By Laxman Nimbale

1. GENOME ORGANIZATION & GENE
EXPRESSION
CELLULAR AND MOLEULAR
PHARMACOLOGY
PRESENTED BY UNDERTHE GUIDELINES OF
RGUHS:
LAXMAN I. NIMBALE
M. Pharmacy
Pharmacology Dept.
1

2. CONTENTS
 INTRODUCTION
 GENOME ORGANIZATION
 CHROMOSOMES
 GENE
 NUCLEIC ACIDS
 HISTORY
 NUCLEOTIDES
 STRUCTURE OF DNA
 GENE EXPRESSION
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3. INTRODUCTION
What is a cell?
 Cell is the structural and functional unit of organism.
 Because the cell carries the entire information of an
organism, if it is multi-cellular in nature. If a single
cellular in nature it does its own function.
 The entire genetic material present in structural form
inside the cell.
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4. Types of cell
Prokaryotic Cell
Eg. Bacteria
Eukaryotic Cell
Eg.Yeast to human cell
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5. Cont…
5

6. GENOME ORGANIZATION
 Genome organization refers to the sequential
organization of the entire genes.
 Genome organization includes regulatory and
coding motifs shared among any loci.They do
not code proteins but acts as a signals
determining genome functions such as
transcription, translation, RNA processing, DNA
replication, chromatin condensation and
packaging.
6

7. CHROMOSOME:
 In the cell DNA is associated with proteins
and each DNA molecules and its associated
protein is called a CHROMOSOMES.
7
This organization holds
true
for prokaryotic and
eukaryotic cells.
Chromatid: A chromatid is one
half of a duplicated
chromosome.

8. 8

9. Number of chromosomes
9

10. GENE
 A gene is a basic unit of heredity and a
sequence of nucleotides in DNA or RNA that
encodes the synthesis of gene product.
 Genes are made up of DNA, some genes act
as an instruction to make molecules called
proteins.
10

11. Cont…
11

12. NUCLEIC ACID
 Nucleic acids serve as repositories and
transmitters of genetic information.
 There are two types of nucleic acids namely
deoxyribonucleic acids DNA and ribonucleic
acids RNA.
12

13. Cont…
13

14. HISTORY
 DNA was discovered in 1869 by Johann
Friedrich Miescher a Swiss researcher.
 The demonstration that DNA contained
genetic information was first made in 1944 by
Avery, Macleod and MacCary.
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15. NUCLEOTIDES
 These are composed of a nitrogenous base, a
pentose sugar and a phosphate
15

16. Cont…
 The bases are of two types as they;
 Purines- Adenine (A), Guanine (G)
 Pyrimidines- Cytosine (C) ,Thymine (T) and
Uracil (U)
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17. IMPORTANT NUCLEOTIDES
 Purines and pyrimidines:These are involved
in a wide variety of metaboli function.
 Sugar derivatives: namely UDP- glucose
participates in the synthesis of glycogen
 cAMP and cGMP are second messengers for
some hormonal action.
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18. STRUCTURE OF DNA
 DNA is a polymer of deoxyribonucleotide. It is
composed of monomeric units namely
deoxyadenylate (dAMP), deoxyguanylate
(dGMP), deoxycytidylate (dCMP),
deoxythymidylate (dTMP).
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19. Cont…
19

20. Cont…
 Chargaff’s rule of DNA composition: Erwin
Chargaff in late 1940 quantitatively analyzed
the DNA hydrolysates from different species.
 He observed that in all the species he studied
DNA had equal numbers of adenine and thymine
residues (A=T) and equal numbers of guanine
and cytosine residues (G=C) .This is known as
the Chargaff’s rule of molar equivalence between
the purine and pyrimidines in DNA.
20

21. Cont…
 DNA is right handed double helix which
contains two polydeoxyribonucleotide chains
twisted around each other on a common axis.
 Two strands are antiparallel
 Width of double helix is 2 nm and each turn of
the helix is 3.4 nm with 10 pairs of nucleotides
each pair placed at a distance of about 0.34
nm .
 Two strands are held together by hydrogen
bonds formed by complementary base pairs.
21

22. Cont…
 The hydrogen bonds are formed between a
purine and pyrimidine only.
 The complementary base pairing in DNA
helix proves Chargaff’s rule.
22

23. 23

24. 24

25. GENOME ORGANIZATION IN EUKARYOTES
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26. GENE EXPRESSION
 GENE EXPRESSION :
 It is the process by which a gene’s DNA sequence is
converted into the structures and functions of a cell.
 Non-protein coding genes are not translated into
protein.
 Genetic information, chemically determined by DNA
structures is transferred to daughter cells by DNA
replication and expressed byTranscription followed by
Translation.
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27. Cont…
 The series of events is called is “Central
Dogma of Life”.
 Biological information flows from DNA to
RNA and from there to proteins.
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28. Cont…
 Gene expression is a multi-step process which
involves
 Replication
 Transcription
 Translation
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29. REPLICATION OF DNA
 It is a process in which DNA copies itself to
produce identical daughter molecules of
DNA.
 DNA strands are anti-parallel and
complementary, each strand can serve as a
template for the reproduction of the opposite
strand.
 This process is called as semi-conservative
replication.
 As the newly synthesized DNA has one half of
the parental DNA and one half of new DNA.
29

30. 30

31. Steps Involved in Replication
Initiation
Elongation
Termination
31

32. INITIATION
 DNA replication starts at specific sites called
origin..
 A specific DNA a protein binds with this site
of origin and separates the double stranded
DNA.
 Separation of two strands of DNA results in
the formation of replication bubble with a
Replication Fork on either strands.
 A Primer recognizes specific sequences of
DNA in the replication bubble and binds to it.
32

33. Cont…
 Helicase- the helicase unwinds the DNA helix
by breaking the hydrogen bonds between the
base pairs.
 Topoisommerase- it introduce negative
supercoils and relieve strains in the double
helix at either end of the bubble.
 SSB proteins-These proteins stabilizes the
single strands thus preventing them to zip
back together.
33

34. 34

35. ELONGATION
 DNA polymerase III binds to the template strand
at the 3’ end of the RNA Primer and starts
polymerizing the nucleotides.
 On leading strand polymerization of nucleotides
proceeds in 5’- 3’ direction towards the
replication fork without interruption
 Lagging strand is replicated in 5’- 3’ direction
away from the replication fork in pieces known
as Okazaki Fragments.
 As DNA polymerase reaches the 5’ end of the
RNA primer of the next Okazaki fragment; it
dissociates and re-associates at the 3’ end of the
primer.
35

36. Cont…
 DNA polymerase I remove the RNA primers
and fills in with DNA.
 DNA ligase seals the nicks and connects the
Okazaki fragments.
 Helicase continues to unwind the DNA into
two single strands ahead of the fork while
topoisomerases relieves the supercoiling
caused by this.
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37. TERMINATION
 Termination occurs when DNA replication forks
meet one another or run to the end of a linear
DNA molecule.
 Also, they may occur when a replication fork is
stopped by a replication terminator protein.
 DNA ligase fills up the gaps between the Okazaki
fragments..
 If mistake or damage occurs, enzymes such as a
nuclease will remove the incorrect DNA.
 DNA polymerase will then fill in the gap..
37

38. TRANSCRIPTION
 Transcription is a process in which ribonucleic
acids (RNA) is synthesized from DNA.The
word gene refers to the functional unit of the
DNA that can be transcribed.
 Transcription involves 3 different stages-
 Initiation
 Elongation and
 Termination.
38

39. Cont…
 RNA polymerase (green) synthesizes RNA by
following a strand of DNA.
 RNA polymerase is an enzyme that is
responsible for copying a DNA sequence into
an RNA sequence, during the process of
transcription.
39

40. Different types of RNAPs
RNA Polymerase I: is located in the nucleolus and
responsible for the synthesis of precursors for
the large ribosomal RNAs.
RNA Polymerase II: is located in the nucleus and
synthesizes the precursors for mRNA and small
nuclear RNAs.
RNA Polymerase III: is located in the nucleus and
participates in the formation of tRNAs and small
ribosomal RNAs.
40

41. Intiation
 RNAP recognizes and binds to a specific
region in the DNA called promoter.
 There are two different base sequence on the
coding strand which the RNA polymerase
recognizes for the initiation of transcription.
 Pribnow box (TATA box) consisting of 6
nucleotide bases (TATAAT) and is located on
the left side about 10 bases away from the
starting point of transcription.
41

42. Cont…
 ‘_35’ sequence: This is the 2nd rcognition site in
the promoter region of DNA.
It contains a base sequenceTTGACA, which is
located about 35 base away on the left side from
the site of transcription start.
 Closed complex- RNAP binds to a double
stranded DNA and this structure .
 Open complex- after binding of RNAP, the DNA
double helix is partially unwound and becomes
single stranded in the vicinity of the initiation
site.
42

43. TRANSCRIPTION
43

44. TERMINATION
 The process of transcription stops by
termination signals.Two types of termination
are identified;
 Rho (ρ) dependent termination: A specific protein,
named ρ factor, binds to the growing RNA or
weakly to DNA and in the bound state it acts as
ATPase and terminates transcription and releases
RNA.
ρ factor is also responsible for the dissociation of
RNA polymerase from DNA.
44

45. Cont…
 Rho (ρ) independent termination: terminator
sequences within the RNA that signals the
RNA polymerase to stop.The terminator
sequence is usually a palindromic sequence
that forms a stem-loop hairpin structure that
leads to the dissociation of the RNAP from
the DNA template. Eg. ‘GCCGCCG’.
 The RNAP fails to proceed beyond this point
and nascent DNA-RNA hybrid dissociates.
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46. TRANSLATION
 The genetic information stored in DNA is passed on to RNA
through transcription and ultimately expressed in the
language of proteins.
 Translation involves “decoding” a messenger RNA (mRNA)
and using its information to build a polypeptide, or chain of
amino acids.
 The biosynthesis of a protein or a polypeptide in a living cell
is referred to asTranslation.
 Genetic code- The codon consist of the four nucleotide
bases, the purines- adenine (A) and guanine (G), and the
pyrimidines- cytosine (C) and uracil (U).
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47. Steps Involved in
Translation
 Initiation ("beginning"): in this stage, the
ribosome gets together with the mRNA and the
first tRNA so translation can begin.
 Elongation ("middle"): in this stage, amino acids
are brought to the ribosome by tRNAs and linked
together to form a chain.
 Termination ("end"): in the last stage, the
finished polypeptide is released to go and do its
job in the cell.
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48. TRANSLATION
48

49.  The initiation of translation in eukaryotes is
complex, involving at least 10 eukaryotic
initiation factors.
 The process of translation initiation can be
divided into 4 steps.
 Ribosomal dissociation
 Formation of 43S pre-initiation complex
 Formation of 48S initiation complex
 Formation of 80S initiation complex
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50. 50
INITIATION

51. 51
ELONGATION

52. 52
TERMINATION

53. 53