Structure of DNA, Organization of DNA, Function of DNA

1. Dr. Ifat Ara Begum
Associate Professor
Dept of Biochemistry
Dhaka Medical College
DNA : Structure,
Organization & Function

2. DN
A

3. Introduction
The largest macromolecules of
human body
Essential for all known forms of life
Carries the genetic instructions used in
the growth, development, functioning
and reproduction of all known
living organisms and many viruses

4. Definition of DNA
DNA may be defined as
polymer
of
deoxy ribonucleotides
connected by 3’-5’ phosphodiester
bond

5. Phosphodiester bond
A covalent bond
The linkage between the 3' carbon atom of
one sugar molecule and the 5' carbon
atom of another sugar molecule
(deoxyribose in DNA and ribose in RNA
It make up the backbone of the strands
of nucleic acid.

7. Contd
Hydrolysis of phosphodiester bonds :
Phosphodiesterases (Has important
role in repairing DNA sequences)
The phosphodiester linkage between
two ribonucleotides can be broken
by alkaline hydrolysis, whereas the
linkage between two deoxy
ribonucleotides is more stable under
these conditions

8. Contd
[Remember,
Ester is a chemical compound derived
from an acid (organic or inorganic) in which
at least one –OH (hydroxyl) group is
replaced by an –O–alkyl (alkoxy) group.]

9. Synthesis of nucleic acid
One nucleotide gets connected with
another nucleotide by 3’-5’
phosphodiester bond.
The 5’ end of newly added
nucleotide makes connection with the
3’end of existing nucleotide (primer)
to elongate the chain.
So, nucleic acid chain always
elongate by polymerization from 5’
end to 3’ end

10. Contd
After completion of synthesis:
 on one side 5’ end will always
remain free
 on the other side, 3’ end will always
remain free.
to provide polarity to nucleic acid
chain with two distinct ends

11. Contd
It is the tradition to read the base
sequence of nucleic acid chain from
5’ end to 3’end

12. Structure of DNA (Watson –
crick DNA double helical
structure)

15. Contd
DNA molecules consist of
two biopolymer chains (strands) coiled
around each other to form a double
helix (like a spiral stair case).
The two strands run in opposite directions to
each other and are thus antiparallel

16. Contd
The strands are
called polynucleotides , since they are
composed of simpler monomer units
called nucleotides (deoxy
ribonucleotides )

17. Contd
Each d-ribonucleotide is composed
of:
I.One of four nitrogen-
containing purine/pyrimidine bases :
cytosine (C), guanine (G), adenine (A)
or thymine (T)
II.A sugar called deoxyribose
III.A phosphate group.
[Nitrogen base remains attached
with 1st
carbon & the phosphate with
5th
carbon of sugar]

19. Contd
The nucleotides are joined to one
another in a chain by covalent
bonds between
the sugar of one nucleotide
and
the phosphate of the next,
resulting in an alternating sugar-
phosphate backbone.

20. Contd
The nitrogen bases of one strand interact
with the bases on the other strand to form
base pair (bp)
by hydrogen bonding between
Purine base of one strand
with
pyrimidine base of other strand.

21. Contd
This bonding occurs according to
“base pairing law”
(Specific hydrogen bonding between A-T &
G-C of two adjacent polynucleotide chains)

23. Contd
This interaction between purine &
pyrimidine bases of two strands is
highly specific to make the two
strands complementary to each other
&
thus the paired bases are called
complementary bp.

24. Contd
The complementary base pairing
always occurs between
A, T
&
G, C
so that in ds-DNA molecule ,
amount of A equals to T
amount of G equals to C
(Chargaff’s rule)

26. Contd
Each A-T base pair is held together
by two hydrogen bonds
Each G-C base pair is held together
by three hydrogen bonds

28. Contd
Two NA chains are regarded
complementary to each other
if their base sequence in their side
by side antiparallel position is found
capable of base pairing
according to “base pairing law”

29. Contd
Two strands of DNA can be
separated after disruption of the
hydrogen bonds between the
complementary base pairs.
Disruption can be done by
alteration of pH or by heating

30. Contd
Remember,
 It is the sequence of the four
nucleobases along the backbone that
encodes biological information
Unit of DNA length: bp
A typical human cell has 7000 Mb
1 Kilo base (Kb) = 1000 bp
1 mega base (Mb) = 10,00000
bp

31. Grooves in DNA
Grooves arise from the unequal
spacing of phosphate- sugar
backbone around the axis of the
helix.

32. Contd
The major groove occurs where the
backbones are far apart. It is 22 Å wide
The minor groove occurs where they are
close together. It is 12 Å wide

33. Contd
]
The width of the major groove means that
the edges of the bases are more
accessible in the major groove than in the
minor groove.

34. Contd
As a result, proteins such as transcription
factors that can bind to specific sequences
in double-stranded DNA usually make
contact with the sides of the bases
exposed in the major groove

35. Types of DNA

36. Mitochondrial DNA (1%
of cellular DNA)
Nuclear DNA
Circular & double
stranded (2-10 copies)
Linear & double stranded
Inherited from mother only Inherited from both of the
parents
37 genes 20000 ? (30000 ?) genes
Codes for 22
mitochondrial tRNA, 2
mitochondrial rRNA & 13
PP that are required in
respiratory chain
Not so

37. Mitochondrial DNA Nuclear DNA
Genetic code differs. e.g.
UGA codes tryptophan
Genetic code differs. . e.g.
UGA is a stop codon
No histones & introns Has histones & introns
No repair /proof reading
mechanism
Has repair /proof reading
mechanism
No recombination Varied by recombination
Rate of mutation : Higher Rate of mutation: Lower

38. Contd
Remember,
 mtDNA has heavy strand ( site of most
genes) & light strand (site of few genes)
 AGA & AGG which are codon for Arg, are
stop codon for mtDNA
 Respiratory chain of mitochondria needs
67 proteins to operate . Only 13 of them
are coded by mtDNA.

40. Coding DNA sequence Non-coding DNA
sequence
Single, non-repetitive,
unique DNA sequence
which includes single
copy genes that code for
proteins
DNA sequence which
does not encode for
proteins. It includes low
copy number DNA
sequence & repetitive
DNA sequence
e.g. exons e.g. introns
Genes only account
for ~ 1.5% of the total
sequence
The rest are non coding.

43. Function of non coding
DNA
i. DNA packaging
ii. Gene expression
iii. Gene mapping
iv. Genetic polymorphism

45. What is it?
It refers to regions of DNA that are
noncoding.
 Almost all (98%) of the DNA is noncoding

46. DNA
Organizatio
n

47. Introduction
Total DNA of cell:
6 x 109
bp
1.5 – 2.0 meter long in uncoiled
straight form
The average diameter of the nucleus is
approximately 6 micrometers (µm), which
occupies about 10% of the
total cell volume.

48. Contd
So, to be accommodated within the nucleus,
DNA is compacted by coiling & super coiling
with the help of histone (H) & nonhistone
nucleoprotein
and finally organized in to chromosomes
[That means, chromosome is nothing but a
long DNA in coiled & folded form]

49. Contd
 Total DNA of a cell is divided among 46
chromosomes (23 pairs), 44 are autosomes
& 2 are sex chromosomes (XY)
 The length of DNA filament of a single
chromosome is about 50 mm which is
reduced to ≤ 5 µm following organization

50. Steps of DNA organization
Four steps:
1.Synthesis of histone core
2.Formation of polynucleosome string
3.Formation of chromatin
4.Formation of chromosome

52. 1. Synthesis of histone core
Globular aggregate of eight (08) histone
proteins forming an octameric histone core
Each core consists of two molecules of
each of the four core histone proteins
(H2A, H2B, H3 and H4).

54. 2. Formation of polynucleosome
string
Helical DNA double strand encircles each
histone core twice
to make
a nucleosome unit

56. Contd
i.e. nucleosome is composed of
DNA
wound around
the octameric histone core

58. Contd
Each nucleosome is separated by
a short segment of DNA (50 bp) called
linker DNA
intercepted with
H1 (linker histone)
between them.

60. Contd
Now, the DNA along with the histone core
takes the look of
beaded string
or
beads on string appearance

61. Contd
Wrapping of histone core accommodates
about 146 bp
&
together with half of the linker DNA with
either side , each of the nucleosome roughly
accommodates about 200 bp by decreasing
the length of DNA with increasing thickness

62. 3. Formation of chromatin
Beaded polynucleosome string is further
coiled into supercoiled solenoid form called
chromatin.
[ i.e. supercoiled form of polynucleosome
string is chromatin]
Chromatin is not visible under microscope
It disperses throughout the nucleus during
interphase of cell cycle

64. 4. Formation of chromosome
Chromatin molecules, during cell division
(esp. at metaphase), are further condensed
100 fold into a giant supercoiled visible form
called chromosome
This progressive folding reduces the length
of DNA to ≤ 5 µm in each chromosome
Non histone protein plays central role here

66. Orders of DNA coiling into
chromosomes
Four orders:
1. Primary coiling of two DNA strands into
Watson-Crick double helical structure
2. Secondary coiling of DNA double helix
around nucleosome to make
polynucleosome string

67. Contd
3. Tertiary coiling of polynucleosome string
to form supercoiled chromatin
4. Quaternary supercoiling of chromatin to
form chromosome

69. Nice to remember
 Total genome of 46 chromosomes (2n)
contains 6 x109
bp
 Haploid genome of 23 chromosomes (n)
contains 3 x109
bp
The entire haploid genome contains sufficient
DNA to code for nearly 1.5 million average
sized genes
(whereas Human gene ≤ 1 lac)

70. Chromosome
Chromosomes are maximum contracted,
condensed & visible threads of chromatin
seen under microscope during metaphase of
cell cycle
Or
A chromosome is an organized package of
DNA found in the nucleus (& mitochondria) of
the cell.

72. Contd
 Excluding sperm and egg cells, humans have
46 chromosomes in each cell, 44 autosomes
& 2 sex chromosomes (XX or XY)
 Each autosome has another chromosome
identical to it & these 2 form a pair of
homologous chromosomes.
Every member of such homologous
chromosome is called homologue.

73. Contd
 So, there are 22 pairs of autosomes & 1 pair
of sex chromosome
 Each parent contributes one chromosome to
each pair so that offspring get half of their
chromosomes from their mother and half from
their father.

74. Contd
 Homologous chromosomes (autosome) are
identical to one another with respect to:
• Length
• Physical look
• Number of :
i. Gene
ii.Gene loci

75. Contd
• Banding pattern
• Position of :
i. centromere
ii.Gene loci

76. Contd
 Paired autosomal chromosomes are
numbered according to their decreasing
length from chromosome 1 to chromosome
22
&
then sex chromosome pair (XX or XY) is
numbered as 23

78. Contd
So,
 The tallest chromosome: 1st
autosomal pair
(chromosome 1)
 The shortest chromosome: Sex
chromosome pair (Y is smaller than X . i.e.
Y chromosome is the shortest one)

79. Contd
 One member from each paired homologous
chromosome makes a set of 23
chromosomes.
Therefore, a complete set of chromosome
(haploid/n chromosome) consists of 22
autosome & 1 sex chromosome.

80. Contd
 Chromosomes are not uniform in width
throughout the whole length.
A constricted (narrowest) area is found
called centromere which divides the
chromosome into 2 arms:
 Short arm denoted by “p”
 Long arm denoted by “q”

82. Terminology
related to
Chromosom
e

83. Cytogenetics
 Morphological study of chromosome directly
under microscope or on photomicrograph
 Needs live dividing cells. e.g. lymphoblast,
fibroblast etc

84. Ploidy
 The number of chromosome set (n) in a cell
is called ploidy.
One set chromosome means 23
chromosomes , selecting one from each of
23 pairs of homologous chromosomes.
 One set of 23 chromosomes is symbolized
as “n”

85. Contd
i.e.
 n (Haploid) chromosome:
22 autosome & 1 sex chromosome .
Found in sperm, ova
 2n (Diploid) chromosome:
Found in normal somatic cell
 3n (Triploid) , 4n (tetraploid) :
Found in chromosomal anomaly

86. Euploidy
 An exact integral multiple of haploid
chromosome number (n) .
 e.g. 2n, 3n, 4n

87. Aneuploidy
 Irregular number of chromosome
 Not an exact integral multiple of haploid
chromosome number (n).
 Involves loss/gain of chromosome
 e.g. 45 chromosome, 47 chromosome

88. Polyploidy
 Any exact integral multiple of haploid
chromosome number (n) except 2n.
 e.g. 3n, 4n

89. Somy
 Number of the copy of individual
chromosome
 Normal somatic cells contain two copies of
each chromosome as homologous pair. So,
they are disomic
 A mature gamet (sperm/ova) contains one
copy of each chromosome, so regarded as
monosomic

90. Metaphase
chromosome

91. Definition
It is the chromosome in a specific stage of
the cell cycle (i.e. metaphase of mitosis)
when it is most condensed and easiest to
distinguish and so to study.
At metaphase, each chromosome replicates
to make a paired structure. Each member of
the replicated paired structure is called sister
chromatid.

93. Contd
Remember,
 Metaphase is the third phase of mitosis
 Mitosis is the process that separates
duplicated genetic material carried in the
nucleus of a parent cell into two identical
daughter cells

94. Important features of
metaphase chromosome

95. 1. Chromatid
 A chromatid is one of two identical halves of a
replicated chromosome
 During cell division, the chromosomes first
replicate so that each daughter cell receives a
complete set of chromosomes.
 Following DNA replication,
the chromosome consists of two identical
structures called sister chromatids, which are
joined at the centromere

97. 2. Centromere
 The part of a chromosome that links sister
chromatids .
 Each metaphase chromosome contains a
centromere (primary constriction),
 It divides the chromosome into two parts
(chromosomal arms)
p; Small arm
q: Large arm

98. Contd
 When chromosomes are represented as a
karyotype, each chromosome is arranged in
such a way that “p” arm lies above the
centromere & “q” arm lies below the
centromere.
 During mitosis, spindle fibers attach to the
centromere via the kinetochore
[Kinetochore: Protein complex on the
centromere to which spindle microtubules
attach]

100. Contd
 The position of centromere & the relative
size of chromosomal arms are used as a
criterion for a morphological classification of
chromosome

101. Metacentric Submetacentri
c
Acrocentric
Centromere is
located approx.
centrally
Centromere is
located slightly
away from the
centre (b/w
midpoint &
endpoint)
Centromere is
located terminally
very close to one
end
Two arms are
almost equal in
length
Two arms are of
unequal length
Two arms are of
unequal length
(one arm is very
short & the other
is long)

102. Metacentric Submetacentric Acrocentric
Example:
chromosome 1
Example:
chromosome 2
Example:
chromosome 13

103. 3. Telomere
 A region of repetitive nucleotide sequences
(3’-TTAGGG-5’) at each end of a
chromosome
 Functions:
• Maintain stability of chromosome
• Assist in chromosome pairing during meiosis
• Ensure complete replication of chromosome
extremities
• Prevent abnormal end to end fusion of
chromosome

104. 4. Chromatin
Two varieties:
1.Euchromatin : Light staining area. It contains
high density of gene & is transcriptionally
active
2.Heterochromatin: Dark staining area. It
contains few/no gene & is transcriptionally
inert

105. 5. Chromosomal banding &
nomenclature
 Each chromosomal arm is subdivided into
regions primarily based on Giemsa staining
of chromosomes, numbered from the
centromere outwards towards the telomere,
e.g. 7p1 means the first region of the short
arm of chromosome 7.

106. Contd
 With increased resolution, further
subdivisions are added depending on
alternating light and dark bands.
e.g. 7q11.22 means the long arm of
chromosome 7 in region 1, band 1, sub-
band 2, sub-sub-band 2.
The correct way to read the notation is
"seven q one one dot two two" and not
"seven q eleven dot twenty-two".

107. Contd
 The ends of the chromosomes are labeled
ptel and qtel.
For example,
The notation 7qtel refers to the end of the
long arm of chromosome 7.
[In fact, these regions , band, sub bands etc
function as physical landmark of
chromosome in gene mapping]

109. Contd
Nice to remember:
 The most commonly used method in human
chromosome banding is G-banding.
 The chromosomes are treated with trypsin &
stained with Giemsa which predominantly
binds AT rich region, producing alternate
dark band (Giemsa positive, AT- rich)
&
light band (Giemsa negative, GC- rich)

110. Contd
 As genes are preferentially associated with
GC rich regions,
Dark bands in G- banding are gene poor
Light bands are gene rich

112. Nucleoprote
in

113. Definition
It is a conjugated protein where nucleic acid
as non protein prosthetic group is conjugated
with protein

114. Types
Protein part of nucleoprotein is of 2 types:
1.Histone protein (H): H1, H2A, H2B, H3 and
H4
2.Non-histone protein: Topoisomerase, DNAP,
RNAP, gene regulatory protein etc

115. 1. Histone protein
LMW
Basic in nature
Strongly cationic
Due to positive charge, they have strong
affinity to associate with the negatively
charged nucleic acid chain

116. 2. Non-histone protein
Acidic in nature
Represent very small amount of
nucleoprotein
Usually these are regulatory proteins &
enzymes of replication, transcription, DNA
repair

117. Function
DNA organization & packing
Stabilization of DNA structure
Regulation of gene expression

118. Functions of
DNA

119. Function
Chemical basis of heredity
 i.e. store, replicate & transmit genetic
information
 Information on how, when & where to make
proteins
 In other words, DNA codes for the primary
structure of protein which impacts the tertiary
structure that determines the function of
protein