Part II

Nucleic Acids
Introduction
• Two types of nucleic acids are important to the cell.
• The first is deoxyribonucleic acid (DNA), which carries all of
the genetic information for an organism.
• The second type is ribonucleic acid (RNA), which is
responsible for interpreting the genetic information into proteins
that will carry out the essential cellular functions.
Structure of Nucleic acids
• The components of these nucleic acids include a five-
carbon sugar, phosphate, and four heterocyclic amines
called nitrogenous bases. The sugar in DNA is 2′-
deoxyribose and the sugar in RNA is ribose. These differ
only in the absence of a hydroxyl group at the carbon-2
position of 2′-deoxyribose.
• The nitrogenous bases are divided into two families known
as pyrimidines and purines.
• The pyrimidine bases in DNA are cytosine and thymine.
• The pyrimidines found in RNA are cytosine and uracil.
• The major purines of both DNA and RNA are adenine and
guanine.
Nucleosides
• Nucleosides are produced by the combination of a sugar, either
ribose (in RNA) or 2′-deoxyribose (in DNA), with a purine or a
pyrimidine base.
• The nucleosides formed with ribose and adenine, or guanine are
called adenosine or guanosine, respectively. If 2′-deoxyribose is the
sugar in these nucleosides, they are called 2′-deoxyadenosine and 2′-
deoxyguanosine.
• The ribonucleosides formed from cytosine and uracil are called
cytidine and uridine, respectively. The deoxyribonucleosides of
cytosine and thymine are called 2′-deoxycytidine and thymidine,
respectively. No prefix is needed for thymidine because it is found
only in DNA.
Nucleosides in RNA Nucleosides in RNA
Nucleosides in RNA Nucleosides in RNA
Nucleotides
• A nucleotide consists of either ribose or deoxyribose, one of the
five nitrogenous bases, and one or more phosphoryl groups.
• A nucleotide with the sugar ribose is a ribonucleotide, and one
having the sugar 2′-deoxyribose is a deoxyribonucleotide.
• The covalent bond between the sugar and the phosphoryl
group is a phosphodiester bond formed by a condensation
reaction between the 5′-OH of the sugar and an -OH of the
phosphoryl group.
Nomenclature of Nucleotides
1) Remove the -ine ending and replace it with either -osine for purines or –idine for pyrimidines.
Uracil is the one exception to this rule. In this case, the –acil ending is replaced with -idine,
producing the name uridine.
2) Nucleotides with the sugar ribose are ribonucleotides, and those having the sugar 2′-
deoxyribose are deoxyribonucleotides.
3) For a deoxyribonucleotide, the prefix deoxy- is placed before the modified nitrogenous base
name. No prefix is required for ribonucleotides, or for thymidine, which is found only in DNA.
4) Add a prefix to indicate the number of phosphoryl groups that are attached. A monophosphate
carries one phosphoryl group; a diphosphate carries two phosphoryl groups; and a triphosphate
carries three phosphoryl groups.
5) Because the full names of the nucleotides are so cumbersome, a simple abbreviation is
generally used.
Nucleotides in RNA
Base Nucleoside Ribonucleotide
Adenine Adenosine Adenosine-5′-phosphate Adenylate
Guanine Guanosine Guanosine-5′-phosphate Guanylate
Cytosine Cytidine Cytidine-5′-phosphate Cytidylate
Uracil Uridine Uridine-5′-phosphate Uridylate

Nucleosides in DNA
Base Nucleoside Deoxyribonucleotide
Adenine 2′-Deoxyadenosine 2′-Deoxyadenosine-5′-phosphate 2′-Deoxyadenylate
Guanine 2′-Deoxyguanosine 2′-Deoxyguanosine-5′-phosphate 2′-Deoxyguanylate
Cytosine 2′-Deoxycytidine 2′-Deoxycytidine-5′-phosphate 2′-Deoxycytidylate
Thymine Thymidine Thymidine-5′-phosphate Thymidylate
Nucleotides in RNA
Base Nucleoside Ribonucleotide
Adenine Adenosine Adenosine-5′-monophosphate AMP
Adenosine-5′-diphosphate ADP
Adenosine-5′-triphosphate ATP
Guanine Guanosine Guanosine-5′-monophosphate GMP
Guanosine-5′-diphosphate GDP
Guanosine-5′-triphosphate GTP
Cytosine Cytidine Cytidine-5′-monophosphate CMP
Cytidine-5′-diphosphate CDP
Cytidine-5′-triphosphate CTP
Uracil Uridine Uridine-5′-monophosphate UMP
Uridine-5′-diphosphate UDP
Uridine-5′-triphosphate UTP
Nucleotides in DNA
Base Nucleoside Deoxyibonucleotide
Adenine Adenosine 2′-Deoxyadenosine-5′-monophosphate dAMP
2′-Deoxyadenosine-5′-diphosphate dADP
2′-Deoxyadenosine-5′-triphosphate dATP
Guanine Guanosine 2′-Deoxyguanosine-5′-monophosphate dGMP
2′-Deoxyguanosine-5′-diphosphate dGDP
2′-Deoxyguanosine-5′-triphosphate dGTP
Cytosine Cytidine 2′-Deoxycytidine-5′-monophosphate dCMP
2′-Deoxycytidine-5′-diphosphate dCDP
2′-Deoxycytidine-5′-triphosphate dCTP
Thymine Thymidine Thymidine-5′-monophosphate TMP
Thymidine-5′-diphosphate TDP
Thymidine-5′-triphosphate TTP
Q) Draw the chemical structure of:
1) dCDP 2) UMP 3) GTP 4) dGMP
5) TTP 6) dATP 7) Cytosine-5′-triphosphate
8) Uridine-5′-triphosphate
9) A nucleotide consisting of 2′-Deoxyribose, thymine, one
phosphoryl group
10) A nucleotide consisting of Ribose, uracil, one phosphoryl
group
Functions of Nucleotides
1) Precursors of DNA and RNA.
2) Activated intermediates in many biosyntheses: e.g UDP-glucose →
glycogen, CDP-diacylglycerol → phosphoglycerides.
3) Nucleotide triphosphates, esp. ATP, as the universal currency of
energy in biological systems.
4) Adenine nucleotides are components of the coenzymes, NAD(P)+,
FAD, and CoA.
5) Metabolic regulators: Ex) c-AMP is the mediator of hormonal
actions.
Nucleotides as Energy Intermediates:
• Nucleotides di and triphosphates
contain high energy phosphate
anhydride bonds.
• Those nucleotides are made during
Catabolism (nutrients breakdown) and
used during the process of biosynthesis.
• ATP or Adenosine triphosphate is the
best known of them besides GTP
[Guanosine triphosphate] and CTP
[Cytidine triphosphate] which are
important in metabolic processes.
Nucleotides as Chemical Messengers:
• 3′,5′-cyclic AMP (cAMP) and 3′,5′-cyclic GMP (cGMP) act as
bio- messengers in hormone- and nerve-mediated signals.
Nucleotides as Redox Factors or Nucleotide Vitamins:
• They are involved in oxidation-reduction reactions in metabolism as cofactors or
enzyme catalysts.
• They are found attaching with water-soluble vitamin as [Nucleotide-Vitamin].
• Vitamin: organic compounds that are essential to life and not synthesized within
the body and obtained through the diet.
• Example: NAD+ and NADH
The structure of DNA:
• A single strand of DNA is a polymer of
nucleotides bonded to one another by
3′–5′ phosphodiester bonds.
• The backbone of the polymer is called
the sugar-phosphate backbone
because it is composed of alternating
units of the five-carbon sugar 2′-
deoxyribose and phosphoryl groups in
phosphodiester linkage.
• A nitrogenous base is bonded to each
sugar by an N-glycosidic linkage
The polymerization of nucleotides into RNA and DNA
DNA Structure: The Double Helix
• X-Ray diffraction proved a helical structure for DNA.
• Chargaff’s rule:
• In the DNA of any species and any organism:
• The amount of guanine should be equal to the amount of cytosine (G = C)
• The amount of adenine should be equal to the amount of thymine (A = T).
• A 1:1 stoichiometric ratio of purine and pyrimidine bases should exist (A+G=T+C)
• Based on these findings, Watson and Crick concluded that:
• DNA is a double helix of two strands ound around one another.
• The sugar-phosphate backbones (S-P) of the two strands of DNA spiral around the outside of the
helix like the handrails on a spiral staircase. The nitrogenous bases extend into the center at right
angles to the axis of the helix
• The double helix structure is partially stabilized by hydrogen bonding between the nitrogenous
bases in the center of the helix. Adenine forms two hydrogen bonds with thymine, and cytosine
forms three hydrogen bonds with guanine. These are called base pairs.
• The two strands of DNA are
complementary strands because the
sequence of bases on one automatically
determines the sequence of bases on the
other.
• The diameter of the double helix is 2.0 nm.
The helix completes one turn every ten base
pairs. One complete turn is 3.4 nm.
• The two strands are antiparallel strands,
i.e. the two strands of the helix run in
opposite directions. Hydrogen bonds that
hold the two strands together.
The Central Dogma (Francic Crick 1957)

• Replication: a process by which DNA is copied with high fidelity.

• Transcription: a process by which DNA genetic code is read and transferred into
messenger RNA (mRNA).

• Translation: a process by which the genetic code is converted to a protein.

• Chromosomes: are pieces of DNA that carry the genetic instructions, or
genes, of an organism.

• Prokaryotes are organisms in which there is no

true nucleus surrounded by a nuclear membrane
and there are no true membrane bound
organelles. Ex) all types of bacteria.
• The prokaryotes have only a single
chromosome.
• Chromosome of prokaryotes is a circular DNA
molecule that is supercoiled, on itself. It is
further attached to a complex of proteins forming
a series of loops. This structure, called the
nucleoid.
• The eukaryotes, have many chromosomes,
each of which has many different levels of
structure.

• The first level of structure is the

nucleosome, which consists of a strand of
DNA wrapped around a small disk made up
of histone proteins. At this level, the DNA
looks like beads along a string.

• The string of beads then coils into a larger

structure called the condensed fiber. This
complex of DNA and protein is termed
chromatin and makes up the eukaryotic
chromosomes.
Q) Write the complementary base sequence for the following
DNA segments:
1) 5′-A-C-G-A-C-T-C-G-G-3′
2) 5′-G-T-A-G-G-C-T-A-C-3′
Q) Give reason:
1) G-C base pair is more stable than A-T pair
2) DNA strands are antiparallel
3) DNA strands are complementary
Q) What is meant by?
1) Chromatin
2) Nucleosome
3) Nucleoid
RNA structure
• The sugar-phosphate backbone of RNA consists of ribonucleotides, also
linked by 3′–5′ phosphodiester bonds.
Differences from DNA:
• The sugar moiety is ribose.
• RNA molecules are usually single-stranded.
• The nitrogenous base uracil (U) replaces thymine (T).
• RNA is much smaller than DNA.
Types of RNA
• Three types of RNA: ribosomal RNA (rRNA), messenger RNA (mRNA),
and transfer RNA (tRNA).
Ribosomal RNA (rRNA)
• The most abundant type of RNA
• It is combined with proteins in the ribosomes.
• Ribosomes are the sites for protein synthesis in the cell.
• It consist of at least two subunits: a large subunit and a small subunit.

Messenger RNA (mRNA)

• It carries genetic information from the DNA, located in the nucleus of the cell, to the
ribosomes located in the cytoplasm.
• Each gene segment of DNA produces a separate mRNA for a particular protein that is
needed in the cell.
• The size of mRNA depends on the number of nucleotides in that gene.
Transfer RNA (tRNA),
• It is the smallest of the RNA molecules.
• It interprets the genetic information in mRNA and brings specific
amino acids to the ribosome for protein synthesis.
• There can be more than one tRNA for each of the 20 amino
acids.
• The structures of the transfer RNAs are similar, consisting of 70
to 90 nucleotides. Hydrogen bonds between some of the
complementary bases in the chain produce loops that give
some double-stranded regions adopting a cloverleaf structure.
• All tRNA molecules have 3′ end with the nucleotide sequence
ACC, which is known as the acceptor stem.
• An enzyme attaches an amino acid by forming an ester bond
with the free -OH at the end of the acceptor stem.
• Each tRNA contains an anticodon, which is a series of three
bases that complements three bases on mRNA
DNA Replication
For replication, DNA must be unknotted, uncoiled, and the double helix must be unwound.
• Topisomerase: Enzyme that unknots and uncoils DNA.
• Helicase: Protein that unwinds the DNA double helix.
• DNA polymerase: Enzyme that replicate DNA using each strand as a template for the newly
synthesized strand. It can only add a nucleotide onto a pre-existing 3′-OH.
• A primer: a short strand of RNA or DNA (about 18-22 bases), built by primase enzyme,
whish serves as a starting point for DNA polymerase.
• DNA ligase: Enzyme that catalyzes the formation of phosphodiester bonds between
pieces of DNA.
• DNA replication is a semi-conservative, i.e. each new strand of DNA contains one parental
(old, template) strand and one daughter (newly synthesized) strand.
Leading strand Lagging strand
1) Its template opens in 3′→5′ direction. 1)
2) Replicated strand that grows continuously. 2) Lagging strand is formed in a short
segments called “Okazaki fragments”. Its
growth is discontinuous.
3) Leading strand is formed immediately at 3) Lagging strand is formed later than
the beginning of replication. leading strand.
4) Only single RNA primer is required. 4) Each Okazaki fragment needs RNA
primer.
5) The direction of growth of leading strand is 5) The direction of growth of leading strand is
5′→3′. 3′→5′, although that that direction of growth
of each of Okazaki fragments is 5′→3′.
6) It does not require DNA ligase. 6) DNA ligase is required for joining Okazaki
fragments.
7) Formation of leading strand is quite rapid. 7) Formation of lagging strand is slower than
leading strand.
Transcription
In prokaryotes, transcription occurs through 3 steps:

1) Initiation: RNA polymerase with one or more transcription factors binds to a

sequence of DNA called “Promoter”, found near the 3′-end of DNA. It forms a
transcription bubble which separates the DNA strands, providing a single strand
template by breaking hydrogen bonds between complementary DNA nucleotides.

2) Elongation: The polymerase builds an RNA molecule out of the complementary

nucleotides, making a chain that grows from 5′ → 3′. The RNA carries the
same information as the non-template (coding) strand of DNA, but it contains
uracil (U) instead of thymine (T).

3) Termination: Sequence called terminator signals that the RNA transcript is

complete. They cause the transcript to be released from the RNA polymerase.
Eukaryotic primary transcripts undergo three post-transcriptional modifications:

1) Addition of a 5′ cap.

• It consists of 7-methylguanosine attached to the 5′ end of the RNA by a 5′–

5′ triphosphate bridge.

• The first two nucleotides of the mRNA are also methylated.

2) Addition of 3′ poly(A) tail.

3) RNA splicing: It involves the removal of portions of the primary transcript that
are not protein coding (introns).
Translation ---- Protein synthesis
Translation occurs through 3 steps:
1) Initiation: The ribosome assembles
around the mRNA to be read, and the first
tRNA (carrying the amino acid
methionine, which matches the start
codon: AUG).
2) Elongation: The ribosome uses the tRNA
anti-codon so that the mRNA is reading
one codon at a time, and the amin acid
matching each codon is added to a
growing protein chain.
3) Termination: The finished polypeptide
chain is released after a stop codon
(UAG, UAA or UGA) enters the ribosome.
Mutation
• Mutation is Changes can occur in the nucleotide sequence of a DNA molecule.
• A chemical that causes DNA mutation is called “Mutagen”.
• Three types of mutations:
1) Point mutation

2) Deletion mutation

3) Insertion mutation
Results of mutation.
• Some mutations are silent mutations; that
Ex) Consider the two codons for glutamic acid: GAA and GAG. A point mutation that
alters the third nucleotide of GAA to GAG will still result in the incorporation of glutamic
acid at the correct position in the protein. Similarly, a GAG to GAA mutation will also be
silent.
• However, most mutations have a negative effect
Ex) Consider the human genetic disorder sickle cell anemia. In the normal β-chain of
hemoglobin, the sixth amino acid is glutamic acid. In the β-chain of sickle cell
hemoglobin, the sixth amino acid is valine. This is due to A point mutation of A → U in
the second nucleotide changes some codons for glutamic acid into codons for valine.