DNA

DEOXY RIBONUCLEIC ACID

INTRODUCTION
CHEMICAL NATURE
STRUCTURE
LOCATION
WATSON AND CRICK PROPOSAL
IMPORTANCE OF WATSON AND CRICK PROPOSAL
TYPES
PROPERTIES , MANAGEMENT AND PROPAGATION OF DNA
ALTERNATE CONFORMATIONS OF DNA

INTRODUCTION :

by 1952,the scientific commmunity had finally accepted the idea that genes were

made of dna.
watson and francis crick at cambridge university in 1n 1953.
information on dna structure had been derived from
1. scattered biochemical studies first begun by friedrich miescher in the year 1860
2.

x-ray diffraction analyses begun by willam astbury in 1940 followed by

rosalindfranklin, linus pauling,maurice wilkins.

CHEMICAL NATURE:the basic building block of dna was known to be a nucleotide.

Five-carbon sugar deoxyribose , to which one phosphate is esterified at the 5` position

of the sugar ring and one nitrogenous base is attached at the 1`site.
there are two types of bases, the smaller pyrimidines and larger purines.
The nucleotides were covalently linked to one another to form a linear polymer or a
strand, with a backbone composed of alternating sugar and phosphate groups joined
by 3`,5`-phosphodiester bonds.

STRUCTURE;Early concept of dna as a simple repeating tetranucleotide.

In1950 ERWIN CHARGAFF of Columbia university proposed chargaff rule.this gave
a blow to tetranucleotide.
CHARGAFF RULE:(A)=(T)
(G)=(C)
(A)+(T)#(G)+(C)

This rule gave dna a SPECIFICITY and INDIVIDUALITY from one organism to
another.
LOCATION:DNA exists in 2 cellular locations (1) nucleus where DNA is in the form of large
extended molecules during replication and in a more condenced state at other times in
the cell cycle, (2) mitochondria in which the organell genome is in a small circular
DNA (maternal)
WATSON AND CRICK PROPOSAL
Watson and crick proposed a model of structure of DNA that includes following
components:1.The molecule is composed of two chains of nucleotides . this conclusion supported
proposal by LinusPauling, who suggested that DNA was composed of 3 nuclotide
strands.
2.The 2 chains spiral around a central axis to form a pair of right handed helices .A
right handed helix turns in a downward clock wise direction. The helix nature of the
DNA was revealed in pattern of spots produced by X-ray diffraction.
3.The sugar ,phosphate ,sugar phosphate back bone is located on the outside of the
molecule with the two sets of bases projecting towards the center.In paulings model ,
the back bones of each strand were erroneously located in the molecule center.The
phosphate groups give the molecule a negative charge.

4. The bases occupy plains that are approximately perpendicular to the long axis of
the molecule and are therefore stacked one on top of another like a pile of
plates.Hydrophobic interactions and vanderwalls forces between the stacked , planar
bases provide stability for the entire DNA molecule.Together the helix turns and
planar base pairs cause the molecule to resemble a spiral stair case.
5.The two chains are held together by hydrogen bonds between each bases of one
chain and an associated base on the other chain. A given hydrogen bond is week and
easily broken, thus allowing the DNA strands to become separated during certain
activities. At the same time , the strengths of the hydrogen bonds are additive , so that
the large number of hydrogen bonds holding the strands together make the double
helix , a stable mo;lecule.
6.The distance from the phosphorus atom of the back bone to the center of the axis is
10 angstronms.
7. The pyrimidine from one chain is always paired with a purine from the other chain .
This relationship would produce a molecule 20 angstroms wide.
8. Nitrogen atoms linked to carbon 4 of cytosine and a carbon 6 of adenine are
predominantly in the amino configuration rather than the immune form. Similarly the
oxygen atoms linked to carbon 6 of guanine and carbon 4 of thiamine are
predominantly in a keto configuration rather than the enol form.
9.Tthe 2 chains composing one double helix run in opposite directions, this is they are
antiparallel .
10. Viewed from outside the molecule the spaces between adjacent turns of the helix
form 2 grooves of different width- a wider major groove and a more narrow minor
groove that spiral around the outer surface of double helix . proteins that bind to the
DNA often fit into these grooves.
11. The double helix makes one complete turn every 10 residues (3.4 nano metres) or,
150 turns per million molecular weight.
12. There is no restriction on the sequence of bases in a given chain of the
molecule.however , once a particular sequence is specified in one chain the sequence
of the other chain is automatically determined. This relation ship between the 2 chains
of the double helix is referred to as copmplementary.
IMPORTANCE OF WATSON AND CRICK PROPOSAL:1. Storage of genetic information DNA is the molecular blueprint a stored record
of precise instructions that determine all the heritable characterstics that an
organism can exhibit.

2. Self duplication and inheritance DNA replication provides the means by which
genetic instructions can be transmitted from one cell to the other cells or from one
individual to its offsprings.
3. Exression of the genetic message:-- a given segment of DNA would correspond to
each gene. The specific sequence of nucleotides in that segment would dictate the
sequence of amino acids in a corresponding polypeptide .a change in the linear
sequence of the nucleotides within the segment would correspond to an inheritable
mutation in that gene.

ALTERNATE CONFORMATION OF DNA :

The x-ray diffraction data utilized by Watson and Crick came from the analysis of fibers of
DNA that had been prepared wet. This wet or fully hydrated form of DNA, which was first
discovered by Rosalind Franklin, is called the B form and is thought to represent the
conformation of molecules as it exists within the cell. Franklin found that the fibers prepared
under conditions of low humidity had a more crystalline structure and generated more sharply
defined x-ray diffraction patterns. The conformation of these molecules in these dried fibers
is somewhat different from the more hydrated fibers and is referred to as A form of DNA.
The transition from the B to the A form is accompanied by numerous changes in the
molecule including a distinct shortening of entire fiber , a change in the steepness of helix
from 3.4 to 2.7 rise per base pair, atilt in the bases relative to the axis of helix, and so on.
TYPES OF DNA
The DNA molecule that Watson and Crick described was in the B form. It is now known that
DNA can exist in several other forms. The primary difference between the forms is the
direction that the helix spirals.
A, B, C = right-handed helix
Z = left-handed helix (found in vitro under high salt)
B is the major form that is found in the cell. Z-DNA was initially found only under high salt
conditions, but the cellular environment is actually a low-salt environment. The question then

is whether type Z exist under cellular conditions. Several features have been discovered that
can stablize Z-DNA under in a low salt environment.

Alternating purine/pyrimidine tracts

o poly GC or poly AT stretches

5-methyl-cytosine

Because both of these conditions can exists in the cell, it is suggested that stretches of Z-DNA
may actually exists in the cell along with other stretches of B-DNA.
In addition to the direction the molecule turns, several other differences exists between the
various forms of DNA. The following table summarizes the features of the different forms of
DNA.
Bases/

Helix

360o Turn

Diameter

Right

11.0

23A

Right

10.0

19A

Right

9.3

19A

Left

12.0

18A

Form

Direction

DNA SUPER COILING :

In 1963 , Jerome Vinograd and co workers of California institute of technology discovered
that two closed, circular DNA molecules of identical molecular weight could exhibit very
different rates of sedimentation. When centrifuged through a density gradient. further analysis
indicate that the DNA molecule sedimenting , more rapidly had a more compact shape
because the molecules was twisted upon itself, Much like a rubber band in which the two
ends are twisted in opposite directions .DNA in this state is said to be supercoiled.Because
super coiled DNA is more compact than its relaxed counter part,it occupies less volumeand it
moves more rapidly in response to a centrifugal force or an electric field.DNA is reffered to
as negatively super coiled when super coiling results from being underwound,and positively
super coiled when overwound.

DNA REPLICATION:
DNA replication. The double helix is unwound and each strand acts as a template. Bases are
matched to synthesize the new partner strands.
DNA replication, the basis for biological inheritance, is a fundamental process occurring in
all living organisms to copy their DNA. This process is "replication" in that each strand of the
original double-stranded DNA molecule serves as template for the reproduction of the
complementary strand. Hence, following DNA replication, two identical DNA molecules
have been produced from a single double-stranded DNA molecule. Cellular proofreading and
error toe-checking mechanisms ensure near perfect fidelity for DNA replication.
In a cell, DNA replication begins at specific locations in the genome, called
"origins".Unwinding of DNA at the origin, and synthesis of new strands, forms a replication
fork. In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding
nucleotides matched to the template strand, a number of other proteins are associated with the
fork and assist in the initiation and continuation of DNA synthesis.
DNA replication can also be performed in vitro (outside a cell). DNA polymerases, isolated
from cells, and artificial DNA primers are used to initiate DNA synthesis at known sequences
in a template molecule. The polymerase chain reaction (PCR), a common laboratory
technique, employs such artificial synthesis in a cyclic manner to amplify a specific target
DNA fragment from a pool of DNA.
Regulation of replication

The cell cycle of eukaryotic cells.

Eukaryotes
Within eukaryotes, DNA replication is controlled within the context of the cell cycle. As the
cell grows and divides, it progresses through stages in the cell cycle; DNA replication occurs
during the S phase (Synthesis phase). The progress of the eukaryotic cell through the cycle is
controlled by cell cycle checkpoints. Progression through checkpoints is controlled through
complex interactions between various proteins, including cyclins and cyclin-dependent
kinases
The G1/S checkpoint (or restriction checkpoint) regulates whether eukaryotic cells enter the
process of DNA replication and subsequent division. Cells which do not proceed through this
checkpoint are quiescent in the "G0" stage and do not replicate their DNA.

Replication of chloroplast and mitochondrial genomes occurs independent of the cell cycle,
through the process of D-loop replication.
Bacteria
Most bacteria do not go through a well-defined cell cycle and instead continuously copy their
DNA; during rapid growth this can result in multiple rounds of replication occurring
concurrentlyWithin E coli, the most well-characterized bacteria, regulation of DNA
replication can be achieved through several mechanisms, including: the hemimethylation and
sequestering of the origin sequence, the ratio of ATP to ADP, and the levels of protein DnaA.
These all control the process of initiator proteins binding to the origin sequences.
Because E coli methylates GATC DNA sequences, DNA synthesis results in hemimethylated
sequences. This hemimethylated DNA is recognized by a protein (SeqA) which binds and
sequesters the origin sequence; in addition, dnaA (required for initiation of replication) binds
less well to hemimethylated DNA. As a result, newly replicated origins are prevented from
immediately initiating another round of DNA replication.[18]
ATP builds up when the cell is in a rich medium, triggering DNA replication once the cell has
reached a specific size. ATP competes with ADP to bind to DnaA, and the DnaA-ATP
complex is able to initiate replication. A certain number of DnaA proteins are also required
for DNA replication each time the origin is copied the number of binding sites for DnaA
doubles, requiring the synthesis of more DnaA to enable another initiation of replication.

ENZYMES :

 An enzyme called DNA gyrase makes a nick in the double helix and each side
separates
An enzyme called helicase unwinds the double-stranded DNA
Several small proteins called single strand binding proteins (SSB) temporarily bind
to each side and keep them separated
An enzyme complex called DNA polymerase "walks" down the DNA strands and
adds new nucleotides to each strand. The nucleotides pair with the complementary
nucleotides on the existing stand (A with T, G with C).
A subunit of the DNA polymerase proofreads the new DNA
An enzyme called DNA ligase seals up the fragments into one long continuous strand
The new copies automatically wind up again
DNA REPAIR :
DNA repair refers to a collection of processes by which a cell identifies and corrects
damage to the DNA molecules that encode its genome.

human cells, both normal metabolic activities and

environmental factors such as UV light and radiation can cause DNA damage,
resulting in as many as 1 million individual molecular lesions per cell per day.