Nucleic acids Get their name because they were first found in the nucleus of cells, but they have since been discovered also to exist outside the nucleus (cytoplasm). Are the molecules within a cell that are responsible for ability to produce exact replicas of themselves. It is called ‘molecules of heredity’. Are the principle genetic materials of all living organisms. It contains C, H, O, N (10%) and P (15%). Are condensation polymers of nucleotides. Are the polynucleotides having high molecular weight. It is a polymer in which the monomer units are nucleotides. Nucleotides: Phosphoric acid esters of nucleosides. Nucleotides = nucleoside + phosphate Nucleotides are carbon ring structures containing nitrogen linked to a 5-carbon sugar. 5-carbon sugar is either a ribose or a deoxy-ribose making the nucleotide either a ribonucleotide or a deoxyribonucleotide. Nucleosides are compounds in which nitrogenous bases (purines and pyrimidines) are conjugated to the pentose sugars (ribose or deoxyribose) by a β-glycosidic linkage. Ribose (RNA) is a sugar, like glucose, but with only five carbon atoms in its molecule. Deoxyribose (DNA) is almost the same but lacks one oxygen atom. In both types of nucleotides the pentoses exist in their ß-furanose (closed five-membered ring) forms. Both molecules may be represented by the symbol: Despite the complexity and diversity of life the structure of DNA is dependent on only 4 different nucleotides. Diversity is dependent on the nucleotide sequence. All nucleotides are 2 ring structures composed of: Despite the complexity and diversity of life the structure of DNA is dependent on only 4 different nucleotides. Diversity is dependent on the nucleotide sequence. All nucleotides are 2 ring structures composed of: A nucleoside consists of a nitrogen base linked by a glycosidic bond to C1’ of a ribose or deoxyribose. Nucleosides are named by changing the nitrogen base ending to -osine for purines and –idine for pyrimidines A nucleotide is a nucleoside that forms a phosphate ester with the C5’ OH group of ribose or deoxyribose Nucleotides are named using the name of the nucleoside followed by 5’-monophosphate

1. Nucleotides and Nucleic acids
 Nucleic acids
 Get their name because they were first found in the nucleus of
cells, but they have since been discovered also to exist outside the
nucleus (cytoplasm).
 Are the molecules within a cell that are responsible for ability to
produce exact replicas of themselves. It is called ‘molecules of
heredity’.
 Are the principle genetic materials of all living organisms.
 It contains C, H, O, N (10%) and P (15%).
 Are condensation polymers of nucleotides.
 Are the polynucleotides having high molecular weight.
 It is a polymer in which the monomer units are nucleotides.
 Nucleotides: Phosphoric acid esters of nucleosides.
 Nucleotides = nucleoside + phosphate
1

2. Cont…
 Nucleotides are carbon ring structures containing nitrogen linked
to a 5-carbon sugar.
 5-carbon sugar is either a ribose or a deoxy-ribose making the
nucleotide either a ribonucleotide or a deoxyribonucleotide.
 Nucleosides are compounds in which nitrogenous bases (purines
and pyrimidines) are conjugated to the pentose sugars (ribose or
deoxyribose) by a β-glycosidic linkage.
2

3. Cont…
 Nucleotide =
– Nitrogeneous base
– Pentose sugars: ribose (RNA) or 2-deoxyribose (DNA)
– Phosphate: The P groups make the links that unite the sugars
(hence a “sugar-phosphate backbone”
 Nucleoside =
– Nitrogeneous base
– Pentose
 Nucleobase =
– Nitrogeneous base

4. 4
sugar base
sugar base
phosphate
sugar base
phosphate
sugar base
phosphate
sugar base
phosphate
nucleoside nucleotides
nucleic acids
 Nucleoside, nucleotides and nucleic acids
 The chemical linkage between monomer units in nucleic acids is a
phosphodiester.

5. Composition of Nucleotides
Nucleotides are made up of three structural subunits.
1. Sugar: ribose in RNA, 2-deoxyribose in DNA
2. Heterocyclic base
3. Phosphate
5

6. Sugar (Pentose)
 Ribose (RNA) is a sugar, like glucose, but with only five carbon
atoms in its molecule.
 Deoxyribose (DNA) is almost the same but lacks one oxygen
atom.
 In both types of nucleotides the pentoses exist in their ß-furanose
(closed five-membered ring) forms.
 Both molecules may be represented by the symbol:
6

7. The most common organic bases are
Adenine (A)
Thymine
(T)
Cytosine (C)
Guanine
(G)
The bases

8.  The bases always pair up in the same way
 Adenine forms a bond with Thymine
 Cytosine bonds with Guanine
Adenine Thymine
Cytosine Guanine

9. Adenine
Deoxyribose
PO4
The deoxyribose, the phosphate and one of
the bases combine to form a nucleotide.

10. Phosphate Groups
 Phosphate groups are what makes a nucleoside a nucleotide.
 Phosphate groups are essential for nucleotide polymerization.
P
O
O
O
O X

11. Cont…
 Number of phosphate groups determines nomenclature.
 Monophosphate, e.g. AMP
 Free = inorganic phosphate (Pi)
 Diphosphate, e.g. ADP
 Free = Pyro- phosphate (PPi)
 Triphosphate, e.g. ATP
 No Free form exists
P
O
O
O
O CH2
P
O
O
O
P
O
O
O
O CH2
P
O
O
O
P
O
O
O
O P
O
O
O CH2

12. Structure of nucleotides and
nucleic acids
 Despite the complexity and diversity of life the structure of DNA
is dependent on only 4 different nucleotides.
 Diversity is dependent on the nucleotide sequence.
 All nucleotides are 2 ring structures composed of:
12
5-carbon sugar b-D-ribose (RNA)
b-D-deoxyribose (DNA)
Base Purine (Double ringed)
Pyrimidine (Single ringed)
Phosphate group A nucleotide WITHOUT a phosphate group is a
NUCLEOSIDE

13. Nucleotide Structure - Sugars
O
HOCH2
5’
1’
4’
3’ 2’
O
HOCH2
OH
OH
OH
O
HOCH2
OH
H
OH
Ribose
Deoxyribose
Generic Ribose
Structure
N.B. Carbons are given
numberings as a prime

14. Nitrogen Bases
 The nitrogen bases in nucleotides consist of two general types:
 Purines: adenine (A) and guanine (G)
 Pyrimidines: cytosine (C), thymine (T) and Uracil (U)

15. Purine and Pyrimidine
 Pyrimidine contains two pyridine-like nitrogens in a six-
membered aromatic ring.
 Purine has 4 N’s in a fused-ring structure. Three are basic like
pyridine-like and one is like that in pyrrole.
15

16. Nucleotide Structure
Bases - Purines
N
N
N
N
1
2
3
4
5
6
7
8
9
Adenine
Guanine
A
G
N
N
N
N
H
NH2
N
N
N
N
H
O
H
NH2

18. Nucleotide Structure
Bases - Pyrimidines
N
N
5
6
1
2
3
4
Thymine
Cytosine
NH
N
O
T
O
H
H3C
C
N
N
NH2
O
H

19. Cont…
N
N
5
6
1
2
3
4
Uracil
NH
N
O
U
O
H
 Thymine is found ONLY in DNA.
 In RNA, thymine is replaced by uracil
 Uracil and Thymine are structurally similar

21. Nucleosides and Nucleotides
 A nucleoside consists of a nitrogen base linked by a glycosidic
bond to C1’ of a ribose or deoxyribose.
 Nucleosides are named by changing the nitrogen base ending to -
osine for purines and –idine for pyrimidines
• A nucleotide is a nucleoside that forms a phosphate ester with the
C5’ OH group of ribose or deoxyribose
• Nucleotides are named using the name of the nucleoside
followed by 5’-monophosphate

22. Names of Nucleosides and Nucleotides

23. 23

24. AMP, ADP and ATP
• Additional phosphate groups can be added to the nucleoside 5’-
monophosphates to form diphosphates and triphosphates
• ATP is the major energy source for cellular activity

25. Nucleic acid
 Nucleic acids are composed of nucleotide monomers, which
themselves are built from a phosphate group, a sugar, and a
nitrogenous base.
 Nucleic acid: One of the family of large molecules which includes
DNA and RNA.
 DNA (deoxyribonucleic acid) which contains the hereditary
information.
 RNA (ribonucleic acid) which delivers the instructions coded in this
information to the cell's protein manufacturing sites.
25

26. Structure of nucleic acid
 Nucleic acid components:
 Sugar - ribose or dexyribose
 Base + sugar = Nucleoside - N - glycoside bond.
 Nucleoside + phosphoric acid = Nucleotide - Ester bond.
 Nucleic Acids - condensation polymer of nucleotide (Nucleotide -
nucleotide) phospho diester bond.
26

27.  A nucleoside is an N-glycoside formed between a base and a sugar
(usually ribose or deoxyribose).
 A nucleotide is a phosphate ester of a nucleoside.
 The chemical linkage between nucleotide units in nucleic acids is a
phosphodiester, which connects the 5’-hydroxyl group of one
nucleotide to the 3’-hydroxyl group of the next nucleotide.
 DNA nucleotides are more stable to acid hydrolysis of the
glycosidic bond, which is one reason that DNA has superceded than
RNA as the main genetic storage molecule; it is less prone to
mutation.
27

28. Base（purine、pyrimdine)+ ribose (deoxyribose)
N-glycosyl linkage
nucleoside + phosphate
phosphoester linkage
nucleotide
phosphodiester linkage
nucleic acid

29. Primary Structure of Nucleic Acids
 Primary Structure: It describes the sequence of bases in the strand.
By convention, the sequence of bases is written in the 5’ to 3’
direction.
 The sequence or order of the nucleotides defines the primary
structure of DNA and RNA.
 The nucleotides of the polymer are linked by phosphodiester bonds
connecting through the oxygen on the 5' carbon of one to the
oxygen on the 3' carbon of another.
 The Oxygen and Nitrogen atoms in the backbone give DNA and
RNA "polarity“.
29

30. Cont…
 The primary structure of a nucleic acid is the nucleotide sequence.
 The nucleotides in nucleic acids are joined by phosphodiester bonds.
 The 3’-OH group of the sugar in one nucleotide forms an ester bond
to the phosphate group on the 5’-carbon of the sugar of the next
nucleotide.

31. Secondary Structure of Nucleic Acids
 DNA consists of two strands of nucleic acids with the sugar-
phosphate backbone outside and the base inside.
 The chains are held together by H-bonding between the base of
one strand with the base of another strand.
 A purine base always pairs with a pyrimidine base or more
specifically Guanine (G) with Cytosine (C) and Adenine (A) with
Thymine (T) or Uracil (U).
 The G-C pair has three hydrogen bonds while the A-T pair has two
hydrogen bonds.
 DNA: The secondary structure of DNA consists of two
polynucleotide chains wrapped around one another to form a
double helix.
 The orientation of the helix is usually right handed with the two
chains running antiparallel to one another.
31

32. 32

33. 33

34. Complementarity
 The sequence of bases on each strand are arranged so that all of
the bases.
 On one strand pair with all of the bases on another strand, i.e. the
number of guanosines always equals the number of cytosines and
the number of adenines always equals the number of thymines.
 There are two grooves, one major and one minor, on the double
helix.
 Proteins and drugs interact with the functional groups on the
bases that are exposed in the grooves.
34

35. 35
DNA double helix
one
helical
turn
34 Å
major
groove
12 Å
minor
groove
6 Å
backbone: deoxyribose and phosphodiester linkage
bases

36. 36

37. Nucleic Acid Structure
The double helix
Major
Groove
Minor
Groove

38. sugar-phosphate
chain
bases
THE DOUBLE HELIX

39. DNA
 DNA stands for deoxyribose nucleic acid.
 This chemical substance is present in the nucleus of all cells in all
living organisms.
 DNA controls all the chemical changes which take place in cells.
 The kind of cell which is formed, (muscle, blood, nerve, etc) is
controlled by DNA.
 DNA is a very large molecule made up of a long chain of sub-
units.
 The sub-units are called nucleotides.
 Each nucleotide is made up of
 A sugar called deoxyribose
 A phosphate group -PO4 and
 An organic base (Adenine, Thymine, cytosine, guanine) 39

40. 40
The Deoxyribonucleotides

41. Example of DNA Primary Structure
 In DNA, A, C, G, and T are linked by 3’-5’ ester bonds between
deoxyribose and phosphate

42.  The strands of DNA are antiparallel
 The strands are complimentary
 There are Hydrogen bond forces
 There are base stacking interactions
 There are 10 base pairs per turn
Properties of a DNA

43. Model of DNA:
• The model was developed by
Watson and Crick in 1953.
• They received a nobel prize
in 1962 for their work.
• The model looks like a
twisted ladder – double helix.

44. 44
 Replication of DNA
The Central Dogma (F. Crick):
DNA replication DNA transcription mRNA translation Protein
(genome) (transcriptome) (proteome)
 Expression and transfer of genetic information:
 Replication: process by which DNA is copied with very high fidelity.
 Transcription: process by which the DNA genetic code is read and
transferred to messenger RNA (mRNA). This is an intermediate step in
protein expression
 Translation: The process by which the genetic code is converted to a
protein, the end product of gene expression.
 The DNA sequence codes for the mRNA sequence, which codes for the
protein sequence

45. Cont…
 DNA is replicated by the coordinated efforts of a number of
proteins and enzymes.
 For replication, DNA must be unknotted, uncoiled and the double
helix unwound.
 Topoisomerase: Enzyme that unknots and uncoils DNA.
 Helicase: Protein that unwinds the DNA double helix.
 DNA polymerase: Enzyme that replicates DNA using each strand
as a template for the newly synthesized strand.
 DNA ligase: enzyme that catalyzes the formation of the
phosphodiester bond between pieces of DNA.
 DNA replication is semi-conservative: Each new strand of DNA
contains one parental (old, template) strand and one daughter
(newly synthesized) strand.
45

46. 46

47. Hydrogen bonds between
base pairs are broken by the
enzyme Helicase and DNA
molecule unzips
DNA molecule
separates into
complementary halves
STEP 1

48. Nucleotides match up with complementary bases
Free nucleotides abundant in nucleus
STEP 2

49. New Strand
Original Strand
Nucleotides are linked into 2 new strands of DNA by the enzyme,
polymerase—DNA polymerase also proof reads for copying errors
STEP 3

50. RNA
 RNA composed of:
1. Ribose sugar
2. Phosphate group
3. One of 4 types of bases (all containing nitrogen):
- Adenine
- Uracyl (only in RNA)
- Cytosine
- Guanine
50

51. Cont…
 RNA is much more abundant than DNA.
 There are several important differences between RNA and DNA:
 The pentose sugar in RNA is ribose, in DNA it’s deoxyribose
 In RNA, uracil replaces the base thymine (U pairs with A)
 RNA is single stranded while DNA is double stranded
 RNA molecules are much smaller than DNA molecules
 RNA is found inside and outside of the nucleus; DNA is found
only inside the nucleus.

53. Characteristics of RNA
 RNA does not self replicate in order to multiply; instead it is
encoded by DNA genes.
 RNA is synthesized in order for the translation of DNA to be
possible.
 The DNA-RNA function is highly interdependable, i.e., if there is
problem with DNA, there will be a problem with the RNA
functions and vice versa (no RNA = no DNA translation can
occur, thus DNA is useless without its RNA genes)
 RNA genes of DNA encode for 3 major types of RNA:
 ribosomal RNA
 messenger RNA
 transfer RNA
53

54. Types of RNA

55. 55
 RNA is a single stranded polymer and does not form double helix.
 There are three types of RNA:
 Messenger RNA (mRNA), whose base sequence specifies the
amino acid sequence in protein.
 ribosomal RNA (rRNA), that comprises the particles on which the
biosynthesis of protein occurs.
 transfer RNA (tRNA), which carries the amino acid that will be
incorporated into the protein.
 tRNAs are shorter than mRNA and rRNA, and folded into a
characteristic cloverleaf like structure. They have a CCA sequence
at the 3’end, and the three bases at the bottom are called
anticoden.
 Each tRNA carries an amino acid as an ester to its terminal 3’OH.
The amino acid will be inserted into a protein during the protein
synthesis.

56. Cont…
 Ribosome: large assembly of proteins and rRNAs that catalyzes
protein and peptide biosynthesis using specific, complementary,
anti-parallel pairing interactions between mRNA and the anti-
codon loop of specific tRNA’s.
 Although single-stranded, there are complementary sequences
within tRNA that give it a defined conformation.
 The three base codon sequence of mRNA are complementary to the
“anti-codon” loops of the appropriate tRNA.
 The base-pairing between the mRNA and the tRNA positions the
tRNAs for amino acid transfer to the growing peptide chain. 56

57. 57
aminoacyl t-RNA
TC loop
D loop
variable loop

58. Reading Assignment
 Protein Biosynthesis
 DNA Sequencing
 PCR (Polymerase Chain Reaction)
58

59. Biological roles of nucleotides and
nucleic acids
 Serving as energy stores for future use in phosphate transfer
reactions. These reactions are predominantly carried out by ATP.
 Forming a portion of several important coenzymes such as
NAD+, NADP+, FAD and coenzyme A.
 Serving as mediators of numerous important cellular processes
such as second messengers in signal transduction events. The
predominant second messenger is cyclic-AMP (cAMP), a cyclic
derivative of AMP formed from ATP.
59

60. Cont…

61. Cont…
 NAD (Nicotinamide Adenine
Dinucleotide) is composed
of two nucleotides.
 NAD is used in many
oxidation-reduction reactions
to accept or donate high-
energy electrons.

62. Cont…
 Serving as neurotransmitters and as signal receptor ligands.
 Adenosine can function as an inhibitory neurotransmitter, while
 ATP also affects synaptic neurotransmission throughout the central
and peripheral nervous systems.
 ADP is an important activator of platelet functions resulting in
control of blood coagulation.
 Controlling numerous enzymatic reactions through allosteric
effects on enzyme activity.
 Serving as activated intermediates in numerous biosynthetic
reactions.
 These activated intermediates include S-adenosylmethionine (S-
AdoMet or SAM) involved in methyl transfer reactions as well as,
 the many sugar coupled nucleotides involved in glycogen and
glycoprotein synthesis. 62

63. Functions of
Nucleotides and Nucleic Acids
 Nucleotide Functions:
– Energy for metabolism (ATP)
– Enzyme cofactors (NAD+)
– Signal transduction (cAMP)
 Nucleic Acid Functions:
– Storage of genetic info (DNA)
– Transmission of genetic info (mRNA)
– Processing of genetic information (ribozymes)
– Protein synthesis (tRNA and rRNA) 63

64. Functions of Nucleic Acids:
1) Transmission of hereditary Characters (DNA)
2) Synthesis of Proteins (RNA)
 DNA: Store house of genetic information control protein synthesis
in cell. Direct synthesis of RNA.
 RNA: Direct synthesis of specific proteins.
 m-RNA: To take genetic massage from RNA.
 t- RNA: Transfer the activated amino acids to the site of protein
synthesis.
 r-RNA: Function not clearly understood. Mostly present in
ribosomes and responsible for stability of m-RNA.
 Properties of Nucleic Acid:
1)Optical Property: Absorbance in UV at 260 nm
2) Melting Temperature: Tm analysis
64