genetics

1. INTRODUCTION
TO GENETICS
SUBMITTED BY: ANUPAM PRAHLAD
FIRST M.PHARM

2. GENETICS
– The branch of biology that deals with heredity,
especially the mechanisms of hereditary transmission
and the variation of inherited characteristics among
similar or related organisms

3. GENE
• Biological unit of heredity
• Gene hold the information to build and maintain
their cells and pass genetic traits to offsprings
• In cells, a gene is portion of DNA

4. Gene (DNA)
RNA formation
Protein formation
Cell structure
Cell enzymes
cell function

5. CHROMOSOMES
• They are the rod-shaped, filamentous bodies
present in the nucleus, which become visible during
cell division.
• They are the carriers of the gene or unit of heredity
• Chromatin: DNA, RNA & proteins that make up
chromosme
• Chromatids: one of the two identical parts of the
chromosome
• Centromere: the point where two chromatids
attach

6. • 46 chromosomes : 22 pairs Autosomes and 1 pair
Sex chromosomes.

7. DNA
• Deoxyribonucleic acid (DNA) is a molecule that carries
the genetic instructions used in the growth, development,
functioning and reproduction of all known
living organisms and many viruses.
• DNA and RNA are nucleic acids.
• They consist of four deoxynucleotides
• DNA has three main components
1. deoxyribose (a pentose sugar)
2. base (there are four different ones)
3. phosphate

8. • Bases are divided into two groups
1.Pyrimidines
2. Purines
PURINE BASES
• Made of a 6 member ring, fused to a 5 membered ring.
• They comprises of adenine and guanine
• Adenine is 6-amino purine and guanine is 2-amino,6-oxypurine

9. PYRIMIDINE BASES
• Made up of a 6member ring.
• The pyrimidine bases are cytosine and thymine.
• Cytosine is present in both DNA and RNA
• Thymine is present only in DNA. uracil is present
in RNA

10. NUCLEOTIDES
• They are phosphate esters of nucleosides
• Base + sugar +phosphate = nucleotide
• The esterification occurs at the fifth and third
hydroxyl group of pentose sugar.
• Nucleotides are linked by covalent bonds
called PHOSPHODIESTER LINKAGES

11. STRUCTURE OF DNA
• DNA is apolymer of deoxribo nucleotides .
• It s made of monomeric units mainly dAMP, dGMP,
dDCMP, dTMP
• Made of two strands of nucleotides that are joined
together by hydrogen bonding
• Hydrogen bonding occurs as a result of
complimentary base pairing.
• Adenine and thymine pair up
• Cytosine and guanine pair up
• Each pair is connected through hydrogen bonding
• Hydrogen bonding always occurs between one
pyrimidine and one purine

12. • The monomeric deoxynucleotides in DNA are
held together by 3’-5’phosphodiester bridges
• DNA structure is often represented in a short
hand form.

13. CHARGAFF’S RULE OF DNA DECOMPOSITION
• Erwin Chargaff in late 1940’s quantitatively
analysed the DNA hydrolysates from different
species.
• He observed that in all species DNA had equal
number of adenine and thymidine residues (
A=T) and equal number of guanine and cytosine
residues(G=C)
• This is known as Chargaff’s rule of molar
equivalence between the purines and
pyrimidenes

14. WATSON AND CRICK MODEL OF DNA
• Watson and Crick used the empirical data of
Franklin, Wilkin, and Chargaff to come up with a
model of the DNA structure.
• It was an important finding to the field of
molecular biology and genetics.
• They published a 900 words paper and Franklin and
Wilkin also published on the same issue of Nature.

15. 1) DNA is a double helix.
• It is aright handed double helix.
2) Two polynucleotides chains
It consist of 2 polydeoxyribonucleotide
chain twisted around each other on a
common axis

16. 3.The two chains wind around right
handedly - right handed double helix.

17. 4. Two chains are in an anti-parallel
orientation. (one strand 5’ – 3’ orientation
and the other 3’ – 5’).

18. 5. Each strand of DNA has a hydrophilic deoxy ribose
phosphate backbone( 3’-5’ phosphodiester bonds) on
the outside of molecule while the hydrobhobic bases
are stacked inside the core
• Sugar-phosphate backbone is located on the outside of
the helix

19. 6. The bases are stacked flat and perpendicular to the
two polynucleotides are bonded together via
hydrogen bonds on the inside of the helix.
The bases are on top of each other following the
twist of the helix.

20. 7. The 2 strands are held together by hydrogen bonds
formed by complementary base pairs.the A-T base air
has 2 hdrogen bonds
• The G-C has 3 hydrogen bonds. The G=C is stronger b
about 50% than A=T

21. 8. The complementary base pairing in DNA helix proves
chargaff’s rule.
9. Bases of the two polynucleotide chains are base-
pairing to maintain similar diameter of the double
helix.

22. 10. The sequence of one chain (strand) is enough to predict
the complementary one in the other orientation
11. there are two grooves found in DNA molecule namely
Major groove and Minor groove
– The width of DNA molecule is 20 Å.
– The strand completes a turn every 34 Å along its length.
– There are ten nucleotides per turn.
– The inter nucleotide distance 3.4 Å.

23. CONFIRMATIONS OF DNA DOUBLE HELIX
• Variation in the confirmation of the nucleotides of DNA
is associated with the confirmational variants of DNA
• The double helical structure of DNA exist in atleast 6
different forms, A-E and Z.
• The B form of DNA double helix described by Watson
and Crick is the most predominant form under
physiological conditions
• Each turn of the B form has 10 base pairing spanning a
distance of 3.4nm.
• The width is about 2 nm.

24. • The A form is also a right handed helix
• It contains 11 base Pair per turning
• There is a tilting of the base air from central axis
• The Z form is left handed helix and contains 12 base pairs
per turn
• The polynucleotide strands of DNA move in a somewhat
zig zag fashion, hence the name Z-DNA

25. COMPARISON OF SRUCTURAL FEATURES OF
DIFFERENT CONFIRMATIONS OF DNA HELIX
FEATURE B-DNA A-DNA Z-DNA
Helix type Right handed Right handed Left handed
Helical
diametre
2.37 2.55 1.84
Distance per
each
complete
turn(nm)
3.4 3.2 4.5
Rise per base
pair
.34 .29 .37
No:of base
pairs per
complete turn
10 11 12
Base pair tilt +19 -1.2 -9
Helix axis
rotation
Major groove Through base
pairs
Minor groove

26. OTHER TYPES OF DNA STRUCTURE
1.Bent DNA
• In general ,adenine base containing DNA tracts are rigid
and straight
• Bent confirmations of DNA occurs when A-tracts are
replaced by other bases or a collapse of the helix into the
minor groove of A tract
• Bending has also been reported due to photochemical
damage or mispairing of bases
• Certain antitumor drugs (cisplatin) produce bent structures
in DNA

27. 2.TRIPLE STRANDED DNA
– Occur due to additional hdrogen bond between the bases
– Thus a thymine can selectively form 2 Hoogsten
hydrogen bonds to the adenine of A-T pair to form T-A-T.
– Likewise, cytosine can form C-G-C.
– They are less stable than double helices due to the fact
that the three negatively charged backbone strands in
triple helix results in increased electrostatic repulsion

28. • Polynucleotide with very high contents of guanine can
form a novel tetrameric structure called G-quartlets
• These structures are planar and are connected by
Hoogsteen bonds
• Antiparallel four stranded DNA structures referred to as G-
tetralexes have also been reported
• G tetralexes have been implicated in the recombination f
immunoglobulin genes and in dimerisation of double
stranded genomic RNA of HIV.

30. DNA REPLICATION

31. • When the cell divides , the daughter cell receive an
identical copy of genetic information from the parent
cell
• Replication is a process in which DNA copies itself to
produce identical daughter molecule of DNA
• It is a complex process that occurs in all living organism
and copies their exact DNA.
• It is the basis for biological inheritance
• Replication is carried out with high tidelity which is
essential for the survival of species
• Delbruck suggested that Watson-Crick model of DNA
could theoritically be replicated by 3 modes
-conservative
-semi conservative
-dispersive

32. • MESELSON and STAHL in 1958 proved that DNA
replication is semi conservative in vivo
• In the daughter cell, one strand is derived from
mother cell while the other strand is newly
synthesised
• This is called semi conservative type of DNA
replication
• Each strand serve as a template over which a
new complementary strand is produced

33. • Parenteral strands are not degraded
• Base pairing allows each strand to serve as a
template strand for a new strand
• New duplex is ½ parent template and ½ new DNA

34. STEPS IN DNA REPLICATION
1) Identification of origin of replication
2) Unwinding of DNA to provide a template strand
3) Formation of replication fork .
4) Direction of DNA replication
5) Synthesis of RNA primer
6) chain elongation
7) Excision of RNA primer and their replacement by DNA
8) DNA ligase action
9) Termination

35. INITIATION
• DNA replication initiate from specific sequences of Origin
of replication (ORI) called Replisomes.
• The origin of replication in bacteria is called ori whereas in
higher organisms known as replicators
• This area is recognized by specific proteins called origin
recognition complex
• Eukaryotic cells have multiple replication sites.
• To initiate replication process, multiple replicative proteins
must assemble on these replication sites.
• It leads to formation of Pre-replication complex (pre-RC).

36. Pre-replication complex has steps :
1.association of Origin recognizing complex (ORC) with
replication origin.
2. binding of Cdc6 protein to ORC
3. binding of Cdt1 and minichromosome maintenance
protein.
• This replicative complex assembly occurs during G1 phase
prior to S phase.
• During the transition between G1 phase to S phase, CDK
proteins and DDK proteins get attached to the Pre-
replication complex.
• It transforms the Pre-replication complex into active
replication fork.

38. REPLICATION FORK
• As the two strands unwind and separate, they form a “Y
shaped” where active synthesis occurs. This region is called
the replication fork.
• DNA helicase unwinds the double helix.
• The replication fork moves at the rate of 1000 nucleotides
per second.
• SSB protein helps to keep the strand separated.
• As the two strands of the double helix are separated, a
problem is encountered, namely, super-coiling in the
region of DNA ahead of the replication fork.

39. • The accumulating positive supercoils interfere with
further unwinding of the double helix
• To solve the problem of super-coiling, there is a group
of enzymes called DNA topoisomerases, which are
responsible for removing supercoils in the helix.
• These enzymes reversibly cut one strand of the double
helix.
• They have both nuclease (strand-cutting) and ligase
(strand- resealing) activities.

40. DIRECTION OF REPLICATION
• The DNA polymerases responsible for replication are
only able to “read” the parental nucleotide sequences
in the 3′→5′ direction, and they synthesize the new
DNA strands only in the 5′→3′ (anti- parallel) direction.
Leading strand
• The leading strand is the strand of nascent DNA which
is being synthesized in the same direction as the
growing replication fork.
• A polymerase "reads" the leading strand template and
adds complementary nucleotides to the nascent
leading strand on a continuous basis.
Lagging strand: This strand is extended away from the
replication fork and synthesized discontinuously in
small fragments known as Okazaki fragments, each
requiring a primer to start the synthesis.

41. RNA PRIMER
• DNA polymerases cannot initiate synthesis of a
complementary strand of DNA on a totally single-stranded
template. Rather, they require an RNA primer, with a free
hydroxyl group on the 3′-end of the RNA strand.
• A specific RNA polymerase, called Primase (DnaG),
synthesizes the short stretches of RNA (approximately ten
nucleotides long) that are complementary and anti-
parallel to the DNA template.
• These short RNA Primer are constantly being synthesized
at the replication fork on the lagging strand, but only one
RNA sequence at the origin of replication is required on
the leading strand.

42. CHAIN ELONGATION
• DNA polymerases elongate a new DNA strand by
adding deoxy- ribonucleotides, one at a time, to the
3′-end of the growing chain.
• DNA chain elongation is catalyzed by DNA
polymerase III.
• The new strand grows in the 5′→3′ direction, anti-
parallel to the parental strand .
• Pyrophosphate (PPi) is released when each new
deoxynucleoside monophosphate is added to the
growing chain.
• This newly added nucleotide would now polymerase
with one another forming the next phosphodiester
bond.

43. EXCISION OF RNA PRIMERS AND THEIR
REPLACEMENT BY DNA
• DNA POL I removes the RNA primer and fills the gap
between Okazaki fragments.
DNA LIGASE ACTION
• The final phosphodiester linkage between the 5′-phosphate
group and the 3′-hydroxyl group on the chain is catalyzed
by DNA ligase.
TERMINATION
• Termination of DNA replication in E. coli is mediated by
binding of the protein, TUS (Terminus Utilization Substance)
to replication termination sites (Ter sites) on the DNA,
stopping the movement of DNA polymerase.

44. TRANSCRIPTIO
N

45. – Transcription is the first step of gene expression, in which a
particular segment of DNA is copied
into RNA (especially mRNA) by the enzyme RNA polymerase.
Transcription proceeds in the following general steps:
– RNA polymerase, together with one or more general
transcription factors, binds to promoter DNA.
– RNA polymerase creates a transcription bubble, which
separates the two strands of the DNA helix. This is done by
breaking the hydrogen bonds between complementary DNA
nucleotides.
– RNA polymerase adds RNA nucleotides (which are
complementary to the nucleotides of one DNA strand).

46. – RNA sugar-phosphate backbone forms with assistance
from RNA polymerase to form an RNA strand.
– Hydrogen bonds of the RNA–DNA helix break, freeing the
newly synthesized RNA strand.
– If the cell has a nucleus, the RNA may be further
processed. This may include polyadenylation, capping,
and splicing.
– The RNA may remain in the nucleus or exit to
the cytoplasm through the nuclear pore complex.

47. TEMPLATE STRAND
– The strand that is transcribed or copied into an RNA
molecule is referred to as the template strand of the DNA.
– The other DNA strand, the non-template strand, is
frequently referred to as the coding strand of that gene.
Biochemistry For Medics- Lecture Notes 6
– The information in the template strand is read out in the
3' to 5' direction
– The sequence of ribonucleotides in the RNA molecule is
complementary to the sequence of deoxy ribonucleotides
in template strand of the double-stranded DNA molecule
– In the coding strand (complementary strand) the
sequence is same as that of the sequence of nucleotides in
the primary transcript.

48. TRANSCRIPTION UNIT
– A transcription unit is defined as that region of DNA that
includes the signals for transcription initiation, elongation,
and termination.
– DNA-dependent RNA polymerase is the enzyme
responsible for the polymerization of ribonucleotides into
a sequence complementary to the template strand of the
gene.
– The enzyme attaches at a specific site—the promoter—on
the template strand.
– This is followed by initiation of RNA synthesis at the
starting point, and the process continues until a
termination sequence is reached.

50. PRIMARY TRANSCRIPT
– The RNA product, which is synthesized in the 5' to 3'
direction, is the primary transcript.
– In prokaryotes, this can represent the product of several
contiguous genes
– In mammalian cells, it usually represents the product of a
single gene
– The 5' terminals of the primary RNA transcript and the
mature cytoplasmic RNA are identical.
– The starting point of transcription corresponds to the 5'
nucleotide of the mRNA.
– This is designated position +1, as is the corresponding
nucleotide in the DNA

51. – The numbers increase as the sequence proceeds
downstream.
– The nucleotide in the promoter adjacent to the
transcription initiation site is designated -1,
– These negative numbers increase as the sequence
proceeds upstream, away from the initiation site

52. DNA-Dependent RNA Polymerase
– The DNA-dependent RNA polymerase (RNAP)is the
complex consisting of
-two identical α subunits
-similar but not identical β and β ' subunits,
-ω subunit
-A sigma subunit (σ)
-Beta is thought to be the catalytic subunit
RNAP, a metalloenzyme, also contains two zinc molecules.
The core RNA polymerase associates with a specific protein
factor (the sigma σ factor) that helps the core enzyme
recognize and bind to the specific deoxynucleotide sequence
of the promoter region to form the preinitiation complex
(PIC)

53. • Mammalian cells possess three distinct nuclear
DNA-Dependent RNA Polymerases
• RNA polymerase I is for the synthesis of r RNA
• RNA polymerase II is for the synthesis of m RNA and
miRNA
• RNA polymerase III is for the synthesis of tRNA/5S
rRNA, snRNA

54. STEPS OF RNA SYNTHESIS
• Initiation phase: RNA-pol recognizes the promoter
and starts the transcription.
• Elongation phase: the RNA strand is continuously
growing.
• Termination phase: the RNA-pol stops synthesis and
the nascent RNA is separated from the DNA
template.

55. i) Initiation of Transcription
– Initiation of transcription involves the binding of the RNA
polymerase holoenzyme to the promoter region on the DNA
to form a preinitiation complex, or PIC
– Characteristic "Consensus" nucleotide sequence of the
prokaryotic promoter region are highly conserved
Pribnow box
– This is a stretch of 6 nucleotides ( 5'- TATAAT-3') centred about
8-10 nucleotides to the left of the transcription start site.
-35 Sequence
– A second consensus nucleotide sequence ( 5'- TTGACA-3'), is
centred about 35 bases to the left of the transcription start
site.

56. – Binding of RNA-polymerase (RNAP) to the promoter region is
followed by a conformational change of the RNAP, and the first
nucleotide (almost always a purine) then associates with the
initiation site on the subunit of the enzyme.
– In the presence of the appropriate nucleotide, RNAP catalyzes
the formation of a phosphodiester bond, and the nascent
chain is now attached to the polymerization site on the
subunit of RNAP.
– In both prokaryotes and eukaryotes, a purine ribonucleotide is
usually the first to be polymerized into the RNA molecule.
– After 10–20 nucleotides have been polymerized, RNAP
undergoes a second conformational change leading to
promoter clearance.
– Once this transition occurs, RNAP physically moves away from
the promoter, transcribing down the transcription unit,
leading to the next phase of the process, elongation.

57. Elongation step of Transcription
– As the elongation complex containing the core RNA
polymerase progresses along the DNA molecule, DNA
unwinding must occur in order to provide access for
the appropriate base pairing to the nucleotides of the
template strand.
– The extent of this transcription bubble (i.e., DNA
unwinding) is constant throughout and is about 20
base pairs per polymerase molecule
– RNA polymerase has associated with it an
"unwindase" activity that opens the DNA helix.
– Topo isomerase both precedes and follows the
progressing RNAP to prevent the formation of super
helical complexes.
– Base pairing rule is followed during the incorporation

59. Termination of transcription
– Termination of the synthesis of the RNA molecule in
bacteria is of two types
a) Rho (ρ) dependent termination
b)Rho (ρ) independent termination
Rho (ρ) dependent termination
The termination process is signalled by a sequence in the
template strand of the DNA molecule—a signal that is
recognized by a termination protein, the rho (ρ) factor.
Rho is an ATP-dependent RNA-stimulated helicase that
disrupts the nascent RNA-DNA complex

61. Rho independent termination
This process requires the presence of intrachain self
complementary sequences in the newly formed primary
transcript so that it can acquire a stable hair pin turn that slows
down the progress of the RNA polymerase and causes it to pause
temporarily.
Near the stem of the hairpin, a sequence occurs that is rich in G
and C.
This stabilizes the secondary structure of the hair pin.

62. – Beyond the hair pin, the RNA transcript contains a strings
of Us, the bonding of Us to the corresponding As is weak.
– This facilitates the dissociation of the primary transcript
from DNA.
– After termination of synthesis of the RNA molecule, the
enzyme separates from the DNA template.
– With the assistance of another factor, the core enzyme
then recognizes a promoter at which the synthesis of a
new RNA molecule commences

63. RNA SPLICING
In eukaryotes RNA transcripts have long non-coding
stretches of nucleotides -these regions will not be
translated .
• The non-coding sections are dispersed between coding
sections
• Introns-non-coding sections of nucleic acid found
between coding regions
• Exons -coding regions of nucleic acids (eventually these
are expressed as amino acids)
• RNA polymerase transcribes introns and exons-this is pre-
mRNA .
• Pre-mRNA never leaves the cell’s nucleus.
• The introns are excised and exons are joined together to
form mRNA

65. THANK YOU