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The Model of a DNA

Name: Anokhi Kashiparekh

Grade: XI
Year: 2013-2014

! -Anokhi Kashiparekh (AK:D)

! ! Acknowledgements

I am greatly thankful to the director of the

school Sir Raja Pathak, the principal of the
school Ma’am Shobha Pathak, the Vice-
Principal of the school Ma’am Jayshri Joshi
and the biology teacher Ma’am Shobha
Menon for having given me this wonderful
opportunity to display my knowledge in the
form of my project.

! -Anokhi Kashiparekh (AK:D)

Contents

Sr No. Title Page

No.

1 The DNA
2 History of DNA Research
3 The Watson and Crick Model
4 DNA: As we know it
5 The Basic Bases
6 DNA packaging and its effects
7 Transcription, Translation and Replication
8 DNA binding proteins
9 DNA Recombination
10 Genetic Disorder
11 My Model

! -Anokhi Kashiparekh (AK:D)

 The DNA
Reproduction and Evolution. The basic fundamentals that
continue the life on Earth as we know it. Every organism
on this planet produces a progeny to ensure the
continuation of its species. These offsprings continue to
show the characters and the traits of the particular specie
that they are born to. The basic requirement for the
continuation of the species and their character is the
DNA.
In simple words we can say that DNA is the nucleic acid
that carries the genetic information in a cell. DNA, that
stands for Deoxyribonucleic Acid, is the molecule made of
nucleic acid, proteins and carbohydrates that encodes the
genetic instructions used in the development and
functioning of all known living organisms and many
viruses.
DNA is organized into structures called the chromosomes
that are found in the cells of the organism.

! -Anokhi Kashiparekh (AK:D)

 History of the DNA Research
First isolated by the Swiss physician Friedrich Meischer, in
1869, DNA was in discovered a microscopic substance in
the pus of discarded surgical bandages. As it resided in the
nuclei of cells, he called it nuclein.

Friedrich Meischer

In 1878, Albrecht Kossel isolated the non-protein

component of nuclein, which was the nucleic acid and
later isolated its five primary nucleobases.
In 1919, Phoebus Levene identified the base, sugar and
phosphate nucleotide unit. Levene suggested that DNA
consisted of a string of nucleotide units linked together
through the phosphate groups. However, Levene thought

! -Anokhi Kashiparekh (AK:D)

the chain was short and the bases repeated in a fixed
order.
In 1937 William Astbury produced the first X-ray
diffraction patterns that showed that DNA had a regular
structure.
In 1927, Nikolai Koltsov proposed that inherited traits
would be inherited through a giant hereditary molecule
made up of ‘two mirror strands that would replicate in a semi-
conservative fashion using each strand as a template’.
In 1928,Fredrick Griffith discovered that traits of the
smooth form of Pneumococcus could be transferred to
the rough form of the same bacteria by mixing killed
smooth bacteria with the live rough form. This system
provided the first clear suggestion that DNA carries
genetic information.
The Avery–MacLeod–McCarty experiment identified DNA as
the transforming principle in 1943, when Oswald Avery,
along with coworkers Colin MacLeod and Maclyn
McCarty reported that DNA is the substance that causes
bacterial transformation.
DNA's role in the heredity function was confirmed in
1952 by Alfred Hershey and Martha Chase in the
Hershey-Chase experiment showed that DNA is the
genetic material of the T2 phage.

! -Anokhi Kashiparekh (AK:D)

 The Watson and Crick Model
In 1953, Francis Crick and James D. Watson published an
article in the scientific journal Nature in its 171st vol. that
was named ‘Molecular Structure of Nucleic Acids: A
Structure for Deoxyribose Nucleic Acid’. It was the first
publication which described the discovery of the double
helix structure of the DNA.
Watson and Crick published this article of the double
helix of the DNA on the basis of the data collected by
researchers all over the world.

! ! ! ! ! ! Experimental evidence
supporting the Watson and
Crick model was published in a
series of five articles in the
same issue of Nature. Of
these, Franklin and Gosling's
paper was the first publication
of their own X-ray diffraction
data and original analysis
method that partially supported the Watson and Crick
model, this issue also contained an article on DNA
structure by Maurice Wilkins and two of his colleagues,
whose analysis and in vivo B-DNA X-ray patterns also
supported the presence in vivo of the double-helical DNA
configurations as proposed by Crick and Watson for their
! -Anokhi Kashiparekh (AK:D)
double-helix molecular model of DNA in the previous
two pages of Nature. In 1962, after Franklin's death,
Watson, Crick, and Wilkins jointly received the Nobel
Prize in Physiology or Medicine . Nobel Prizes were
awarded only to living recipients at the time. A debate
continues about who should receive credit for the
discovery.
In an influential presentation in 1957, Crick laid out the
central dogma of Biology which foretold the relationship
between DNA, RNA, and proteins, and articulated the
‘adaptor hypothesis’.
The central dogma of molecular biology deals with the detailed
residue-by-residue transfer of sequential information. It states that
such information cannot be transferred back from protein to either
protein or nucleic acid.
Final confirmation of the replication mechanism that was
implied by the double-helical structure followed in 1958
through the Meselson–Stahl experiment. Further work by
Crick and coworkers showed that the genetic code was
based on non-overlapping triplets of bases, called codons,
allowing Har Gobind Khorana, Robert W. Holley and
Marshall Warren Nirenberg to decipher the genetic
code.These findings represent the birth of molecular
biology wherein there was a research that helped to show
how the nucleotides in nucleic acids, which carry the
genetic code of the cell, control the cell’s synthesis of
proteins.

! -Anokhi Kashiparekh (AK:D)

 DNA: As we know it
The structure of DNA of all species comprises two helical
chains each coiled round the same axis, and each with a
pitch of 34 angstroms (3.4 nanometers) and a radius of
10 angstroms (1.0 nm). According to another study, when
measured in a particular solution, the DNA chain
measured 22 to 26 angstroms wide (2.2 to 2.6 nm), and
one nucleotide unit measured 3.3 Å (0.33 nm) long.
Although each individual repeating unit is very small,
DNA polymers can be very large molecules containing
millions of nucleotides. For instance, the largest human
chromosome, chromosome number 1, consists of
approximately 220 million base pairs and is 85 mm long.

The helix structure consists of two strands of DNA

running in the opposite direction to each other and are
anti-parallel one having the 3rd while the other having the
5th carbon as the backbone.
Attached to each sugar is one of four types of molecules
called nucleobases. It is the sequence of these four
nucleobases along the backbone that encodes genetic
information. This information is read using the genetic
code, which specifies the sequence of the amino acids
within proteins. The code is read by copying stretches of
DNA into the related nucleic acid RNA in a process called
transcription.
! -Anokhi Kashiparekh (AK:D)
During cell division these chromosomes are duplicated in
the process of DNA replication, providing each cell its
own complete set of chromosomes. Eukaryotic organisms
i.e. animals, protists, fungi and plants, store most of their
DNA inside the cell nucleus and some of their DNA in
organelles, such as mitochondris or chloroplasts. In
contrast, prokaryotes like bacteria and archaea store their
DNA only in the cytoplasm. Within the chromosomes,
chromatin proteins such as histones compact and organize
DNA. These compact structures guide the interactions
between DNA and other proteins, helping control which
parts of the DNA are transcribed.

In living organisms DNA does not usually exist as a single

molecule, but instead as a pair of molecules that are held
tightly together. These two long strands entwine like vines,
in the shape of a double hilex. The nucleotide repeats
contain both the segment of the backbone of the
molecule, which holds the chain together, and a
nucleobase, which interacts with the other DNA strand in
the helix. A nucleobase linked to a sugar is called a
nucleoside and a base linked to a sugar and one or more
phosphate groups is called a nucleotide. A polymer
comprising multiple linked nucleotides (as in DNA) is
called a polynucleotide.
The DNA double helix is stabilized primarily by two
forces: hydrogen bonds between nucleotides and base-
staching interactions among aromatic nucleobases.
! -Anokhi Kashiparekh (AK:D)
The four bases found in DNA are adenine (A), cytosine
(C), guanine (G) and thymine (T). These four bases are
attached to the sugar/phosphate to form the complete
nucleotide, as shown for adenosine monophosphate.

Adenosine Monophosphate

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 The Basic Bases
1. Adenine- Adenine is a nucleobase with a variety of
roles in biochemistry including cellular respiration, in
the form of both the energy-rich adenosine
triphosphate (ATP) and the cofactors nicotinamide
adenine dinucleotide (NAD) and flavin adenine
dinucleotide (FAD), and protein synthesis, as a chemical
component of DNA and RNA.The shape of adenine is
complementary to either thymine in DNA or uracil in
RNA. It has the IUPAC name of 9H-purin-6-amine.

2. Cytosine- Cytosine is one of the four main bases found

in DNA and RNA, along with adenine, guanine, and
thymine (uracil in RNA). It is a pyrimidine derivative,
with a heterocyclic aromatic ring and two substituents
attached (an amine group at position 4 and a keto
group at position 2). The nucleoside of cytosine is
cytidine. In Watson-Crick base pairing, it forms three
hydrogen bonds with guanine. It has the IUPAC name
of 4-aminopyrimidin-2(1H)-one.

3. Guanine- Guanine is another of the four main bases

found in DNA and RNA. In DNA, guanine is paired
with cytosine. With the formula C5H5N5O, guanine is a
derivative of purine, consisting of a fused pyrimidine-
imidazole ring system with conjugated double bonds.
! -Anokhi Kashiparekh (AK:D)
 Being unsaturated, the bicyclic molecule is planar. The
guanine nucleoside is called guanosine. It has the
IUPAC name of 2-amino-1H-purin-6(9H)-one.

4. Thymine- As the name suggests, thymine may be

derived by methylation of uracil at the 5th carbon. In
RNA, thymine is replaced with uracil in most cases. In
DNA, thymine binds to adenine via two hydrogen
bonds, thus stabilizing the nucleic acid structures.
Thymine combined with deoxyribose creates the
nucleoside deoxythymidine. Its IUPAC name is 5-
Methylpyrimidine-2,4(1H,3H)-dione.

The two types of base pairs form different numbers of

hydrogen bonds, AT forming two hydrogen bonds, and
GC forming three hydrogen bonds. DNA with high GC-
content is more stable than DNA with low GC-content.

! -Anokhi Kashiparekh (AK:D)

Most DNA molecules are actually two polymer strands,
bound together in a helical fashion by noncovalent bonds;
this double stranded structure (dsDNA) is maintained
largely by the intrastrand base stacking interactions, which
are strongest for G,C stacks. The two strands can come
apart – a process known as melting – to form two single-
stranded DNA molecules (ssDNA) molecules. Melting
occurs at high temperature, low salt and high pH. Low
pH also melts DNA, but since DNA is unstable due to
acid depurination, low pH is rarely used.
When all the base pairs in a DNA double helix melt, the
strands separate and exist in solution as two entirely
independent molecules. These single-stranded DNA
molecules (ssDNA) have no single common shape, but
some conformations are more stable than others.

! -Anokhi Kashiparekh (AK:D)

 DNA packaging and its effects
The expression of genes is influenced by how the DNA is
packaged in chromosomes, in a structure called
chromatin. Base modifications can be involved in
packaging, with regions that have low or no gene
expression usually containing high levels of methylation of
cytosine bases. DNA packaging and its influence on gene
expression can also occur by covalent modifications of the
histone protein core around which DNA is wrapped in the
chromatin structure or else by remodeling carried out by
chromatin remodeling complexes. There is, further,
crosstalk between DNA methylation and histone
modification, so they can coordinately affect chromatin
and gene expression.

Damage
DNA can be damaged by many sorts of mutagens, which
change the DNA sequence. Mutagens include oxidizing
agents, alkylating agents and also high-energy
electromagnetic radiations such as ultraviolet light and X-
rays. The type of DNA damage produced depends on the
type of mutagen.

! -Anokhi Kashiparekh (AK:D)

For example, UV light can damage DNA by producing
thymine dimers, which are cross-links between pyrimidine
bases. On the other hand, oxidants such as free radicals or
hydrogen peroxide produce multiple forms of damage,
including base modifications, particularly of guanosine,
and double-strand breaks. A typical human cell contains
about 150,000 bases that have suffered oxidative damage.
Of these oxidative lesions, the most dangerous are double-
strand breaks, as these are difficult to repair and can
produce point mutations, insertions and deletions from the
DNA sequence, as well as chromosomal
translocations.These mutations can cause cancer. Because
of inherent limitations in the DNA repair mechanisms, if
humans lived long enough, they would all eventually
develop cancer. DNA damages that are naturally
occurring, due to normal cellular processes that produce
reactive oxygen species, the hydrolytic activities of cellular
water, etc., also occur frequently. Although most of these
damages are repaired, in any cell some DNA damage may
remain despite the action of repair processes. These
remaining DNA damages accumulate with age in
mammalian post mitotic tissues. This accumulation
appears to be an important underlying cause of aging.
Many mutagens fit into the space between two adjacent
base pairs, this is called intercalation. Most intercalators
are aromatic and planar molecules. For an intercalator to
fit between base pairs, the bases must separate, distorting
the DNA strands by unwinding of the double helix. This
! -Anokhi Kashiparekh (AK:D)
inhibits both transcription and DNA replication, causing
toxicity and mutations. As a result, DNA intercalators may
be carcinogens. Nevertheless, due to their ability to inhibit
DNA transcription and replication, other similar toxins
are also used in chemotherapy to inhibit rapidly growing
cancer cells.

Mutation
In genetics, a mutation is a change of the nucleotide
sequence of the genome of an organism, virus, or
extrachromosomal genetic element. Mutations result from
unrepaired damage to DNA or to RNA genomes that are
typically caused by radiation or chemical mutagens, errors
in the process of replication, or from the insertion or
deletion of segments of DNA by mobile genetic elements.
Mutations may or may not produce discernible changes in
the observable characteristics of an organism. Mutations
play a part in both normal and abnormal biological
processes including: evolution, cancer, and the
development of the immune system.

! -Anokhi Kashiparekh (AK:D)

Mutation can result in several different types of change in
sequences. Mutations in genes can either have no effect,
alter the product of a gene, or prevent the gene from
functioning properly or completely. Mutations can also
occur in nongenic regions. One study on genetic
variations between
different species of
Drosophila suggests that if
a mutation changes a
protein produced by a
gene, the result is likely to
be harmful, with an
estimated 70 percent of
amino acid
polymorphisms which
have damaging effects,
and the remainder being
either neutral or weakly
beneficial. Due to the
damaging effects that
mutations can have on
genes, organisms have
mechanisms such as DNA
repair to prevent or
correct mutations i.e.
revert the mutated
sequence back to its
original state.
! -Anokhi Kashiparekh (AK:D)
 Transcription, Translation
and Replication:
A gene is a sequence of DNA that contains genetic
information and can influence the phenotype of an
organism. Within a gene, the sequence of bases along a
DNA strand defines a messenger RNA sequence, which
then defines one or more protein sequences. The
relationship between the nucleotide sequences of genes
and the amino-acid sequences of proteins is determined
by the rules of translation, known collectively as the
genetic code. The genetic code consists of three-letter
'words' called codons formed from a sequence of three
nucleotides (e.g. ACT, CAG, TTT).
In transcription, the codons of a gene are copied into
messenger RNA by RNA polymerase. This RNA copy is
then decoded by a ribosome that reads the RNA sequence
by base-pairing the messenger RNA to transfer RNA,
which carries amino acids. Since there are 4 bases in 3-
letter combinations, there are 64 possible codons. These
encode the twenty standard amino acids, giving most
amino acids more than one possible codon. There are also
three 'stop' or 'nonsense' codons signifying the end of the
coding region; these are the TAA, TGA and TAG codons.

! -Anokhi Kashiparekh (AK:D)

Cell Division is essential for an organism to grow, but,
when a cell divides, it must replicate the DNA in its
genome so that the two daughter cells have the same
genetic information as their parent. The double-stranded
structure of DNA provides a simple mechanism for DNA
replication. Here, the two strands are separated and then
each strand's complementary DNA sequence is recreated
by an enzyme called DNA polymerase. This enzyme
makes the complementary strand by finding the correct
base through complementary base pairing, and bonding it
onto the original strand. As DNA polymerases can only
extend a DNA strand in a 5! to 3! direction, different
mechanisms are used to copy the antiparallel strands of
the double helix. In this way, the base on the old strand
dictates which base appears on the new strand, and the
cell ends up with a perfect copy of its DNA.

! -Anokhi Kashiparekh (AK:D)

DNA-binding proteins

Structural proteins that bind DNA are well-understood

examples of non-specific DNA-protein interactions.
Within chromosomes, DNA is held in complexes with
structural proteins. These proteins organize the DNA into
a compact structure called chromatin. In eukaryotes this
structure involves DNA binding to a complex of small
basic proteins called histones, while in prokaryotes
multiple types of proteins are involved. The histones form
a disk-shaped complex called a nucleosome, which
contains two complete turns of double-stranded DNA
wrapped around its surface. These non-specific
interactions are formed through basic residues in the
histones making ionic bonds to the acidic sugar-phosphate
backbone of the DNA, and are therefore largely
independent of the base sequence. These chemical
changes alter the strength of the interaction between the
DNA and the histones, making the DNA more or less
accessible to transcription factors and changing the rate of
transcription. Other non-specific DNA-binding proteins in
chromatin include the high-mobility group proteins,
which bind to bent or distorted DNA.These proteins are
important in bending arrays of nucleosomes and
arranging them into the larger structures that make up
chromosomes. In contrast, other proteins have evolved to
! -Anokhi Kashiparekh (AK:D)
bind to particular DNA sequences. The most intensively
studied of these are the various transcription factors,
which are proteins that regulate transcription. Each
transcription factor binds to one particular set of DNA
sequences and activates or inhibits the transcription of
genes that have these sequences close to their promoters.
The transcription factors do this in two ways. Firstly, they
can bind the RNA polymerase responsible for
transcription, either directly or through other mediator
proteins; this locates the polymerase at the promoter and
allows it to begin transcription. Alternatively, transcription
factors can bind enzymes that modify the histones at the
promoter. This changes the accessibility of the DNA
template to the polymerase.

! -Anokhi Kashiparekh (AK:D)

 Genetic Recombination
Recombination allows chromosomes to exchange genetic
information and produces new combinations of genes,
which increases the efficiency of natural selection and can
be important in the rapid evolution of new proteins.
Genetic recombination can also be involved in DNA
repair, particularly in the cell's response to double-strand
breaks.

Chromosomal crossover is when two DNA helices break,

swap a section and then rejoin. The most common form
of chromosomal crossover is homologous recombinations,
where the two chromosomes involved share very similar
sequences. Non-homologous recombination can be
damaging to cells, as it can produce chromosomal
translocations and genetic abnormalities.

! -Anokhi Kashiparekh (AK:D)

In eukaryotes, recombination
also occurs in meiosis, where
it facilitates chromosomal
crossover. The crossover
process leads to offspring having
different combinations of genes from those of their
parents, and can occasionally produce new chimeric
alleles. The shuffling of genes brought about by genetic
recombination is thought to have many advantages, as it is
a major engine of genetic variation and also allows
sexually reproducing organisms to avoid Muller’s ratchet ,
in which the genomes of an asexual population
accumulate deleterious mutations in an irreversible
manner.
Chromosomal crossover refers to recombination between
the paired chromosomes inherited from each of one's
parents, generally occurring during meiosis. During
prophase I the four available chromatids are in tight
formation with one another. While in this formation,
homologous sites on two chromatids can mesh with one
another, and may exchange genetic information.

! -Anokhi Kashiparekh (AK:D)

 Genetic Disorder
A genetic disorder is an illness caused by one or more
abnormalities in the geome, especially a condition that is
present from birth i.e congenital. Most genetic disorders
are quite rare and affect one person in every several
thousands or millions.
Genetic disorders are heritable, and are passed down from
the parents' genes. Other defects may be caused by new
mutations or changes to the DNA. In such cases, the
defect will only be heritable if it occurs in the germ line.
The same disease, such as some forms of cancer, may be
caused by an inherited genetic condition in some people,
by new mutations in other people, and by non-genetic
causes in still other people.
Some types of recessive gene disorders confer an
advantage in certain environments when only one copy of
the gene is present.
DNA is constantly subject to mutations, accidental
changes in its code. Mutations can lead to missing or
malformed proteins, and that can lead to disease. We all
start out our lives with some mutations. These mutations
inherited from your parents are called germ-line
mutations. However, you can also acquire mutations
during your lifetime. Some mutations happen during cell
division, when DNA gets duplicated. Still other mutations
! -Anokhi Kashiparekh (AK:D)
are caused when DNA gets damaged by environmental
factors, including UV radiation, chemicals, and viruses.
Few mutations are bad for you. In fact, some mutations
can be beneficial. Over time, genetic mutations create
genetic diversity, which keeps populations healthy. Many
mutations have no effect at all. These are called silent
mutations. But the mutations we hear about most often
are the ones that cause disease. Some well-known
inherited genetic disorders include cystic fibrosis, sickle cell
anemia, Tay-Sachs disease, phenylketonuria and color-blindness,
among many others. All of these disorders are caused by
the mutation of a single gene. Most inherited genetic
diseases are recessive, which means that a person must
inherit two copies of the mutated gene to inherit a
disorder. This is one reason that marriage between close
relatives is discouraged; two genetically similar adults are
more likely to give a child two copies of a defective gene.
Diseases caused by just one copy of a defective gene, such
as Huntington's disease, are rare. Thanks to natural selection,
these dominant genetic diseases tend to get weeded out of
populations over time, because afflicted carriers are more
likely to die before reproducing. Scientists estimate that
every one of us has between 5 and 10 potentially deadly
mutations in our genes-the good news is that because
there's usually only one copy of the bad gene, these
diseases don't manifest. Cancer usually results from a series
of mutations within a single cell. Often, a faulty, damaged,
or missing p53 gene is to blame. The p53 gene makes a
! -Anokhi Kashiparekh (AK:D)
protein that stops mutated cells from dividing. Without
this protein, cells divide unchecked and become tumors.

Huntington's disease

Sickle cell anaemia

Cystic Fibrosis

Cancer

! -Anokhi Kashiparekh (AK:D)

 My Model
For Identification:
Red Beads- Phosphates
Blue Beads- Deoxyribose Sugars
Green Beads- Thymine
Orange Beads- Guanine
Yellow Beads- Cytosine
White Beads- Adenine

Sequence:
G-C
G-C
T-A
C-G
T-A
A-T
G-C
C-G
T-A
G-C
A-T
A-T
C-G
T-A
G-C
A-T
C-G
G-C
A-T
! -Anokhi Kashiparekh (AK:D)