Report to

Department of Chemical Engineering

University of EGE
for
Course:OMY 160 Technical English

DNA

Prepared by
ERDEM BÜLBÜL
05992900

May 10, 2001

BORNOVA-İZMİR
 Summary

DNA is a polymer. The monomer units of DNA are nucleotides, and the polymer is known as a
"polynucleotide." Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base
attached to the sugar, and a phosphate group. There are four different types of nucleotides found in DNA,
differing only in the nitrogenous base. The four nucleotides are given one letter abbreviations as shorthand for
the four bases.

• A is for adenine
• G is for guanine
• C is for cytosine
• T is for thymine

Adenine and guanine are purines. Purines are the larger of the two types of bases found in DNA.
Cytosine and thymine are pyrimidines. Like purines, all pyrimidine ring atoms lie in the same plane.

The deoxyribose sugar of the DNA backbone has 5 carbons and 3 oxygens. The hydroxyl groups on the
carbons link to the phosphate groups to form the DNA backbone. Deoxyribose lacks an hydroxyl group when
compared to ribose, the sugar component of RNA.

DNA is a normally double stranded macromolecule. Two polynucleotide chains, held together by weak
thermodynamic forces, form a DNA molecule.

Features of the DNA Double Helix are:

• Two DNA strands form a helical spiral, winding around a helix axis in a right-handed spiral
• The two polynucleotide chains run in opposite directions
• The sugar-phosphate backbones of the two DNA strands wind around the helix axis like the
railing of a sprial staircase

The bases of the individual nucleotides are on the inside of the helix, stacked on top of each other like
the steps of a spiral staircase.
 Introduction
Although scientists as far back in history as Aristotle recognized that the features of one
generation are passed on to the next (...like begets like...) it was not until the 1860's that the
fundamental principles of genetic inheritance were described by Gregor Mendel. His theories were,
however, widely disregarded by scientists of the time. In the last quarter of the 19th century, however,
microscopists and cytologists, interested in the process of cell division, developed both the equipment
and the methods needed to visualize chromosomes and their division in the processes of mitosis and of
meiosis.

As the 20th century began many scientists noticed similarities in the theoretical behavior of
Mendel's particles, and the visible behavior of the newly discovered chromosomes. It wasn't long
before most scientists were convinced that the hereditary material responsible for giving living things
their characteristic traits, and chromosomes must be one in the same. Yet, questions still remained.
Chemical analysis of chromosomes showed them to be composed of both protein and DNA. Which
substance carried the hereditary information? For many years most scientists favored the hypothesis
that protein was the responsible molecule because of its comparative complexity when compared with
DNA. After all, DNA is composed of a mere 4 subunits while protein is composed of 20, and DNA
molecules are linear while proteins range from linear to multiply branched to globular. It appeared
clear that the relatively simple structure of a DNA molecule could not carry all of the genetic
information needed to account for the richly varied life in the world around us!

In 1951, the then 23-year old biologist James Watson traveled from the United States to work
with Francis Crick, an English physicist at the University of Cambridge. Crick was already using the
process of X-ray crystallography to study the structure of protein molecules. Together, Watson and
Crick used X-ray crystallography data, produced by Rosalind Franklin and Maurice Wilkins at King's
College in London, to decipher DNA's structure.

Working with nucleotide models made of wire, Watson and Crick attempted to put together the
puzzle of DNA structure in such a way that their model would account for the variety of facts that they
knew described the molecule. Once satisfied with their model, they published their hypothesis, entitled
"Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" in the British
journal Nature. It is interesting to note that this paper has been cited over 800 times since its first
appearance!
 Here are their words:

"...This (DNA) structure has two helical chains each coiled round the same axis...Both chains
follow right handed helices...the two chains run in opposite directions. ..The bases are on the inside of
the helix and the phosphates on the outside..."

"The novel feature of the structure is the manner in which the two chains are held together by
the purine and pyrimidine bases... The (bases) are joined together in pairs, a single base from one
chain being hydrogen-bonded to a single base from the other chain, so that the two lie side by
side...One of the pair must be a purine and the other a pyrimidine for bonding to occur. ...Only specific
pairs of bases can bond together. These pairs are: adenine (purine) with thymine (pyrimidine), and
guanine (purine) with cytosine (pyrimidine)."

"...in other words, if an adenine forms one member of a pair, on either chain, then on these assumptions
the other member must be thymine; similarly for guanine and cytosine. The sequence of bases on a
single chain does not appear to be restricted in any way. However, if only specific pairs of bases can
be formed, it follows that if the sequence of bases on one chain is given, then the sequence on the
other chain is automatically determined."

"...It has not escaped our notice that the specific pairing we have postulated immediately suggests a
possible copying mechanism for the genetic material."

And with these words, the way was made clear for tremendous strides in our understanding of the
structure of DNA and, as a result our ability to work with and manipulate the information-rich DNA
molecule.

1.0. Historical Past of Knowledge about DNA:

1.1 From 1870s to Watson-Crick:

The processes of mitosis and meiosis were discovered in the 1870s and 1890s. It was observed
that, as cells divided, chromosomes moved around in a cell, and people began to wonder what their
function was. It was determined that chromosomes were made of protein and a chemical called DNA,
about which people knew almost nothing. People began to suspect that chromosomes had something to
do with genetics, but couldn’t explain what/how. When enough evidence was accumulated to confirm
that chromosomes did, indeed, have something to do with genetics, most people thought that in some
way the protein in the chromosomes served as the genetic material. People knew that DNA was also in
the chromosomes, but because its structure was unknown and people didn’t know much about it, few
people thought it was the genetic material.

In 1928, Frederick Griffith performed an experiment using pneumonia bacteria and mice. This
was one of the first experiments that hinted that DNA was the genetic code material. Follow the links
to study his experiment. He used two strains of Streptococcus pneumoniae: a “smooth” strain which
has a polysaccharide coating around it that makes it look smooth when viewed with a microscope, and
a “rough” strain which doesn’t have the coating, thus looks rough under the microscope. When he
injected live S strain into mice, the mice contracted pneumonia and died. When he injected live R
strain, a strain which typically does not cause illness, into mice, as predicted, they did not get sick, but
lived. Thinking that perhaps the coating on the bacteria somehow caused the illness, Griffith then used
heat to kill some of the S strain bacteria and injected that into mice. This failed to infect/kill the mice,
indicating that the polysaccharide coating was not what caused the disease, but rather, something
within the living cell. Since Griffith had used heat to kill the bacteria and heat denatures protein, he
next hypothesized that perhaps some protein within the living cells, that was denatured by the heat,
caused the disease. He then injected another group of mice with a mixture of heat-killed S and live R,
and the mice died! When he did a necropsy on the dead mice, he isolated live S strain bacteria from
the corpses. Griffith concluded that therefore, the live R strain bacteria must have absorbed genetic
material from the dead S strain bacteria, and since heat denatures protein, the protein in the bacterial
chromosomes was not the genetic material. This evidence pointed to DNA as being the genetic
material. Transformation is the process whereby one strain of a bacterium absorbs genetic material
from another strain of bacteria and “turns into” the type of bacterium whose genetic material it
absorbed. Because DNA was so poorly understood, scientists remained skeptical up through the 1940s

In 1952, Alfred Hershey and Martha Chase did an experiment which is so significant, it has been
named the “Hershey-Chase Experiment”. They used a bacterium named Escherichia coli, or E. coli
for short, named after a scientist whose last name was Escher. They also used a virus called T2 that
infects E. coli. T2 is a bacteriophage. Isolated T2, like other viruses, is just a crystal of DNA and
protein, so it must live inside E. coli in order to make more virus like itself. When the new T2 viruses
are ready to leave the host E. coli cell (and go infect others), they burst the E. coli cell open, killing it
(hence the name “bacteriophage”). Hershey and Chase were seeking an answer to the question, “Is it
the viral DNA or viral protein coat (capsid) that is the viral genetic code material which gets injected
into the E. coli?” Their results indicated that the viral DNA, not the protein, is its genetic code
material. At this time, people knew that viruses were composed of DNA inside a protein coat/shell
called a capsid. It was also known that viruses replicate by taking over the host cell’s metabolic
functions to make more virus, then in the case of a bacteriophage, killing the host bacterium cell as the
virus left. In order to do all this, the virus (T2) must inject whatever is the viral genetic code into the
host cell (E. coli). Hershey and Chase were seeking an answer to the question, “Is it the viral DNA or
viral protein coat (capsid) that’s the genetic material that gets injected into the E. coli?”

They tested this by using radioactive labeling. Since some amino acids contain sulfur in their
side chains, if T2 is grown in E. coli with a source of radioactive sulfur, the sulfur will be incorporated
into the T2 protein coat making it radioactive. Since DNA has lots of phosphorus in its -PO4 groups,
if T2 is grown in E. coli with a source of radioactive phosphorus, the phosphorus will be incorporated
into the viral DNA, making it radioactive. Hershey and Chase grew two batches of T2 and E. coli: one
with radioactive sulfur and one with radioactive phosphorus to get batches of T2 “labeled” with either
radioactive S or radioactive P. Then, these radioactive T2 were placed in separate, new batches of E.
coli, but were left there only 10 minutes. This was to give the T2 time to inject their genetic material
into the bacteria, but not reproduce. In the next step, still in separate batches, the mixtures were
agitated in a kitchen blender to knock loose any viral parts not inside the E. coli but perhaps stuck on
the outer surface. Hopefully, this would differentiate between the protein and DNA portions of the
virus. Then, each mixture was spun in a centrifuge to separate the heavy bacteria (with any viral parts
that had gone into them) from the liquid solution they were in (including any viral parts that had not
entered the bacteria). The centrifuge causes the heavier bacteria to be pulled to the bottom of the tube
where they form a pellet, while the light-weight viral “left-overs" stay suspended in the liquid portion
called the supernatant. In the subsequent step, the pellet and supernatant from each tube were
separated and tested for the presence of radioactivity. Radioactive sufur was found in the supernatant,
indicating that the viral protein did not go into the bacteria. Radioactive phosphorus was found in the
bacterial pellet, indicating that viral DNA did go into the bacteria.

Based on these results, Hershey and Chase concluded that DNA must be the genetic code
material, not protein as many people believed. When their experiment was published and people
finally acknowledged that DNA was the genetic material, there was a lot of competition to be the first
to discover its chemical structure.

What was known is that DNA contains a nitrogenous base. There are two kinds of these,
which include:

Each nitrogenous base is connected to a molecule of ribose sugar (- 1 oxygen in DNA) to form
a nucleoside like the adenosine in ATP.
 Each nucleoside is joined to a PO4 (phosphate group) to form a nucleotide like adenosine
monophosphate (which can be turned into ATP by adding phosphate groups).

People also knew that nucleotides were somehow linked by dehydration synthesis to form
DNA, but the exact structure/arrangement was unknown.

In the early 1950s, Rosalind Franklin, an Englishwoman, was doing research which involved
bouncing x-rays off crystals of various substances (a process which is called x-ray crystallography),
including DNA, then exposing photographic film to the x-rays. She was studying the scatter patterns
made by the x-rays bouncing off the crystals of various substances (Unfortunately, she died of cancer
soon afterwards, or she might have been more famous). Other people like Linus Pauling were also
attempting to figure out the structure of DNA.

1.2. Watson-Crick:

James Watson, a young American scientist went to England to visit Francis Crick, another
young researcher. When they went to visit Franklin, they saw her photographs of DNA x-ray
crystallography. From her pictures, they were able to determine that the structure of DNA was
organized into a spiral or helix. Based on this information, in 1953, Watson and Crick published a
paper in which they proposed and described a theoretical structure for DNA. Subsequent research by
many other people has since proven their idea to be correct. For their discovery, they received the
Nobel prize in 1962. Since the Nobel prize is not awarded posthumously, people have often wondered
if the Nobel committee would have included Franklin if she had still been alive.

DNA is a double helix. The outer edges are formed of alternating ribose sugar molecules and
phosphate groups. The two strands go in opposite directions (1 “up” and 1 “down”). The nitrogenous
bases are “inside” like rungs on a ladder. Adenine on one side pairs with thymine (uracil in RNA) on
the other by hydrogen bonding, and cytosine pairs with guanine.

Note that the C-G pair has three hydrogen bonds while the A-T pair has only two, which keeps
them from pairing wrong. This dictates side-to-side pairing, but says nothing about the order along the
molecule. Watson and Crick said this variability along the molecule can account for the variety in the
genetic code. Their model also accounts for how DNA can replicate itself. They said the molecule
“unzips” and new matching bases are added in to create two new molecules. They called this
semiconservative replication because each new molecule has one “old” and one “new” strand of
DNA.
 DNA codes for protein synthesis by first coding for RNA. First, the DNA code is transcribed
to RNA code, which is still in the “language” of nitrogenous bases, except that adenine on the DNA
pairs with uracil (in place of thymine) on the RNA. The RNA code is then translated to protein code,
which is a different “language.” This process involves ribosomes and two kinds of RNA: mRNA and
tRNA. The mRNA codes for the gene in question and is copied off the DNA, while tRNA matches a
specific group of nucleotides with a specific amino acid. A “unit” of three nucleotides on the tRNA
codes for one amino acid. Each of these “units” is called an anticodon. These match up with
corresponding three-nucleotide sequences on the mRNA called codons, and in this manner the amino
acids are organized into the correct sequence to build a protein. The ribosome works with the mRNA
and tRNA to hook the amino acids together to form a protein.(Look Figure 1 for Watson-Crick Model)

Figure 1:Watson-Crick Model

2.0 Structure of DNA :

2.1. Components of DNA:

The fundamental chemical building block of deoxyribonucleic acid (DNA) is the nucleotide. A
nucleotide consists of three parts(See Appendix A :The average mass of Dna and nucleotide Sub-units
as they appear in Dna)
 • A nitrogen-containing pyrimidine or purine base (Nitrogenous base)

• A deoxyribose sugar(5-Carbon sugar)

• A phosphate group; that acts as a bridge between adjacent deoxyribose sugars. Each
deoxyribose sugar unit contains five carbon atoms joined in a ring structure with an oxygen atom. The
carbon atoms of the deoxyribose sugar are designated by numbering them sequentially from one to five.
The first carbon atom, the 1´ carbon, is by definition the carbon atom covalently attached to one of four
organic bases: guanine (G), adenine (A), thymine (T), or cytosine (C). Adenine and guanine are purines,
and cytosine and thymine are pyrimidines. Phosphate groups are attached to the third (3´) and fifth (5´)
carbon atoms. In DNA, the term nucleotide refers to the complete assemblage of a nitrogenous base (A,
G, C, or T), a five-carbon deoxyribose sugar, and a phosphate group.(See Figure 2)

Figure 2 :Structure of DNA

2.2 Chemical Structure Of DNA

 Figure 3:Chemical Structure of Dna
DNA is a linear polymer that is
made up of nucleotide units. The
nucleotide unit consists of a base, a
deoxyribose sugar, and a phosphate.
There are four types of bases: adenine
(A), thymine (T), guanine (G), and
cytosine (C). Each base is connected to a
sugar via a ß glycosyl linkage. The
nucleotide units are connected via the
O3' and O5' atoms forming
phosphodiester linkages. (See in Figure
3)
In normal DNA, the bases form pairs:
A to T and G to C. This is called
complementarity. A duplex of DNA is
formed by two complementary chains
that are arranged in an anti-parallel
manner.
The results of fiber and single crystal
x-ray crystallographic studies have
shown that DNA can have several
conformations. The most common one is
called B-DNA. B-DNA is a right-handed
double helix with a wide and narrow
groove. Tha bases are perpendicular to
the helix axis.
DNA can also be found in the A form
in which the major groove is very deep
and the minor groove is quite shallow.
A very unusual form of DNA is the
left-handed Z-DNA. In this DNA, the
basic building block consists of two
nucleotides, each with different
conformations. Z-DNA forms excellent
crystals. building block consists of two
nucleotides, each with different
conformations. Z-DNA forms excellent
crystals.
 Several years ago it was discovered that nucleic acids
can form four stranded structures and a few examples
of these molecules now exist. Occasionally mutations occur in
which a base is changed. Base pairs
still form, but they are not in the usual Watson-Crick geometry.
Examples of these mismatches have been characterized.

Very recently, DNA structures have appeared that are unusual

in that the end pairs are flipped out or there are

Figure 4:Chemical Structure of Adenine

bulges.(Seechemical structure of Dna’s bases in Figure 4,5,6,7)

Figure 5:Chemical Structure Figure 6:Chemical Structure

of Thymine of Cytosine

Figure 7:Chemical Structure of Quanine

3.0. Replication of DNA:

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3.1 Types of Replication:

  Conservative replication would leave intact the original DNA molecule and generate a completely new
molecule.
 Dispersive replication would produce two DNA molecules with sections of both old and new DNA
interspersed along each strand.

• Semiconservative replication would produce molecules with both old and new DNA, but
each molecule would be composed of one old strand and one new one.

See posible Models of Replication below in Figure 8.

Figure 8: Types of Dna Replication

3.2 Dna Replication:

The replication is semiconservative. Each strand acts as a template for the synthesis of a new DNA
molecule by the sequential addition of complementary base pairs, thereby generating a new DNA strand
that is the complementary sequence to the parental DNA. Each daughter DNA molecule ends up with one
of the original strands and one newly synthesized strand.
 A simplified representation of a DNA molecule separating to form two new molecules.
To reproduce, a cell must copy and transmit its genetic information (DNA) to all of its progeny.
To do so, DNA replicates, following the process of semiconservative replication Each strand of the
original molecule acts as a template for the synthesis of a new complementary DNA molecule.(Figure 9)

The two strands of the double helix are first separated by enzymes. With the assistance of other
enzymes, spare parts available inside the cell are bound to the individual strands following the rules of
complementary base pairing: adenine (A) to thymine (T) and guanine (G) to cytosine (C).

Figure 9 :Dna Replication

By this way DNA replicates its body and makes one hand old and other hand new body. The genetic codes
of new bodies are same with the part of separated DNA that makes a new helix DNA structure together.

Two strands of DNA are obtained from one, having produced two daughter molecules which are
identical to one another and to the parent molecule.
3.3 Messelson and Stahl’s Experiment

In 1957, Matthew Meselson and Franklin Stahl did an experiment to determine which of the following
models best represented DNA replication:

1. Did the two strands unwind and each act as a template for new strands? This is
semiconservative replication, because each new strand is half comprised of molecules from
the old strand.

2. Did the strands not unwind, but somehow generate a new double stranded DNA copy
of entirely new molecules? This is conservative replication.

In order to determine which of these models was true, the following experiment was performed: The
original DNA strand was labelled with the heavy isotope of nitrogen, N-15. This DNA was allowed to go
through one round of replication with N-14, and then the mixture was centrifuged so that the heavier DNA
would form a band lower in the tube, and the intermediate (one N-15 strand and one N-14 strand) and
light DNA (all N-14) would appear as a band higher in the tube.

The expected results for this experiment:

• Replication Of DNA is semiconservative.

• Not all but some of the genetic information is preserved by semiconservative replication.(Look to
replications effects in generations in Figure 10)
Figure 10: Replication Results in Generations
 4.0. Genetic Code

4.1. Order Of Nucleotids Make The Genetic Code

In 1943, Oswald Avery, Colin Macleod, and Maclyn McCarty, at the Rockefeller Institute,
discovered that different strains of the bacterium Strepotococcus pneumonae could have different
effects on a mouse. One virulent strain could kill an injected mouse, and another avirulent strain
had no effect. When the virulent strain was heat-killed and injected into mice, there was no effect.
But when a heat-killed virulent strain was coinjected with the avirulent strain, the mice died. What
transforming principle was the dead virulent strain giving to the avirulent strain to make it lethal?

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Figure 11:Experiment on mouse

Avery and his colleagues separated the dead virulent cells into fractions and coinjected them with the
avirulent strain, to see which fraction contained the transforming principle. They discovered that
the fraction was DNA. Most scientists at the time, in favour of the theory of protein as genetic
 material, discounted this result and said that there must have been some protein in the fraction that
conferred virulence.

This Experiment show us the genetic information is based on DNA and all the genetic happens
become in DNA.(See Figure 11)

DNA writes the genetic code on the views by nucleotides likes AGC, TTA, CTG ect. And this codes
are replicates in DNA replication before the protein synthesis.

Amino acids specified by each codon sequence on mRNA. Key for the above table 1 :

Table 1: Amino acids specified by each codon sequence on mRNA

Ala: Alanine Cys: Cysteine Asp: Aspartic acid Glu: Glutamic acid
Phe: Phenylalanine Gly: Glycine His: Histidine Ile: Isoleucine
Lys: Lysine Leu: Leucine Met: Methionine Asn: Asparagine
Pro : Proline Gln: Glutamine Arg: Arginine Ser: Serine
Thr: Threonine Val: Valine Trp: TryptophaneTyr: Tyrosisne

DNA nucleotides bases. During protein synthesis, ribosomes move along the
mRNA molecule and "read" its sequence three nucleotides at a time (codon) from the 5' end to the
3' end. Each amino acid is specified by the mRNA's codon, and then pairs with a sequence of three
complementary nucleotides carried by a particular tRNA (anticodon).

Since RNA is constructed from four types of nucleotides, there are 64 possible triplet sequences or
codons (4x4x4). Three of these possible codons specify the termination of the polypeptide chain.
They are called "stop codons". That leaves 61 codons to specify only 20 different amino acids.
Therefore, most of the amino acids are represented by more than one codon. The genetic code is
said to be degenerate. (Look Appendix B About Genetic Code)

4.2.Mutations :
Mutations can be caused by a change in the sequence of the nucleotides. Some mutations have more
effect than others, depending on where in the code they are and how important that area is to the
code. While mutations in some areas of some genes have little effect, sickle cell anemia is caused
by a mutation in only one nucleotide. This changes the codon at that location to code for a different
amino acid, and that, in turn, significantly changes the shape of the hemoglobin molecules in that
person’s blood.

When some viruses infect us, they insert their DNA15into our cells’ DNA (for example, Herpes virus),
and stay resident in our cells for the rest of our lives. These can potentially become active again
either making a person sick again (like Shingles in a person who has had Chicken Pox) or just
being shed from a person’s body (to infect others) without obvious symptoms of illness (like
Mononucleosis). Some kinds of cancer may be caused this way. The AIDS virus does things
“backwards”. This virus contains RNA rather than DNA, yet when it gets into someone’s cells, it
can do reverse transcription and code from its RNA to make DNA which, then, can code to make
more virus.

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