BIO CHEM: BIOCHEMISTRY

LECTURE 9: NUCLEIC ACIDS

1st SEMESTER | A.Y. 2023-2024

NUCLEIC ACIDS
• Two kinds of nucleic acids are found in the cells:
• Ribonucleic Acid (RNA) and Deoxyribonucleic Acid (DNA)
• Both DNA and RNA are polymers
• The building blocks of nucleic acid chains are the nucleotides
• Nucleotides themselves, however, are composed of three
simpler units: a base, a sugar, and a phosphate.

Nitrogenous Base
Phosphate Sugar
PURINES PYRIMIDINE
Adenine Cytosine
Guanine Thymine
Uracil

Nucleotide

NITROGEN CONTAINING HETEROCYCLIC BASES

• All are aromatic amines
• Adenine (A) and Guanine (G) are Purines; Cytosine (C),
Thymine (T) and uracil (U) are pyrimidines
• Adenine, Guanine and Cytosine are found in both DNA and
RNA, but Uracil is found only in RNA and Thymine is found only PENTOSE SUGAR
in DNA.
• The sugar component of RNA is D- ribose and in the DNA is 2-
deoxy-D- ribose
PURINE STRUCTURE
• A bicyclic base with fused five
and six membraned rings
• 2 purine derivatives: adenine
and guanine
• adenine is the 6-amino
derivative and guanine is the
2-amino-6-oxo purine
derivative. PHOSPHATE
• Derived from phosphoric acid (H3PO4) the phosphoric acid
loses two of its hydrogen atoms to give a hydrogen phosphate
ion (HPO4¯)

NUCLEOSIDE FORMATION
Important characteristics of the nucleoside formation process of
combining two molecules into one
• The base is always attached to C1’ of the sugar which is
PYRIMIDINE STRUCTURE always in a β configuration
• A monocyclic base with a 6 • A molecule of water is formed as the two molecules bond
membraned ring together and condensation reaction occurs
• Derivatives are the thymine,
Cytosine and Uracil
• Thymine is the 5 methyl -2, 4
dioxo derivative
• Cytosine is the 4-amino-2-oxo
derivative
• Uracil is the 2, 4 dioxo derivative
 5’ carbon of one sugar unit and a phosphoester bond to the
3’ carbon of the other sugar.
• A nucleotide chain has directionality. One end of the
nucleotide chain, the 5’ end normally carries a free phosphate
group attached to the 5’ carbon atom. The other end of the
nucleotide chain, the 3’ end normally has a free hydroxyl
group attached to the 3’ carbon atom.
• Each nonterminal phosphate group in the backbone of a
nucleic acid carries 1- charge.

PHOSPHATE - PHOSPHORIC ACID

Three parallels between primary nucleic acid structure and primary

protein structure are worth noting:

NUCLEOTIDE FORMATION
Formation of nucleotide from a sugar, a base and a phosphate can
be visualized as a two-step process:
• First the pentose sugar and nitrogen containing base react to
form a two-subunit entity called a NUCLEOSIDE.
• The nucleoside reacts with a phosphate group to form the
three-subunit entity called a NUCLEOTIDE.

• DNAs and RNAs and proteins all have backbone that do not
vary in structure.
• The sequence of attachments to the backbone (nitrogen
bases in nucleic acids and amino acid R groups in proteins )
distinguishes one DNA from another, one RNA from another
and one protein from another.
• Both nucleic acid polymer chains and protein polymer chains
have directionality: for nucleic acids, there is a 5’ end and a
Important characteristics of the nucleotide formation process by
3’ end, and for proteins there is an N-terminal end and a C
adding a phosphate group to a nucleoside are the following:
terminal end.
• The phosphate group is attached to the sugar at the C5’
position through a phosphoester linkage
DEOXYRIBONUCLEIC ACID (DNA)
• As with nucleoside formation, a molecule of water is
produced in nucleotide formation. Thus, overall, two • The DNA double helix involves two polynucleotide strands coiled
molecules of water are produced in combining a sugar, base around each other in a manner somewhat like a spiral structure.
and phosphate into a nucleotide.

THE GENERAL STRUCTURE OF A NUCLEIC ACID IN TERMS

OF NUCLEOTIDE SUBUNITS

Some important points about nucleic acid structure:

• Each nonterminal phosphate group of the sugar phosphate
backbone is bonded to two sugar molecules through a 3’ , 5’
phosphodiester linkage. There is a phosphoester bond to the
 oriented in the 5’ to 3’ (away from the replication fork), this is the
lagging strand.

LEADING STRAND
• A short piece of RNA called a primer (produced by an enzyme
called primase) comes along and binds to the end of the leading
strand. The primer acts as the starting point for DNA synthesis.
• DNA polymerase binds to the leading strand and then ‘walks’
along it, adding new complementary nucleotide bases. This
replication is continuous leading to 3’ to 5’ strand
o DNA polymerases are responsible for synthesizing DNA:
they add nucleotides one by one to the growing DNA chain,
incorporating only those that are complementary to the
template.
o They catalyze the formation of a phosphodiester linkage
between the end of a growing strand and an incoming
The base sequence of a single strand of a DNA molecule segment
nucleotide. The latter must complement a nucleotide in the
is always written in a direction from the 5’ end to the 3’ end of the
template strand.
segment. 5’ A-A-G-C-T-A-G-C-T-T-A-C-T 3’
o They verify if the pairing of nitrogenous pairing is correct.

PREDICTING BASE SEQUENCE IN A COMPLEMENTARY

DNA STRAND LAGGING STRAND

Predict the sequence of bases in the DNA strand that is • Discontinuous strand along 5’ to 3’ strand
complementary to the DNA strand shown • The result of DNA replication is two DNA molecules consisting
of one new and one old chain of nucleotides.
5’ C-G-A-A-T-C-C-T-A 3’
• Following replication the new DNA automatically winds up into a
double helix.
Solution: Because only A forms a complementary base pair with T
and only G with C , the complementary strand is as follow RIBONUCLEIC ACID (RNA)
3’ G-C-T-T-A-G-G-A-T 5’ Four Major Differences Exist Between RNA molecules and DNA
molecules:
Note the reversal of the numbering of the ends of the 1. The sugar unit in the backbone of RNA is ribose; it is
complementary strand compared to the given strand. This is due deoxyribose in DNA.
to the antiparallel nature of the two strands in a double helix. 2. The base thymine found in DNA is replaced by uracil in RNA.
In RNA, uracil instead of thymine, pairs with adenine.
3. RNA is a single stranded molecule; DNA is double stranded.
REPLICATION OF DNA MOLECULES 4. RNA molecules are much smaller than DNA molecules,
DNA REPLICATION is the biochemical process by which DNA ranging from 75 nucleotides to a few thousand nucleotides.
molecules produce exact duplicates of themselves.
DIFFERENT CLASSES OF RNA
A. Messenger RNA ( mRNA )
a. Produced in the process called transcription
i. Transcription is the process by which the information in
a strand of DNA is copied into a new molecule of
messenger RNA (mRNA).
b. Carry the genetic information from the DNA in the nucleus
directly to the cytoplasm
c. Its concentration is very low
d. Not long lived
e. Size varies widely, with an average unit containing perhaps
750 nucleotides.
f. Only synthesized when needed

• DNA are anti parallel meaning they ran in opposite direction.

• The first step in DNA replication is to ‘unzip’ the double helix
structure of the DNA molecule.
• This is carried out by an enzyme called helicase which breaks
the hydrogen bonds holding the complementary bases of DNA
together (A with T, C with G).
• The separation of the two single strands of DNA creates a ‘Y’
B. Transfer RNA (tRNA)
shape called a replication ‘fork’. The two separated strands will
a. Containing from 73 to 93 nucleotides per chain.
act as templates for making the new strands of DNA.
b. 3 dimensional type of RNA
• One of the strands is oriented in the 3’ to 5’ (towards the c. Relatively small molecules
replication fork), this is the leading strand. The other strand is d. There is at least one different tRNA molecule for each of
the 20 amino acids from which the body makes its proteins
 e. Contains not only cytosine, guanine, adenine and uracil but
also several other modified nucleotides such as 1- I. Circular RNA
methylguanosine. a. The most recent RNA discovery
b. Acts as miRNA sponge, thus controlling the effects of
miRNA.

TRANSCRIPTION
The process by which DNA directs the synthesis of mRNA
molecules that carry the coded information needed for protein
synthesis the mRNA molecule produces serve as the carrier of the
information needed to direct protein synthesis.

STEPS IN THE TRANCRIPTION PROCESS

1. A portion of the DNA double helix unwinds, exposing a
C. Ribosomal RNA (rRNA)
sequence of bases.
a. The RNA complexed with proteins in ribosomes.
2. Free ribonucleotides, one nucleotide at a time, align along one
b. Ribosome synthesize proteins, specifically the histones.
of the exposed strands of the DNA bases, the template strand,
c. 35% proteins 65% rRNA
forming new base pairs.
3. RNA polymerase is involved in the linkage of ribonucleotides,
D. Small Nuclear RNA (snRNA)
one by one, to the growing mRNA molecule
a. Found in the nucleus of eukaryotic cells
4. Transcription ends when the RNA polymerase enzyme
b. Small, about 100 to 200 nucleotides long
encounters a sequence of bases that is “ read” as a stop signal.
c. Facilitates the conversion of heterogenous nuclear RNA to
messenger RNA.
d. Helps the processing of initial mRNA that is being
transcribed into mature form
e. Great help in initial mRNA synthesis

E. Micro RNA (miRNA)

a. These RNAs are only 20-22 nucleotides long but are
important in the timing of an organism’s development
b. Play an important roles in cancer, stress responses and
viral infections.
c. Inhibit translation of mRNA into protein and promote the
degradation of mRNA.
d. Also stimulate protein production in cells when the cell
cycle has been arrested.

F. Small Interfering RNA ( siRNA)

a. These are short stretches of RNA ( 20-30 nucleotides long)
b. Have been found to have a control in gene expression.
c. The serve as protective mechanism for some species
d. They eliminate undesirable gene, specifically genes that
come from virus or uncontrolled DNA
e. Break specific RNA molecules just to control gene

G. Long non coding RNA (lncRNA)

a. Do not fit in other RNA classes
b. RNA molecules greater than 100 nucleotides in length
c. Used to silence a specific chromosomes
d. Others involved in imprinting
i. IMPRINTING: specific gene from one parent are being
favored
e. Activates specific genes

H. Piwi – Associated RNA (piRNA)

a. RNA molecules with 21-31 nucleotides long
b. Found only in animal cells
c. Used to bind to and lead to the destruction of transposons
i. Transposons: DNA segment that can move around the
chains
d. “Jumping genes” can disrupt the normal cellular processes
and even lead to cancer.
e. Some referred this as the genome’s own immune system.