Watson & Crick DNA Model

Academic Script

1. History
The foundation of genetics as a molecular science dates back to 1869, just three
years after Mendel reported his experiments. It was in 1869 that Friedrich Miescher
discovered a new type of weak acid, abundant in the nuclei of white blood cells.
Miescher‟s weak acid turned out to be the chemical substance we now call DNA
(deoxyribonucleic acid).

For many years the biological function of DNA was unknown, and no role in heredity
was ascribed to it. An important first step was taken by Frederick Griffith in 1928
when he demonstrated that a physical trait can be passed from one cell to another
called as transformation.

In a milestone experiment, Oswald Avery, Colin MacLeod, and Maclyn McCarty this
three person showed that the substance causing the transformation of cells was only
DNA. These experiments implied that the substance responsible for genetic
transformation was the DNA of the cell—hence that DNA is the genetic material.

A second pivotal finding was reported by Alfred Harshey and Martha Chase in 1952.
They demonstrated that the outer protein coat of a phage (virus) does not enter the
bacterium it infects, whereas the phage‟s inner material, consisting of DNA, does
enter the bacterial cell. Since the DNA is responsible for the production of the new
phages during the infection process, the DNA, not the protein, must be the genetic
material.
In some viruses, RNA (ribonucleic acid) is the genetic material. Example is the
tobacco mosaic virus that infects tobacco plants consists only of RNA and protein.
Not the DNA.

2. Components of nucleic acids

Nucleic acids are made by joining nucleotides in a repetitive way into long, chainlike
polymers. Nucleotides are made of main three components
1) Phosphate
2) Sugar
3) Nitrogenous base

Nucleotides:
As already said, the nucleotide consists of phosphate, nitrogenous base and sugar. A
nucleoside is a sugar-base compound. Thus, phosphate-containing nucleoside
called as nucleotide.

Sugar + nitrogenous base = nucleoside

Nucleoside + phosphate = nucleotide

Nitrogenous base: The nitrogenous bases are aromatic heterocyclic compounds.

DNA and RNA both have four bases (two purines and two pyrimidines) in their
nucleotide chains. Both molecules have the purines adenine and guanine and the
pyrimidine cytosine. DNA has the pyrimidine thymine; while RNA has the pyrimidine
uracil. Thus, three of the nitrogenous bases are found in both the DNA and RNA,
whereas thymine is unique to DNA, and uracil is unique to RNA.

Sugars: Both DNA and RNA have five carbon sugars and all sugars are pentoses.
But DNA contains D-deoxyribose and RNA contains D-ribose. Deoxyribose has one
oxygen less at C2 compared to ribose.

Nomenclature of nucleotides
Nitrogenous base and sugar combine to produce nucleoside. If ribose sugar is
present in nucleoside, it‟s called as ribonucleosides. So ribonucleosides of A, G, C
and U are named as adenosine, guanosine, cytidine and uridine respectively.

The binding of nucleotide components

It is customary to number the carbon atoms of the nitrogenous base and deoxyribose
molecule. The carbon atoms in the deoxyribose are numbered 1‟ to 5‟. The
numbering begins to the right of the oxygen atom and proceeds clockwise. The
atoms in the purine ring are numbered as 1 to 9 and for pyrimidine as 1 to 6 why it is
because purine is having 9 carbon while pyrimidine having 6. The carbons of sugars
are differentiated with an associated prime („).
The sugars are bound to nitrogenous bases by β-N-glycosidic bonds. The N9 of a
purine ring binds with 1‟carbon of a pentose sugar to form a covalent bond in the
purine nucleoside. While in case of pyrimidine nucleosides, the linkage is between N1
of a pyrimidine and 1‟ carbon of a pentose. The hydroxyl groups of nucleoside are
esterified with the phosphates to produce 5‟ or 3‟-mono phosphate. Nucleoside mono
phosphate possesses one phosphate moiety. The binding of second or third
phosphate moieties to the nucleoside produce nucleoside diphosphate or nucleoside
triphosphate respectively.

3. Biologically Active Structure of DNA

In the early 1950s, a number of researchers began to try to understand the detailed
molecular structure of DNA in hopes that the structure alone would suggest answers
to these questions.

The general feeling was that the biologically active structure of DNA was more
complex than a single thread of nucleotides linked together by phosphor diester
bonds, and that several interacting strands were involved. But in 1953, Linus Pauling,
a Nobel laureate who had discovered the helical structure of proteins, was
investigating a three-stranded structure for the genetic material.

In 1953 James Watson and Francis Crick at Cambridge University published a well
known two-page paper in the journal Nature entitled “Molecular Structure of Nucleic
Acids: A Structure for Deoxyribose Nucleic Acid”. This paper, which first put forth the
correct model of DNA structure, is a milestone in the modern era of molecular
genetics. They had decided that a two-stranded structure was more consistent with
available evidence. Three lines of evidence directed Watson and Crick: is the
chemical nature of the components of DNA, X-ray crystallography, and the Chargaff‟s
ratios.

DNA X-Ray Crystallography

When Watson and Crick were studying DNA structure, Maurice Wilkins, Rosalind
Franklin, and their colleagues were using X-ray crystallography to analyze the
structure of DNA. The molecules in a crystal are arranged in an orderly way, so that
when a beam of X ray is aimed at the crystal, the beam scatters in an orderly fashion.
The scatter pattern can be recorded on photographic film or computer-controlled
devices. The nature of this pattern depends on the structure of the crystal.

The cross in the center of the photograph indicates that the molecule is a helix; the
dark areas at the top and bottom come from the bases, stacked perpendicularly to
the main axis of the molecule. This image of the DNA molecule stimulated Watson
and Crick‟s understanding of its structure.
Chargaff ’s Ratios
Chargaff‟s rules disproved the tetranucleotide hypothesis; the four bases of DNA did
not occur in a 1:1:1:1 ratio. His results gave insight to Watson and Crick in the
development of their model.

Until Erwin Chargaff‟s work, scientists had labored under the erroneous
tetranucleotide hypothesis. This hypothesis proposed that DNA was made up of
equal quantities of the four bases; therefore, a subunit of this DNA consisted of one
copy of each base. Chargaff carefully analyzed the base composition of DNA in
various species. He found that although the relative amount of a given nucleotide
differs among species, the amount of adenine equaled to that of thymine and the
amount of guanine equaled to that of cytosine. That is, in the DNA of all the
organisms studied, a 1:1 correspondence exists between the purine and pyrimidine
bases. This is known as Chargaff’s rule.

The Watson-Crick Model

With the information available, Watson and Crick began constructing molecular
models. They found that a possible structure for DNA was one in which two helices
coiled around one another (a double helix), with the sugar-phosphate backbones on
the outside and the bases on the inside. This structure would fit the dimensions X-ray
crystallography had established for DNA if the bases from the two strands were
opposite each other and formed “stair” in the helical “ladder”. The diameter of the
helix could only be kept constant at about 20 Å, if one purine and one pyrimidine
base made up each rung. Two purines per stair would be too big, and two
pyrimidines would be too small.

After further experimentation with models, Watson and Crick found that the hydrogen
bonding necessary to form the rungs of their helical ladder could occur readily
between certain base pairs, the pairs that Chargaff found in equal frequencies.
(Hydrogen bonds are very weak bonds in which two electronegative atoms, such as
O and N, share a hydrogen atom between them. They have 3 to 5% of the strength
of a covalent bond.) Thermodynamically stable hydrogen bonding occurs between
thymine and adenine and between cytosine and guanine only.

The relationship is one of complementarity. There are two hydrogen bonds between
adenine and thymine while three between cytosine and guanine.
Another point about DNA structure relates to the polarity that exists in each strand.
That is, one end of a DNA strand has a 5’ phosphate and the other end has a 3’
hydroxyl group. Watson and Crick found that hydrogen bonding would occur if the
polarity of the two strands ran in opposite directions; that is, if the two strands were
antiparallel.

Other types of DNA structure:

Bent DNA: Adenine containing DNA tracts are rigid and straight. Bent conformation
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 in DNA structure has also been reported
due to photochemical damage or mispairing of bases also.

Triple-stranded DNA: Triple-stranded DNA formation is less stable than double

helix. A thymine can form two Hoogsteen hydrogen bonds to the adenine of A-T pair
that form T-A-T.
A protonated cytosine can also form teo hydrogen bonds with guanine of G-C pairs
that and results in protonated C+-G-C.

Four-stranded DNA: The ends of eukaryotic chromosomes namely telomeres are

rich in guanine, and therefore form G-tetraplexes. Polynucleotides with very high
contents of guanine can form a novel tetrameric structure called G-quartets. These
structures are planar and are connected by Hoogsteen hydrogen bonds. Antiparaller
four-stranded DNA structures, referred to as G-tetraplexes have also been reported.
Telomeres have become the targets for anticancer chemotherapies.

4. RNA
RNA means Ribonucleoacids.
RNA has certain similarities with DNA structure and also specific differences also.
Main difference is
 RNA is generally a single stranded polynucleotide.
 RNA contains ribose sugar in place of deoxyribose in DNA.
 In case of nitrogenous base, Uracil is present in contrast to thymine in DNA.
 Chargaff‟s rule is not followed in case of RNA due to single stranded structure. So,
cytosine and guanine content is not equal in RNA.
In the protein synthesis process, three different kinds of RNA serve in three different
roles.
mRNA (messenger RNA)
tRNA (transfer RNA)
rRNA (ribosomal RNA)

Apart from these three RNAs found in cells, other RNAs namely SnRNA (small
nuclear RNA), hnRNA (heterogenous nuclear RNA), ScRNA (small cytoplasmic
RNA), and SnoRNA (small nucleolar RNA) are also found in the cells.

mRNA
The mRNA is synthesized from DNA. In eukaryotes, it is synthesized as
heterogenous nuclear RNA in the nucleus. During processing, hnRNA liberates the
functional mRNA which enters into the cytoplasm for protein synthesis. The
eukaryotic mRNA is capped at the 5‟-terminal end by 7-methylguanosine
triphosphate. This capping helps to prevent mRNA from hydrolysis by enzyme 5‟-
exonucleases and help in recognition of mRNA for protein synthesis.

tRNA
Holly elucidated the structure of tRNA. Transfer RNA is an important example of a
hybrid molecule. The RNA part contains 73 to 93 nucleotides that form three loops
and an acceptor stem formed by hydrogen bonding between complementary
ribonucleotides (C-G, A-U).

The structure of tRNA contains mainly four arms

The acceptor arm:

This arm is capped with a sequence CCA (5‟ to 3‟). The amino acid attached to the
acceptor arm.

The anticodon arm: The center loop of transfer RNA is the anticodon loop. The
anticodon contains three nucleotides that create a code. The acceptor binds to one
amino acid, which is specific to the code of the anticodon. And the three-base
anticodon complements a three-base sequence in the mRNA. In this way, the rnRNA
directs the synthesis of proteins by telling the order of amino acids.

Most of the amino acids have more than one mRNA code, a tract called as
degeneracy. In these cases, the third base can vary or wobble also called as wobble
hypothesis. Four three-base codes have specific functions. AUG indicates exactly
where reading of the three-base codes should begin. Because the bases on the
mRNA are read as triplets, and almost all triplets code an amino acid, it is essential
that the starting point be exact. AUG also codes for methionine within the RNA code,
but N-formyl methionine is coded when AUG is used as the start signal. Other three
UAA, UAG, and UGA are the stop signals. The start and stop codons are very useful
for identifying genes within the DNA sequences.

The D arm: It is named due to the presence of di hydro uridine.

The TΨC arm: This arm contains sequence of thyamine, pseudouridine (psi, Ψ) and
cytosine.
The variable arm: This arm is the most variable in tRNA.

Ribosomal RNA (rRNA)

The matching of the mRNA codon and the tRNA anticodon occurs within the
ribosome, which is a very complex assembly of rRNA and proteins.
The rRNA is made up of two major subunits that are identified by their size as
measured by sedimentation rate: for prokaryotes, they are 50S and 30S. The 30S
subunit is further subdivided into 5S, 16S, and 23S components. But 5S is having
120 nucleotides long, 16S is 1500 nucleotides long and while 23S is 2900
nucleotides long.

The ribosome is a large structure, on the order of 150 to 250 A. They are
approximately 60 percent RNA and 40 percent protein.

The three-base code of the mRNA is translated into an amino-acid polymer, or a

protein. Starting with the initial AUC sequence, the ribosome reads the mRNA code
three bases at a time. It finds the matching tRNA and binds the codon and anticodon
through hydrogen bonding. The ribosome keeps two sites side-by-side. Because this
allows it to covalently link the incoming amino acid to the last amino acid of the
growing chain via a peptide bond that releases H20. Then, the ribosome shifts its
position three bases further to the 3' end of the mRNA and repeats the process. Now
the ribosome keeps elongating the protein until it reaches one of the stop codons. A
cell has thousands of ribosomes, and some microorganisms increase the number
when they are growing rapidly.

5. Function of nucleic Acids

Effective storage, expression, and reproduction of the genetic message characterize
individual species and also discriminate them from one another, and assure their
stability over successive generations. Because DNA is the repository of genetic
information in each living cell, its integrity and stability are significant to life. The main
function of nucleic acids is to store and transmit genetic information.

REPLICATION
The structure of DNA allows for its replication and repair with near-perfect fidelity.
The capacity of living cells to preserve their genetic material and to duplicate it for the
next generation results from the structural complementarity between the two halves
of the DNA molecule. The basic unit of DNA is a linear polymer of four different
monomeric subunits, deoxyribonucleotides, arranged in a precise linear sequence. It
is this linear sequence that encodes the genetic information.

DNA Repair
DNA is not inert; rather, it is a chemical entity subject to assault from the
environment, and any resulting damage, if not repaired, will lead to mutation and
possibly disease also.

Best-known example of the link between environmental-induced DNA damage and

disease is that of skin cancer, which can be caused by excessive exposure to UV
radiation in the form of sunlight (and, to a lesser degree, tanning beds also).

In addition to genetic insults caused by the environment, the very process of DNA
replication during cell division is prone to error. The rate at which DNA polymerase
adds incorrect nucleotides during DNA replication is a major factor in determining the
spontaneous mutation rate in an organism. While a "proofreading" enzyme normally
recognizes and corrects many of these errors, some mutations survive this process.
Estimates of the frequency at which human DNA undergoes lasting, uncorrected
errors range from 1 x 10-4 to 1 x 10-6 mutations per gamete for a given gene. A rate of
1 x 10-6 means that a scientist would expect to find one mutation at a specific locus
per one million gametes.

The gene is a segment of DNA, or a sequence of deoxyribonucleotides. The

sequence of deoxy-ribonucleotides is faithfully copied to a complementary (i.e.,
matching) sequence the messenger RNA, or mRNA. By copying the DNA code into
mRNA, the cells can use the information on the DNA without destroying or distorting
it.
Within the ribosome, the mRNA directs· the assembly of the protein by indicating the
order in which the amino acids are to be joined. The code on the mRNA identifies
which type of transfer RNA, or tRNA, should enter the ribosome and supply a
particular amino acid to the growing protein chain.

Different tRNA molecules binds specifically to the range of amino acids needed to
make enzymes and match specifically with the code on the mRNA. The mechanism
of bringing tRNA and mRNA together in a ribosome is a versatile and efficient way for
the cells to be able to synthesize any and all types of enzymes as they need them
and use that information to direct the synthesis of new protein.