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Dna Structure and Function
Dna Structure and Function
From the work of biochemist Phoebus Levene and others, scientists in Watson and Crick's time knew
that DNA was composed of subunits called nucleotides^11start superscript, 1, end superscript. A
nucleotide is made up of a sugar (deoxyribose), a phosphate group, and one of four nitrogenous bases:
C and T bases, which have just one ring, are called pyrimidines, while A and G bases, which have
Left panel: structure of a DNA nucleotide. The deoxyribose sugar is attached to a phosphate group and
to a nitrogenous base. The base may be any one of four possible options: cytosine (C), thymine (T),
adenine (A), and guanine (G). The four bases have differences in their structure and functional groups.
Cytosine and thymine are pyrimidines and have just one ring in their chemical structures. Adenine
and guanine are purines and have two rings in their structures.
Right panel: a strand of linked DNA nucleotides. The sugars are connected by phosphodiester bonds.
A phosphodiester bond consists of a phosphate group in which two of the oxygen atoms are bonded to
other atoms - in this case, to carbon atoms of the neighboring deoxyribose sugars. The DNA strand
consists of alternating phosphate groups and deoxyribose sugars (sugar-phosphate backbone), with the
DNA nucleotides assemble in chains linked by covalent bonds, which form between the deoxyribose
sugar of one nucleotide and the phosphate group of the next. This arrangement makes an alternating
chain of deoxyribose sugar and phosphate groups in the DNA polymer, a structure known as
Chargaff's rules
One other key piece of information related to the structure of DNA came from Austrian biochemist
Erwin Chargaff. Chargaff analyzed the DNA of different species, determining its composition of A,
A, T, C, and G were not found in equal quantities (as some models at the time would have
predicted)
The amounts of the bases varied among species, but not between individuals of the same
species
The amount of A always equalled the amount of T, and the amount of C always equalled the
amount of G (A = T and G = C)
These findings, called Chargaff's rules, turned out to be crucial to Watson and Crick's model of the
In the early 1950s, American biologist James Watson and British physicist Francis Crick came up
with their famous model of the DNA double helix. They were the first to cross the finish line in this
scientific "race," with others such as Linus Pauling (who discovered protein secondary structure) also
Rather than carrying out new experiments in the lab, Watson and Crick mostly collected and analyzed
existing pieces of data, putting them together in new and insightful ways^22start superscript, 2, end
superscript. Some of their most crucial clues to DNA's structure came from Rosalind Franklin, a
Franklin was an expert in a powerful technique for determining the structure of molecules, known
as X-ray crystallography. When the crystallized form of a molecule such as DNA is exposed to X-
rays, some of the rays are deflected by the atoms in the crystal, forming a diffraction pattern that
X-ray diffraction image of DNA. The diffraction pattern has an X shape representative of the two-stranded,
Franklin’s crystallography gave Watson and Crick important clues to the structure of DNA. Some of
these came from the famous “image 51,” a remarkably clear and striking X-ray diffraction image of
DNA produced by Franklin and her graduate student. (A modern example of the diffraction pattern
produced by DNA is shown above.) To Watson, the X-shaped diffraction pattern of Franklin's image
superscript.
Watson and Crick brought together data from a number of researchers (including Franklin, Wilkins,
Chargaff, and others) to assemble their celebrated model of the 3D structure of DNA. In 1962, James
Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine.
Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.
right-handed helix. The sugar-phosphate backbones of the DNA strands make up the outside of the
helix, while the nitrogenous bases are found on the inside and form hydrogen-bonded pairs that hold
In the model below, the orange and red atoms mark the phosphates of the sugar-phosphate backbones,
while the blue atoms on the interior of the helix belong to the nitrogenous bases.
Antiparallel orientation
Double-stranded DNA is an antiparallel molecule, meaning that it's composed of two strands that run
alongside each other but point in opposite directions. In a double-stranded DNA molecule, the 5' end
(phosphate-bearing end) of one strand aligns with the 3' end (hydroxyl-bearing end) of its partner, and
vice versa.
Structure of a DNA nucleotide, showing the numbering of the sugar carbons as well as the numbering
of ring carbon and nitrogen atoms in the four potential nitrogenous bases (as well as uracil, a base
found in RNA but not DNA). The nitrogenous bases are labeled with plain numbers, while the
Left panel: illustration of the antiparallel structure of DNA. A short segment of DNA double helix is
shown, composed of two DNA strands held together by hydrogen bonds between the bases. The
strand on the left has a phosphate group exposed at its top (5' end) and a hydroxyl group exposed at its
bottom (3' end). The strand on the right has the opposite orientation, with a phosphate group exposed
at its bottom (5' end) and a hydroxyl exposed at its top (3' end). The 5' end of one strand thus ends up
next to the 3' end of the other, and vice versa.
Right panel: structure of a nucleotide, illustrating the 5' phosphate group and 3' hydroxyl group. These
groups get their names from their positions on the deoxyribose sugar's ring. The ring carbons of the
sugar are labeled from 1' (the carbon bearing the nitrogenous base) to 5' (the carbon bearing the
phosphate group). The 3' carbon in the middle bears the hydroxyl group.
Right-handed helix
In Watson and Crick's model, the two strands of DNA twist around each other to form a right-
handed helix. All helices have a handedness, which is a property that describes how their grooves are
oriented in space.
Image of a DNA double helix, illustrating its right-handed structure. The major groove is a wider gap
that spirals up the length of the molecule, while the minor groove is a smaller gap that runs in parallel
to the major groove. The base pairs are found in the center of the helix, while the sugar-phosphate
The twisting of the DNA double helix and the geometry of the bases creates a wider gap (called
the major groove) and a narrower gap (called the minor groove) that run along the length of the
molecule, as shown in the figure above. These grooves are important binding sites for proteins that
Base pairing
In Watson and Crick's model, the two strands of the DNA double helix are held together by hydrogen
bonds between nitrogenous bases on opposite strands. Each pair of bases lies flat, forming a "rung" on
Base pairs aren't made up of just any combination of bases. Instead, if there is an A found on one
strand, it must be paired with a T on the other (and vice versa). Similarly, an G found on one strand
must always have a C for a partner on the opposite strand. These A-T and G-C associations are known
other on the two strands of the helix, and their functional groups form two hydrogen bonds that hold
the strands together. Similarly, G and C are found opposite to each other on the two strands, and their
functional groups form three hydrogen bonds that hold the strands together.
Base pairing explains Chargaff's rules, that is, why the composition of A always equals that of T, and
the composition of C equals that of G. Where there is an A in one strand, there must be a T in the
other, and the same is true for G and C. Because a large purine (A or G) is always paired with a small
pyrimidine (T or C), the diameter of the helix is uniform, coming in at about 222 nanometers.
Although Watson and Crick's original model proposed that there were two hydrogen bonds between
the bases of each pair, we know today that G and C form an additional bond (such that A-T pairs form
The structure of DNA unlocked the door to understanding many aspects of DNA's function, such as
how it was copied and how the information it carried was used by the cell to make proteins.
As we'll see in upcoming articles and videos, Watson and Crick's model ushered in a new era of
discovery in molecular biology. The model and the discoveries that it enabled form the foundations
In the mid-twentieth century, scientists were still unsure as to whether DNA or protein was the
genetic material of the cell
It was known that some viruses consisted solely of DNA and a protein coat and could transfer
their genetic material into hosts
In 1952, Alfred Hershey and Martha Chase conducted a series of experiments to prove that DNA was
the genetic material
Viruses (T2 bacteriophage) were grown in one of two isotopic mediums in order to
radioactively label a specific viral component
Viruses grown in radioactive sulfur (S) had radiolabelled proteins (sulfur is present in
proteins but not DNA)
Viruses grown in radioactive phosphorus (P) had radiolabeled DNA (phosphorus is
present in DNA but not proteins)
The viruses were then allowed to infect a bacterium (E. coli) and then the virus and bacteria were
separated via centrifugation
The larger bacteria formed a solid pellet while the smaller viruses remained in the supernatant
The bacterial pellet was found to be radioactive when infected by the 32P–viruses (DNA) but not
the 35S–viruses (protein)
This demonstrated that DNA, not protein, was the genetic material because DNA was
transferred to the bacteria
This occurs because each nitrogenous base can only pair with its complementary partner
Consequently, when DNA is replicated by the combined action of helicase and DNA polymerase:
Each new strand formed will be identical to the original strand separated from the template
The two semi-conservative molecules formed will have an identical base sequence to the
original molecule
Prior to this experiment, three hypotheses had been proposed for the method of replication of DNA:
Conservative Model – An entirely new molecule is synthesised from a DNA template (which
remains unaltered)
Semi-Conservative Model – Each new molecule consists of one newly synthesised strand and
one template strand
Dispersive Model – New molecules are made of segments of new and old DNA
Meselson and Stahl were able to experimentally test the validity of these three models using
radioactive isotopes of nitrogen
Nitrogen is a key component of DNA and can exist as a heavier 15N or a lighter 14N
DNA molecules were prepared using the heavier 15N and then induced to replicate in the presence of
the lighter 14N
DNA samples were then separated via centrifugation to determine the composition of DNA in
the replicated molecules
The results after two divisions supported the semi-conservative model of DNA replication
After one division, DNA molecules were found to contain a mix of 15N and 14N, disproving
the conservative model
After two divisions, some molecules of DNA were found to consist solely of 14N, disproving
the dispersive model
Results of the Meselson-Stahl Experiment
DNA replication is a semi-conservative process whereby pre-existing strands act as templates for
newly synthesised strands
The process of DNA replication is coordinated by two key enzymes – helicase and DNA polymerase
Helicase
Helicase unwinds the double helix and separates the two polynucleotide strands
It does this by breaking the hydrogen bonds that exist between complementary base pairs
The two separated polynucleotide strands will act as templates for the synthesis of new
complementary strands
DNA Polymerase
DNA polymerase synthesises new strands from the two parental template strands
Free deoxynucleoside triphosphates (nucleotides with 3 phosphate groups) align opposite
their complementary base partner
DNA polymerase cleaves the two excess phosphates and uses the energy released to link the
nucleotide to the new strand
DNA Replication Summary