CHEMISTRY OF NUCLEIC ACID

BCH 204
(MEDICAL BIOCHEMISTRY III)
 INTRODUCTION

• Nucleic acids are macromolecules present in all living cells in

combination with proteins to form nucleoproteins, the protein is
usually basic in nature e.g., protamines and histones containing a
high concentration of basic amino acids (arg, lys, his)
• Nucleic acids have a variety of roles in organisms; genetic
information is encoded in a nucleic acid molecule, the cell
interprets this information as sequences of amino acid in protein
and peptide molecules
• Nucleic acids are polymers of a specific sequence of subunits or
monomers called nucleotides, they are therefore polynucleotides
• Simply put, nucleic acid is the general term used for DNA and RNA.
DNA means Deoxyribonucleic acid while RNA means Ribonucleic
acid. DNA is present in nuclei and small amounts are also present
in the mitochondria, whereas 90% of RNA is present in the cell
cytoplasm and 10% in the nucleolus
• Nucleotides are the monomeric units of the nucleic acids, DNA
(deoxyribonucleic acid) and RNA (ribonucleic acid). Each
nucleotide consists of a heterocyclic nitrogenous base, a sugar,
and phosphate.
• In DNA, the sugar is deoxyribose; lacking a hydroxyl
group on carbon 2, whereas in RNA it is ribose.
• A gene is defined as a segment of the DNA molecule that contains
the information required for the synthesis of a functional
biological product, whether protein or RNA
• A cell typically has many thousands of genes, and DNA molecules,
not surprisingly, tend to be very large. The storage and
transmission of biological information are the only known
functions of DNA
• RNAs have a broader range of functions, and several classes are
found in cells
• Ribosomal RNAs (rRNAs) are components of ribosomes, the complexes
that carry out the synthesis of proteins.
• Messenger RNAs (mRNAs) are intermediaries, carrying genetic
information from one or a few genes to a ribosome, where the
corresponding proteins can be synthesized.
• Transfer RNAs (tRNAs) are adapter molecules that faithfully translate the
information in mRNA into a specific sequence of amino 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 present in nucleic acids are purine and
pyrimidine
• purine bases are adenine (A) and guanine (G) while pyrimidine bases
are cytosine (C) and thymine (T).
• RNA contains A, G, and C, but it has uracil (U) instead of thymine
• Ribose sugar is present in RNA while deoxyribose is the sugar in DNA
• PURINE BASES

Adenine is 6-aminopurine
Guanine is 2-amino-6-oxypurine
 PYRIMIDINE BASES

Uracil is 2, 4 dioxy pyrimidine

Cytosine is 2-oxy-4-amino pyrimidine
Thymine is 2,4-dioxy, 5-methyl pyrimidine
 SUGARS IN NUCLEIC ACIDS

The sugar is either β-D-ribose or β-D-2-deoxyribose

DNA and RNA are distinguished on the basis of the
sugar present
DNA contains β-D-2-deoxyribose (lacking a hydroxyl
group on carbon 2)
RNA contains β-D-ribose
 NUCLEOSIDES AND NUCLEOTIDES
• Nucleosides are derivatives of purines and pyrimidines that have a sugar
linked to a ring nitrogen of a purine or pyrimidine. Numerals with a prime
(e.g, 2' or 3') distinguish atoms of the sugar from those of the base
• The sugar in ribonucleosides is D-ribose, and in deoxyribonucleosides is
2-deoxy-D-ribose. Both sugars are linked to the base by a -N-glycosidic
bond, almost always to the N-1 of a pyrimidine or to N-9 of a purine
• nucleotides are nucleosides with a phosphoryl group esterified to a
hydroxyl group of the sugar. The 3'- and 5'-nucleotides are nucleosides
with a phosphoryl group on the 3'- or 5'-hydroxyl group of the sugar,
respectively.
• Since most nucleotides are 5'-, the prefix "5'-" usually is omitted when
naming them. UMP and dAMP thus represent nucleotides with a
phosphoryl group on C-5 of the pentose. Nucleotides could be mono, di
or triphosphates depending on the number of phosphate group that is
esterified to the hydroxyl group of the sugar
Structure of Adenosine and Deoxycytidine
 NUCLEOTIDES

PURINE NUCLEOTIDES PYRIMIDINE NUCLEOTIDES

 NAMES OF BASES AND THEIR CORRESPONDING NUCLEOSIDES AND
NUCLEOTIDES
Base Nucleoside Nucleotide
Adenine (A) Adenosine AMP, ADP, ATP, cAMP, etc
Guanine (G) Guanosine GDP, GTP, cGMP
Thymine (T) Thymidine
Uracil (U) Uridine UDP-sugar
Cytosine (C) Cytidine CTP, CDP-choline
Hypoxanthine Inosine IMP
• Deoxyribonucleotides: These nucleotides contain pentose sugar,
deoxyribose and are monomeric units of DNA
• Ribonucleotides: These nucleotides contain pentose sugar, D-
ribose and are monomeric units of RNA
• • Mononucleotides are nucleosides in which single phosphate
group is attached to hydroxyl group of the pentose sugar. For
example, AMP (adenosine monophosphate) is adenine + ribose +
phosphate.
• If an additional phosphate group is attached to the pre-existing
phosphate of mononucleotide
• – A nucleoside diphosphate, e.g. ADP
• – A nucleoside triphosphate, e.g. ATP results
Structure of ATP and its components
 FUNCTIONS OF SOME NUCLEOTIDES

• 1. ATP, GTP, CTP, UTP, NAD, FAD and CoA are important
ribonucleotides which act as coenzymes.
• 2. Deoxyribonucleotides are required for DNA replication and
repair. Ribonucleotides are required for RNA.
• 3. They are used in biosynthetic reactions like UDP-glucose, in
glycogen synthesis and UDPgalactose in lactose synthesis.
• 4. ATP acts as currency of free energy for all cellular activities like
muscle contraction, biosynthesis of molecules and transfer
reactions.
• 5. Some nucleotides act as intracellular messenger’s .eg, c AMP, c
GMP are involved in peptide hormone action
• 6. GTP is used in protein synthesis.
• 7. S-adenosyl methionine participates in transmethylation
reactions.
 Concept of Base-Pairing
• As proposed by Watson and Crick, each DNA molecule consists of two
polynucleotide chains joined by hydrogen bonds between the bases
• In each base pair, a purine on one strand forms hydrogen bonds with a
pyrimidine on the other strand. In one type of base pair, adenine on one
strand pairs with thymine on the other strand
• This base pair is stabilized by two hydrogen bonds. The other base pair,
formed between guanine and cytosine, is stabilized by three hydrogen
bonds.
• As a consequence of base-pairing, the two strands of DNA are
complementary, that is, adenine on one strand corresponds to thymine
on the other strand, and guanine corresponds to cytosine.
• The concept of base-pairing proved to be essential for determining the
mechanism of DNA replication (in which the copies of DNA are produced
that are distributed to daughter cells) and the mechanisms of
transcription and translation
• A=T, G C RNA contains Uracil instead of thymine, so
Adenine pairs with uracil in RNA
HYDROGEN BOND FORMATION BETWEEN PURINE AND PYRIMIDINE
BASES
 Primary Structure of DNA

• The deoxyribonucleotides are linked together by phosphodiester

bonds between the 3' –hydroxyl of the sugar of one nucleotide
through a phosphate molecule to the 5' – hydroxyl on the sugar of
another nucleotide
• The sugar – phosphate linkages form the backbone of the polymer
to which the variable bases are attached
• The nucleotide polymer has a free phosphate group attached to 5'
– position of sugar and a free 3' –hydroxyl group.
• The sequence of the polymer is written in the 5’ to 3’ direction
with abbreviations to different bases
The bond between the
base and the sugar is β-
N-glycosidic bond
between the N-9 of
Guanine and C-1 of the
sugar, the bond between
the sugar and the
phosphate group is an
ester bond between the
C-5 of the sugar and the
phosphate group. The
bond between a
nucleotide and another
PRIMARY STRUCTURE OF DNA
is phosphodiester bond
 Secondary Structure of DNA

• The secondary structure of DNA is performed when the two

strands of DNA are paired together
• In the secondary structure of DNA, the two strands are anti-
parallel. That means, the 5’ ---- 3’ of one strand is in opposite
direction to the other strand
• The bases are stacked in the inside of the two strands
• The bases of one strand pairs with the bases of the other strand of
the same plane such that adenine always pairs with thymine with
two bonds, guanine always pairs with cytosine with three bonds
• The negatively charged phosphate group and the sugar units
expose themselves to the outside of the chain
• The two strands of DNA coil around a single axis forming right
handed double helix
• Watson - Crick proposed a double helical model of DNA, having
the following important characteristic features.
1. Two helical polynucleotide chains are coiled around a common axis. The
chains run in opposite directions, (anti parallel)
2. The two antiparallel polynucleotide chains are not identical, but they are
complimentary.
3. The purine, pyrimidine bases are on the inside of the helix, the phosphate
and deoxyribose groups are on the outside. The planes of the sugars are at
right angles to that of the bases.
4. The diameter of the helix is 20 A0,adjascent bases are separated by 3.4 A0
5. The helical structure repeats after 10 residues on each chain.
6. The two chains are held together by hydrogen bonds between pairs of
bases. Adenine is always paired with thymine, Guanine always paired with
cytosine. A to T is bonded by two hydrogen bonds (A= T), Guanine is bonded
to cytosine by three hydrogen bonds
7. The double helix is stabilized by interaction between stacked bases of the
same strand.
8. Watson - Crick Model of DNA is also referred as B-DNA, which is the most
stable one under physiological conditions.
9. The mitochondrial DNA is circular and there can be formation of Z-DNA
and C-DNA which can be performed during either replication or
transcription.
DOUBLE HELICAL STRUCTURE OF DNA
 Chargaff’s Rule
• Ervin Chargaff discovered that in DNA of all species, quantity of
purines is the same as that of pyrimidines (A+G=T+C). He observed
that in DNA, content of adenine equals that of thymin (A=T) and
content of guanine equals that of cytosine (G=C).
• Watson and Crick deduced that adenine must pair with thymine
and guanine with cytosine, because of stearic and hydrogen
bonding factors. Adenine cannot pair with cytosine; guanine
cannot pair with thymine.
• Thus, one member of a base pair in a DNA must always be a
purine and the other a pyrimidine.
• This base pairing restriction explains that in a double stranded
DNA molecule, the content of A equals that of T and the content of
G equals that of C.
• The ratio of purine to pyrimidine bases in the DNA is always one,
i.e. G+A : T+C = 1.
 The Structure of RNA

• The building unit of RNA is ribonucleotide. Ribonucleotide differs

from deoxyribonucleotide in that ribonucleotide contains “O” in
the carbon 2’ sugar ribose.
• Uracil is found in RNA while Thymine is found in DNA.
• The nuclear DNA is in secondary structure, but RNA is the primary
structure. Only t-RNA after post transcriptional process can be
changed to tertiary structure
• The three RNAs that have important role in protein synthesis are:
• 1. Messenger RNA (mRNA)
• 2. Transfer RNA (tRNA)
• 3. Ribosomal RNA (rRNA)
• Messenger RNA (mRNA)
• The mRNA comprises only about 5-10% of total cellular RNA
• The mRNA carries the genetic information in the form codons. Codons
are a group of three adjacent nucleotides that code for the amino acids
of protein.
• In eukaryotes mRNAs have some unique characteristics, e.g. the 5' end
of mRNA is “capped” by a 7-methyl-guanosine triphosphate
• mRNAs serve as template for protein biosynthesis and transfer genetic
information from DNA to protein synthesizing machinery.
• If the mRNA codes for only one peptide, the mRNA is monocistronic. If it
codes for two or more different polypeptides, the mRNA is
polycistronic. In eukaryotes most mRNA are monocistronic.
• Transfer RNA (tRNA)
• tRNA molecules vary in length from 74 to 95 nucleotides. In eukaryotic
cells, 10-20% of the nucleotides of tRNA may be modified and known as
unusual nucleotides, e.g., Ribothymidine (T), in which methyl group is
added to uracil to form thymine and Pseudouridine (ψ), in which uracil is
attached to ribose by a carbon-carbon bond rather than a nitrogen bond
• All single stranded transfer RNA molecules get folded into a structure
that appears like a clover leaf.
• All tRNA have 4 arms.
• 1. Amino acid arm: the one that carries amino acid
• 2. The D arm: the one that binds with active center of the enzyme
aminoacyl tRNA synthetase.
• 3. TψC arm: the one that binds to ribosome during protein synthesis.
• 4. Anticodon arm: which pairs with the codon of mRNA during protein
synthesis.
• Ribosomal RNA (rRNA)
• rRNA is highly methylated as compared to the other RNAs. rRNA
participates in the structure of ribosome. rRNA, ribosomal
proteins and Mg++ constitute ribosome. The ribosome is made of
two subunits (big and small).
• Ribosomes are ribonucleotide-protein particles, serve as work
benches for protein synthesis, about 2/3 of the mass is RNA and
rest is protein. In prokaryotes, they float freely in cytoplasm or
attach to plasma membrane. Each ribosome consists of a large
subunit and a small subunit .
• They are held together by non-covalent interactions.
• Ribosomes are not only found in cytosol but also in mitochondria.
• According to their sedimentation rates, the subunits are referred
as 30S, & 50S, together they form 70S unit. 30S has 21 proteins
and 16 S r-RNA. 50S has 34 proteins and 23S, 5S r-RNA.
components of 70s prokaryotic rRNAs are identified
ribosome 1. In prokaryotic cells as 23s,
16s, and 5s
2. In eukaryotic cells as 28s,
18s, 7s and 5s.
 DIFFERENCES BETWEEN DNA AND RNA
• Both have adenine, guanine and cytosine. Both have nucleotides
linked by phosphodiester bond, in 3’-5’direction. Both have
important role in protein synthesis
DNA RNA

Uracil absent Present

sugar deoxyribose ribose
site Nucleus, Nucleus, cytosol,
mitochondria but ribosome
never in the cytosol
strands Double-stranded Single stranded
types A, B and Z tRNa, mRNa, rRNA
Carries genetic Only mRNA carries
information genetic information
thymine present absent
Number of bases equal Not equal