Nucleotides and Nucleic Acids

Nucleotides have three characteristic components:

(1) a nitrogenous (nitrogen-containing) base, (2) a pentose, and (3) a phosphate. The molecule
without the phosphate group is called a nucleoside. The nitrogenous bases are derivatives of two
parent compounds, pyrimidine and purine. The bases and pentoses of the common nucleotides
are heterocyclic compounds. The carbon and nitrogen atoms in the parent structures are
conventionally numbered to facilitate the naming and identification of the many derivative
compounds.
The pentoses of nucleotides and nucleosides the carbon numbers are given a prime ()
designation to distinguish them from the numbered atoms of the nitrogenous bases. The base of a
nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N--glycosyl
bond to the 1 carbon of the pentose, and the phosphate is esterified to the 5 carbon. The N-glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose
and hydrogen from the base), as in O-glycosidic bond formation.
Both DNA and RNA contain two major purine bases, adenine (A) and guanine (G), and two
major pyrimidines. In both DNA and RNA one of the pyrimidines is cytosine (C), but the second
major pyrimidine is not the same in both: it is thymine (T) in DNA and uracil (U) in RNA. Only
rarely does thymine occur in RNA or uracil in DNA. Nucleic acids have two kinds of pentoses.
The recurring deoxyribonucleotide units of DNA contain 2-deoxy-D-ribose, and the
ribonucleotide units of RNA contain D-ribose. In nucleotides, both types of pentoses are in their
-furanose (closed five-membered ring) form. The pentose ring is not planar but occurs in one of a
variety of conformations generally described as puckered. Specific long sequences of A, T, G,
and C nucleotides in DNA are the repository of genetic information.

Phosphodiester Bonds
The successive nucleotides of both DNA and RNA are covalently linked through phosphategroup bridges, in which the 5-phosphate group of one nucleotide unit is joined to the 3hydroxyl group of the next nucleotide, creating a phosphodiester linkage.Thus the covalent
backbones of nucleic acids consist of alternating phosphate and pentose residues, and the
nitrogenous bases may be regarded as side groups joined to the backbone at regular intervals.
The backbones of both DNA and RNA are hydrophilic. The hydroxyl groups of the sugar
residues form hydrogen bonds with water. The phosphate groups, with a pKa near 0, are
completely ionized and negatively charged at pH 7, and the negative charges are generally
neutralized by ionic interactions with positive charges on proteins, metal ions, and polyamines.
All the phosphodiester linkages have the same orientation along the chain, giving each linear
nucleic acid strand a specific polarity and distinct 5and 3 ends. By definition, the 5end lacks a
nucleotide at the 5position and the 3 end lacks a nucleotide at the 3 position. Other groups

(most often one or more phosphates) may be present on one or both ends. The covalent backbone
of DNA and RNA is subject to slow, non enzymatic hydrolysis of the phosphodiester bonds. In
the test tube, RNA is hydrolyzed rapidly under alkaline conditions, but DNA is not; the 2hydroxyl groups in RNA (absent in DNA) are directly involved in the process. Cyclic 2,3monophosphate nucleotides are the first products of the action of alkali on RNA and are rapidly
hydrolyzed further to yield a mixture of 2- and 3-nucleoside mono phosphates. A short nucleic
acid is referred to as an oligonucleotide. The definition of short is somewhat arbitrary, but
polymers containing 50 or fewer nucleotides are generally called oligonucleotides. A longer
nucleic acid is called a polynucleotide.

DNA Molecules Have Distinctive Base Compositions

A most important clue to the structure of DNA came from the work of Erwin Chargaff and his
colleagues in the late 1940s. They found that the four nucleotide bases of DNA occur in different
ratios in the DNAs of different organisms and that the amounts of certain bases are closely
related. These data, collected from DNAs of a great many different species, led Chargaff to the
following conclusions:
1. The base composition of DNA generally varies from one species to another.
2. DNA specimens isolated from different tissues of the same species have the same base
composition.
3. The base composition of DNA in a given species does not change with an organisms age,
nutritional state, or changing environment.
4. In all cellular DNAs, regardless of the species, the number of adenosine residues is equal to
the number of thymidine residues (that is, A= T), and the number of guanosine residues is equal

to the number of cytidine residues (G =C). From these relationships it follows that the sum of the
purine residues equals the sum of the pyrimidine residues; that is, A+ G= T +C.
These quantitative relationships, sometimes called Chargaffs rules, were confirmed by many
subsequent researchers. They were a key to establishing the three dimensional structure of DNA
and yielded clues to how genetic information is encoded in DNA and passed from one generation
to the next.

DNA Is a Double Helix

To shed more light on the structure of DNA, Rosalind Franklin and Maurice Wilkins used the
powerful method of x-ray diffraction to analyze DNA fibers. They showed in the early 1950s that
DNA produces a characteristic x-ray diffraction pattern. From this pattern it was deduced that
DNA molecules are helical with two periodicities along their long axis, a primary one of 3.4
and a secondary one of 34 . The problem then was to formulate a three-dimensional model of
the DNA molecule that could account not only for the x-ray diffraction data but also for the
specific A= T and G=C base equivalences discovered by Chargaff and for the other chemical
properties of DNA.
In 1953 Watson and Crick postulated a three dimensional model of DNA structure that accounted
for all the available data. It consists of two helical DNA chains wound around the same axis to
form a right handed double helix. The hydrophilic backbones of alternating deoxyribose and
phosphate groups are on the outside of the double helix, facing the surrounding water. The
furanose ring of each deoxyribose is in the C-2 endo conformation. The purine and pyrimidine
bases of both strands are stacked inside the double helix, with their hydrophobic and nearly
planar ring structures very close together and perpendicular to the long axis. The offset pairing of
the two strands creates a major groove and minor groove on the surface of the duplex. Each
nucleotide base of one strand is paired in the same plane with a base of the other strand. Watson
and Crick found that the hydrogen-bonded base pairs illustrated in G with C and A with T, are
those that fit best within the structure, providing a rationale for Chargaffs rule that in any DNA,
G = C and A = T. It is important to note that three hydrogen bonds can form between G and C,
symbolized G=C, but only two can form between A and T, symbolized A=T. This is one reason
for the finding that separation of paired DNA strands is more difficult the higher the ratio of G=C
to A=T base pairs. Other pairings of bases tend to destabilize the double-helical structure. When
Watson and Crick constructed their model, they had to decide at the outset whether the strands of
DNA should be parallel or anti parallelwhether their 5,3-phosphodiester bonds should run in
the same or opposite directions. An anti parallel orientation produced the most convincing
model, and later work with DNA polymerases provided experimental evidence that the strands
are indeed anti parallel, a finding ultimately confirmed by x-ray analysis.

Watson-Crick model for the structure of DNA. The original model proposed by Watson and
Crick had 10 base pairs, or 34 (3.4 nm), per turn of the helix; subsequent measurements
revealed 10.5 base pairs, or 36 (3.6 nm), per turn. (a) Schematic representation, showing
dimensions of the helix. (b) Stick representation showing the backbone and stacking of the bases.
(c) Space-filling model
To account for the periodicities observed in the X ray diffraction patterns of DNA fibers, Watson
and Crick manipulated molecular models to arrive at a structure in which the vertically stacked
bases inside the double helix would be 3.4 apart; the secondary repeat distance of about 34
was accounted for by the presence of 10 base pairs in each complete turn of the double helix. In
aqueous solution the structure differs slightly from that in fibers, having 10.5 base pairs per
helical turn.
The two anti parallel polynucleotide chains of double-helical DNA are not identical in either base
sequence or composition. Instead they are complementary to each other. Wherever adenine
occurs in one chain, thymine is found in the other; similarly, wherever guanine occurs in one
chain, cytosine is found in the other. The DNA double helix, or duplex, is held together by two
forces: hydrogen bonding between complementary base pairs and base-stacking interactions. The
complementarity between the DNA strands is attributable to the hydrogen bonding between base
pairs. The base-stacking interactions, which are largely nonspecific with respect to the identity of
the stacked bases, make the major contribution to the stability of the double helix. The important
features of the double-helical model of DNA structure are supported by much chemical and
biological evidence. Moreover, the model immediately suggested a mechanism for the
transmission of genetic information. The essential feature of the model is the complementarity of
the two DNA strands.

RNA
We now turn our attention to RNA, which differs from DNA in three respects. First, the
backbone of RNA contains ribose rather than 2-deoxyribose. That is, ribose has a hydroxyl group
at the2-position. Second, RNA contains uracil in place of thymine. Uracil has the same singleringed structure as thymine, except that it lacks the 5- methyl group. Thymine is in effect 5methyl-uracil. Third, RNA is usually found as a single polynucleotide chain. Except for the case
of certain viruses, RNA is not the genetic material and does not need to be capable of serving as
a template for its own replication. Rather, RNA functions as the intermediate, the mRNA,
between the gene and the protein-synthesizing machinery. Another function of RNA is as an
adaptor, the tRNA, between the codons in the mRNA and amino acids. RNA can also play a
structural role as in the case of the RNA components of the ribosome. Yet another role for RNA
is as a regulatory molecule, which through sequence complementarity binds to, and interferes
with the translation of, certain mRNAs. Finally, some RNAs (including one of the structural
RNAs of the ribosome) are enzymes that catalyze essential reactions in the cell. In all of these
cases, the RNA is copied as a single strand off only one of the two strands of the DNA template,
and its complementary strand does not exist. RNA is capable of forming long double helices, but
these are unusual in nature.

Difference between DNA and RNA

DNA
Difference: 1.Found in nucleus 2. sugar is
deoxyribose 3. Bases are A,T,C,G
Bases
& DNA is a long polymer with a
Sugars:
deoxyribose and phosphate backbone
and four different bases: adenine,
guanine, cytosine and thymine
Definition: A nucleic acid that contains the genetic
instructions used in the development and
functioning of all known living
organisms
Job/Role:

Medium of long-term storage and

transmission of genetic information

Stands for:
Predomina
nt
Structure:
Pairing of
Bases:
Stability:

DeoxyriboNucleicAcid
Typically a double- stranded molecule
with a long chain of nucleotides

Unique
Features:

Gene

A-T(Adenine-Thymine), G-C(GuanineCytosine)
Deoxyribose sugar in DNA is less
reactive because of C-H bonds. Stable in
alkaline conditions. DNA has smaller
grooves where the damaging enzyme can
attach which makes it harder for the
enzyme to attack DNA.
The helix geometry of DNA is of BForm. DNA is completely protected by
the body i.e. the body destroys enzymes
that cleave DNA. DNA can be damaged
by exposure to Ultra-violet rays

RNA
1.Found in nucleus and cytoplasm 2.sugar is
ribose. 3. Bases are A,U,C,G
RNA is a polymer with a ribose and
phosphate backbone and four different
bases: adenine, guanine, cytosine, and uracil
RNA, single-stranded chain of alternating
phosphate and ribose units with the bases
adenine, guanine, cytosine, and uracil
bonded to the ribose. RNA molecules are
involved in protein synthesis and sometimes
in the transmission of genetic information.
The main job of RNA is to transfer the
genetic code need for the creation of
proteins from the nucleus to the ribosome.
this process prevents the DNA from having
to leave the nucleus, so it stays safe.
Without RNA, proteins could never be
made.
RiboNucleicAcid
A single-stranded molecule in most of its
biological roles and has a shorter chain of
nucleotides
A-U(Adenine-Uracil),
G-C(GuanineCytosine)
Ribose sugar is more reactive because of COH (hydroxyl) bonds. Not stable in alkaline
conditions. RNA on the other hand has
larger grooves which makes it easier to be
attacked by enzymes.
The helix geometry of RNA is of A-Form.
RNA strands are continually made, broken
down and reused. RNA is more resistant to
damage by Ultra-violet rays.

A gene is the molecular unit of heredity of a living organism. It is used extensively by the
scientific community as a name given to some stretches of deoxyribonucleic acids (DNA) and
ribonucleic acids (RNA) that code for a polypeptide or for an RNA chain that has a function in
the organism. Living beings depend on genes, as they specify all proteins and functional RNA
chains. Genes hold the information to build and maintain an organism's cells and pass genetic
traits to offspring. All organisms have genes corresponding to various biological traits, some of
which are instantly visible, such as eye color or number of limbs, and some of which are not,
such as blood type, increased risk for specific diseases, or the thousands of basic biochemical
processes that comprise life.
Genes that are expressed usually have introns that interrupt the coding sequences. A typical
eukaryotic gene, therefore, consists of a set of sequences that appear in mature mRNA (called
exons) interrupted by introns. The regions between genes are likewise not expressed, but may
help with chromatin assembly, contain promoters, and so forth. Intron sequences contain some
common features. Most introns begin with the sequence GT (GU in RNA) and end with the
sequence AG. Otherwise, very little similarity exists among them. Intron sequences may be large
relative to coding sequences; in some genes, over 90 percent of the sequence between the 5 and
3 ends of the mRNA is introns. RNA polymerase transcribes intron sequences. This means that
eukaryotic mRNA precursors must be processed to remove introns as well as to add the caps at
the 5 end and polyadenylic acid (poly A) sequences at the 3 end.

The Central Dogma

Transcription of DNA to RNA to protein: This dogma forms the backbone of molecular biology
and is represented by four major stages.
1. The DNA replicates its information in a process that involves many enzymes: replication.
2. The DNA codes for the production of messenger RNA (mRNA) during transcription.
3. In eucaryotic cells, the mRNA is processed (essentially by splicing) and migrates from the
nucleus to the cytoplasm.
4. Messenger RNA carries coded information to ribosomes. The ribosomes "read" this
information and use it for protein synthesis. This process is called translation.
Proteins do not code for the production of protein, RNA or DNA.
They are involved in almost all biological activities, structural or enzymatic.

Replication

DNA replication is the process of producing two identical replicas from one original DNA
molecule. This biological process occurs in all living organisms and is the basis for biological
inheritance. DNA is made up of two strands and each strand of the original DNA molecule serves
as template for the production of the complementary strand, a process referred to as
semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near
perfect fidelity for DNA replication

When DNA replicates, many different proteins work together to accomplish the following steps:
1. The two parent strands are unwound with the help of DNA helicases.
2. Single stranded DNA binding proteins attach to the unwound strands, preventing them
from winding back together.
3. The strands are held in position, binding easily to DNA polymerase, which catalyzes the
elongation of the leading and lagging strands. (DNA polymerase also checks the accuracy
of its own work!).
4. While the DNA polymerase on the leading strand can operate in a continuous fashion,
RNA primer is needed repeatedly on the lagging strand to facilitate synthesis of Okazaki
fragments. DNA primase, which is one of several polypeptides bound together in a group
called primosomes, helps to build the primer.
5. Finally, each new Okazaki fragment is attached to the completed portion of the lagging
strand in a reaction catalyzed by DNA ligase

Transcription
Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA
transcription. One strand of the DNA double helix is used as a template by the RNA polymerase
to synthesize a messenger RNA (mRNA). This mRNA migrates from the nucleus to the
cytoplasm. During this step, mRNA goes through different types of maturation including one
called splicing when the non-coding sequences are eliminated. The coding mRNA sequence can
be described as a unit of three nucleotides called a codon.
Transcription proceeds in the following general steps:
1 One or more sigma factor protein binds to the RNA polymerase holoenzyme, allowing it to
bind to promoter DNA.
2 RNA polymerase creates a transcription bubble, which separates the two strands of the DNA
helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides.
3 RNA polymerase adds matching RNA nucleotides to the complementary nucleotides of one
DNA strand
4 RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA
strand.
5 Hydrogen bonds of the untwisted RNA-DNA helix break, freeing the newly synthesized RNA
strand.
6 If the cell has a nucleus, the RNA may be further processed. This may include polyadenylation,
capping, and splicing.
7The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear pore complex

Translation
The ribosome binds to the mRNA at the start codon (AUG) that is recognized only by the
initiator tRNA. The ribosome proceeds to the elongation phase of protein synthesis. During this
stage, complexes, composed of an amino acid linked to tRNA, sequentially bind to the
appropriate codon in mRNA by forming complementary base pairs with the tRNA anticodon.
The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one,
translated into polypeptidic sequences dictated by DNA and represented by mRNA. At the end, a
release factor binds to the stop codon, terminating translation and releasing the complete
polypeptide from the ribosome.