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Structure of DNA, Its
Organization & Functions
Dr. Ifat Ara Begum
Associate Professor
Department of Biochemistry
Dhaka Medical College, Dhaka
Structure of DNA, Its Organization & Functions
Different types of RNA , Cell Cycle
Presented by:
Dr. Sharmin Sultana
M.Phil Student, Part II
Department of Biochemistry
Dhaka Medical College, Dhaka
DNA
 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
Definition of DNA
 Polymer of deoxyribonucleotide / d-ribonucleotide
connected by 3’-5’ phosphodiester bond
d-ribonucleotide
=
deoxy ribose sugar + phosphate + nitrogen base
3′-5′ phosphodiester bond
 A covalent bond between
adjacent nucleotides
 It is formed between:
the phosphate group (attached to
5’ carbon of sugar) of one
nucleotide & the OH group
(attached to 3’ carbon of sugar)
of next nucleotide
 Very strong bond, so, DNA is
remarkably stable
 It makes up the backbone of
the strands of nucleic acid
 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 this condition
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
 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
 It is the tradition to read the
base sequence of nucleic acid
chain from 5’ end to 3’end
Structure of DNA
(Watson –Crick double helix)
 DNA molecule consists
of two polynucleotide
strands
 Each strand is a polymer
of deoxyribonucleotides
connected by
3’-5’ phosphodiester
bond
A 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
Deoxyribonucleotide
 Phosphate remains attached with 5th carbon of pentose sugar
 Nitrogen base remains attached with 1st carbon of pentose sugar
 A phosphodiester bond is a
covalent bond that is formed
between the phosphate
group and two 5-carbon ring
carbohydrates (pentoses)
over two ester bonds.
 In this manner, each strand of
DNA has an
alternating sugar-phosphate
backbone
 The two strands run in
opposite directions to each
other and are
thus antiparallel
 The two strands wound
around each other in a
double helix form like a
spiral stair case
 Type of DNA helical
structure here: B-form.
i.e.
A right handed helical
structure containing 10 bp
per turn
 The purine bases of one strand
connect with the pyrimidine bases on
the other strand by hydrogen bonds
to form base pair (bp)
 This interaction between purine and
pyrimidine bases of two strands is
highly specific to make the two strand
complementary to each other
and
the paired bases may be called
complementary base pair (bp)
 Complementary base pairing always
occur between adenine (A) of one strand
& thymine (T) of other strand
Or
between guanine (G) of one strand &
cytosine (C) of other strand
(Base Pairing Law)
 Thus in dsDNA molecule, the amount of
adenine equals to thymine & the amount
of guanine equals to cytosine
(Chargaff’s rule)
 Base pairing law:
 Specific hydrogen bonding between
adenine – thymine and guanine –
cytosine of two adjacent polynucleotide
chains
 Each A-T base pair is held together by
two hydrogen bonds
 Each G-C base pair is held together by
three hydrogen bonds.
Chargaff’s rule:
DNA from any cell of any organisms
should have a 1:1 ratio of pyrimidine
and purine bases
i.e.
The amount of guanine should be
equal to cytosine and the amount of
adenine should be equal to thymine.
 The two polynucleotide chains
may be 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
Grooves in DNA:
 Grooves arise from the
unequal spacing of
phosphate- sugar backbone
around the axis of the helix
 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
 ]The edges of the bases are more accessible in the
major groove than in the minor groove.
 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
Types of DNA Helical
Structure
B - Form A - Form Z - Form
Right handed
helical structure
first described by
Watson- Crick
Right handed helical
structure but more
compact
Left handed helical structure
having base positioned more
toward the periphery of helix
It contains 10 bp
per turn
It contains 11 bp per
turn
It contains 12 bp per turn
Stabilizing factors for DNA
double helix , Related Terms
Factors responsible for stabilizing the DNA double helix
 Hydrogen bonds present in between purine &
pyrimidine base pair
 pH of DNA solution
 Temperature of DNA solution
Melting of DNA:
 Synonym: Denaturation /
Dissociation / Unwinding /
Helix to coil transition
 Separation of DNA double
helix by disruption of
hydrogen bonds between
complementary base pairs
 It spares phosphodiester
bonds of nucleic acid chain
 It is done by exposing DNA to a
solution of extreme pH ,
extreme temperature or high
urea concentration
 Use:
 To initiate replication &
transcription
 In genetic engineering
Melting Temperature (Tm) :
 Temperature at which 50%
of helical structure of DNA is
lost
 For mammals (40% G-C bp) :
87 degree C
Annealing /
Renaturation:
 Reassociation of two
complimentary
separated DNA strands
to make a ds DNA
Hybridization of DNA:
 Synthesis of new ds nucleic
acid chain (esp. DNA) by
annealing of two different
complementary nucleic acid
chains derived from different
sources
 It may be DNA-DNA hybrid,
RNA-RNA hybrid or DNA-RNA
hybrid
 Unlike annealing, two chains
are derived from different
sources, one of them acts as
probe for identification
 Use:
 Evaluation of DNA homology
between different species
 Detection of frequency of a
given DNA sequence in the
genome
 Gene mapping
DNA sequences
DNA sequence
Coding sequence Non coding sequence
Low copy number
DNA sequence
(60 – 70 %)
Repetitive DNA sequence
(30 – 40 %)
(copy number as many as 107 per
haploid genome)
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.
e.g. exons e.g. introns
<10% of genome >90% of genome
Function of non coding DNA:
i. DNA packaging
ii. Gene expression
iii. Gene mapping
iv. Genetic polymorphism
• It refers to regions of DNA
that are noncoding.
Types of DNA
Mitochondrial DNA Nuclear DNA
Circular, has 16500 base pair Linear , has 7000 maga base
Inherited from mother only Inherited from both of the parents
Contain 37 genes
that codes for 22 mitochondrial
tRNA, 2 mitochondrial rRNA & 13
proteins of respiratory chain
Contain >30000 genes
<1% of cellular DNA >99% of cellular DNA
Mitochondrial DNA Nuclear DNA
Genetic code differs slightly from
standard code of nuclear DNA.
e.g. UAG sense codon for tryptophan
Genetic code differs.
e.g. UAG is a stop codon
No histones & introns Has histones & introns
Majority genes on one stand (heavy
strand)
Light strand has few genes
Genes on both strand
Rate of mutation : High (10 times of
nuclear DNA) due to ineffective DNA
repair system
Rate of mutation: Less
Functions of DNA
Organization of DNA
 Total DNA of cell is made of
6 x 109 bp which is about
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.
 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
 The length of DNA filament of
a single chromosome is about
50 mm which is reduced to ≤ 5
µm following organization
Nucleoproteins
A conjugate protein
where nucleic acid as non
protein prosthetic group
is conjugated with
protein at the ratio of 1:1
Function:
DNA organization & packing
Stabilization of DNA
structure
Regulation of gene
expression
Nucleoprotein
Protein part of nucleoprotein is of two types:
1. Histone protein (H): H1, H2A, H2B, H3 and H4
2. Non-histone protein: Topoisomerase, DNAP, RNAP etc
Histone Proteins:
 LMW
 Basic in nature containing
25% basic amino acids
 Strongly cationic
 Due to positive charge, they
have strong affinity to
associate with the
negatively charged nucleic
acid chain
Non Histone Proteins:
 Acidic in nature
 Represent very small amount
of nucleoprotein
 Usually these are regulatory
proteins & enzymes of
 Replication
 Transcription
 DNA repair
Steps of DNA
organization
Four steps in DNA
organization:
1. Synthesis of histone
core
2. Formation of
polynucleosome string
3. Formation of
chromatin
4. Formation of
chromosome
 Synthesis of histone core:
 Globular aggregate of
eight (08) histone proteins
forming an octameric histone
core (Histone bead)
Each core consists of two
molecules of each of the
four core histone proteins
(H2A, H2B, H3 and H4).
 Formation of polynucleosome
string:
Helical DNA double strand
encircles each histone core twice
to make a nucleosome unit
 Nucleosome
=
DNA wound around octameric
histone core
 25 million nucleosome in
each nucleus
 Each nucleosome is separated
by a short segment of DNA (50
bp) called linker DNA
intercepted with H1 (linker
histone) between them.
 Now, the DNA along with the
histone core takes the look of
beaded string
or
beads on string appearance
 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
 Formation of Chromatin:
Chromatin is the supercoiled
form of the polynucleosome
string
 It is formed when beaded
polynucleosome string is further
coiled
It is not visible under
microscope
 It disperses throughout the
nucleus during interphase of cell
cycle
 Formation of Chromosome:
 In simple sense, a chromosome is a
long DNA in coiled & folded form
or
 Maximum contracted, condensed &
visible threads of chromatin seen
under microscope during metaphase
of cell cycle
 Chromatin molecules are further
condensed (100 folds) during mitosis
& meiosis (esp. at metaphase) into
this giant, supercoiled visible form.
 This progressive folding reduces
the length of DNA to ≤ 5 µm in each
chromosome
Non histone protein plays central
role here
 Total DNA of a cell is distributed
in condensed & compact form into
46 chromosomes (23 pairs): 44 (22
pairs)are autosomes & 02 are sex
chromosomes (XY)
 Total genome of 46
chromosomes (2n) contains 6 x 109
bp
 Total genome of 23
chromosomes (n) contains 3 x 109
bp
The entire haploid genome contains sufficient DNA to code
for nearly 1.5 million average sized genes
But human has ≤ 1 lac gene which represents <10% of DNA
(coding / exonic DNA)
Rest 90% is non coding DNA
Four Orders of DNA coiling
into chromosome
 Primary coiling of two
DNA strands into
Watson-Crick double
helical structure
 Secondary coiling of
DNA double helix
around nucleosome to
make polynucleosome
string
 Tertiary coiling of
polynucleosome string to
form supercoiled
chromatin
 Quaternary supercoiling
of chromatin to form
chromosome
Structure of dna, its organization &amp; functions, july 2020

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Structure of dna, its organization &amp; functions, july 2020

  • 1. Structure of DNA, Its Organization & Functions Dr. Ifat Ara Begum Associate Professor Department of Biochemistry Dhaka Medical College, Dhaka
  • 2. Structure of DNA, Its Organization & Functions Different types of RNA , Cell Cycle Presented by: Dr. Sharmin Sultana M.Phil Student, Part II Department of Biochemistry Dhaka Medical College, Dhaka
  • 3. DNA
  • 4.  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
  • 6.  Polymer of deoxyribonucleotide / d-ribonucleotide connected by 3’-5’ phosphodiester bond d-ribonucleotide = deoxy ribose sugar + phosphate + nitrogen base
  • 8.  A covalent bond between adjacent nucleotides  It is formed between: the phosphate group (attached to 5’ carbon of sugar) of one nucleotide & the OH group (attached to 3’ carbon of sugar) of next nucleotide  Very strong bond, so, DNA is remarkably stable  It makes up the backbone of the strands of nucleic acid
  • 9.
  • 10.
  • 11.  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 this condition
  • 13.  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
  • 14.  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  It is the tradition to read the base sequence of nucleic acid chain from 5’ end to 3’end
  • 15. Structure of DNA (Watson –Crick double helix)
  • 16.  DNA molecule consists of two polynucleotide strands  Each strand is a polymer of deoxyribonucleotides connected by 3’-5’ phosphodiester bond
  • 17. A 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 Deoxyribonucleotide  Phosphate remains attached with 5th carbon of pentose sugar  Nitrogen base remains attached with 1st carbon of pentose sugar
  • 18.  A phosphodiester bond is a covalent bond that is formed between the phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds.
  • 19.  In this manner, each strand of DNA has an alternating sugar-phosphate backbone  The two strands run in opposite directions to each other and are thus antiparallel
  • 20.  The two strands wound around each other in a double helix form like a spiral stair case  Type of DNA helical structure here: B-form. i.e. A right handed helical structure containing 10 bp per turn
  • 21.  The purine bases of one strand connect with the pyrimidine bases on the other strand by hydrogen bonds to form base pair (bp)  This interaction between purine and pyrimidine bases of two strands is highly specific to make the two strand complementary to each other and the paired bases may be called complementary base pair (bp)
  • 22.  Complementary base pairing always occur between adenine (A) of one strand & thymine (T) of other strand Or between guanine (G) of one strand & cytosine (C) of other strand (Base Pairing Law)  Thus in dsDNA molecule, the amount of adenine equals to thymine & the amount of guanine equals to cytosine (Chargaff’s rule)
  • 23.  Base pairing law:  Specific hydrogen bonding between adenine – thymine and guanine – cytosine of two adjacent polynucleotide chains  Each A-T base pair is held together by two hydrogen bonds  Each G-C base pair is held together by three hydrogen bonds.
  • 24. Chargaff’s rule: DNA from any cell of any organisms should have a 1:1 ratio of pyrimidine and purine bases i.e. The amount of guanine should be equal to cytosine and the amount of adenine should be equal to thymine.
  • 25.  The two polynucleotide chains may be 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
  • 26. Grooves in DNA:  Grooves arise from the unequal spacing of phosphate- sugar backbone around the axis of the helix  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
  • 27.  ]The edges of the bases are more accessible in the major groove than in the minor groove.  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
  • 28.
  • 29. Types of DNA Helical Structure
  • 30. B - Form A - Form Z - Form Right handed helical structure first described by Watson- Crick Right handed helical structure but more compact Left handed helical structure having base positioned more toward the periphery of helix It contains 10 bp per turn It contains 11 bp per turn It contains 12 bp per turn
  • 31.
  • 32. Stabilizing factors for DNA double helix , Related Terms
  • 33. Factors responsible for stabilizing the DNA double helix  Hydrogen bonds present in between purine & pyrimidine base pair  pH of DNA solution  Temperature of DNA solution
  • 34. Melting of DNA:  Synonym: Denaturation / Dissociation / Unwinding / Helix to coil transition  Separation of DNA double helix by disruption of hydrogen bonds between complementary base pairs  It spares phosphodiester bonds of nucleic acid chain  It is done by exposing DNA to a solution of extreme pH , extreme temperature or high urea concentration  Use:  To initiate replication & transcription  In genetic engineering
  • 35. Melting Temperature (Tm) :  Temperature at which 50% of helical structure of DNA is lost  For mammals (40% G-C bp) : 87 degree C
  • 36. Annealing / Renaturation:  Reassociation of two complimentary separated DNA strands to make a ds DNA
  • 37. Hybridization of DNA:  Synthesis of new ds nucleic acid chain (esp. DNA) by annealing of two different complementary nucleic acid chains derived from different sources  It may be DNA-DNA hybrid, RNA-RNA hybrid or DNA-RNA hybrid  Unlike annealing, two chains are derived from different sources, one of them acts as probe for identification  Use:  Evaluation of DNA homology between different species  Detection of frequency of a given DNA sequence in the genome  Gene mapping
  • 38.
  • 40. DNA sequence Coding sequence Non coding sequence Low copy number DNA sequence (60 – 70 %) Repetitive DNA sequence (30 – 40 %) (copy number as many as 107 per haploid genome)
  • 41. 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. e.g. exons e.g. introns <10% of genome >90% of genome
  • 42.
  • 43.
  • 44. Function of non coding DNA: i. DNA packaging ii. Gene expression iii. Gene mapping iv. Genetic polymorphism • It refers to regions of DNA that are noncoding.
  • 46.
  • 47. Mitochondrial DNA Nuclear DNA Circular, has 16500 base pair Linear , has 7000 maga base Inherited from mother only Inherited from both of the parents Contain 37 genes that codes for 22 mitochondrial tRNA, 2 mitochondrial rRNA & 13 proteins of respiratory chain Contain >30000 genes <1% of cellular DNA >99% of cellular DNA
  • 48. Mitochondrial DNA Nuclear DNA Genetic code differs slightly from standard code of nuclear DNA. e.g. UAG sense codon for tryptophan Genetic code differs. e.g. UAG is a stop codon No histones & introns Has histones & introns Majority genes on one stand (heavy strand) Light strand has few genes Genes on both strand Rate of mutation : High (10 times of nuclear DNA) due to ineffective DNA repair system Rate of mutation: Less
  • 50.
  • 52.  Total DNA of cell is made of 6 x 109 bp which is about 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.  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  The length of DNA filament of a single chromosome is about 50 mm which is reduced to ≤ 5 µm following organization
  • 54. A conjugate protein where nucleic acid as non protein prosthetic group is conjugated with protein at the ratio of 1:1 Function: DNA organization & packing Stabilization of DNA structure Regulation of gene expression Nucleoprotein Protein part of nucleoprotein is of two types: 1. Histone protein (H): H1, H2A, H2B, H3 and H4 2. Non-histone protein: Topoisomerase, DNAP, RNAP etc
  • 55. Histone Proteins:  LMW  Basic in nature containing 25% basic amino acids  Strongly cationic  Due to positive charge, they have strong affinity to associate with the negatively charged nucleic acid chain Non Histone Proteins:  Acidic in nature  Represent very small amount of nucleoprotein  Usually these are regulatory proteins & enzymes of  Replication  Transcription  DNA repair
  • 57. Four steps in DNA organization: 1. Synthesis of histone core 2. Formation of polynucleosome string 3. Formation of chromatin 4. Formation of chromosome
  • 58.  Synthesis of histone core:  Globular aggregate of eight (08) histone proteins forming an octameric histone core (Histone bead) Each core consists of two molecules of each of the four core histone proteins (H2A, H2B, H3 and H4).
  • 59.  Formation of polynucleosome string: Helical DNA double strand encircles each histone core twice to make a nucleosome unit
  • 60.  Nucleosome = DNA wound around octameric histone core  25 million nucleosome in each nucleus
  • 61.  Each nucleosome is separated by a short segment of DNA (50 bp) called linker DNA intercepted with H1 (linker histone) between them.  Now, the DNA along with the histone core takes the look of beaded string or beads on string appearance
  • 62.  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
  • 63.  Formation of Chromatin: Chromatin is the supercoiled form of the polynucleosome string  It is formed when beaded polynucleosome string is further coiled It is not visible under microscope  It disperses throughout the nucleus during interphase of cell cycle
  • 64.
  • 65.  Formation of Chromosome:  In simple sense, a chromosome is a long DNA in coiled & folded form or  Maximum contracted, condensed & visible threads of chromatin seen under microscope during metaphase of cell cycle
  • 66.  Chromatin molecules are further condensed (100 folds) during mitosis & meiosis (esp. at metaphase) into this giant, supercoiled visible form.  This progressive folding reduces the length of DNA to ≤ 5 µm in each chromosome Non histone protein plays central role here
  • 67.  Total DNA of a cell is distributed in condensed & compact form into 46 chromosomes (23 pairs): 44 (22 pairs)are autosomes & 02 are sex chromosomes (XY)  Total genome of 46 chromosomes (2n) contains 6 x 109 bp  Total genome of 23 chromosomes (n) contains 3 x 109 bp
  • 68. The entire haploid genome contains sufficient DNA to code for nearly 1.5 million average sized genes But human has ≤ 1 lac gene which represents <10% of DNA (coding / exonic DNA) Rest 90% is non coding DNA
  • 69. Four Orders of DNA coiling into chromosome
  • 70.
  • 71.  Primary coiling of two DNA strands into Watson-Crick double helical structure  Secondary coiling of DNA double helix around nucleosome to make polynucleosome string  Tertiary coiling of polynucleosome string to form supercoiled chromatin  Quaternary supercoiling of chromatin to form chromosome