Principles of Biochemistry

BOI206
Lecture 1
Introduction to the Study of Cell

Course:

PRINCIPLES OF BIOCHEMISTRY (BOI206)

Type:

Compulsory

Total Units:

3 (3 x 1 h lecture per week)

No. of Lectures: 42
Lecturers:

Dr. Intan Haslina Ishak

Dr. Rashidah Abdul Rahim

Prof. Dr. K. Sudesh Kumar

Dr. Intan Haslina Ishak

intanishak@usm.my
Ext. 5137
Room G08/131

Course outline
1. An introduction to biochemistry
2. Organisation of cell
Prokaryotic and eukaryotic cells.

3. Components of cells: Structure and function

Water and buffer, Acid amino and protein, Fatty acid and lipid, Monosaccharides and
carbohydrates, & DNA and RNA, Membrane and membrane transportation.

4. Enzymology
Enzyme as biological catalyst, Enzyme kinetics, Enzyme inhibitions, Enzyme regulation,
Allosteric enzymes.

5. Energetics and Metabolism

Principle of bioenergetics, Carbohydrate metabolism (glycolysis, citric acid cycle, pentose
phosphate pathway, gluconeogenesis), Photosynthesis, Oxidation in biology, Oxidation
of fatty acids (lipid metabolism).

Objectives:

Introduction to cells, organelles, molecules; structure &

function relationship; working of a cell

Course contents are divided into 4 major sections:

1. Concept of a cell: Prokaryote, Eukaryote, Animal and

Plant Cells; cellular organelles

2. Cell components (Structure & Function): Water and

buffer, amino acids and protein, fatty acids and lipid,
monosaccharide and carbohydrate, nucleotides and
DNA, RNA, membrane and membrane transport

3. Enzymology: Enzyme as catalysts, enzyme kinetics,

inhibitor effects, enzyme regulations, allosteric enzymes

4. Energetics and metabolisms: Bioenergetic principles,

carbohydrate metabolisms (glycolysis), TCA cycle,
pentose phosphate pathway, gluconeogenesis and
photosynthesis, fatty acid oxidation

Course evaluation:

Test/Quiz/Assignment/Practical: 50%
Final Exam: 50%

Laboratory Practical:

30%

Test/Quiz/Assignment:

20%

Tests:

Test 1: Will be determined later

Test 2: Will be determined later

Come to class!!!!!!

 Review lecture notes. (Will be uploaded on

elearn)

Read book chapters.

Biochemistry, 5th edition, Campbell, M. K. & Farrel, S.O,
Thomson-Brooks/Cole.
Principles of Biochemistry, 4th edition, Voet, D. & Voet,
J.G., John Wiley & Sons, Inc.

Principles of
Biochemistry
4th Edition

Biochemistry
5th Edition

Biochemistry
Chemistry of living organisms.
The study of biology at the molecular level.

Scientists study cells from various perspectives such as:

1. Cytology: what we learn with a microscope

2. Genetics: what we learn using genetic techniques
3. Biochemistry: what we learn through biochemical
analysis

Characteristics of Life: All Living Things

1. Have metabolic activity; ability to acquire and use
energy
2. Use homeostatic controls which respond to environmental change

3. Show growth, development and reproduction

4. DNA is molecule of inheritance

5. Have adaptive potential; heritable variation in form,

function and behavior allow changes to accommodate
changing environment
6. Display diversity; variations in form, function and
behavior as a result of natural selection and
environmental change

Levels of Organization of Life

biosphere

tissue

ecosystem

community

Cell: smallest
living unit

population

organelle

multicellular
organism
organ system

molecule

organ

subatomic particle

atom

CLASSIFICATION: THE THREE DOMAIN SYSTEM

Eukarya
(eukaryotes)

This system proposes that a common ancestor cell ("Cenancestor") gave

rise to three different cell types, each representing a domain. The three
domains are the Archaea (archaebacteria), the Bacteria (eubacteria), and
the Eukarya (eukaryotes). The Eukarya are then divided into 4 kingdoms:
Protists, Fungi, Animalia, and Plantae.

The Three Domain System, proposed by Woese and others,

is an evolutionary model of classification based on:
i) differences in the sequences of nucleotides in the
cell's ribosomal RNAs (rRNA),
ii) the cell's membrane lipid structure
iii) its sensitivity to antibiotics.
Comparing rRNA structure is especially useful. Because
rRNA molecules throughout nature carry out the same
function, their structure changes very little over time.
Therefore similarities and dissimilarities in rRNA nucleotide
sequence are a good indication of how related or unrelated
different cells and organisms are.

The Bacteria and the Eukarya

have membranes composed of
unbranched fatty acid chains
attached to glycerol by ester
linkages.
The Archaea have membranes
composed of branched
hydrocarbon chains attached to
glycerol by ether linkages.

Prokaryotic cells are generally much smaller and more simple

than eukaryotic.
The smaller a cell, the greater is its surface-to-volume
ratio.
A large surface-to-volume ratio, as seen in smaller
prokaryotic cells, means that nutrients can easily and
rapidly reach any part of the cells interior.
In the larger eukaryotic cell, the limited surface area when
compared to its volume means nutrients cannot rapidly diffuse
to all interior parts of the cell.
That is why eukaryotic cells require a variety of specialized
internal organelles to carry out metabolism, provide
energy, and transport chemicals throughout the cell.
Both, have to carry out the same life biochemical processes.

Cells with a high metabolic rate are usually small.

Why?

Structure of virus:
nucleic acid with a protein envelope

Virus: genetic parasite! Is it a cell?

T4 Bacteriophage:
infects prokaryotes
Used by
scientists to
introduce
foreign genetic
material into
bacterial cells:
genetic
engineering/
recombinant
technology

Adenovirus (cold)

Important terms: Definitions?

Nucleus
Cytoplasm
Plasma membrane
Protoplasm/protoplast

Nuclear membrane
Mitochondrion

Golgi apparatus/body
Cytosol

Plastid

Endoplasmic reticulum
(smooth &
rough/granulated)

Chloroplast

Centriole

Nuclear plasma

Centrosome

Nucleolus

Ribosome

Chromatin

Liposome

Cell wall

Vacuole

PROKARYOTE
Bacterial cell

Bacterial nucleoid (EM)

Bacterial spore

Bacterial (E. coli) flagellar

monotrichous

lophotrichous
amphitrichous

peritrichous

Locomotor organelles
Eukaryotic cell
May have flagella or cilia. Flagella and cilia are organelles
involved in locomotion and in eukaryotic cells consist of a
distinct arrangement of sliding microtubules surrounded by
a membrane. The microtubule arrangement is referred to
as a 2X9+2 arrangement.
Prokaryotic cell

Some have flagella, each composed of a single, rotating

fibril and not surrounded by a membrane. No cilia.

Flagella
composition: A bacterial flagellum has 3 basic parts: a filament, a hook, and a
basal body.

Transmission Electron
Micrograph of Escherichia coli
O157:H7

Structure of an eukaryotic cell

Structure of an eukaryotic cell

Plant Cell

Scytonemia (blue-green algae)

Mitochondria

Lysosome

Centriole & centrosome

Microfilament & Microtubule:

Cytoskeleton

Nucleus

Nuclear body
Eukaryotic cell
a. Bounded by a nuclear membrane having pores connecting
it with the endoplasmic reticulum
b. Contains one or more paired, linear chromosomes
composed of deoxyribonucleic acid (DNA) associated with
histone proteins
c. Nucleolus present.
d. Nuclear body is called a nucleus

Prokaryotic cell
a. Not bounded by a nuclear membrane
b. Usually contains one circular chromosome composed of
deoxyribonucleic acid (DNA) associated with histone-like
proteins.
c. No nucleolus.
d. Nuclear body is called a nucleoid

Chromosome

Cell division
Eukaryotic cell
a. By mitosis
b. Sex cells in diploid organisms are produced through
meiosis

Prokaryotic cell
a. Usually by binary fission. No mitosis.
b. Organisms are haploid. No meiosis needed.

Nucleic acid

Endoplasmic reticulum
(smooth & rough)

EM

Rough endoplasmic reticulum (EM)

Golgi apparatus

Lipid assembly, polypeptide chain modification,

packaging of polypeptides for transport to other
various locations in cell

Plasma membrane

Cytoplasmic membrane (cell membrane, plasma

membrane)
Eukaryotic cell
a. Cytoplasmic membrane is a fluid phospholipid bilayer
containing sterols as well as carbohydrates.
b. Capable of endocytosis (phagocytosis and pinocytosis) and
exocytosis.

Prokaryotic cell
a. Cytoplasmic membrane; is a fluid phospholipid bilayer
without carbohydrates and usually lacking sterols . Many
bacteria do contain sterol-like molecules called hopanoids.
b. Incapable of endocytosis and exocytosis.

Size comparison of cellular components

Comparison of eukaryotic and prokaryotic cells and

selected organels

THANK YOU