 Structure of DNA:

◦ The most important clue to the structure of

DNA came from the work of Erwin Chargaff
and his colleagues in the late 1940s.

◦ The data collected from DNAs of a great many

different species led Chargaff to some
important conclusions.

These conclusions are as follows…

 Late 1940s

 Base composition of DNA generally varies from

one species to another.

 DNA specimens isolated from different tissues

of the same species generally have the same base
composition.

 The base composition of DNA in a given species

does not change with the organism’s age,
nutritional state, or changing environment.
 In all cellular DNAs, regardless of the
species, the number of adenine residues is
equal to the number of thymine residues
(i.e., A=T), and the number of guanine
residues is equal to the number of cytosine
residue (i.e., G=C).

 Fromthis relationships, it follows that the

sum of the purine residues equals the sum
of the pyrimidine residues, that is A+G =
T+C
 Key
to establishing the 3D structure of
DNA

 Provide clues as to how genetic

information is encoded in DNA and
passed from one generation to the next.
What are nucleic acids in biology?
 Nucleic acids, which are composed of
nucleotides, are very large and complex
organic molecules that contain the genetic
code for that organism.

 Two closely related types are needed to

transmit the genetic information from
parent to offspring: DNA and RNA.
 The other type of nucleic acid, RNA, is
mostly involved in protein synthesis.
 Just like in DNA, RNA is made of
monomers called nucleotides.
 Each nucleotide is made up of
three components: a nitrogenous base, a
pentose (five-carbon) sugar called
ribose, and a phosphate group.
a colorless crystalline compound with basic
properties, forming uric acid on oxidation.
 a substituted derivative of purine, especially
the bases adenine and guanine present in
DNA.
 Purine is a heterocyclic aromatic organic
compound that consists of a pyrimidine ring
fused to an imidazole ring. It is water-soluble.
Purine also gives its name to the wider class
of molecules, purines, which include
substituted purines and their tautomer's.
 A colorless crystalline compound with basic
properties.
 A substituted derivative of pyrimidine, especially
the bases thymine and cytosine present in DNA.
 Pyrimidine is an aromatic heterocyclic organic
compound similar to pyridine. One of the three
diazines, it has the nitrogen atoms at positions 1
and 3 in the ring.
 In nucleic acids, three types of nucleobases are
pyrimidine derivatives: cytosine, thymine, and
uracil.
 DNA or RNA are called nucleic
acids because of the acidic nature of
the phosphate group attached to them.

 Hence it's the acidic part of the

molecule that dominates, and that is
why we know DNA as an acid.
 Nucleic acids are
polynucleotides—that is, long
chainlike molecules composed
of a series of nearly identical
building blocks called
nucleotides. Each nucleotide
consists of a nitrogen-
containing aromatic base
attached to a pentose (five-
carbon) sugar, which is in turn
attached to a phosphate
group.
 1950s: Rosalind Franklin and Maurice
Wilkins obtained X-ray diffraction
pattern of DNA
• deduced that DNA was helical.

 The pattern also indicated that the

molecule contained two strands, a clue
that was crucial to determining the
structure.
 The X-ray diffraction
pattern of DNA
The spots forming across in the center denote a
helical structure. The heavy bands at the top and
bottom correspond to the recurring bases.
 The problem was to formulate a three-
dimensional model of DNA molecule that
could account not only the X-ray
diffraction data, but also

• Needed to be a helical structure, also satisfy

Chargoff’s rules (A=T, C=G) and

• Satisfied other chemical properties of DNA

 In 1953, Watson and Crick postulated that,
◦ It consists of two helical DNA chains coiled
around the same axis to form a right-handed
double helix. The strands of DNA comprising
the double helix run in opposite direction

◦ The spatial relationship between the two

strands creates a major groove and a minor
groove between the two strands

◦ The three - dimensional model of DNA structure

confirms the Chargaff’s rules
Hydrogen bonding pattern
in the base pairs defined
by Watson and Crick
Schematic drawings of complementary anti
parallel strand of DNA following the pairing
rules proposed by Watson and Crick
Watson-Crick model for the structure of DNA
 Watson and Crick postulated that DNA is a
double helix where
- Two helical DNA strands coiled around
same axis to form right-handed double helix

- Hydrophilic backbone of alternating

sugar/phosphate units of the nucleotides are
on outside of DNA molecule exposed to water
 Hydrophobic bases (complementary base
pairs) are stacked neatly inside the
molecule.
 The hydrogen bond between the base
pairs hold the double helix together.

 Strands are anti parallel.

Note That

 The two DNA strands in the “double

helix” are anti parallel.

 Thetwo DNA strands are not IDENTICAL,

but they are COMPLEMENTARY.
 The model explained many unusual
physical properties of DNA.

 It immediately suggested a mechanism

for the transmission of genetic
information.

 It suggested a means by which DNA

could be replicated.
 The central dogma outlines the plan for the storage
and transmission of hereditary information.
 Now we know that DNA is the bearer of genetic
information in all living organisms.
 The entire basis of information storage and
transmission in the cell is embodied in three steps:

REPLICATION

TRANSCRIPTION

TRANSLATION
Watson and Crick model for DNA replication
 They suggested that DNA is replicated on a
DNA template.
- Each strand of DNA in the double helix acts
as a template – a pattern for the synthesis of
its complement.

 Since DNA is double-stranded, complementary

replication would produce two double-helical
DNA molecules, each containing a strand of the
original DNA and a new strand complementary
to it.
- This type of replication is called semi conservative
replication, which was confirmed by M.S. Meselson
and F.W. Stahl in 1957.

- In 1955, Arthur Kornberg and his associates

discovered DNA polymerase — a large
protein which catalyses the formation of DNA.

- DNA strand elongates. Elongation or the chain

growth is always from the 5 end to the 3 end of the
elongating DNA molecules
Replication of DNA as suggested by
Watson and Crick
 DNA replication is the process by
which DNA makes a copy of itself
during cell division.
 The first step in DNA replication is to
'unzip' the double helix structure of
the DNA? molecule.
 The two separated strands will act as
templates for making the new strands
of DNA.
 The amino acids sequence of every protein
and nucleotides sequence of every RNA
molecule in cell is specified by that cell’s
DNA.
A segment of DNA that contains the
information required for the synthesis of a
functional biological product is referred to as
a GENE.
 Ribosomal RNAs (rRNA) are the structural
component of ribosome, the large complexes
carry out the synthesis of protein.
 Messenger RNAs (mRNA) are nucleic acids
that carry the information from one or a few
genes to the ribosome, where the
corresponding protein can be synthesized.

 Transfer RNAs (tRNA) are adaptor

molecules that faithfully translate the
information in mRNA into a specific sequence
of amino acids.
 RNA is made on a DNA template

 The information contained in DNA is passed to

a form of RNA called messenger RNA (mRNA)
by transcription (“rewriting”).

 The mechanics of transcription is quite similar

to the mechanics of replication because DNA
is the template upon which RNA is formed.

 The major difference is that—

The enzyme is RNA polymerase instead of
DNA polymerase

Sugar units of the nucleoside used to

make RNA is ribose rather than
deoxyribose, and the u (uracil) substitutes
for T (Thymidine) in RNA.
Translation involves tRNA, mRNA, ribosome
and Enzymes
The synthesis of specific protein under the
direction of specific gene is complex.
Proteins are the polymer of 20 different
amino acids and there are only four different
nucleotide monomers in DNA.
Hence, there can not be a one-to-one
relationship between the sequence of
nucleotides in the DNA molecule and the
sequence of amino acids in a protein.
The protein-coding information is read by
the cells in blocks of three nucleotides
residues, or codons.

Each codon specifies a different amino

acids.

The set of rules that specifies which

nucleic acid codon corresponds to which
amino acid is known as genetic code.
Crick’s adaptor hypothesis
A mRNA molecule is bound to a ribosome.

The transfer RNA(tRNA) molecules bring

amino acids to the ribosome one at a time.

Each tRNA identifies the appropriate codon

on the mRNA and add this amino acid to the
growing protein chain.
The first tRNA is released and the
ribosome moves one codon length along the
message, allowing the next tRNA to come
into place, carrying its amino acid.
Energy in the form of ATP is required at
each step in the movement.
As the ribosome moves along the mRNA , it
eventually encounters a ‘stop’ codon. At this
point, the polypeptide chain is released.
 Steps in protein synthesis
Bacterial ribosomes
have 3 sites that bind
aminoacyl-tRNAs
A site (aminoacyl)
P site (peptidyl)
E site (exit) (largely on
50s)
Formation of the
initiation complex. (in
bacteria)
Steps in protein synthesis
First step in
elongation (in
bacteria)

- binding of
the second

aminoacyl-
tRNA
 Steps in protein synthesis

Second step in
elongation (in
bacteria): formation
of the first peptide
bond

-peptide bond is formed

 Steps in protein synthesis
Third step in elongation
(in bacteria):
translocatoin
ribosome moves one
codon towards the 3’end
of mRNA.
the didpeptidyl-tRNA
is now entirely in the P
site
A site is open (for
incoming tRNA)
uncharged tRNA
moves first to E site,
then leaves.
 Steps in protein synthesis
Termination of protein synthesis
in bacteria
-occurs in response to a
termination codon in A site.

-a Release Factor binds to A

site, leads to hydrolysis of ester
linkage between nascent
polypeptide and the tRNA.

-polypeptide thus released.

-mRNA, deacylated tRNA, and

Release Factor leave ribosome.
Ribosome dissociates into 30S and
50S subunits.
Most common forms of
DNA damage
Bulges due to deletions or insertions
Missing, altered, or incorrect base
UV-induced pyrimidine dimers
Strand breaks at phosphodiester bonds or
within deoxyribose rings
Covalent cross-linking of strands
 Mutations
 Mutation means alterations in DNA
structure that produce permanent
changes in the genetic information
encoded therein.

There is a strong link between

accumulation of mutations and the
processes of aging and carcinogenesis.
 There are no cure for molecular diseases. But
medical scientists dream to correct these
inborn errors by replacing a nonfunctional
gene on a human chromosome with one that
is functional.
 The research involves experiments with
recombinant DNA.
 Recombination consists of cleaving DNA
chains, inserting a new piece of DNA into
the gap created by the cleavage, and
resealing the chains.
 Gene mutations are the changes in the base sequence of
DNA

 Substitution, addition, or deletion of one or more

nucleotides in the DNA molecule are called gene
mutation
Example: SHESAWTHEBADBOYHITTHEDOG

SHE SAW THE BAD BOY HIT THE DOG

SHE SAW THE BAD TBO YHI TTH EDO G—Addition of one
letter
Sense Nonsense
SHE SAW THE ADB OYH ITT HED O G —Deletion of one
letter
Sense Nonsense

SHE SAW THE BAE BOY HIT THE DOG—Replacement of one

letter
Sense Nonsense
Sickle cell anemia and other molecular diseases
are the products of mutation
 Mutation may be harmful or beneficial: Sickle
cell trait and sickle cell anemia illustrate both
the harm and benefit

 People with sickle cell trait have immunity to

malaria, so in this sense mutation is beneficial

 People with sickle cell anemia are very sick and

often die young, which certainly is a harmful
effect of mutation
Xeroderma pigmentosum
(XP)
 Disease caused by defect in the
nucleotide-excision repair system.
 People with XP are extremely light
sensitive, and readily develop sunlight-
induced cancers.
 They also have neurological
abnormalities, presumably due to inability
to repair certain lesions caused by high
rate of oxidative metabolism in neurons
DNA Damage by Radiation
We are constantly exposed to radiation due to,
• near UV radiation (in sunlight)
• constant field of ionizing radiation in form of
cosmic rays
• constant exposure to radiation from radioactive
elements (radium, plutonium, uranium, radon, 14C,
and 3H)
• X-rays (medical and dental examinations)
• radiation therapy (cancer and other diseases)
UV and ionizing radiations cause about 10% of
all DNA damage caused by environmental agents
Oxidative damage to DNA
Oxidative damage is possibly the most
important source of mutagenic
alterations in DNA.

Excited oxygen species such as

hydrogen peroxide, hydroxyl radicals, and
superoxide radicals arise during
irradiation or as a byproduct of aerobic
metabolism
 Reactive oxygen species (ROS) are critical
components of the antimicrobial repertoire of
macrophages, yet the mechanisms by which
ROS damage bacteria in the phagosome are
unclear.
 The NADH-dependent phagocytic oxidase
produces superoxide, which dismutes to form
H2O2.
 Macrophages engulf and kill bacteria.
Oxidative damage to DNA
 Cells have elaborate defense system to
destroy these reactive species. Theses includes
enzymes catalase and superoxide dismutase
that convert reactive oxygen species to
harmless products.
A fraction of these species will escape
cellular defenses, and cause damage (ranging
from oxidation of deoxyribose and base
moieties to strand breaks)
Data related to this type of damage is not
available. However, every day DNA of each
human cell exposed to thousands of such
reactions.
Hereditary nonpolyposis
colon cancer (HNPCC)
 This type of cancer generally
develops at an early age.

 This is caused by defects in

mismatch repair. Defects in at least
five different mismatch repair genes
can give rise to HNPCC.
 Breast cancer
• Mostly occurs in women with no known
predisposition
• At least 10% of cases are associated
with defects in two genes (Brca1 and
Brca2) associated with DNA repair.
• Women with defects in either of these
genes have a >80% chance of developing
breast cancer.
 DNA repair
• Biological macromolecules are susceptible
to chemical alterations that arise from
environmental damage or errors during
synthesis.

• For RNAs, proteins, or other cellular

molecules, most consequences of such
damage are circumvented through normal
turnover (synthesis and degradation).
 DNA repair
• However, integrity of DNA is vital to cell
survival and reproduction.

• Its information content must be protected

over the life span of the cell and
preserved from generation to generation.
 DNA repair
 DNA is the only molecule that, if damaged, is
repaired by the cell.
 Such repair is possible because the
information content of duplex DNA is
inherently redundant.
 Human DNA replication has an error rate of
about three base-pair mistakes during copying
of 6 billion base pairs in the diploid human
genome.
•low error rate is due to DNA repair
systems that review and edit the newly
replicated DNA
 DNA Repair
 Further, about 10,000 bases (mostly
purines) are lost per cell per day from
spontaneous breakdown in human DNA; the
repair systems must replace these bases to
maintain the fidelity of the encoded
information.
Usually, the complementary structure of
DNA ensures that the information lost
through damage to one strand can be
recovered from the other.
 DNA Repair
•However, even errors involving both
strands can be corrected through
recombination.

•Double-stranded breaks (potentially the

most serious lesions) can be repaired by
recombination events.
 Double – helical DNA and RNA can be
denatured (extreme pH and heat)

 Nucleic acids from different species can form

hybrids

 Nucleotides and nucleic acids undergo non

enzymatic browning

 DNA is often methylated

 Long DNA sequences can be determined

 Nucleotides carry chemical energy in
cells.

 Nucleotidesare components of many

enzyme cofactors.

 Some nucleotides are intermediates in

cellular communications.