodynamics. It is the
science of energy transformations.

 The principles of thermodynamics are used to evaluate

the flow and interchanges of matter and energy.

 Bioenergetics is the study of energy in living organisms.

It is useful in determining the direction and extent to
which specific biochemical reactions occur.
 LAWS OF THERMODYNAMICS
 FIRST LAW: In all physical and chemical changes, energy is neither
created or destroyed.
The total amount of energy in the universe is constant.

 SECOND LAW: The disorder “S” or entropy in the universe always

increases. All chemical and physical occur spontaneously when
disorder is increased.
The universe equals, the system + the surrounding, where according
to the Second Law, a spontaneous change in a system proceeds in the
direction of decreasing free energy.

 THIRD LAW: As the temperature of a perfect crystalline solid

approaches absolute zero (0o K), disorder approaches zero.
 FACTORS AFFECTING BIOCHEMICAL
REACTIONS

ENTHALPY (Total heat content)- related to the

First Law of Thermodynamics

ENTROPY (Disorder)- related to the second Law

of Thermdynamics

FREE ENERGY (Energy available to do chemical

work)- is derived from the mathematical
relationship between enthalpy and entropy
GIBBS FREE ENERGY: Energy and Change,
Spontaneity in biochemical reactions
• Spontaneous means “fast”
• Free Energy of a System
 G < 0 spontaneous exergonic- energy released
 G = 0 Equilibrium
 G > 0 Nonspontaneous endergonic- energy required
• Life and Thermodynamics
 G = H - TS
 H is heat of a reaction at constant pressure
 S is the change in entropy
 G is the change in free energy
• T is the temperature
 Rections Associated with Thermodynamic
Laws
Associated with the First Law:
Exothermic: In a reaction or process, heat is given off.
Endothermic: In a reaction or process, heat is absorbed from the
surrounding.
Isothermic: In a reaction or process, heat is not exchanged with the
surrounding.
Associated with the Third Law
In a chemical reaction, we have the reactants which react to produce
the products.
In exergonic reaction (energy released): The products have a lower free
energy than the reactants. The reaction proceeds spontaneously and
yields energy.
In endergonic reaction (energy dependent): The products have a higher
free energy than the reactants and the reaction does not proceed
spontaneously and requires energy to occur.
 METABOLISM
LIFE OBEYS THE LAWS OF THERMODYNAMICS
Principles of Metabolism: Reactions in cells are catalyzed
by enzymes, which are proteins catalysts. The reactions
are grouped together in sequences called pathways.

Types of pathways:
Catabolism: reactions which break down molecules; delta
G is negative. Energy is given off and can be captured as
ATP.
Anabolism: synthetic reactions; delta G is positive; energy
input is required.
The Biggest Biological Distinction-Prokaryotes
and Eukaryotes
• Prokaryote: Greek derivation meaning “before
the nucleus”
◦ single-celled organisms
◦ include bacteria and cyanobacteria
• Eukaryote: Greek derivation meaning “true
nucleus”
• contain a well-defined nucleus surrounded by a
nuclear membrane
• can be single celled, such as yeasts and Paramecium,
or multicellular, such as animals and plants
Similarities between Eukaryotes and Prokaryotes

 Both have DNA as their genetic material.

1. Both are membrane bound.
2. Both have ribosomes.
3. Both have similar basic metabolism.
4. Both amazingly diverse in forms.
 DIFFERENTIATING PROKARYOTES AND
EUKARYOTES
SIZE
Prokaryotes are usually much smaller than
eukaryotic cells
Eukaryotic cells are, on average, ten times the size
of prokaryotic cells.

CELL WALL
Prokaryotes have cell wall composed of peptidoglycan (a
single large polymer of amino acid and sugar). Cell wall of
eukaryotes is not made up of this polymer.

SURFACE AREA
Prokaryotes have a large surface area /volume ratio giving
them the advantage of having a higher metabolic and growth
rate with smaller generation time as compared to the
eukaryotes.
 DIFFERENTIATING PROKARYOTES AND
EUKARYOTES

1. SUPPORT
In Eukaryotes provided by cytoskeleton;
none in Prokaryotes

2. PROTEIN SYNTHESIS
In Eukaryotes (animals) Rough Endoplasmic Reticulum (Rough ER)
is involved
In Prokaryotes ribosomes are involved

3. FAT SYNTHESIS
In Eukaryotes – Smooth ER involved
No fat synthesis in Prokaryotes
 DIFFERENTIATING PROKARYOTES AND
EUKARYOTES

4. ENERGY PRODUCTION
In Eukaryotes – chloroplasts (plants); mitochondrion
(Kreb’s cycle)
In Prokaryotes – chlorophyll (if present) but has no covering
or chloroplast; no mitochondrion and Kreb’s cycle
replaced by fermentation

5. ENERGY DIGESTION
Lysosomes involved in aging process of cell in Eukaryotes
No lysosomes in Prokaryotes
 DIFFERENTIATING PROKARYOTES AND
EUKARYOTES

6. MOVEMENT
In Eukaryotes – cilia, flagella and pseudopod movement
In Prokaryotes – flagella of different structure involved in
locomotion

7. REPRODUCTION - DNA control

In Eukaryotes – DNA in chromosomes inside nucleus
In Prokaryotes – DNA in single strand and floating freely
without a nucleus
Summary of Organelles and their Function(s)
Water
About 60-90 percent
of an organism is water

Water is used in
most reactions in
the body

Water is called the

universal solvent

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