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Honors Biology DNA

By Matt Wedekind
Honors Challenge Activity #1:
Essay Question Set #1:
1.) The four nitrogenous bases found in DNA include guanine (G), cytosine (C), adenine
(A), and thymine (T). In DNA, a purine nitrogenous base (guanine and adenine) always binds
with a pyrimidine nitrogenous base (cytosine and thymine). Therefore, the base pairs found in
DNA are guanine-cytosine and thymine-adenine, or the reverse of those two. (Cytosine-guanine
and adenine-thymine).
2.) If a double-stranded DNA molecule has 15% thymine, this means that adenine, its
reverse, must also consist of 15% of the molecule. This is because thymine and adenine are
always bound together in a base pair. Knowing that thymine and adenine consist of 30% of the
DNA molecule, we can subtract 30% from the 100% total of the DNA molecule to figure that
cytosine and guanine consist of the other 70% of the molecule. Because cytosine and guanine
always pair together, half of 70% is 35%. Therefore, to answer the question, adenine consists of
15% of the DNA molecule, cytosine consists of 35%, and guanine consists of 35%.
3.) If there were no base pair rules, DNAs ability to serve as a source of genetic
information would be rendered completely inoperable. We can know this by possessing a basic
understanding of the processes of transcription and translation. Starting with transcription, when
the messenger RNA reads the unzipped gene in the DNA, the RNA polymerase has to call for the
opposite nitrogenous base, with uracil replacing thymine. However, if there was no rule for base
pairs, this entire process would be impossible and there would be no code read, as the opposite
nitrogenous bases spell out the code of the respective gene in the DNA. There would be no way
for transcription to occur, and because of this, there would be no way for translation to occur,
and because of this, no proteins would be created. The process wholly relies on base pair rules.
4.) First, lets look at Virus I. We can tell right away that its genetic material consists of
RNA. This is because it contains uracil, but no thymine, and we know this to be a property of
RNA. We can also tell that it is double-stranded, because there is an equal amount of uracils to
adenines, and an equal amount of cytosines to guanines. This is because double-stranded
molecules have base pairs, and because of this, there can never be more of one nitrogenous base
than its respective base pair.
Next, lets look at Virus II. Its genetic material consists of DNA, not RNA. We can know
this because it contains thymine, but no uracil, and thymine is only found in DNA. Additionally,
this viruss genetic material is double-stranded, because there is an equal amount of uracils to
adenines, and an equal amount of cytosines to guanines, and this means that the viruss genetic
material consists of a molecule with base pairs.
What about Virus III? Its genetic material consists of DNA, like Virus II. Just like Virus
II, we know this because the molecule contains thymine, but no uracil, and thymine is found only
in DNA. However, Virus III is different than Virus II. Virus IIIs genetic material is single-
stranded. This is because there is not an equal number of nitrogenous bases in each base pair.
There are more adenines than thymines, and more cytosines than guanines. This would be
impossible in a double-stranded molecule, as the nitrogenous bases come in pairs.
Finally, Virus IVs genetic material consists of RNA. This is because the molecule
contains uracil, but no thymine, and uracil is only found in RNA. Virus IVs genetic material is
single-stranded. This is because there is not an equal number of nitrogenous bases in each base
pair. There are more uracils than adenines, and more guanines than cytosines. This would be
impossible in a double-stranded molecule, as the nitrogenous bases come in pairs.
Essay Question #2:
1.) See attached loose-leaf paper.
2.) The direction of replication is shown on the paper. All replication moves from 5 to
3. This causes problems, as the helicase unzips in one direction only, thus creating lagging and
leading strands. The leading strands replicates with the helicase, the 3 lying at the very end of
the strand and the 5 lying where the helicase begins to unzip. The DNA polymerase adds
respective nucleotides as the helicase unzips, making it very simple. However, in the case of the
lagging strand, it is much more difficult. The helicase begins to unzip at the 3, and replication
does not begin at 3. A complicated process begins in which DNA polymerase creates new DNA
in pieces known as Okazaki fragments, named for one of their discoverers, Reiji Okazaki.
These fragments are linked together with DNA ligase, and new, replicated DNA is created
discontinuously.
3.) Semi-conservative replication is one of three postulates related to how DNA could
possibly replicate. It can be described as two new, identical DNA molecules being created, each
containing one of the original strands and one new strand, a replica of the opposite strand. This is
how DNA replicates, as the helicase separates the DNA into two separate strands, and the DNA
polymerase adds new DNA to the single strands.
4.) DNA is anti-parallel, with the 5 and 3 being on opposite sides of each othee (On one
strand, the 5 is on one end, while the opposite strand has 5 on the opposite end, rather than the
must be copied in a unique way, as described before. This is because while helicase unzips the
DNA molecule in one direction, the DNA is not replicated in the same direction because of its
anti-parallel nature, thus leading to the creation of Okazaki fragments.
Option #1: Chargaffs data
1.) Mycobacterium tuberculosis has a higher concentration of guanine and cytosine than
adenine and thymine. However, the eukaryotes (the mammals, fish, invertebrates, plants, fungi)
all have a higher concentration of thymine and adenine in their base composition.
2.) Humans: 31 + 19.1 = 50.1, 31.5 + 18.4 = 49.9
50.1 / 49.9 = 1.004, approx. 1
Mycobacterium tuberculosis: 15.1 + 34.9 = 50, 14.6 + 35.4 = 50
50 / 50 = 1
3.) This claim is true, and I have proven it using Chargaffs data. In question 2, I
demonstrated that the ratio of purines over pyrimidines in humans and in mycobacterium
tuberculosis were exactly or almost exactly 1. This means that there is always a C to go with a G,
or a T to go with an A. It means that the DNA is double-stranded. Because this ratio is 1, the
amount of adenine to thymine is equal, and the amount of guanine to cytosine is equal.
4.) In terms of structure, the DNA is double-stranded, and this means that there is always
a base pair of nitrogenous bases. If there is a cytosine, a guanine accompanies it, and if there is
an adenine, a thymine accompanies it, and vice-versa.
5.) This would be because the viruses are single-stranded. They are not prokaryotes or
eukaryotes, as they are not living things, therefore their genetic material can be single-stranded.
Additionally, the polio virus could have 0.0% thymine because its genetic material could
possibly be RNA as opposed to DNA, where uracil is found instead of thymine.
Honors Challenge Activity #2:
a.) James D. Watson interest in genetics stemmed from his teacher at Indiana University,
Salvador Luria. He was curious as to the nature of the gene, and he realized that in order to make
a discovery, he would have to delve into biochemistry, which was something he was not fond of.
Regardless, he decided to travel to Europe to study it. While there, he met Maurice Wilkins, an
X-ray crystallographer. X-ray crystallography was important in the discoveries of the structure of
nucleic acids and proteins, and when Watson met Wilkins, he grew interested in Wilkinss field.
Once he had gained enough money, Watson moved to Cambridge and met Francis Crick.
Francis Crick was a visionary, who was especially interested in radical theories of all sorts of
kinds. They became a partnership, but there was a problem: They were inexperienced in the field
they wanted to research! Neither knew any biochemistry, (that ship had sailed for Watson) and
X-ray crystallography was not a primary focus of Crick, although he had basic understanding of
it.
In Kings College of London, where Maurice Wilkins hailed from, him and his partner in
science, Rosalind Franklin, were conducting thorough, painstaking work on X-ray
crystallography. They collected large amounts of data on DNA, but were unable to draw any sort
of conclusion as to what the shape could be. This was unacceptable for Watson and Crick, who
were eager to theorize and make game-changing discoveries.
Linus Pauling was a brilliant man who studied structure furiously. He leaned towards a
triple-stranded DNA model, although he was not adamant in his theory. Watson and Crick
looked to him as an opponent, a challenge, and were determined to prove his theories wrong and
take all recognition for themselves. Linuss son Peter was often inadvertently giving information
to Watson and Crick regarding his fathers latest discoveries and scrapped ideas. Watson and
Crick took this information eagerly.
Watson and Crick were also excited in the work of Erwin Chargaff, who had discovered
the ratio of adenine to thymine and the ratio of guanine to cytosine in all living things was
approximately 1:1. When Watson and Crick discovered this, they took note. They could not
prove anything without X-ray crystallography, but it definitely pointed to a connection between
purines and pyrimidines.
Watson and Crick visited the laboratory of Rosalind Franklin where Watson tried to take
a mental note of all data he could find. Luckily, some unpublished data by Franklin and Wilkins
was passed on to Watson and Crick.
A chemist sharing a desk with Crick suggested a ground-breaking idea. He suggested a
different chemical form of DNA, keto rather than enol, would allow for hydrogen bonding,
which would explain how the molecule is held together AND the meaning behind Chargaffs 1:1
ratio data.
Watson and Crick took their passed on data, lazy research, and stolen ideas and published
their Nature article documenting their discoveries, and finally proposed the double-helix model
we all know today. They won the Nobel Prize and left all the people who practically carried their
findings in the dust.

Its simple: Watson and Crick did not deserve full credit for their discoveries. They were
not studying in their own field of science, and their data was taken from other sources, such as
Wilkins and Franklin. If anything, the credit should go to Wilkins and Franklin for their X-ray
crystallography that Watson and Crick never actually took part in, to Chargaff, for his discovery
of the 1:1 purine-pyrimidine ratio, and to Cricks fellow chemist, who suggested the keto vs. enol
idea. Watson and Crick certainly put the puzzle together, but none of this would have been
possible without the others mentioned, and Watson and Crick never looked back or
acknowledged them. Even when their X-ray crystallography data was practically stolen from
the laboratory of Wilkins and Franklin, Watson even went as far as to demonize Franklin in his
book, The Double Helix.

Even if Watson and Cricks discoveries were wrought with injustice, it provided ground
for many other discoveries in the field of genetics, such as replication, by Meselson and Stahl in
1958. The double helix is the center-point of this idea, and without it, you simply cannot explain
how DNA replicates itself.
The double helix model is celebrated as a bare necessity of understanding in modern
biology. It is the foundation of genetics and without it, many magnificent breakthroughs such as
the human genome could never begin to have been discovered. Under all processes of genetics
lies the double helix model, and these processes are incredibly crucial to understanding the most
important part of science: the function of life.

Regardless the importance of the discovery, the race that Watson and Crick created
against other scientists such as Linus Pauling seems to be absurd and antagonistic. But how
uncommon is it, really? The race for the human genome fought between public government
organizations such as the US National Institutes of Health and private companies such as Celera
Genomics eerily echo the race for the structure of DNA of the 1950s. Looking at these so-called
races, and the mind-blowing discoveries that result from them, is this product of human self-
importance really such a bad thing?
In most cases, these races stem from the fact that a scientist wants his name in the history
books, and that he wants to be known as the one man who discovered it. This eager
competitiveness fuels progress, and without it, there would be no incentive to be productive and
efficient. This is why races occur. Because a man wants to be the first, and he will do anything
in his power to accomplish this.