This slide might be helpful to the students of BSc and MSc who are interested in molecular biology

1. Nucleic acids:
Structure,
nature as genetic material, and replication
Dr. Anand Kumar Chaudhari (M.Sc., Ph.D)
Assistant Professor
Govt. Girls’ P.G. College, Ghazipur, 233001,
UP, India

2. Chromosomes are composed of two types of large organic molecules
(macromolecules): nucleic acids and proteins
There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA).
In 1868, Johann Friedrich Miescher, a young Swiss medical student, became fascinated with
an acidic substance that he isolated from pus cells obtained from bandages used to dress
human wounds. After the pepsin treatment, he recovered an acidic substance that
he called “nuclein” that contained a novel substance that was slightly acidic and high in
phosphorus. The substance was later renamed nucleic acid by one of his students.
Structure of nucleic acids (DNA & RNA)
1. DNA
It is useful to consider the structure of DNA at three levels of increasing complexity, known
as the primary, secondary, and tertiary structures of DNA. The primary structure of DNA
refers to its nucleotide structure and how the nucleotides are joined together. The
secondary structure refers to DNA’s stable three dimensional configuration, the helical
structure worked out by Watson and Crick. Tertiary structures are the complex packing
arrangements of double-stranded DNA in chromosomes.

3. The structure of DNA can be studied at three levels
1. The Primary Structure of DNA
The primary structure of DNA consists of a string of nucleotides joined together by
phosphodiester linkages.
DNA and RNA is made from simple subunits, called nucleotides, each comprising
three parts: (1) a sugar, (2) a phosphate, and (3) a nitrogen-containing base.
The sugars of nucleic acids—called pentose sugars—have five carbon atoms. The
sugars of DNA and RNA are slightly different in structure. RNA’s sugar, called
ribose, has a hydroxyl group (–OH) attached to the 2′-carbon atom, whereas
DNA’s sugar, or deoxyribose, has a hydrogen atom (–H) at this position and
therefore contains one oxygen atom fewer overall.
The Structure of DNA & RNA

4. The second component of a nucleotide is its nitrogenous base, which may be of two
types—a purine or a pyrimidine.
Both DNA and RNA contain two purines, adenine and guanine (A and G). Three
pyrimidines are common in nucleic acids: cytosine (C), thymine (T), and uracil (U).
The third component of a nucleotide is the phosphate group, which consists of a
phosphorus atom bonded to four oxygen atoms. Phosphate groups are found in every
nucleotide and frequently carry a negative charge, which makes DNA acidic.

5. The secondary structure of DNA refers to its three-dimensional
configuration—its fundamental helical structure.
DNA consists of two polynucleotide strands. The sugar–phosphate groups of
each polynucleotide strand are on the outside of the molecule, and the bases
are in the interior. Hydrogen bonding joins the bases of the two strands:
guanine pairs with cytosine, and adenine pairs with thymine. The two
polynucleotide strands of a DNA molecule are complementary and antiparallel
X-ray Diffraction Studies Provides the detailed molecular structure of DNA by three
different molecular biologist
Watson, Crick, and Wilkins shared the 1962 Nobel Prize in Physiology or Medicine for
their work on the double-helix model. Unfortunately, Franklin died prematurely (age
37) in 1958, and Nobel Prizes cannot be awarded posthumously.
2. The Secondary Structures (Watson and Crick model, April 25, 1953)

6. The important features of Watson-Crick
model or double helix model of DNA are as
follows:
The DNA molecule consists of two polynucleotide
chains or strands that spirally twisted around
each other and coiled around a common axis to
form a right-handed double-helix.
The two strands are antiparallel i.e. they run in
opposite directions so that the 3′ end of one
chain facing the 5′ end of the other.
The sugar-phosphate backbones remain on the
outside, while the core of the helix contains the
purine and pyrimidine bases.
The two strands are held together by hydrogen
bonds between the purine and pyrimidine bases
of the opposite strands.
Adenine (A) always pairs with thymine & Uridine (T
& U) by two hydrogen bonds and guanine (G)
always pairs with cytosine (C) by three
hydrogen bonds. This complementarity is
known as the base pairing rule. Thus, the two
stands are complementary to one another.

8. 2. The Tertiary structures (The complex structure resulting in the
formation of chromosome)
Nucleosome : (DNA + Histones octamer (H2A, H2B, H3, and H4 basic proteins)
Chromatosome: Nucleosome + H1 linker

9. Types of DNA
A-DNA B-DNA Z-DNA
That exists when little
water is present.
Present in cell when
abundant water is present
When high salt
concentration
Right handed Right handed Left handed
Not common Most common type of DNA
in cell
Not common
11 bp 10 bp 12 bp
Width 23 A (2.3 nm) Width 20 A (2.0 nm) 18 A (1.8 nm)

10. DNA AS THE SOURCE OF GENETIC INFORMATION
Some important works in molecular biology
Mendal 1866: Principle of heredity: called them as Factor, but what is factor then don’t
explaine ???
F. Miescher 1868: Discovered Nuclein (nucleic acid)
Griffith 1928: Principle of transformation
Avery, MacLeod, and McCarty 1944: First evidence proved DNA as a genetic material
Harshey and Chase 1952: Second evidence that proof that DNA is genetic material not the
protein
Urey Miller 1953: Origin of life inorganic to organic molecule
Watson and Crick 1953 (25 April) : DNA double helix model
Franckel Conrat and Bea Singer 1956 : RNA as genetic material in certain viruses
Meselson and Stahl 1958: The nature of replicating DNA

11. The discovery of the transforming principle
The first clue that DNA was the carrier of hereditary information came with the
demonstration that DNA was responsible for a phenomenon called transformation.
The phenomenon was first observed in 1928 by Fred Griffith, whose special interest was
the bacterium that causes pneumonia, Streptococcus pneumoniae
Griffith had succeeded in isolating several different strains of S. pneumoniae (type I, II, III,
and so forth). In the virulent (disease-causing) forms of a strain, each bacterium is
surrounded by a polysaccharide coat, which makes the bacterial colony appear smooth
when grown on an agar plate; these forms are referred to as S, for smooth. Griffith found
that these virulent forms occasionally mutated to non-virulent forms, which lack a
polysaccharide coat and produce a rough-appearing colony; these forms are referred to
as R, for rough.

12. Transformation experiment and results
Griffith observed that small amounts of
living type IIIS bacteria injected into mice
caused the mice to develop pneumonia
and die; on autopsy, he found large
amounts of type IIIS bacteria in the blood
of the mice.
When Griffith injected type IIR bacteria
into mice, the mice lived, and no bacteria
were recovered from their blood .
Griffith knew that boiling killed all the
bacteria and destroyed their virulence;
when he injected large amounts of heat-
killed type IIIS bacteria into mice, the mice
lived and no type IIIS bacteria were
recovered from their blood
However, Griffith got a surprise when he
infected his mice with a small amount of
living type IIR bacteria along with a large
amount of heat-killed type IIIS bacteria.

13. Because both the type IIR bacteria and the heat-killed type IIIS bacteria were nonvirulent,
he expected these mice to live.
Surprisingly, 5 days after the injections, the mice became infected with pneumonia and
died.
When Griffith examined blood from the hearts of these mice, he observed live type IIIS
bacteria. Furthermore, these bacteria retained their type IIIS characteristics through several
generations; so the infectivity was heritable.
Griffith’s results had several possible interpretations,
First, it could have been the case that he had not sufficiently sterilized the type IIIS bacteria
and thus a few live bacteria remained in the culture. Any live bacteria injected into the
mice would have multiplied and caused pneumonia. Griffith knew that this possibility was
unlikely, because he had used only heat-killed type IIIS bacteria in the control experiment,
and they never produced pneumonia in the mice.
A second interpretation was that the live, type IIR bacteria had mutated to the virulent S
form. Such a mutation would cause pneumonia in the mice, but it would produce type IIS
bacteria, not the type IIIS that Griffith found in the dead mice.
Many mutations would be required for type II bacteria to mutate to type III bacteria, and
the chance of all the mutations occurring simultaneously was impossibly low.
Griffith finally concluded that the type IIR bacteria had somehow been transformed,
acquiring the genetic virulence of the dead type IIIS bacteria. This transformation had
produced a permanent, genetic change in the bacteria. He called this substance the
transforming principle

14. Identification of the transforming principle
Question: What is the chemical nature of the
transforming substance ??
After 10 years of research, Avery, Colin MacLeod,
and Maclyn McCarty succeeded in isolating and
purifying the transforming substance.
They showed that Enzymes such as trypsin and
chymotrypsin, known to break down proteins,
had no effect on the transforming substance.
Ribonuclease, an enzyme that destroys RNA,
also had no effect.
Enzymes capable of destroying DNA, however,
eliminated the biological activity of the
transforming substance (Figur).
These results, published in 1944, provided
compelling evidence that the transforming
principle-and therefore genetic information—
resides in DNA.

15. The Hershey–Chase experiment
A second piece of evidence implicating DNA as
the genetic material resulted from a study of the
T2 virus conducted by Hershey and Chase. The
T2 virus is a bacteriophage (phage) that infects
the bacterium Escherichia coli.
As stated in figure, a phage reproduces by
attaching to the outer wall of a bacterial cell and
injecting its DNA into the cell, where it replicates
and directs the cell to synthesize phage protein.
The phage DNA becomes encapsulated within
the proteins, producing progeny phages that
lyse (break open) the cell and escape (Figure).

17. Hershey and Chase designed a series of experiments to determine whether the phage
protein or the phage DNA is transmitted in phage reproduction
To follow the fate of protein and DNA, they used radioactive forms, or isotopes, of
phosphorus and sulfur. DNA contains phosphorus but not sulfur; so Hershey and Chase
used 32P to follow phage DNA during reproduction. Protein contains sulfur but not
phosphorus; so they used 35S to follow the protein.
They grew one batch of E. coli in a medium containing 32P and infected the bacteria with
T2 phage so that all the new phages would have DNA labeled with 32P (Figure). They grew a
second batch of E. coli in a medium containing 35S and infected these bacteria with T2
phage so that all these new phages would have protein labeled with 35S.
Hershey and Chase then infected separate batches of unlabeled E. coli with the 35S- and
32P-labeled phages. After allowing time for the phages to infect the cells, they placed the E.
coli cells in a blender and sheared off the then-empty protein coats (ghosts) from the cell
walls. They separated out the protein coats and cultured the infected bacterial cells. When
phages labeled with 35S infected the bacteria, most of the radioactivity was detected in the
protein ghosts and little was detected in the cells. Furthermore, when new phages emerged
from the cell, they contained almost no 35S (see Figure). This result indicated that, although
the protein component of a phage is necessary for infection, it does not enter the cell and is
not transmitted to progeny phages. In contrast, when Hershey and Chase infected bacteria
with 32P-labeled phages and removed the protein ghosts, the bacteria were still radioactive.
Most significantly, after the cells lysed and new progeny phages emerged, many of these
phages emitted radioactivity from 32P, demonstrating that DNA from the infecting phages
had been passed on to the progeny (see Figure). These results confirmed that DNA, not
protein, is the genetic material of phages.

18. PROOF THAT RNA STORES THE GENETIC INFORMATION IN SOME VIRUSES
As more and more viruses were identified and studied, it became apparent that many of
them contain RNA, but no DNA.
One of the first experiments that established RNA as the genetic material in RNA viruses
was the so-called reconstitution experiment of Fraenkel-Conrat and Bea Singer (1956).
Their simple, but definitive, experiment was done with tobacco mosaic virus (TMV), a virus
composed of a single molecule of RNA encapsulated in a protein coat

19. They treated TMV particles of two different strains with chemicals that dissociate the
protein coats of the viruses from the RNA molecules and separated the proteins from the
RNA.
Then they mixed the proteins from one strain with the RNA molecules from the other
strain under conditions that result in the reconstitution of complete, infective viruses
composed of proteins from one strain and RNA from the other strain.
When tobacco leaves were infected with these reconstituted mixed viruses, the progeny
viruses were always phenotypically and genotypically identical to the parent strain from
which the RNA had been obtained (Figure).
This result confirmed that, the genetic information of TMV is stored in RNA, not in
protein.

20. DNA REPLICATION
Genetic Information Must Be Accurately Copied Every Time a Cell Divides
The cell cycle comprises of three phases:
Interphase, Mitotic (M) phase and
Cytokinesis
interphase is divided into three sub phases:
G1, S, and G2. DNA replication takes place
in S-phase
M-phase : Nucleus devides with equal
amount of DNA
Cytokinesis: Cell devides into two daughter
types
So the question arises how DNA devides
and distributed equally in two cells
(produced as a result of cytokinesis)

21. All DNA Replication Takes Place in a Semi-conservative Manner
Initially, three models were proposed for DNA replication: conservative, semi-conservative
and dispersive replication.

22. In conservative replication, the entire double-stranded DNA molecule serves as a
template for a whole new molecule of DNA, and the original DNA molecule is fully
conserved during replication
Semiconservative replication is intermediate between these two models; the two
nucleotide strands unwind and each serves as a template for a new DNA molecule
In dispersive replication, both nucleotide strands break down (disperse) into fragments,
which serve as templates for the synthesis of new DNA fragments, and then somehow
reassemble into two complete DNA molecules.
These three models allow different predictions to be made about the distribution of
original DNA and newly synthesized DNA after replication.???
Then, Meselson and Stahl’s (1958) proved that DNA replication is semi-conservative in all
organisms

23. To determine which of the three
models of replication applied to E.
coli cells, Matthew Meselson and
Franklin Stahl needed a way to
distinguish old and new DNA.
They did so by using two isotopes of
nitrogen, 14N (the common form)
and 15N (a rare, heavy form).
Meselson and Stahl distinguished
between the heavy 15N laden DNA
and the light 14N-containing DNA
with the use of equilibrium density
gradient centrifugation
Meselson and Stahl’s Experiment
N15 N14
Equilibrium density gradient centrifugation : to distinguish
between heavy, 15N-laden DNA and lighter, 14N-laden DNA.

25. FINDINGS :
E.coli cells are grown on 15N for several generations and DNA is extracted and analyzed by
CsCl density gradient centrifugation (Generation 0; control). DNA from bacteria that had
been grown on medium containing 15N appeared as a single band (all DNA become heavy).
Cells are then transferred to medium containing 14N for one generation. DNA is extracted
and analyzed (20 minute) . After one round of replication, the DNA appeared as a single
band at intermediate weight (conservative hypothesis rejected, means replicated in semi-
conservative manner).
For two generations. DNA is extracted and analyzed (40 minute). After a second round of
replication, DNA appeared as two bands, one light and the other intermediate in weight.
(means replicated in semi-conservative manner).
For three generations. DNA is extracted and analyzed (60 minute). Samples taken after
additional rounds of replication appeared as two bands, as in part c. (if dispersive then no
any light bands appears in subsequent round of replication, means only hybrid appears:
dispersive concept rejected)
Now it is confirmed that DNA Replication is semi-conservative: each DNA strand serves as a
template for the synthesis of a new DNA molecule.

26. Modes of Replication
After Meselson and Stahl’s work, investigators confirmed that other organisms
also use semi-conservative replication. Scientist needs to know how this takes
place
There are, however, several different ways in which semi-conservative replication
can take place, differing principally in the nature of the template DNA—that is,
whether it is circular (prokaryotic) or linear (eukaryotic).
Individual units of replication are called replicons, each of which contains a
replication origin. Replication starts at the origin and continues until the entire
replicon has been replicated. Bacterial chromosomes have a single replication
origin, whereas eukaryotic chromosomes contain many.
There are three possible ways by which semi-conservative replication takes place
in different organisms

27. 1. Theta replication
Takes place in circular DNA, such as that found in E. coli and other bacteria.
It is named because it generates a structure that resembles the Greek letter
theta (θ).

28. In theta replication, double-stranded DNA begins to unwind at the replication origin,
producing single stranded nucleotide strands that then serve as templates on which new
DNA can be synthesized. The unwinding of the double helix generates a loop, termed a
replication bubble.
Unwinding may be at one or both ends of the bubble, making it progressively larger. The
DNA replication on both of the template strands is simultaneous with unwinding point of
unwinding, where the two single nucleotide strands separate from the double-stranded
DNA helix, is called a replication fork, called bidirectional replication.
If a single replication fork is present, it proceeds around the entire circle to “produce two
complete circular DNA molecules”, each consisting of one old and one new nucleotide
strand.

29. 2. Rolling-circle replication
Takes place in some viruses and in the F factor of E. coli.

30. This form of replication is initiated by a break in one of the nucleotide strands that creates
a 3′-OH group and a 5′- phosphate group. New nucleotides are added to the 3′ end of the
broken strand, with the inner (unbroken) strand used as a template. As new nucleotides
are added to the 3′ end, the 5′ end of the broken strand is displaced from the template,
rolling out like thread being pulled off a spool. The 3′ end grows around the circle, giving
rise to the name rolling-circle model.
With each revolution around the circle, the growing 3′ end displaces the nucleotide strand
synthesized in the preceding revolution. Eventually, the linear DNA molecule is cleaved
from the circle, resulting in a double stranded circular DNA molecule and a single-
stranded linear DNA molecule. The linear molecule circularizes either before or after
serving as a template for the synthesis of a complementary strand.

31. 3. Linear eukaryotic replication

32. Eukaryotic replication proceeds at a rate ranging from 500 to 5000 nucleotides per minute
at each replication fork (considerably slower than bacterial replication). Even at 5000
nucleotides per minute at each fork, DNA synthesis starting from a single origin would
require 7 days to replicate a typical human chromosome consisting of 100 million base
pairs of DNA. The replication of eukaryotic chromosomes actually takes place in a matter
of minutes or hours, not days. This rate is possible because replication initiates at
thousands of origins.
At each replication origin, the DNA unwinds and produces a replication bubble.
Replication takes place on both strands at each end of the bubble, with the two replication
forks spreading outward. Eventually, the replication forks of adjacent replicons run into
each other, and the replicons fuse to form long stretches of newly synthesized DNA.
Replication and fusion of all the replicons leads to two identical DNA molecules.

33. The semi-conservative replication of eukaryotic chromosomes was first demonstrated in
1957 by the results of experiments carried out by J. Herbert Taylor, Philip Woods, and
Walter Hughes on root-tip cells of the broad bean, Vicia faba

34. Requirements of Replication
Although the process of replication includes many components, they can be
combined into three major groups:
1. template consisting of single-stranded DNA,
2. 2. raw materials that to be assembled into a new nucleotide strand, and
3. enzymes and other proteins that “read” the template and assemble the
substrates into a DNA molecule.
Because of the semi-conservative nature of DNA replication, a double-stranded
DNA molecule must unwind to expose the bases that act as a template for the
assembly of new polynucleotide strands, which will be complementary and
antiparallel to the template strands.
The raw materials are incoming nucleotides (e.g., primers) each consisting of a
deoxyribose sugar and a base (a nucleoside) attached to three phosphate
groups .
In DNA synthesis, nucleotides are added to the 3′-OH group of the growing
nucleotide strand. The 3′-OH group of the last nucleotide on the strand attacks
the 5′-phosphate group of the incoming nucleotides.

35. Replication takes place and completed in four different stages: initiation, unwinding,
elongation (or extension), and termination
1. Initiation
The replication of the E. coli chromosome begins at
oriC, the unique sequence at which replication is
initiated.
The first step appears to be the binding of four DnaA
protein—to the four 9-base-pair (bp) repeats in oriC.
Next, DnaA proteins bind cooperatively to form a core
of proteins with oriC DNA wound on the surface of the
protein complex.
Strand separation begins within the three tandem 13-
bp repeats in oriC and spreads until the replication
bubble is created.
A complex of DnaB protein (the DNA helicase) and
DnaC protein joins the initiation complex and
contributes to the formation of two bi-directional
replication forks.

36. 2. Unwinding of DNA strands
Helicases, Single stranded Binding Proteins (SSBs), and Topoisomerases (I and II, also
known as DNA gyrase) play important roles

37. Because DNA synthesis requires a single-stranded template and because double-stranded
DNA must be unwound before DNA synthesis can take place, the cell relies on several
proteins and enzymes to accomplish the unwinding.
DNA helicase:
A DNA helicase breaks the hydrogen bonds between the N-bases of the two nucleotide
strands
Single-strand-binding proteins:
single-strand-binding proteins (SSBs) attach tightly to the exposed single-stranded DNA
These proteins protect the single-stranded nucleotide chains and prevent the formation of
secondary structures
Topoisomerases :
Another protein essential for the unwinding process is the enzyme topoisomerases. There
are two types of topoisomerase:
Topoisomerase I : reduces the torsional strain (torque) that builds up ahead of the
replication fork by cutting single strand by removing phosphodiester bond.
Topoisomerase II (DNA gyrase) : reduces the torsional strain (torque) that builds up ahead
of the replication fork by cutting both the strands by removing phosphodiester bond.

38. 3. Elongation / Extension
During the elongation phase of replication, single-stranded DNA is used as a template for
the synthesis of DNA. This process requires a series of steps and enzymes.
Synthesis of primers
DNA polymerases require a
nucleotide with a 3′-OH group to
which a new nucleotide can be
added.
Because of this requirement, DNA
polymerases cannot initiate DNA
synthesis on a bare template;
rather, they require a primer—an
existing 3′-OH group—to get
started.
How, then, does DNA synthesis
begin? An enzyme called DNA
primase synthesizes short stretches
of nucleotides, or primers, to get
DNA replication started

39. DNA synthesis by DNA polymerases
After DNA is unwound and a primer has been added, DNA polymerases elongate the new
polynucleotide strand by catalyzing DNA polymerization.
At least five different DNA polymerases (In prokaryotes & 15 in eukaryotes). Two of them,
DNA polymerase I and DNA polymerase III, carry out DNA synthesis in replication; the other
three have specialized functions in DNA repair
DNA polymerase III
That acts as the main workhorse of replication. DNA polymerase III synthesizes nucleotide
strands by adding new nucleotides to the 3′ end of a growing DNA molecule. This enzyme
has two enzymatic activities. Its 5′→3′ polymerase activity allows it to add new nucleotides
in the 5′→3′ direction. Its 3′→5′ exonuclease activity allows it to remove nucleotides in the
3′→5′ direction, enabling it to correct errors (proof-reading). If a nucleotide having an
incorrect base is inserted into the growing DNA molecule, DNA polymerase III uses its 3′→5′
exonuclease activity to back up and remove the incorrect nucleotide.
Because these two strands have opposite polarity, one is being extended in an overall 5’-3'
direction and the other is being extended in an overall 3’-5' direction. However, the
enzymes that catalyze DNA synthesis (DNA polymerases) can only add nucleotides onto the
3' end of a DNA strand—that is, they synthesize DNA only in the 5’-3' direction

40. One, called the leading strand / continuous strand, is extended continuously (synthesized
towards the replication fork) by the sequential addition of nucleotides to its 3' end. The
other, called the lagging strand / discontinuous strand / Okazaki fragments, synthesized
apposite to replication fork.
These small fragments of DNA have been named Okazaki fragments after Reiji Okazaki
(Husband) and Tuneko Okazaki (wife) who first time reported in E. coli.
DNA polymerase I
Has 5′→3′ polymerase (synthesize new nucleotides), 5′→3′ exonuclease and 3′→5′
exonuclease activities (replaces RNA primers with DNA).

42. DNA ligase
Seals the nicks (okazaki fragments) in DNA after replacement of RNA primers by DNA
If the lagging strand of DNA is synthesized
discontinuously/ okazaki fragments, a
mechanism is needed to link the fragments
together to produce the large DNA strands
present in mature chromosomes.
This mechanism is provided by the enzyme
DNA ligase by using energy from NAD or ATP.
First, adenosine monophosphate (AMP) of the
ligase-AMP intermediate forms a phosphoester
linkage with the 5'-phosphate at the nick, and
then a nucleophilic attack by the 3'-OH at the
nick on the DNA-proximal phosphorus atom
produces a phosphodiester linkage between the
adjacent nucleotides at the site of the nick.

43. 4. Termination
In some DNA molecules, replication is terminated whenever two
replication forks meet. In others, specific termination sequences block
further replication. A termination protein, called Tus in E. coli, binds to
these sequences. Tus blocks the movement of helicase, thus stalling the
replication fork and preventing further DNA replication.

44. An overview of DNA
replication
(must draw in Exam)

45. Thank
You