Lecture 3

Molecular Biology ٣٢٥ Sabah Linjawi ١

 What is nucleic acid?

„ A nucleic acid is a macromolecule composed of

chains of monomeric nucleotides
„ These molecules carry genetic information or form
structures within cells.
„ The most common nucleic acids are
deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA).
„ Nucleic acids are universal in living things, as they
are found in all cells and viruses.
„ Nucleic acids were first discovered by Friedrich
Miescher in 1871.

Molecular Biology ٣٢٥ Sabah Linjawi ٢

 What is nucleic acid?

„ The term "nucleic acid" is the generic name

for a family of biopolymers, named for their
role in the cell nucleus.
„ The monomers from which nucleic acids are
constructed are called nucleotides.
„ Each nucleotide consists of three
components: a nitrogenous heterocyclic
base, which is either a purine or a pyrimidine;
a pentose sugar; and a phosphate group.
Molecular Biology ٣٢٥ Sabah Linjawi ٣
 Building Blocks - Nucleotides

„ A nucleotide is composed of
three parts: pentose, base
and phosphate group.
„ In DNA or RNA, a pentose
is associated with only one
phosphate group
„ but a cellular free
nucleotide (such as ATP)
may contain more than one
phosphate group.
„ If all phosphate groups are
removed, a nucleotide
becomes a nucleoside

Molecular Biology ٣٢٥ Sabah Linjawi ٤

 Pentose

„ The chemical structure of

pentose which contains five
carbon atoms, labeled as
C1' to C5'.
„ The pentose is called
ribose in RNA and
deoxyribose in DNA
„ because the DNA's
pentose lacks an oxygen
atom at C2'.
„ Recalling that RNA stands
for "ribonucleic acid", and
DNA for "deoxyribonucleic
acid".

Molecular Biology ٣٢٥ Sabah Linjawi ٥

 Bases
„ There are five different bases, each
is denoted by a single letter as given
in the parenthesis:
„ Adenine (A), Cytosine (C),
Guanine (G), Thymine (T), and
Uracil (U).
„ Among them,
„ A, C, G and T exist in DNA;
„ A, C, G and U exist in RNA.
„ Their chemical structures are shown
in the following figure. A and G
contain a pair of fused rings,
classified as purines. C, T, and U
contain only one ring, classified as
pyrimidines.

Molecular Biology ٣٢٥ Sabah Linjawi ٦

 Cellular Nucleotides and Nucleosides

„ In cells, a free nucleotide

may contain one, two or
three phosphate groups.
„ The energy carrier ATP
(adenosine triphosphate)
has three phosphate
groups
„ ADP (adenosine
diphosphate) has two
„ AMP (adenosine
monophosphate) has
one.
„ Their structures are
shown in the following
figure.

Molecular Biology ٣٢٥ Sabah Linjawi ٧

 The Nucleic Acid Chain
„ In a nucleic acid chain,
two nucleotides are
linked by a
phosphodiester bond,
which may be formed by
the condensation
reaction similar to the
formation of the peptide
bond.
„ In cells, such process
has been found in the
ligation between two
nucleic acid fragments.
„ However, the whole
nucleic acid chain is
usually synthesized by
RNA polymerase or
DNA polymerase.

Molecular Biology ٣٢٥ Sabah Linjawi ٨

 DNA Structure
„ In a normal DNA molecule, adenine
(A) is paired with thymine (T)
„ guanine (G) is paired with cytosine
(C).
„ The uracil (U) of RNA can also pair
with adenine (A)
„ U differs from T by only a methyl
group located on the other side of
hydrogen bonding.
„ A DNA molecule has two strands,
held together by the hydrogen
bonding between their bases
„ adenine can form two hydrogen
bonds with thymine
„ cytosine can form three hydrogen
bonds with guanine.

Molecular Biology ٣٢٥ Sabah Linjawi ٩

 DNA's B Form, A Form and Z Form

„ In a DNA molecule, the two strands

are not parallel, but intertwined with
each other. Each strand looks like a
helix.
„ The two strands form a "double
helix" structure, which was first
discovered by James D. Watson
and Francis Crick in 1953.
„ This structure, also known as the B
form, the helix makes a turn every
3.4 nm
„ The distance between two
neighboring base pairs is 0.34 nm.
„ There are about 10 pairs per turn.
„ The intertwined strands make two
grooves of different widths
„ The major groove and the minor
groove, which may facilitate binding
with specific proteins.

Molecular Biology ٣٢٥ Sabah Linjawi ١٠

 DNA's B Form, A Form and Z Form

„ In a solution with higher

salt concentrations or with
alcohol added, the DNA
structure may change to an
A form, which is still right-
handed, but every 2.3 nm
makes a turn and there are
11 base pairs per turn.
„ Another DNA structure is
called the Z form, because
its bases seem to zigzag.
„ Z DNA is left-handed. One
turn spans 4.6 nm,
comprising 12 base pairs.

Molecular Biology ٣٢٥ Sabah Linjawi ١١

 RNA Structure and Function

„ Most cellular RNA molecules are single stranded.

„ They may form secondary structures such as stem-
loop and hairpin.

Molecular Biology ٣٢٥ Sabah Linjawi ١٢

 RNA Structure and Function

„ The major role of RNA is to participate in protein

synthesis, which requires three classes of RNA:
„ messenger RNA (mRNA)
„ transfer RNA (tRNA)
„ ribosomal RNA (rRNA)
„ Other classes of RNA include
„ Ribozymes
The RNA molecules with catalytic activity.
„ Small RNA molecules
RNA interference and other functions.

Molecular Biology ٣٢٥ Sabah Linjawi ١٣

 The mRNA-ribosome-tRNA complex
formed during protein synthesis

Molecular Biology ٣٢٥ Sabah Linjawi ١٤

 References
„ Wolfram Saenger, Principles of Nucleic Acid Structure, 1984, Springer-Verlag New York
Inc.
„ Keith Roberts, Martin Raff, Bruce Alberts, Peter Walter, Julian Lewis and Alexander
Johnson, Molecular Biology of the Cell 4th Edition, Routledge, March, 2002, hardcover,
1616 pages, 7.6 pounds, ISBN 0-8153-3218-1
„ The Biochemistry of the Nucleic Acids - by Roger Lionel Poulter Adams, John T Knowler -
708 pages
„ Nucleic Acids in Chemistry and Biology - by G Michael Blackburn, ... - 503 pages
„ The Double Helix: A Personal Account of the ... - by James D Watson, Gunther Siegmund
Stent - 264 pages
„ Links
„ Interview with Aaron Klug, Nobel Laureate for structural elucidation of biologically important
nucleic-acid protein complexes provided by the Vega Science Trust.
„ Nucleic Acid Research Journal
„ UC Berkeley video lecture on nucleic acids
„ www.visionlearning.com/library/module_viewer.php?mid
„ www.answers.com/topic/nucleic-acid

Molecular Biology ٣٢٥ Sabah Linjawi ١٥