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1. introdakshen
 Chapter One
 Introduction

2. Outline
1. Introduction
2. Historical overview of molecular biology
3. Overview of cells & Biologically important
molecules
4. Cellular genetic components
5. The central dogma of molecular biology

3. 1. Introduction
 Molecular biology is the study of biological
phenomena at the molecular level, in particular the
study of the molecular structure of DNA and the
information it encodes, and the biochemical basis of
gene expression and its regulation.
 Molecular biology is a melding of aspects of genetics
and biochemistry

4. 2. History overview of molecular biology

5. Cont’d

6. Cont’d

7. 3. Overview of cells & Biologically important molecules
3.1 Overview of cells
 Fundamental working units of every living system.
 Every organism is composed of one of the two types
of cells:
1. Prokaryotic cells
2. Eukaryotic cells
 Distinguished on the basis of their structure and
complexity of their organization.

8. Prokaryotic cells Eukaryotic cells

9. 1. Prokaryotic cells
Less complex cells consisting of single (haploid) and
circular chromosomes lacking a nuclear membrane
Their DNA has not associated with histones
Bounded by semi rigid cell wall
Include Bacteria (eubacteria) & the Archae
(Archaebacteria)

10.  The cell contents inside the membrane are liquid and
includes:
 Cytoplasm; - helps in maintain and allowing for
cell respiration (energy production).
 Nuclear material (DNA); - genetic material which
is not bounded by nuclear membrane.
 Ribosome; - for protein synthesis and composed
of three kind of rRNA and about fifty kind of
protein.

11.  Extracellular structure or structure present outside of
the cell includes
 Flagella; - which helps in movement of the cell.
 Capsule; - structure which protects bacteria from
being engulfed by other phagocytes cells.
 Pilli; - a hair like structure present in some bacteria.
 Prokaryotic cells multiply by dividing into two by
binary fission, a means of multiplication in which the
nuclear material (DNA) replicates simply and the cell
divided into two and the resulting cells that produced
will have identical genetic material.

12. 2. Eukaryotic cells
 Eu means true and karyoten means nucleus
 Have more a complex cytoplasm, has nuclear
material (DNA) covered by nuclear membrane and
membrane bounded organelles.
 The outer boundary of those cells is formed of cell
membrane,
 It contains one or more paired, linear
chromosomes composed of DNA associated with
histone and non-histones proteins
 Includes plants, animals, fungi and certain algae

13.  The cytoplasm of eukaryotic cells include: -
 Nucleus; - surrounded by nuclear membrane and
contain DNA and nucleoli.
 Endoplasmic reticulum(ER); - transport protein,
lipid and other materials.
 Ribosome
 Produce protein
 Larger and more complex than those of the
prokaryotic cell and composed of five kinds of
rRNA and about eighty kinds of proteins.

14.  Mitochondria:
 Respiration/ energy production for the cell
 Contains self replicating, circular, dsDNA molecule
 Golgi complex; - secretion of substance from the cell
 Lysosome; - produced by Golgi complex and
breakdown foreign substance.
 Cell division in eukaryotes: Mitosis and Meiosis

15. Mitosis
 Results in the formation of two daughter cells
having the same number of chromosomes as the
parent cell.
 The nucleus divides by mitosis.
 This is the mechanisms by which most cells
reproduce.
Meiosis
 Formation of four daughter cells, each having
half number of chromosomes as the parent cell.
 Haploid (1N) sex cells in diploid (2N) organisms
are produced through meiosis.

16.  Common features of organisms
• Chemical energy is stored in ATP
• Genetic information is encoded by DNA
• Information is transcribed into RNA
• There is a common triplet genetic code
• Translation into proteins involves ribosomes
• Shared metabolic pathways
• Similar proteins among diverse groups of organisms

17. The three domains of life
Current research theories
support the division of living
organisms into three domains
1. Bacteria
2. Eukaryotes
3. Achaea living in the
most inhospitable regions
of the earth
• Thermophiles
• Halophiles
• Methanogens

18. Phases of the Cell cycle
Cell cycle alternates between interphase & cell division
(karyokinesis; mitosis or meiosis & cytokinesis)

19. cont’d
Interphase
non-dividing phase
Cell is preparing for division
nucleus is visible & chromosomes are uncoiled &
invisible.
Includes G1, S & G2

20. cont’d
A. G1 phase
 Each chromosome has one chromatid
 The cell grows in size and synthesis of organelles
occurs.
B. S phase
 DNA duplicates when DNA synthesis occurs
C. G2 phase
 The chromosomes have two chromatids.
 Synthesis of enzymes & other proteins in
preparation for mitosis

21. Cell division
A. Mitosis/ one nuclear division
 Produces two daughter cells
that are identical to the parent
cell.
2n 2n
 Division of somatic (body)
cells
 Phases included: prophase,
metaphase, anaphase, and
telophase

22. Function of mitosis
Single celled organisms: reproduction
Multicellular organisms:
• Growth/development (asexual reproduction),
• Differentiation: specialization & division of labor
• Repair: replacement of dying cells e.g. skin, RBCs
Reproduction (multi-cellular to produce sex cells
(gametes) (meiosis)

23. B. Meiosis/two nuclear
division
 Four daughter cells
produced
 Each daughter cell has
half the chromosomes of
the parent
2n ------->n
 Two sets of cell division
involved: meiosis I and II

24. Difference b/n mitosis & meiosis
Mitosis Meiosis
Purpose Produces somatic cells (Body,
growth)
produces reproductive cells
Process cell duplication (Diploid -> diploid) reduction division (Diploid ->
haploid)
Number of
Divisions
One cell division Two cell division
Product 1 -> 2 identical daughter cells To
each other & mother cell
1 -> 4 cells (gametes) daughter
cells different
Occurrence More often At a certain time in the life cycle
Crossing-
over
No Yes
Chromosome
separation
Sister chromatids Homologous chromosomes

25. 3.2 Overview Biological important molecules
 Most organic molecules fall into one of four
classes:
A. Carbohydrates
B. Lipids
C. Proteins
D. Nucleic acids

26. 1. Carbohydrates
It is a common class of simple organic compounds
Function of Carbohydrates
Energy source
Give structure to cell membranes and cell walls
(in plants)
Recognition markers-e.g. A,B,O blood types
Structural component of nucleic acids (DNA and
RNA)
Serve as metabolic intermediates

27. Major groups of Carbohydrate
Monosaccharides (Simple Sugars)
Have basic structure (CH2O)n, where n is ≥ 3
Cannot be hydrolyzed any further (e.g., Glucose,
Galactose , and Fructose)
Monosaccharide's link to each other through glycoside
bond to form other groups.

28. Disaccharides
 Formed from two monosaccharides linked through
glycosidic bond
 Include: Maltose, sucrose, and lactose

29. Polysaccharides
 More than 10 monosaccharids joined together by glycoside
bond
 They vary in monomeric composition, bond type, degree of
branching, and biological function.
Starches: major storage form of Glucose in most plants
 Two main constituents of starch are Amylopectin and Amylose
 Amylose composed only of glucose units joined in an alpha (α)
-1,4- linkage.
 Amylopectin composed only of glucose units are joined together
by α 1-4 linkages predominate, but every 30-50 residues, a
‘branch’ arises from an α-1,6- linkage.

30.  Un branched starch: amylose:- joined by α-1,4- &
α-1,6-glycosidic bond
 Branched starch: amylopectin:- joined by α-1,4- &
α-1,6-glycosidic bond
H O
OH
H
OH
H
OH
CH2OH
H
O H
H
OH
H
OH
CH2OH
H
O
H
H H O
O
H
OH
H
OH
CH2
H
H H O
H
OH
H
OH
CH2OH
H
OH
H
H O
O
H
OH
H
OH
CH2OH
H
O
H
O
1 4
6
H O
H
OH
H
OH
CH2OH
H
H H O
H
OH
H
OH
CH2OH
H
H
O
1
OH
3
4
5
2
amylopectin

31. Glycogen
 Storage polysaccharide in animals (liver and muscles)
 Glycogen is a polysaccharide that is physically related to
amylopectin in being built only of glucose and in having a
mix of α-1,4- and α-1,6- bonds.
 Glycogen, however, has many more α-1,6- branches than
amylopectin, with such bonds occurring about every 10
residues.
H O
OH
H
OH
H
OH
CH 2OH
H
O H
H
OH
H
OH
CH 2OH
H
O
H
H H O
O
H
OH
H
OH
CH 2
H
H H O
H
OH
H
OH
CH 2OH
H
OH
H
H O
O
H
OH
H
OH
CH 2OH
H
O
H
O
1 4
6
H O
H
OH
H
OH
CH 2OH
H
H H O
H
OH
H
OH
CH 2OH
H
H
O
1
OH
3
4
5
2
glycogen

32. Cellulose
 It is a polymer of glucose used to give plant cell
walls structural integrity and has the individual units
joined only in a β -1,4-configuration
 Very few organisms produce cellulase, enzyme that
hydrolyze cellulose
cellulose
H O
OH
H
OH
H
OH
CH 2OH
H
O
H
OH
H
OH
CH 2OH
H
O
H H O
O H
OH
H
OH
CH 2OH
H
H O
H
OH
H
OH
CH 2OH
H
H
OH
H O
O H
OH
H
OH
CH 2OH
H
O
H H H H
1
6
5
4
3
1
2

33. 2. Proteins
Proteins are polymers of monomers called amino acids
Amino acid contains amino & carboxyl groups cause
protein to have a positively charged end & a negatively
charged end & an alpha carbon bonded to 4 different
covalent partners Structure of an amino acid
Different amino acids
differ in their R-group
that determines physical &
chemical characteristics of amino acid (aa).

34.  Amino acids form polymers when the negative
carboxyl group(COO-
) of one amino acid react with
amino group of the other amino acid.
 During this process there is releasing a molecule of
water and a formation of an amid link or a peptide
bond (-CONH-) thereby forming a polypeptide chain.
 In a reverse reaction, the peptide bond can be cleaved
by water (hydrolysis).
NH3-CH-COO + NH3-CH-COO ↔NH3-CH-CO- NH-CH-COO
R R’ R
R’
-H2O
Peptide
bond
- - -
+
+ +

35. Function of proteins
Proteins do all essential work for the cell
– build cellular structures
– digest nutrients
– execute metabolic functions
– mediate information flow within a cell and among
cellular communities.

36. Protein Structure
A protein molecule may consist of one very long
polypeptide chain or it may consist of several polypeptide
chains joined together in which case linkage other than
peptide bonds is involved.
When cells make a polypeptide, the chain folds
spontaneously to assume the functional conformation of
that protein
4 superimposed levels of structure

37. A. Primary protein structure
It is the sequence of aas held together by covalent bond.
Each protein has not only a definite aas composition, but
also a unique sequence
The aa sequence has a profound effect on the resulting 3D
structure and on the function of protein. Changes in it can
affect every other level of structure as well as the
properties of a protein

38. B. Secondary protein structure
Regular repeating structures arising when H-bonds b/n
the peptide backbone amide hydrogen (N-H) and
carbonyl oxygen (C=O) occur at regular intervals within
a given linear sequence (strand) of a protein (as in the
alpha helix) or b/n two adjacent strands (as in beta
sheets)
Include the well known alpha-helix and beta strands
Alpha helix: forms coil as a result of H-bonding b/n
a,as separated by 4 residue.

39. Beta strands
Consists of two or more aa sequence that are arranged
adjacently and the 2 or more strands are joined by
hydrogen bond
Adjacent β strands can form hydrogen bonds in
antiparallel or parallel arrangements
In an antiparallel arrangement, the successive β strands
alternate directions
In a parallel arrangement, all of the N-termini of
successive strands are oriented in the same direction

40. C. Tertiary protein structure
Arises from interactions b/n aas more distant in primary
structure. Besides the peptide bond, interactions also
involve b/n side chains
Proteins with such structures are referred to as ‘globular’
and they are, by far, the most abundant class of proteins
H-bonds, ionic interactions, & disulfide bridges of side
chains also involved in stabilizing the tertiary structure.

41. D. Quaternary protein structure
The last level of protein structure we will consider is
that of quaternary structure
Results from the union of more than one protein
molecules, which function as part of the larger
assembly or protein complex
Consider hemoglobin, the oxygen carrying protein of
our blood, contains two alpha and beta subunits
Multiple subunit proteins are common in cells and
they give rise to very useful properties not found in
single subunit proteins

42. 04/12/25
42
Structure of human hemoglobin. The protein's α and β subunits
are in red and blue, and the iron-containing heme groups in
green.

43. Protein Denaturation
Proteins denature when they lose their 3-D structure
>>their chemical conformation and thus their
chemical characteristic folded structure
Proteins may be denatured at secondary, tertiary and
quaternary structural levels, but not at the primary
structural level
Denaturation is usually caused by heat, acids, bases,
detergents, alcohols, heavy metals, reducing agents or
certain chemicals such as urea
Denatured proteins can be irreversible or reversible
denaturation, when the denaturing influence is removed.

44. 3. Lipids
Biological molecules that are insoluble in aqueous
solutions and soluble in organic solvents are classified
as lipids
Composed of monomers of alcohol (glycerol) & fatty
acids
Fats (solid) & oils (liquid at room temp.)
 Fats associated with animals - butter
 Oils associated with plants - corn oil, olive oil

45. Types of lipids
 Four important families of lipids are:
1. Triglycerides (fats & oils) = 1 Glycerol & 3 fatty
acids
2. Phospholipids = 1Glycerol + 2 fatty acids +
Phosphate
3. Steroids = Lipids fused in rings (cholesterol)
4. Waxes (cutin, suberin) = Alcohol & 1 fatty acid

46. Function of lipids
 Provide energy reserves- fats & oils
 Insulation (subcutaneous fat) & Cushions of internal
organs
 Serve as structural components of biological
membranes
 Message (signaling) & membrane fluidity – steroids
 Hormones (testosterone, estrogen) - steroids

47. 4. Nucleic acids
 Nucleic acids are very large and complex molecules
responsible for storage, transmission, and translation
of genetic information
 Found in all cells (inside nucleus, mitochondria and
chloroplast)
 They are long chain or polymers of repeating
subunits, called nucleotides, with 4 bases [adenine,
guanine, cytosine, and thymine (in DNA) or uracil
(in RNA)]

48. They have three components
1. Nitrogeneous bases (either as purine or
pyrimidine ring)
2. Sugar (ribose or deoxyribose)
3. Phosphate groups
P
Pentose
sugar
Nitrogenous
bases

49.  There are basically two types of nucleic acids
1. DNA (Deoxyribonucleic acid)
2. RNA (Ribonucleic acid )
DNA
 Contain deoxyribose sugar
 made of two polynucleotide strands
 have thymine rather than uracil
RNA
 contain ribose sugar
 made of a single polynucleotide strand
 have uracil instead of thymine

50. 1. Nitrogenous bases
They are nitrogen-containing molecules having the
chemical properties of a base (a substance that accepts
an H+ ion or proton in solution).
Fall into two types: Pyrimidine (Cytosine, Thymine
and Uracil) and Purine (Adenine and Guanine).
The Nitrogenous bases pair up with other bases.
 specific one purine to one pyrimidine
Components of nucleotides

51. A. Pyrimidines
Are single carbon- nitrogen ring and the 6 atoms
(4 carbons, 2 nitrogen) are numbered 1-6
The two pyrimidines in DNA are cytosine and
thymine; in RNA uracil is found instead of thymine.
The only difference b/n uracil and thymine is the
presence of a methyl substituent at C5.

52. B. Purines
Are double carbon – nitrogen ring
The 9 atoms that make up the fused rings (5 carbons, 4
nitrogen atoms) are numbered 1-9.
The same two purines, adenine and guanine, are
present in both DNA and RNA.

53.  In Base pairing, always
adenine is paired with
thymine (or uracil if RNA)
and guanine is always
paired with cytosine
◦ A = T and G = C
 Once the sequence of bases
in one strand of DNA
double helix is known, it is
possible to know the other
strand sequence of base
because of specific base
pairing.

54. 2. Pentose sugar
It is a 5-carbon sugar molecule numbered as 1', 2', 3', 4' &
5', using a prime (') is to differentiate them from the
numbering of the bases
Exists as β-D-ribose (in RNA) or as β-D-2-deoxyribose
(in DNA)
The only difference b/n the two sugars is that ribose has a
-OH on 2‘-C, whereas deoxyribose has only -H in that
position.

55. 3. Phosphate group (PO4)
 It gives an acidic character of nucleotides because it dissociate
at the PH found in the cells, freeing H+
ions & leaving the
phosphate negatively charged
 Two sugars in polymerised RNA or DNA molecule are joined
by a phosphoric acid molecule which is forming an ester bond
with the 5' and 3' C.

56.  A DNA or RNA chain is
formed in a series of three
steps.
 In the first reaction, each
base is chemically linked to
one molecule of sugar at the
1′-carbon of the sugar,
forming a compound called
a nucleoside.
 The bond between the base
and sugar is called a
glycosidic bond. Nucleoside
Nucleosides and nucleotides

57.  When a phosphate group is also attached to the 5′-
carbon of the same sugar, the nucleoside becomes a
nucleotide.
 Nucleotides can possess 1, 2, or 3 phosphate groups &
labeled with α, β & γ phosphate, respectively.
 Finally, nucleotides are joined (polymerized) by
condensation reactions to form a chain (strand).
 The OH on the 3′-carbon of a sugar of one nucleotide
forms an ester bond to the phosphate of another
nucleotide, eliminating a molecule of water.
 This chemical bond linking the sugar components of
adjacent nucleotides is called a phosphodiester bond,
or 5′ → 3′ phosphodiester bond, indicating the
polarity of the strand.

58.  The structure of a nucleoside and 3 nucleotides with
differing numbers of phosphates

59.  Formation of nucleic acid chain

60.  Nucleotides may contain 1 phosphate unit
(monophosphate), two such (diphosphate), or three
(triphosphate).
 When free in the cell pool, nucleotides usually occur
as triphosphates: deoxynucleoside triphosphates
(dNTPs) and nucleoside triphosphates (NTPs)
 The triphosphate (dNTPs and NTPs) form serves as
the precursor building block for a DNA or RNA chain
during synthesis.
 Nomenclature of the nucleotides use shorthand. E.g.,
deoxycytidine triphosphate (DNA) and cytidine
triphosphate (RNA) are abbreviated to dCTP and CTP,
respectively.

61.  The letters A, G, C, T, and U stand for the bases but, in
practice, they are commonly used to represent the
whole nucleotides containing these bases.

62. Significance of 5′ and 3′
The ends of a DNA or RNA chain are distinct and
have different chemical properties. The two ends are
designated by the symbols 5′ and 3′.
The symbol 5′ refers to the carbon in the sugar to
which a phosphate (PO4) functional group is attached.
The symbol 3′ refers to the carbon in the sugar ring to
which a hydroxyl (OH) functional group is attached.
The asymmetry of the ends of a DNA strand implies
that each strand has a polarity determined by which
end bears the 5′-phosphate and which end bears the 3′-
hydroxyl group.

63.  This 5′ → 3′ directionality of a
nucleic acid strand is an extremely
important property of the molecule.
 Understanding this directionality
(polarity) is critical for
understanding aspects of replication
and transcription, for reading a
DNA sequence, and for carrying out
experiments in the lab.
 By convention, a DNA sequence is
written with the 5′ end to the left,
and the 3′ end to the right. This is
also the direction of synthesis.

64. The Central dogma of molecular genetics
Defines the relationships b/n DNA, RNA, & protein in
the transmission of genetic information into functional
units of biological activity
The flow of information from DNA to RNA to protein, but
not the reverse