structure of DNA and RNA

1. Structure of DNA and RNA

2. NUCLEOTIDE
Composition of Nucleotides
A nucleotide is made up of 3 components:
I. Nitrogenous base (a purine or a pyrimidine)
II. Pentose sugar, either ribose or deoxyribose
III. Phosphate groups esterified to the sugar.
When a base combines with a pentose sugar, a nucleoside is
formed.

4. NUCLEOSIDE
NUCLEOTIDE

5.  When the nucleoside is esterified to a phosphate group, it
is called a nucleotide or nucleoside monophosphate.
 When a second phosphate gets esterified to the existing
phosphate group, a nucleoside diphosphate is generated.
The attachment of a 3rd phosphate group results in the
formation of a nucleoside triphosphate.
 The nucleic acids (DNA and RNA) are polymers of
nucleoside monophosphates.

6. Nitrogenous Bases of RNA and DNA
Two classes of nitrogenous bases namely purines and
pyrimidines are present in RNA and DNA.
Purine Bases
Two principal purine bases found in DNAs, as well as
RNAs
 Adenine (A)
 Guanine (G).

7. Pyrimidine Bases
Three major pyrimidine bases are:
 Cytosine (C)
 Uracil (U)
 Thymine (T)

8.  Cytosine and uracil are found in RNAs and cytosine and
thymine in DNA.
 Both DNA and RNA contain the pyrimidine cytosine but
they differ in their second pyrimidine base.
 DNA contains thymine whereas RNA contains uracil.

10.  All the pyrimidine bases can exist in lactam form and
Lactim form.
 If the group is –HN–CO–, it is called the Lactam type
(keto), while the same if isomerises to – N = C – OH, it
is called Lactim form (enol).
 At the physiological pH, the lactam (keto) forms are
predominant.

11. Minor bases seen in nucleic acids

12. You read 3' or 5' as "3-prime" or "5-
prime".
(Ribose is the sugar
in the backbone of
RNA, ribonucleic
acid.)

13. A phosphate group is attached to the sugar
molecule in place of the -OH group on the 5'
carbon.
Nitrogenous bases attach in place of the -OH
group on the 1' carbon atom in the sugar
ring.
Nucleotide
The phosphate group on one
nucleotide links to the 3' carbon
atom on the sugar of another
one forming 3’,5’ phosphodiester
bridges

14. Sources of carbon and nitrogen in
purine ring
1. N1 of purine is derived from amino group of aspartate
2. C2 and C8 arise from formate of N10 formyl THF
3. N3 and N9 are obtained from amide group of glutamate
4. C4,C5 and C7 are contributed by glycine
5. C6 directly from CO2

16. Different major bases with their corresponding nucleosides
and nucleotides
Base Ribonucleoside Ribonucleotide
Adenine (A) Adenosine Adenosine monophosphate
(AMP)
Guanine (G) Guanosine Guanosine monophosphate
(GMP)
Uracil (U) Uridine Uridine monophosphate
(UMP)
Cytosine (C) Cytidine Cytidine monophosphate
(CMP)

17. Base Deoxyribonucleoside Deoxyribonucleotide
Adenine Deoxyadenosine Deoxyadenosine
monophosphate (dAMP)
Guanine Deoxyguanosine Deoxyguanosine
monophosphate (dGMP)
Cytosine Deoxycytidine Deoxycytidine monophosphate
(dCMP)
Thymine Deoxythymidine Deoxythymidine
monophosphate (dTMP)

18. Structure of ATP and its components

19. BIOLOGICALLY IMPORTANT NUCLEOTIDES
 Adenosine nucleotides: ATP, ADP, AMP and Cyclic
AMP.
 Guanosine nucleotides: GTP, GDP, GMP and cyclic
GMP.
 Uridine nucleotides: UTP, UDP, UMP, UDP-G.
 Cytidine nucleotides: CTP, CDP, CMP and certain deoxy
CDP derivatives of glucose, choline, ethanolamine

20. ATP
 ATP serves as the main biological source of energy in the
cell.
 ATP is required as a source of energy in several metabolic
pathways, e.g. fatty acid synthesis, glycolysis, cholesterol
synthesis, protein synthesis, gluconeogenesis, etc. and in
physiologic functions such as muscle contraction, nerve
impulse transmission, etc.

21. AMP
AMP is the component of many coenzymes such as NAD+,
NADP+, FAD, coenzyme A, etc. These coenzymes are
essential for the metabolism of carbohydrate, lipid and
protein.

22.  C-AMP (Cyclic adenosine 3', 5'-monophosphate)
 c-AMP is formed from ATP by the action of adenylate
cyclase.
 c-AMP acts as a second messenger for many hormones,
e.g. epinephrine, glucagon, etc.

23.  GDP and GTP
 These guanosine nucleotides participate in the
conversion of succinyl-CoA to succinate.
 GTP is required for activation of adenylate cyclase by
some hormones.
 GTP serves as an energy source for protein synthesis.

24. C-GMP (Cyclic guanosine 3', 5’-monophosphate)
 c-GMP is formed from GTP by guanylyl cyclase.
 c-GMP is an intracellular signal or second messenger
that can act antagonistically to c-AMP.
 c-GMP is involved in relaxation of smooth muscle and
vasodilation

25. UDP (Uridine diphosphate)
 UDP participates in glycogenesis.
 UDP-glucose and UDP-galactose take part in galactose
metabolism and required for synthesis of lactose and
cerebrosides.
 UDP-glucuronic acid is required in detoxification
processes and for biosynthesis of mucopolysaccharides
such as heparin, hyaluronic acid, etc.

26. CTP (Cytidine triphosphate) and CDP (Cytidine
diphosphate)
CTP and CDP are required for the biosynthesis of some
phospholipids. CDP-choline is involved in the synthesis of
sphingomyelin.

27. PURINE, PYRIMTDTNE AND NUCLEOTIDE ANALOGS
 Allopurinol is used in the treatment of hyperuricemia and gout
 6 – thio-guanine and 6 – Mercaptopurine: In both of these naturally
occurring purines, –OH groups are replaced by “thiol” (–SH) group
at 6 – position of purine, widely used in clinical medicine.
 Azathioprine (which gets degraded to 6-mercaptopurine) is used to
suppress immunological rejection during transplantation.
 Arabinosyladenine is used for the treatment of neurological
disease.

28. DNA STRUCTURE AND FUNCTION

29. DNA is a polymer of deoxyribonucleotides (or simply
deoxynucleotides )
Deoxyribonucleotide is composed of a nitrogenous base,
a sugar and phosphate group.
The bases of DNA molecule carry genetic information,
whereas their sugar and phosphate groups perform a
structural role

30.  The sugar in a deoxyribonucleotide is deoxyribose.
 The purine bases in DNA are adenine (A), and guanine (G).
 Pyrimidine bases are thymine (T) and cytosine (C).
 The 3′-hydroxyl of one sugar is linked to the 5′-hydroxyl of
another sugar through a phosphate group.
Polarity of DNA molecule
 In the case of DNA, the base sequence is always written from
the 5′ end to the 3′ end. This is called the polarity of the DNA
chain.

32.  Watson-Crick Model of DNA Structure
A diagrammatic
representation of the
Watson and Crick model of
the double-helical structure
of the B form of DNA

33. Base pairing rule. Base pairing of A with T and G with C.
Hydrogen bonds between bases

34.  Features of DNA double helix are
 The DNA is right handed double helix. It consists of 2
polydeoxyribonucleotide chains ( strands ) twisted around
each other on a common axis.
 The 2 strands are antiparallel i.e. one strand runs in 5’ to
3’ direaction and other in 3’ to 5’ direaction.
 The width/diameter of double helix is 20 angstrom( 2nm)

35.  Each turn of the helix is 34 angstrom ( 3.4 nm ) with 10
pairs of nucleotides, each pair placed at a distance of 3.4
angstrom
 Each strand of DNA has a hydrophilic deoxyribose
phosphate backbone on outside or periphery and
hydrophobic bases at inside or core of the molecule.
 The 2 strands are not identical but complementary to
each other due to base pairing.

36.  The 2 strands are held together by hydrogen bonds formed
by complementary base pairs. The A-T pair is double
bond and G-C pair is triple bond.
 The hydrogen bonds are formed between a purine and a
pyrimidine only. If 2 purines face each other they would
not fit in the allowable space and 2 pyrimidine would be
too far away to form bonds. Hence the possible spatial
arrangements are A-T,T-A,G-C and C-G.

37.  The complementary base pairing proves Chargaff’s rule.
The amount of adenine = thymine and guanine =
cytosine.
 One strand has genetic information and is known as sense
strand or coding strand and the opposite strand is known
as antisense strand.
 The double helix as wide/major grooves and
narrow/minor grooves. Proteins can interact with DNA at
these grooves without distrupting the base pairs.

38. Chargaff’s Rule
 Erwin Chargaff ( 1940 ) observed that in all species,
 The overall base composition of an organism is invariant. It
can not be changed by changing environmental conditions, age
or nutrition.
 The base composition of one species is different from another
species.
 The base composition is the same in all the tissues of an
organism.
 Also, the total sum of the purines is equal to the total sum of
pyrimidines (A + G = T + C).
 Chargaff’s rule: The number of adenine is always equal to
the number of thymine and the number of cytosines are always
equal to the number of guanines and the sum of the total
purines are equal to the sum of the total pyrimidines

39. Types of DNA
 The double helical structure exists in atleast 6
different forms A to E and Z based on variation in
conformation of nucleotides
 B-DNA ( described by Watson and Crick ) is most
predominant under physiological conditions.
 The Z-form is left handed and arranged in “zig zag”
fashion.

41. Triple-stranded DNA
Triple-stranded DNA formation occur due to additional hydrogen
bonds between the bases. Thus, a thymine can selectively form two
Hoogsteen hydrogen bonds to the adenine of A-T pair to form T-A-T
Likewise, a protonated cytosine can also form two hydrogen bonds
with guanine of G-C pairs that results in C-G-C. Triple-helical
structure is less stable than double helix. This is due to three
negatively charged backbone strands in triple helix results in an
increased electrostatic repulsion.

42. Four-stranded DNA
Polynucleotides with very high contents of guanine can form a novel
tetrameric structure. called G-quartets. These structures are planar and
are connected by Hoogsteen hydrogen bonds. Antiparallel four-
stranded DNA structures, referred to as G-tetraplexes have also been
reported. The ends of eukaryotic chromosomes namely telomeres are
rich in guanine, and therefore form G-tetraplexes.

43. DNA Denaturation
 Separation of double-stranded DNA into 2 single strands
by breaking of hydrogen bonds between the bases is
known as DNA denaturation
 It can be done by change in pH or increasing temperature
or use of chemical agents ( Formamide )
 Loss in helical structure can be measured by increase in
absorbance at 260 nm in spectrophotometer.
 Tm ( Melting temperature ) – The temperature at which
half of DNA has denatured

44.  Above Tm DNA is single strands and below Tm DNA is
double strand
 G-C base pairs ( 3 hydrogen bonds ) are stronger than A-
T base pairs ( double bond ) so DNA with more G-C
content have greater Tm.
 Renaturation ( reannealing ) – is process by which the
seperated complementary DNA strands can form double
helix

46. Organization of DNA
 DNA is a long structure. i.e In a Diploid Human cell, the
DNA size is 6.0 x 109 bp and contour length 2 meter. Such
a long DNA has to be packed in a nucleus of about 10um
size.
 In prokaryotes DNA is organized as a single chromosome
in form of a double stranded circle

47. Organization in Eukaryotes
 DNA double helix wrap around a core of eight histone
proteins. The DNA-histone complex is called chromatin.
 The double helix of DNA is highly negatively charged
due to all the negatively charged phosphates in the
backbone.
 Histones are positively charged proteins due to being
rich in arginine and lysine amino acids so histones bind
with DNA very tightly.
 Core histones are H2A, H2B, H3, and H4

48.  Two each of the histones (H2A, H2B, H3, and H4) come
together to form a histone octamer which binds and wraps
approximately 2 turns of DNA, or about 150 base pairs.
This complex is known as nucleosome.
 Two adjacent nucleosomes are connected by linker DNA
to which H1 histone is attached.
 These Nucleosome chain gives a ‘beads on string’
appearance and length of DNA is now condensed to 10
nm fibre

49.  which gets further condensed and coiled to produce a
solenoid of 30 nm diameter. This solenoid structure
undergoes further coiling to produce a chromatid of 700
nm.
 Chromatin is held over a scaffold of non-histone
chromosomal or NHC proteins.

50.  chromatin is densely packed to form darkly staining
heterochromatin. At other places, chromatin is loosely
packed to form euchromatin which is lightly stained.
Euchromatin is transcriptionally active chromatin whereas
heterochromatin is transcriptionally inactive
 During the course of mitosis the loops are further coil
becomes highly compacted into chromosomes that
become visible under light microscope ( during metaphase

51. DNA wraps twice around histone octamer to form one
nucleosome

52. Ribonucleic acid (RNA)
DNA is double stranded, while RNA single stranded

53.  RNA is a polymer of ribonucleotides held together by
3',5'-phosphodiester bridges.
 Although RNA has certain similarities with DNA
structure, they have specific difference

54.  Pentose : The sugar in RNA is ribose in contrast to
deoxyribose in DNA.
 Pyrimidine : RNA contains the pyrimidine uracil in place
of thymine (in DNA).
 Single strand : RNA is usually a single stranded
polynucleotide.
 Chargaff's rule-not obeyed : Due to the single-stranded
nature, there is no specific relation between purine and
pyrimidine contents. Thus the guanine content is not
equal to cytosine

55.  Susceptibility to alkali hydrolysis : Alkali can hydrolyse
RNA to 2',3'-cyclic diesters. This is possible due to the
presence of a hydroxyl group at 2' position. DNA cannot
be subjected to alkali hydrolysis due to lack of this group.

56. Types of RNA
The 3 major types of RNA are
1. Messenger RNA (mRNA)
2. Transfrer RNA (tRNA)
3. Ribosomal RNA (rRNA)
All of these are involved in the process of protein
biosynthesis. Each differs from the others by size and
function.

57. Messenger RNA (mRNA): The gene present in DNA is
transcribed into mRNA. This constitutes about 2–5% of
total RNA in the cell. They are generally degraded quickly.
Ribosomal RNA (rRNA): This constitutes about 80% of all
RNA in the cell. 28S, 18S and 5S are the major varieties.
They are involved in protein biosynthesis and are very
stable.

58.  Transfer RNA (tRNA): There are about 60 different
species present. They constitute about 15% of the total
RNA in the cell. They are very stable.
 Micro RNA (miRNA): They alter the function of mRNA.
They are moderately stable.

59. Small RNA: They constitute about 1–2% of total RNA
in the cell. There are about 30 different varieties. They
are very stable.
 Small Nuclear RNAs (SnRNAs) are a subgroup of small
RNA.
 Some important species of SnRNAs are U1 (165
nucleotides), U2 (188 nucleotides), U3 (216), U4 (139),
U5 (118), U6 (106). They are involved in mRNA splicing

60. Structure of mRNA
 mRNA is synthesized in the nucleus as heterogenous RNA
(hnRNA), which are processed into functional mRNA.
 The mRNA carries the genetic information in the form of
codons. Codons are a group of three adjacent nucleotides that
code for the amino acids of protein.

61. • In eukaryotes mRNAs have some unique characteristics,
e.g. the 5' end of mRNA is “capped” by a 7- methyl-
guanosine triphosphate.
• The cap is involved in the recognition of mRNA in
protein biosynthesis and it helps to stabilize the mRNA
by preventing attack of 5'-exonucleases.

62.  A poly (A) “tail” is attached to the other 3'-end of mRNA.
This tail consists of series of adenylate residues, 20-250
nucleotides in length joined by 3' to 5' phosphodiester
bonds.

63. Function of mRNA
 mRNAs serve as template for protein biosynthesis and
transfer genetic information from DNA to protein
synthesizing machinery.
 If the mRNA codes for only one peptide, the mRNA is
monocistronic. If it codes for two or more different
polypeptides, the mRNA is polycistronic. In eukaryotes
most mRNA are monocistronic.

64. Transfer RNA (tRNA)
 All single stranded transfer RNA molecules get folded
into a structure that appears like a clover leaf.
 They contain a significant proportion of unusual bases.
 These include dihydrouracil (DHU), pseudouridine (Ψ)
and hypoxanthine . Moreover, many bases are
methylated.

65. Three unusual (modified) nucleosides present in tRNA

66. All t-RNAs contain four main arms:
 The acceptor arm.
 The D arm
 The anticodon arm
 The TψC arm.

67. Structure of clover leaf transfer RNA

68.  The acceptor arm : This arm is capped with a sequence
CCA (5'to 3'). The amino acid is attached to the acceptor
arm.
 The anticodon arm : This arm, with the three specific
nucleotide bases (anticodon), is responsible for the
recognition of triplet codon of mRNA. The codon and
anticodon are complementary to each other.
 The D arm : lt is so named due to the presence of
dihydrouridine.

69.  The TψC arm contains both ribothymidine (T) and
pseudouridine (ψ, psi).
 The extra arm is also known as variable arm because it
varies in size, is found between the anticodon and TψC
arms.

70. Ribosomal RNA (rRNA)
 The ribosomes are the factories of protein synthesis. The
eukaryotic ribosomes are composed of two major
nucleoprotein complexes-60S subunit and 40S subunit.
The 60S subunit contains 28S rRNA, 5S rRNA and 5.8S
rRNA . while the 40S subunit contains 18S rRNA.