Nucleic acids are polymers made of nucleotides that serve as the repository of genetic information. There are two main types of nucleic acids: DNA and RNA. DNA is found in cell nuclei and contains the genetic blueprint. RNA is found throughout the cell and assists in protein synthesis. A nucleotide contains a nitrogenous base (purine or pyrimidine), a 5-carbon sugar (deoxyribose in DNA and ribose in RNA), and one or more phosphate groups. Nucleotides bond together via phosphodiester linkages between the sugar and phosphate to form polynucleotide chains. DNA exists as a double helix with the bases on the inside bonded via hydrogen bonds in a complementary and antiparallel fashion

1. NUCLEIC ACIDS
Chasama Costantine, MD

2. Introduction
• Discovered in 1869 by a Swiss physiologist Johan
Friedrich Miescher while studying the nuclei of
white blood cells.
– Thus called Nucleic acids.
• However it is now known that nucleic acids are
found throughout a cell, not just in the nucleus.
• They serve as the repository and transmitter of
genetic information in every cell and organism.
• Due to their ability of self replication

3. Definition
• Nucleic Acids
– Polymers in which the repeating unit is a nucleotide
• A nucleotide has three components:
–pentose sugar - a monosaccharide
–phosphate group (PO43-)
–heterocyclic base

4. Two types of Nucleic Acids:
• DNA: Deoxyribonucleic Acid:
– Found within cell nucleus
– The pentose sugar is a Deoxyribose
– Storage and transfer of genetic information
– Passed from one cell to other during cell division
• RNA: Ribonucleic Acid:
– Occurs in all parts of cell
– The pentose sugar is Ribose
– Primary function is to synthesize proteins

7. Nitrogenous bases
 There are two kinds of nitrogen-containing
bases Purines and Pyrimidines
 Purines
 2 rings
 Six-membered and a Five-membered nitrogen-
containing rings fused together
 Pyridmidines
 One ring
 Six-membered nitrogen-containing ring.

8. Purines
 Adenine = 6-amino purine
 Guanine = 2-amino-6-oxy purine
 Hypoxanthine = 6-oxy purine
 Xanthine = 2,6-dioxy purine

10.  Adenine and Guanine
 Found in both DNA and RNA
 Hypoxanthine and Xanthine
 Not found in nucleic acids
 Important intermediates in purine metabolism

11. Pyrimidines
 Uracil = 2,4-dioxy pyrimidine
 Thymine = 2,4-dioxy-5-methyl pyrimidine
 Cytosine = 2-oxy-4-amino pyrimidine
 Orotic acid = 2,4-dioxy-6-carboxy pyrimidine

13. pyrimidines
 Cytosine is found in both DNA and RNA
 Uracil is found only in RNA
 Thymine is normally found in DNA and not in
RNA
 Sometimes tRNA may contain some Thymine as
well as Uracil

14. Important Nitrogenous Bases

15. Nucleotide formation
Step 1- Nucleoside formation:
– Condensation reaction between a five-carbon
monosaccharide and a purine or pyrimidine base
derivative.
– The N9 of a purine or N1 of a pyrimidine base is
attached to C1’ position of sugar (beta-
conformation) in an N-C-glycosidic linkage

17.  Nucleoside nomenclature:
– For pyrimidine bases
• suffix -idine is used (cytidine, thymidine, uridine)
– For purine bases
• suffix -osine is used (adenosine, guanosine)
– prefix “-deoxy” is used to indicate deoxyribose
present (e.g: deoxythymidine )

19. Nucleotide formation…
Step 2 - Nucleotide Formation
• Phosphate group is added to a nucleoside
– Attached to C5’ position through a phosphoester
bond
– Condensation reaction (H2O released)

21. Nucleotide

22. Nucleotide nomenclature
• Named by appending 5’-monophosphate to nucleoside
name

23. Nucleotides functions
 Nucleotides make DNA and RNA
 Nucleotides are structural components of
several essential co-enzymes:
• Coenzyme A
• NAD+
• NADP+

24. Nucleotides functions…
 Nucleotides serve as carriers of activated
intermediates in the synthesis of some
biomolecules:
• Carbohydrate, Lipids and Proteins
 Serve as the second messengers in signal
transduction pathways:
• cyclic adenosine monophosphate (cAMP)
• cyclic guanosine monophosphate (cGMP).

25. Nucleotide functions…
 Nucleotide plays an important role as Energy
currency in the cell
• ATP, GTP
 Nucleotides are important regulatory
compounds for many of the pathways of
intermediary metabolism, inhibiting or
activating key enzymes

26. Polynucleotide formation
 The nucleotides of a polynucleotide chain are
linked to one another in 3’,5’-phosphodiester
bonds
 Phosphoric acid forms a phosphate ester to
connect the 3’-hydroxyl group of one pentose
to the 5’-carbon on another pentose
 Sugar-phosphate groups are referred to as
nucleic acid backbone
• This backbone is found in all nucleic acids
• Sugars are different in DNA and RNA

28.  5’ end has free phosphate group and 3’ end
has a free OH group
 The sequence of bases is read from 5’ to 3’
 The next nucleotide binds at the 3’ end

30. DNA
• It is the chemical basis of heredity and may be
regarded as the reserve bank of genetic
inforormation.
• The genetic information is encoded in its
primary structure (nucleotide sequence)
• It controls every aspect of cellular function

31. DNA…
• DNA is organized into genes, the fundamental
units of genetic information.
• Gene is a segment of DNA which specifies the
chain of amino acids that comprises the
protein molecule
– Most human genes are ~1000–3500 nucleotide
units long
• Genome:
– All of the genetic material (the total DNA)
contained in the chromosomes of an organism
– Human genome is about 20,000–25,000 genes

32. The central dogma of molecular biology
• A theory that describes interrelationship of
the three classes of biomolecules (DNA, RNA
and proteins) constitutes

33.  A DNA molecule must comprise many
nucleotides to carry the genetic information
necessary for even the simplest organisms
 E.g., the RNA of a virus such as HIV, which
causes AIDS, is 9719 nucleotides in length
 The E. coli genome is a single DNA molecule
consisting of 4.6 million nucleotides( 4.6 x 106
base pairs =4.6 x 103 kilo base pairs) kbp

34. DNA molecules from higher organisms can be
much larger
The human genome comprises of 3 billion
nucleotides [3 x 109], divided among 23 distinct
DNA molecules (chromosomes) of different
sizes.
One of the largest known DNA molecules is
found in the Indian muntjak, an Asiatic deer; its
genome is nearly as large as the human genome
but is distributed on only 3 chromosomes

35. The Indian Muntjak
and Its
Chromosomes.
Cells from a female
Indian muntjak
contain three pairs of
very large
chromosomes
(stained orange).
The cell shown is a
hybrid containing a
pair of human
chromosomes
(stained green) for
comparison.

36. DNA structure
 DNA structure is a double helix whose chains
are complementary and antiparallel
o 1953, Watson & Crick- x-ray diffraction
 Complementary
–A binds to T and C to G between the chains
–The sequence of bases on one strand
automatically determines the sequence of
bases on the other

37.  Antiparallel
– Each end of the helix contains the 5’ end of one
strand and the 3’ end of the other.
• The chains travel in opposite directions
• This allows for formation of H-bonds
between base pairs

39. Forces in DNA Double Helix
1. Hydrogen bonds
o linkage between bases, although weak energy-
wise, is able to stabilize the helix because of the
large number present in DNA molecule;
o 2 Hydrogen bonds in A-T pair and 3 Hydrogen
bonds in G-C pair
• This ensures that DNA would never
spontaneously separate under physiological
conditions

40.  Chargaff’s rule of base pairing
 Molar equivalence between the purines
and pyrimidines in DNA (A=T and GΞC)
• %A = %T and %C = %G
• Human DNA contains 30% adenine,
30% thymine, 20% guanine and 20%
cytosine

42. Forces in DNA Double Helix…
2. Stacking interactions
o Also known as Van der Waals interactions
o Also occur between bases and are weak,
o The large amounts of these interactions
help to stabilize the overall structure of the
helix.

43. Forces in the DNA strand

44. Significance of complementary base
pairing
• Complementary base pairing is very
important in the conservation of the base
sequence of DNA.
• Each strand of DNA can act as a template
to direct the synthesis of another strand
similar to its complementary one and thus
DNA is capable of directing its own self
replication.

45. exercise
• Predict the sequence of bases in the DNA
strand complementary to the single DNA
strand shown below
–5’ A–A–T–G–C–A–G–C–T 3’

46. The Watson and Crick Model of DNA
• Named after American Biologist James
Watson and English Physicist Francis Crick.
• B DNA was the form upon which the model
is derived. DNA occurs primarily in this form
in vivo
• The important features of this model of DNA
are:

47. Features of the Watson and Crick DNA
model
 The DNA molecule consists of two helical
polynucleotide chains or strands coiled
around a common axis.
 The two strands are antiparallel in polarity;
they run in opposite directions so that the 3’
end of one chain faces the 5’ end of the
other

48.  The purine and pyrimidine bases are inside
the helix, whereas the phosphate and
deoxyribose(sugar) backbones are on the
outside.
 The two chains are held together by
hydrogen bonds between (the purine and
pyrimidine) pairs of bases of the opposite
strands

49.  Adenine (A) always pairs with thymine (T) by
two hydrogen bonds and Guanine (G) always
pairs with cytosine (C) by three hydrogen
bonds.
 This complementarity is known as the base
pairing rule.
 Thus the two strands are complementary to
one another.

50.  The base sequence along a polynucleotide
chain is variable and a specific sequence of
bases carries the genetic information.
 The base compositions of DNA obey Chargaff’s
rule according to which:
i. A=T and G=C.
ii. (A+C) = (G+T)
iii. The ratio of (A+T) and (G+C) is constant for a
species (range 0.4 -1.9)

51. Base compositions experimentally determined for a variety
of organisms
Species A:T G:C A:G
Human being 1.00 1.00 1.56
Salmon 1.02 1.02 1.43
Wheat 1.00 0.97 1.22
Yeast 1.03 1.02 1.67
Escherichia coli 1.09 0.99 1.05
Serratia
marcescens
0.95 0.86 0.70

52. • Measurements
– The helix diameter is 20Å or 2 nm
– Adjacent bases are spaced 3.4Å or 0.34 nm
along the helix axis
– The length of a complete turn of helix is 34 Å or
3.4nm
– There are 10 bases per turn
– There is a rotation of 36 degrees per base (360
degrees per full turn).

53. • The DNA helix has a shallow groove called
minor groove (-1.2nm) and a deep groove
called major groove (- 2.2nm) across.
• NB:
• An angstrom is a unit of length equal to
10−10 m or 0.1 nanometer.

55. FORMS OF DNA
• Three helical forms of DNA are recognized
to exist: A, B, and Z.
• The B conformation is the dominate form
under physiological conditions.
• In B DNA, the basepairs are stacked 0.34 nm
apart, with 10 basepairs per turn of the
right-handed double helix and a diameter of
approx 2 nm.

56. • Like B DNA, the A conformer is also a right-
handed helix.
• However, A DNA exhibits a larger diameter
(2.6 nm), with 11 bases per turn of the helix,
and the bases are stacked closer together in
the helix (0.25 nm apart).
• Both A and B DNA conformers have a major
groove and a minor grove

57. • These grooves (particularly the minor
groove) contain many water molecules that
interact favorably with the amino and keto
groups of the bases.
• In these grooves, DNA-binding proteins can
interact with specific DNA sequences
without disrupting the base-pairing of the
molecule.

58. • In contrast to the A and B conformers of
DNA, Z DNA is a left handed helix.
• This form of DNA has been observed
primarily in synthetic double-stranded
oligonucleotides, especially those with
purine and pyrimidines alternating in the
polynucleotide strands.

59. • In addition, high salt concentrations are
required for the maintenance of the Z DNA
conformer.
• Z DNA possesses a minor groove but no
major groove, and the minor groove is
sufficiently deep that it reaches the axis of
the DNA helix.

60. • The natural occurrence and potential
physiological significance of Z DNA in living
cells has been the subject of much
speculation.
• However, these issues with respect to Z DNA
have not yet been fully resolved.

61. Right vs Left Handed Helix

62. A Summary of the features of the DNA
forms

63. A B Z

64. Denaturation of DNA
• The loss of helical structure due to disruption
of H–bonds is called denaturation or melting,
where the double strands separate into single
strands.
• This can be due to extremes of pH, heat, or
chemicals that disrupt H-bonds.
• DNAs which are G-C rich denature at a higher
temperature (Tm) than those which are A-T
rich

65. Types of DNA sequences:
• Exons
– The coding sequences; interrupted by noncoding
sequences
• Introns
– The noncoding sequences; from 10 to 10,000 bases
long
• Palindrome
– Also known as inverted repeats
– DNA sequence that contains the same information
whether it is read forward or backward; e.g. CGAAGC
– Tendency to form hairpin loops and a snapback
(cruciform)

67. RNA
• Like DNA, RNA is composed of repeating
purine and pyrimidine nucleotide subunits.
• However, several distinctions can be made
with respect to the chemical nature of RNA
and DNA.
• Unlike the 2′-deoxyribose sugar moiety of
DNA, the sugar moiety in RNA is ribose.

68. • Like DNA, RNA usually contains adenine,
guanine, and cytosine, but does not contain
thymidine.
• In place of thymidine, RNA contains uracil.
• The concentration of purines and pyrimidine
bases do not necessarily equal one another
in RNA because of the single-stranded
nature of the molecule.

69. • The monomeric units of RNA are linked
together by 3′,5′-phosphodiester bonds
analogous to those in DNA.
• RNAs have molecular weights between 1 ×
104 Daltons for transfer RNA (tRNA) and 1 ×
107 Daltons for ribosomal RNA (rRNA).

70. • Three major classes of RNA are found in
eukaryotic organisms: messenger RNA (mRNA),
transfer RNA (tRNA), and ribosomal RNA
(rRNA).
• Each class differs from the others in the size,
function, and general stability of the RNA
molecules.
• Minor classes of RNA include heterogeneous
nuclear RNA (hnRNA), small nuclear RNA
(snRNA), and small cytoplasmic RNA (scRNA).