Nucleic acid structure notes

1. Module [1]: Molecular Science
1- Nucleic Acid Chemistry
Omer B Mohamed, M.Sc., MB (ASCPi) cm

2. Objectives
• Diagram the structure of nitrogen bases, nucleosides and
nucleotides.
• Describe the nucleic acid structure as a polymer of
nucleotides.
• Describe nucleotides, nucleic acid and DNA, RNA.

3. Nucleotides & Nucleosides
Biomedical importance:
In addition to serving as precursors of nucleic acids, purine and
pyrimidine nucleotides participate in metabolic functions as
diverse as energy metabolism, protein synthesis, regulation of
enzyme activity, and signal transduction. When linked to vitamins
or vitamin derivatives, nucleotides form a portion
of many coenzymes.

4. Nucleotides & Nucleosides
• A nucleotide is the basic building block of nucleic acid (DNA
& RNA).
• Are molecules of about 700 kd. Each nucleotide consists of a
five carbon sugar (D-ribose or 2-deoxy D-ribose), the first
carbon of which is covalently joined to a nitrogen bases
(purine and pyrimidine) and the fifth carbon to a triphosphate
moiety. A nitrogen base bound to an un phosphorylated sugar
is a nucleoside.
Keyword: D-ribose, Purine, Pyrimidine, Triphosphate

5. D-ribose & 2-deoxy D-ribose
• D-ribose is a natural simple aldopentose sugar with molecular
formula C5H10O5
• 2-deoxy D-ribose is ribose with the number two carbon of
deoxyribose linked to a hydrogen atom rather than a hydroxyl
group

6. Nitrogen bases (purine and pyrimidine)
• Purines and pyrimidines are aromatic heterocycles, cyclic
structures that contain, in addition to carbon, other (hetero)
atoms such as nitrogen.
• Note that the smaller pyrimidine molecule has the longer name
and the larger purine molecule the shorter name, and that their
six-atom rings are numbered in opposite directions.
• Nitrogen bases with a single ring (thymine, cytosine and
uracil) are pyrimidines. Bases with a double ring (guanine,
adenine) are purines.

7. Nitrogen bases (purine and pyrimidine)

8. Nucleosides
• 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 (eg, 2′ or 3′) distinguish
atoms of the sugar from those of the heterocycle.
 Nucleosides Are N-Glycosides:
• The sugars in ribonucleosides are linked to the heterocycle by
an a-N-glycosidic bond, almost always to the N-1 of a
pyrimidine or to N-9 of a purine

10. Nucleotides Are Phosphorylated Nucleosides
Mononucleotides 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. Additional phosphoryl
groups, ligated by acid anhydride bonds to the phosphoryl
group of a mononucleotide, form nucleoside diphosphates and
triphosphates

13. Nucleic Acid
The 5′-phosphoryl group of a mononucleotide can esterify a
second hydroxyl group, forming a phosphodiester. Most
commonly, this second hydroxyl group is the 3′-OH of the
pentose of a second nucleotide. This forms a dinucleotide in
which the pentose moieties are linked by a 3′,5′-phosphodiester
bond to form the “backbone” of RNA and DNA.
Addition of nucleotides in this way gives the N.A chain a
polarity; that is, it has a 5 ′ phosphate end and a 3 ′ hydroxyl end.
We refer to N.A as oriented in a 5 ′ to 3 ′ direction, and the linear
sequence of the nucleotides, by convention, is read in that order.

14. Nucleic Acid Are Directional Macromolecules
Directional 3′ → 5′ phosphodiester bonds link the monomers of
polynucleotides. Since each end of a polynucleotide thus is
distinct, we reefer to the “5′-end” or the “3′-end” of a
polynucleotide. Since the phosphodiester bonds all are 3′ → 5′,
the representation pGpGpApTpCpA indicates that the terminal 5′-
hydroxyl is phosphorylated. More concisely, the representation
GGATC, which shows only the base sequence, is by convention
written with the 5′-base (G) at the left and the 3′-base (C) at the
right.

17.  This polymeric molecule, deoxyribonucleic acid (DNA), is the
chemical basis of heredity and is organized into genes, the
fundamental units of genetic information. The basic
information pathway—that is.
 The chemical nature of the monomeric deoxynucleotide units
of DNA:
1. Deoxyadenylate
2. Deoxyguanylate
3. Deoxycytidylate
4. Thymidylate
Deoxyribonucleic Acid (DNA)

18. Model of A Double-stranded (Ds) DNA
Molecule
 Since the genetic information resides in the order of the
monomeric units within the polymers, there must exist a
mechanism of reproducing or replicating this specific
information with a high degree of fidelity.
 That requirement, together with x-ray diffraction data from the
DNA molecule generated by Franklin, and the observation of
Chargaff that in DNA molecules the concentration of
deoxyadenosine (A) nucleotides equals that of thymidine (T)
nucleotides (A = T), while the concentration of
deoxyguanosine (G) nucleotides equals that of deoxycytidine
(C) nucleotides (G = C), led Watson, Crick, and Wilkins to
propose the modle in the early 1950s.

19. Double Helix

20. Cooperative interaction
Base Pairing & Base Stacking:
The two strands of this double-stranded helix are held in register
by both hydrogen bonds between the purine and pyrimidine bases
of the respective linear molecules and by van der Waals and
hydrophobic interactions between the stacked adjacent base pairs.

21. DNA Grooves
The sugar-phosphate backbones are arranged at specific distances
from one another in the double helix. The two regions formed in
the helix by the backbones are called the (Major Groove and
Minor Groove). The major and minor grooves are sites of
interaction with the many proteins that bind to specific nucleotide
sequences in DNA (binding or recognition sites ). The double
helix can also be penetrated by intercalating agents, molecules
that slide transversely into the center of the helix. Denaturing
agents such as formamide and urea displace the hydrogen bonds
and separate the two strands of the helix.

22. Structural forms of the double helix
There are three major structural forms of DNA: the B form (described
by Watson and Crick in 1953), the A form, and the Z form.
 B Form
Right-handed helix with 10 base pairs per 360° turn (or twist) of the
helix, and with the planes of the bases perpendicular to the helical axis.
Chromosomal DNA is thought to consist primarily of B-DNA
 A Form
The A form is produced by moderately dehydrating the B form. It is
also a right-handed helix, but there are 11 base pairs per turn, and
the planes of the base pairs are tilted 20° away from the perpendicular
to the helical axis. The conformation found in DNA–RNA hybrids or
RNA–RNA double-stranded regions is probably very close to the A
form.

23.  Z form
Z-DNA is a left-handed helix that contains 12 base pairs per turn.
[Note: The deoxyribose– phosphate backbone “zigzags,” hence,
the name “Z”-DNA.] Stretches of Z-DNA can occur naturally in
regions of DNA that have a sequence of alternating purines and
pyrimidines (for example, poly GC). Transitions between the B
and Z helical forms of DNA may play a role in regulating gene
expression.

24. Linear and circular DNA molecules
 Each chromosome in the nucleus of a eukaryote contains one
long, linear molecule of dsDNA, which is bound to a complex
mixture of proteins (histone and nonhistone, to form
chromatin. Eukaryotes have closed, circular, dsDNA
molecules in their mitochondria, as do plant chloroplasts.
 A prokaryotic organism typically contains a single, circular,
dsDNA molecule. [Note: Circular DNA is “supercoiled”, that
is, the double helix crosses over on itself one or more times.

25. DNA Supercoil & Topology
Supercoiling (by certine enzymes like Topoisomerases) can
result in overwinding (positive supercoiling) or underwinding
(negative supercoiling) of DNA. Supercoiling, a type of tertiary
structure, compacts DNA.] Each prokaryotic chromosome is
associated with nonhistone proteins that help compact the DNA
to form a nucleoid. In addition, most species of bacteria also
contain small, circular, extrachromosomal DNA molecules called
plasmids. Plasmid DNA carries genetic information, and
undergoes replication that may or may not be synchronized to
chromosomal division.