DNA

Introduction: What is DNA?

DNA (Deoxyribonucleic acid)
• A complex molecule containing all necessary information to build and maintain
an organism.
• All living things have DNA within their cells
• It serves as the primary unit of heredity in organisms, used in reproduction of
cells. A portion of the DNA is passed along to the next generation allowing for
slight changes.

1.1DNA Is a structure that encodes information

– DNA or deoxyribonucleic acid contains the molecular instructions for life.
– found in nearly all living cells
– exact location within a cell depends on whether that cell possesses a special
membrane-bound organelle called a nucleus
 Organisms composed of cells that contain nuclei are classified as
eukaryotes
 Organisms composed of cells that lack nuclei are classified as
prokaryotes.
– In eukaryotes, DNA is housed within the nucleus
– In prokaryotes, DNA is located directly within the cellular cytoplasm, as there is
no nucleus available.
What is DNA exactly?
– DNA is a complex molecule that consists of many components, a portion of
which are passed from parent organisms to their offspring during the process of
reproduction.
– DNA is composed of the same nitrogen-based molecules
– DNA differs from organism to organism as it is simply the order in which these
smaller molecules are arranged that differs among individuals.
– this pattern of arrangement ultimately determines each organism's unique
characteristics by another set of molecules that "read" the pattern and stimulate
the chemical and physical processes it calls for.

What components make up DNA?

– All DNA is composed of a series of smaller molecules called nucleotides.
– A nucleotide is made up of three primary components:
1. A nitrogen-containing region known as a nitrogenous
base
2. A carbon-based sugar molecule called deoxyribose,
3. A phosphorus-containing region known as a phosphate
group attached to the sugar molecule
There are four different DNA nucleotide
1. adenine “A”
Figure 1: A single nucleotide contains a
nitrogenous base (red) and a deoxyribose sugar
2. thymine "T"
molecule (grey). One side of the sugar molecule
is refered to as 3' end (dark grey) and the other 5'
3. guanine "G"The 5' side has a phosphate
end (dark grey).
group attached.
4. cytosine "C"

Adenine, thymine

– NUCLEOTIDES owe much of their structure and bonding

capabilities to the deoxyribose
– The central portion of this molecule (deoxyribose) contains five carbon atoms arranged in
the shape of a ring, and each carbon in the ring is referred to by a number followed by the
prime symbol (').
– 5' carbon atom is particularly notable, it is the site at which the phosphate group is attached
to the nucleotide.
– The area surrounding this carbon atom is known as the 5' end of the nucleotide.
– Opposite the 5' carbon, on the other side of the deoxyribose ring, is the 3' carbon, which is
NOT attached to a phosphate group. This portion of the nucleotide is typically referred to as
the 3' end.
– Polynucleotide is when nucleotides join together in a series to form a structure.
– At each point of juncture within a polynucleotide, the 5' end of one nucleotide attaches to the
3' end of the adjacent nucleotide through a connection called a phosphodiester bond. It is
this alternating sugar-phosphate arrangement that forms the "backbone" of a DNA molecule.

Figure 3: All polynucleotides contain

an alternating sugar-phosphate
backbone. This backbone is formed
when the 3' end (dark gray) of one
nucleotide attaches to the 5'
phosphate end (light gray) of an
How is the DNA strand organized? adjacent nucleotide by way of a
phosphodiester bond.
– Although DNA is often found as a single-stranded polynucleotide, it assumes its
most stable form when double stranded.
– Double-stranded DNA consists of two polynucleotides that are arranged such that the
nitrogenous bases within one polynucleotide are attached to the nitrogenous bases
within another polynucleotide by way of special chemical bonds called hydrogen
bonds.
– Each A in one strand always pairs with a T in the other strand, and each C always
pairs with a G.
– The double-stranded DNA that results from this pattern of bonding looks much like a
ladder with sugar-phosphate side supports and base-pair rungs.
**Note that because the two polynucleotides that make up double-stranded DNA are "upside
down" relative to each other, their sugar-phosphate ends are anti-parallel, or arranged in opposite
orientations. This means that one strand's sugar-phosphate chain runs in the 5' to 3' direction,
whereas the other's runs in the 3' to 5' direction (Figure 4). The specific sequence of A, T, C, and
G nucleotides within an organism's DNA is unique to that individual, and it is this sequence that
controls not only the operations within a particular cell, but within the organism as a whole
Figure 4: Double-stranded DNA consists of
two polynucleotide chains whose
nitrogenous bases are connected by
hydrogen bonds. Within this arrangement,
each strand mirrors the other as a result of
the anti-parallel orientation of the sugar-
phosphate backbones, as well as the
complementary nature of the A-T and C-G
base pairing.

– Other than the ladder-like structure described above, another key

characteristic of double-stranded DNA is its unique three-dimensional
shape.
– In 1952, scientist Rosalind Franklin used a process called X-ray diffraction to
capture images of DNA molecules (Figure 5). Although the black lines in these
photos look relatively sparse, Dr. Franklin interpreted them as representing distances
between specific molecules that were arranged in a spiral shape called a helix.
– Researchers James Watson and Francis Crick were pursuing a
definitive model for the stable structure of DNA inside cell nuclei.
They used Franklin's images, along with their own evidence for the
double-stranded nature of DNA, to argue that DNA actually takes
the form of a double helix, a ladder-like structure that is twisted
along its entire length (Figure 6).
How is DNA packaged inside cells?

-DNA packaging, which is the phenomenon of fitting

DNA into dense compact forms. Long pieces of double-
stranded DNA are tightly looped, coiled, and folded so
that they fit easily within the cell.

-Eukaryotes do this by wrapping their DNA around

special proteins called histones, thereby compacting it
enough to fit inside the nucleus.
Figure 7: To better fit within the cell,
long pieces of double-stranded DNA are
tightly packed into structures called
chromosomes.
-Prokaryotes, compress their DNA through a twisting process called supercoiling

-In both eukaryotes and prokaryotes, this highly compacted DNA is then arranged into
structures called chromosomes.
-Chromosomes take different shapes in different types of organisms.
-Chromosomes exist in pairs, which means that there are two copies of each chromosome
in most cells that compose these organisms' bodies. (Humans, for instance, have 23 pairs
of chromosomes, for a total of 46 individual chromosomes.)
– Figure 8: Double-
stranded DNA (grey)
is wrapped around
histone proteins (red),
and that structure is
itself coiled.

How do scientists visualize DNA?

-It is impossible to see double-stranded DNA with the naked eye - unless, that is, they
have a large amount of it.
-Scientists extract DNA from tissue samples, thereby pooling together miniscule amounts
of DNA from thousands of individual cells. When this DNA is collected and purified, the
result is a whitish, sticky substance that is somewhat translucent.
-To actually visualize the double-helical structure of DNA, researchers require special
imaging technology.
-It is possible to see chromosomes with a standard light microscope, as long as the
chromosomes are in their most condensed form.
– To see chromosomes in this way, scientists must first use a chemical process that attaches the
chromosomes to a glass slide and stains or "paints" them. Staining makes the chromosomes easier
to see under the microscope. In addition, the banding patterns that appear on individual
chromosomes as a result of the staining process are unique to each pair of chromosomes, so they
allow researchers to distinguish different chromosomes from one another. Then, after a scientist
has visualized all of the chromosomes within a cell and captured images of them, he or she can
arrange these images to make a composite picture called a karyotype

1.2 The Discovery of DNA Function Involved Multiple Scientists

Who first identified DNA?
– James Watson and Frances Crick are often credited with discovering DNA.
– However this substance was identified nearly 90 years earlier by Swiss chemist
Friedrich Miescher. While studying white blood cells, Miescher isolated a
previously unknown type of molecule that was slightly acidic and contained a
high percentage of phosphorus. Miescher named this molecule "nuclein," which
was later changed to "nucleic acid" and eventually to "deoxyribonucleic acid.”
Interestingly, Miescher did not believe that nuclein, Miescher believed that
 proteins were responsible for heredity, because they existed in such a wide variety
of forms.
Who linked DNA to heredity?
– Most scientists believed that protein, not DNA, was the carrier of hereditary
information.
– This changed in 1944, when biologist Oswald Avery performed a series of
groundbreaking experiments with the bacteria that cause pneumonia. At the time,
scientists knew that some types of these bacteria (called "S type") had an outer
layer called a capsule, but other types (called "R type") did not. Through a series
of experiments, Avery and his colleagues found that only DNA could change R
type bacteria into S type.
 This meant that something about DNA allowed it to carry
instructions from one cell to another. This result highlighted DNA
as the "transforming factor," thereby making it the best candidate
for the hereditary material
Who confirmed Avery's findings?
– Avery's findings were largely unaccepted as evidence for DNA as the hereditary
material until separate experiments were performed by other scientists.
– Thus, eight years later, Alfred Hershey and Martha Chase further confirmed that
protein was not the hereditary material through their work with bacteriophages,
which are viruses that infect bacteria.
– Bacteriophages are composed of only two substances: protein and DNA. By using radioactive labels
that would integrate specifically to either DNA or protein, but not both, Hershey and Chase were able
to show that DNA is the only material transferred directly from bacteriophages into bacteria when the
bacteria are infected by these viruses. This observation was important, because Hershey and Chase
knew that the end result of bacteriophage infection was the production of more viruses in multiple
copies

– DNA in a virus can take over a bacterial cell, causing it to replicate only the viral
DNA and to create new viruses. This process is a form of hijacking, wherein the
viral life-form takes over the regular machinery inside another life-form (in this case,
a single bacterial cell).
– Hershey and Chase had presented experiments that clearly suggested that DNA
controls the production of more DNA, and that DNA itself was that substance that
controlled life-forms.
Only one year after Hershey and Chase performed these experiments, the structure of
DNA was determined by James Watson and Francis Crick. This allowed investigators to
put together the pieces of the story about how DNA carries hereditary information from
cell to cell. Indeed, the experimental work connecting heredity and the structure of DNA
were happening in parallel, so the next few years would be an exciting time for the
discovery of DNA function.