Chemistry of nucleic acids for I year Allied Health Sciences .pdf

Chemistry of nucleic acids, Nucleosides, Nucleotides for I year Allied Health Sciences. RGUHS RS4 Syllabus

1. CHEMISTRY OF
NUCLEIC ACIDS
P. SANTOSH KUMAR

2. DISCUSSED UNDER FOLLOWING
HEADINGS
▪Nitrogenous base- purine and pyrimidine, major, minor bases
▪Nucleosides and Nucleotides- structure, examples, and importance
▪Synthetic nucleoside and nucleotide analogues and their
applications
▪Structure and functions of DNA
▪Different types of RNA and their functions

3. Definition: Nucleic acids are non protein nitrogenous substances
made up of monomeric units of nucleotides.
Chemistry of purines, pyrimidines, nucleosides and nucleotides
•Purines are nine numbered ring
structure consisting of pyrimidine
ring attached to imidazole ring. The
atoms of purine ring are numbered
in anti-clock wise direction.
Structure of purine ring - the
sources of carbon and nitrogen
atoms of purine ring

4. ▪Major purine bases present in nucleic acids are Adenine and
Guanine
▪Minor purine bases present in nucleic acids are Hypoxanthine
and Xanthine
▪Purine bases present in plants are Caffeine-acts as stimulant and
Theophylline present in tea acts as smooth muscle relaxant
▪Purine analogues- these have structural similarity to purine.
Ex: Allopurinol used in the treatment of gout
6-Mercaptopurine used as anticancer drug

6. ▪Pyrimidine bases- are six numbered ring structure and the atoms
of pyrimidine ring numbered in clockwise direction.
From
carbamoyl
phosphate
From
Aspartic
acid

7. ▪The major pyrimidine bases present in nucleic acids are
cytosine, thymine and uracil.
▪Cytosine present in both RNA & DNA
▪Thymine present only in DNA
▪Uracil present only in RNA
▪Minor pyrimidine bases present in nucleic acids are
▪Methyl cytosine present in DNA
▪Dihydrouracil present in tRNA
▪Pyrimidine analogues- structural similarity to pyrimidine-
5-Fluorouracil used in the treatment of cancer

9. ▪Chemistry of nucleosides - Nucleosides consisting of purine or
pyrimidine bases linked to pentose sugar. Pentose sugar may be
ribose in ribonucleoside or 2-deoxyribose in deoxyribonucleoside.
▪Purine/pyrimidine bases are attached covalently by
β-N glycosidic linkage formed between C
1 of pentose sugar may be
ribose or deoxyribose with N
9 of purine and N
1 of pyrimidine base.

10. Different types of nucleosides present in ribonucleic acids or Ribonucleosides

Different types of nucleosides present in deoxyribonucleic acids or
Deoxyribonucleosides
Nucleosidebase + pentose sugar
AdenosineAdenine + ribosugar
GuanosineGuanine + ribosugar
Cytidine Cytosine + ribosugar
Uridine Uracil + ribosugar
Nucleoside base + pentose sugar
d-AdenosineAdenine + deoxyribosugar
d-GuanosineGuanine + deoxyribosugar
d-Cytidine Cytosine + deoxyribosugar
d-ThymidineThymine + deoxyribosugar

11. ▪Chemistry of Nucleotides- are phosphorylated nucleosides
made up of nitrogenous base may be purine or pyrimidine,
pentose sugar may be ribose or deoxyribose and phosphate
group. (Ex: AMP, TMP)
▪The Purine/pyrimidine bases are attached to C
1 of pentose sugar
and N
9 of purine and N
1 of pyrimidine through β-N glycosidic
linkage.
▪Esterification of phosphate group occurs at 3
rd
OH group or 5
th

OH of pentose sugar.

12. ▪Most of the biologically important nucleotides are 5’-phosphate
esters. Further esterification leads to corresponding diphosphates
and triphosphates. (Ex: ADP, ATP, TTP)
▪These nucleosides present in nucleic acids are joint together by
phosphodiester bonds formed between 3
rd
-OH group of sugar
moiety of one nucleotide with 5
th
OH group sugar of another
nucleotide

13. Different types of nucleotides present in ribonucleic acids or
Ribonucleotides
Nucleotide base pentose sugar Phosphate
Adenylate/AMP Adenosine + ribosugar + phosphoric acid
Guanylate/GMP Guanosine + ribosugar + phosphoric acid
Cytidylate/CMP Cytidine + ribosugar + phosphoric acid
Uridylate/UMP Uridine + ribosugar + phosphoric acid
Different types of nucleotides present in deoxyribonucleic acids or
Deoxyribonucleotides
Nucleotide base pentose sugar Phosphate
d-Adenylate/dAMP d-adenosine + deoxyribosugar + phosphoric acid
d-Guanylate/dGMP d-guanosine + deoxyribosugar + phosphoric acid
d-Cytidylate/dCMP d-cytidine + deoxyribosugar + phosphoric acid
d-Thymidylate/dTMP d-thymidne + deoxyribosugar + phosphoric acid

14. Functions of nucleotides:
▪Used for synthesis of Nucleic acids
▪Required for activation intermediates of metabolic pathways
like UDP glucose
▪Acts as carrier of methyl groups in the formation of SAM (S-
Adenosyl metheionine)
▪ATP Acts as universal currency of energy
▪Involved in protein biosynthesis
▪Composition of coenzymes like NAD, FAD, Coenyme-A
▪Acts as metabolic regulators like c-AMP, c-GMP

15. Structure of Nucleotides

16. Poly deoxyribonucleotides showing phosphodiester bond

18. ▪Biologically important nucleotides- Nucleotides are integral part of
nucleic acids, besides nucleotides present in various tissues and cells
place an important role in many biologically important reactions and
are called as biologically important nucleotides
Mainly classified into
▪Adenosine nucleotide derivatives- ATP, ADP, AMP, c-AMP, etc.
▪Guanosine nucleotide derivatives- GTP, GDP, GMP, c-GMP, etc.
▪Cytidine nucleotide derivatives- CTP, CDP, CMP, c-CMP, etc.
▪Uridine nucleotide derivatives- UTP, UDP, UMP, UDP- glucose,
etc.
▪Miscellaneous- PAPS, SAM, NAD, NADP, Coenzyme A

19. ▪Adenosine triphosphate (ATP)- formed during oxidative
phosphorylation by combing with ADP and Pi in ETC.
▪Also called as universal currency of energy, its high energy
compound consisting of two high energy bonds, on hydrolysis
yields -7.6 kcal/moles and the energy produced is used for many
endergonic reactions in the body like
▪Arginino succinate reaction in urea cycle
▪Synthesis of creatine phosphate from creatine
▪Synthesis of SAM
▪Synthesis of coenzyme A from Pantothenic acid
▪Synthesis of oxaloacetate from pyruvate
▪Conversion of glucose to glucose 6-phosphate

20. Adenosine diphosphate (ADP)- Is an primary phosphate acceptor
in oxidative and substrate level phosphorylation
Place an important role in cellular respiration
Activates the enzyme glutamate dehydrogenase
Adenosine monophosphate (AMP)- Formed from IMP, and also
from degradation of 3’-5’ c-AMP, by an enzyme phosphodiesterase
Activates the activity of an enzyme glycogen phosph.
Inhibits the activity of an enzyme fru.1,6 bisphosphatase

21. Cyclic AMP- Clinically it is 3’-5’ adenosine monophosphate
formed in the tissues from the ATP under the influence of an
enzyme adenylate cyclase
▪Acts as second messenger
▪Plays an important glycogen metabolism
▪Increases the lipolysis
▪Inhibits the cholesterol synthesis
▪Increases the steroid synthesis

22. Guanosine Tri Phosphate (GTP)-
Require for protein biosynthesis
Plays an important role in gluconeogenesis
Cyclic GMP- clinically it is 3’-5’ guanosine monophosphate
formed in the tissues from the GTP under the influence of an
enzyme guanylate cyclase
▪Acts as second messenger
▪Plays an important role in neurotransmission
▪Plays an important role in insulin secretion
▪Plays an important role in opening and closing of ion channels

23. CTP (Cytidine Triphosphate) and CDP (Cytidine Diphosphate)
▪CTP & CDP are involved in the formation of phospholipids
▪CDP-choline is involved in the synthesis of sphingomyelin

24. UDP-glucose- Formed from glucose with the help of UTP, used for
synthesis of glycogen, GAGs, UDP glucoronic acid
Phospho Adenosyl Phospho Sulfate (PAPS)- High energy
compound formed from ATP and sulfate in the liver
▪Used in various trans-sulfuration reactions
▪Synthesis of sulpholipids and GAGs
▪Plays an important role in detoxification of various xenobiotics like
phenols, indoles, skatols and indoxyl compounds which are
catabolic end product of amino acid tryptophan
S-adenosyl methionine (SAM)- also called as active methionine,
formed from methionine by the transfer of adenosyl group from
ATP to sulfur group of methionine

25. ▪Active methionine formed from methionine plays an important role in
transmethylation reactions
Methionine
Active methionine
(SAM)
Methionine adenosyl trasferase
ATP
PPi +Pi
Nor-epinephrine
Epinephrine
Methyl trasferase
SAM SAH
Guanido acetic acid creatine
Methyl trasferase
SAM SAH
N-acetyl seritonine Melatonine
Methyl trasferase
SAM SAH
Carnosine
Anserine
Methyl trasferase
SAM SAH
•Active methionine also plays an important role in detoxification of
various xenobiotics

26. Nucleic acids are non protein nitrogenous substances made up of
monomeric units of nucleotides. Two types of nucleic acids present in all
living organisms mainly
▪Deoxyribonucleic acid (DNA)
▪Ribonucleic acid (RNA)
Deoxyribonucleic acid (DNA)
▪Present in every nucleated cells and mitochondria but never in cytoplasm
▪Carries genetic information
Structure of DNA is described as
▪Primary structure of DNA
▪Secondary or double helical structure of DNA or Watson-Crick model of
DNA
▪Higher organization of DNA

27. Primary structure of DNA
▪Consisting of 10
10
deoxyribonucleotides composed of four
deoxyribonucleotides namely deoxyadenylate, deoxyguanylate
deoxycytidilate, deoxythymidilate.
▪These deoxyribonucleotides are joined together by
phosphodiester bonds formed between 3rd OH deoxyribose sugar
of one nucleotide with 5th OH deoxyribose sugar of another or
adjacent nucleotide. This leads to the formation of linear
polydeoxyribonucleotide strands with two free ends on both sides
▪The end of the strand which bares 5’ phosphate without
phosphodister bond is called as 5’ end and The end of the strand
which bares 3’ OH without phosphodister bond is called as 3’ end.

28. ▪So primary structure denotes the
number and sequence of
deoxyribonucleotide in a strand
joined together by phosphodiester
bond.
▪In primary structure sugar and
phosphate groups forms the back
bone where as purine and
pyrimidine bases projects
laterally from back bone
PRIMARY STRUCTURE OF DNA

29. Salient features of Watson - Crick Model of
DNA
1.DNA consist of two polydeoxyribonucleotide
chains twisted around in a right handed
Double stranded helix.
2.Four deoxyribonucleotides in DNA are
deoxyadenylate, deoxyguanylate,
deoxycytidylate and thymidylate.
3.Two chains in DNA run in antiparallel
direction, One strand runs in 3’ - 5’ direction
and another strand runs in 5’ - 3’ direction.
One complete turn of 10 nucleotide residues, 3.4nm
Axis of
symmetry
Widt
h
Secondary structure of DNA/ Watson-Crick model of DNA / Watson-
Crick model of double stranded DNA- it was first described by Watson-
Crick in 1953

30. THE DOUBLE HELIX (1953)
www.chem.ucsb.edu/.../images/WatsonCrick.jpg
© 2016 Paul Billiet ODWS
Watson-Crick

31. 4.The backbone of DNA is made up of
alternating deoxyribose and phosphate
groups. Nitrogenous bases are towards
the core of double helix are arranged
perpendicular to the axis of helix.
5.Each strand acts as a template for
synthesis of daughter DNA strand
(replication).
5’
5’
3’
3’

32. 6.In DNA two strands are complementary to each other and are held
together by hydrogen bonds between the purine and pyrimidine bases.
7.Base pairing rule: Adenine of one strand pair with thymine of
opposite strand by two hydrogen bonds. Whereas Guanine will pair
with Cytosine of opposite strand by three hydrogen bonds, So the
GC bond is stronger than A=T bond.
8.Chargoff’s rule: it states that number of adenine bases are equal to
number thymine (A=T) and number Guanine bases are equal to
number Cytosine (G=C) bases.

33. 9.The spiral is pitch of 3.4 nm per
turn. Each single turn
consisting of 10 base pairs and
the adjacent bases are separated
by 0.34 nm.
10.The diameter or width of helix
is 2.0 nm.
11.Helical forms has two grooves
– minor (0.6nm) and major
(0.12nm) grooves. In these
grooves proteins interact with
exposed bases and drugs
One complete turn of 10 nucleotide residues, 3.4nm
Axis of symmetry
Width

34. Different types of DNA- DNA exits in at least 6 different
conformational forms A to E and Z. Among these B, A and Z
forms are important. B-DNA is more common predominant and
physiological form of DNA
Differences between A, B and Z forms of DNA
Features A B Z
Helix turn Right handed Right handed Left handed
Shape Broad Intermediate Elongated
Width/diameter2.3 nm 2.0 nm 1.8 nm
Base pairs /turn11 10 12
Pitch/base pair 0.256 0.34 0.571

35. Higher organization of DNA-
In higher animals inside the nucleus. DNA is further organized to
complex structure
−DNA bound and wrapped around histones to form Nucleosomes,
−Repeating units of nucleosomes coiled to form chromatin fiber.
▪Supercoiled loops to produce chromosomes.
▪Extra – chromosomal DNA include plasmids which are found in
most bacteria and other organisms.

36. Higher organization of DNA-

37. Denaturation of DNA :
▪Denaturation of DNA means lose of double stranded DNA resulting
in the formation of single stranded DNA. During denaturation
hydrogen bonds are broken down and the base pairs are separated.
▪Factors causing denaturation are: High temperature, chemicals
like formamide, increased pH and decreased salt content.
Melting of DNA:
▪The temperature at which the DNA is half denatured is called as
melting temperature of DNA (Tm).
▪Under physiological condition the melting temperature of DNA is
usually 90
o
C and melting point mainly depending on G-C content.
▪At low temperature i.e, 5-20
o
C these denatured DNA strands are
renatured called as Annealing of DNA.

38. Functions of DNA
▪Storage of genetic information
▪DNA act as carrier of genetic information from generation to
generation. Replicates itself so each new cell has identical copy.
▪Expression of coded information present in in nucleotide
sequence is transcribed into RNA and then translated to
sequence of amino acids in proteins.
▪Controls the activities of cell by determining which proteins are
produced.
▪Undergo mutations which accounts for variety of living things
on earth

39. Differences between DNA and RNA
DNA RNA
Present in nucleus, mitochondria not in
cytoplasm
Present in nucleus and cytoplasm
Double stranded helix Single stranded
Contains millions of base pairs (bp)Contains 300 – 500 bp
Bases present are Adenine, Guanine,
Cytosine and Thymine, Uracil absent
Bases present are Adenine, Guanine,
Cytosine and Uracil, Thymine absent
Obeys Chargoff’s rule Doesn’t Obeys Chargoff’s rule
Sugar is deoxyribose Sugar is ribose
Resistant to alkali Easily destroyed by alkali
A, B and Z are different types of DNAmRNA, tRNA, rRNA, hnRNA and
snRNA

40. Ribonucleic acid (RNA)-
▪RNA is the polymer of ribonucleotides joined together by phosphodiester
bonds.
▪The sugar is ribose. Bases present in RNA are adenine, guanine, cytosine
and uracil, thymine is absent.
▪RNA present in both in nucleus and cytoplasm.
Primary structure of RNA- denotes the number and sequence of
ribonucleotide in its chain joined together by phosphodiester bonds
formed between 3
rd
OH sugar group of one ribonucleotide with 5
th
OH
group sugar of adjacent or next ribonucleotide.
Secondary structure of RNA- denotes the various coiled formation of
ribonucleotide chains. These coils are stabilized by intrachain hydrogen
bonds between purine and pyrimidine bases i.e A = U, and CG

41. Types of RNA and their functions- cellular RNAs are 5 types
▪m-RNA – carries genetic information from DNA to ribosomes for
protein biosynthesis
▪t-RNA- transfer of amino acids from cytoplasm to site of protein
biosynthesis
▪r-RNA – helps in binding of mRNA to ribosomes
▪hn-RNA – acts as precursor for synthesis of mRNA
▪sn-RNA (small nuclear RNA) – takes part in the formation of
spliceosomes which plays an important role in processing of
RNA (hnRNA to mRNA)

42. Messenger RNA (m-RNA):
▪Because it carries genetic information from DNA to ribosomes
hence the name messenger RNA.
▪Single stranded mRNA consisting of 10
3
to 10
4
ribonucleotides
formed from precursor hn-RNA.
▪m-RNA contains adenine, Guanine, Cytosine and Uracil as major
bases, Minor bases are methyl pyrimidine and methyl purines.
▪Structure of m-RNA includes Cap region, 5’UTR (Untranslated
Regions), coding region, 3’ UTR and poly A tail.

43. poly A tail: 3’ end of RNA contains a polymer of adenylate
nucleotides consisting of 200 to 300 residues called as poly A tail.
−Poly A tail helps in maintaining intracellular stability of and
protect from 3’ exonucleases action.
Cap region: 5’end of mRNA contains cap structure consisting of
7-methyl GTP.
−Helps in maintaining intracellular stability of specific mRNA and
protect from 5’ exonucleases action.
−The cap structure is involved in recognition of protein
synthesizing machinery.
−The protein biosynthesis begins from 5’end of cap structure of
mRNA.

44. ▪The mRNA also contains specific sequence of nucleotides in
triplets called as codons which are responsible for synthesis of
specific proteins.
▪Initiating codon always AUG for methionine
▪Specific codon for different amino acids, UUU for Phe Ala
▪Terminating codons UGA, UAA and UAG collectively called as
Terminating codons
▪The mRNA also contains 3’ and 5’ untranslated region (UTR)

45. Functions of mRNA:
▪Each codon is a sequence of 3 bases (triplet codon). Using 4
types of nucleotides (A, G, C and U) 64 triplet codons are
possible.
▪Out of these 64, 61 codons codes for amino acids, other 3
codons (UAA, UGA and UAG ) are called the nonsense
codons or chain termination codons, because protein synthesis
stops or ends when these codons occurs on mRNA.
▪Since these codons code for 20 amino acids, some amino acids
are coded by more than 1 codon.
▪AUG is the chain initiation codon which codes for
methionine.

46. Transfer RNA (t-RNA)- Single stranded, globular in nature.
tRNA makes up to 20 % of total RNA.
Primary structure of t-RNA-
•Consisting of about 70 to 90 ribonucleotides.
•The major bases present in t-RNA are Adenine, Guanine,
Cytosine and Uracil.
•The unusual bases present in t-RNA are thymine, dihydrouracil,
hypoxanthine and methyl adenine.
•The most of the bases present in t-RNA are methylated

47. SECONDARY STRUCTURE OF T -RNA
Clever leaf

48. Secondary structure of t-RNA- single stranded RNA folded to
form a clover leaf appearance. These foldings are stabilized by
intrachain hydrogen bonds formed between purine and
pyrimidine ribonucleotides
• Clover leaf structure of t-RNA consisting of 5 arms namely
acceptor arm, anticodon arm, D-arm/ DHU arm, Pseudouridine
arm, Variable arm
i. Acceptor arm (CCA arm): containing unpaired base sequence
of cytosine, cytosine and adenine at 3’ OH end.
•It has 7 base pairs, carries amino acids from cytoplasm to
ribosomes for protein biosynthesis.

49. ii. Anti-codon arm: opposite to acceptor arm, contains 3 bases
triplets anticodons that are complementary to codons of mRNA.
•It has 5 base pairs.
•The specificity of tRNA resides in this anticodon arm
•This arm contains unusual base hypoxanthine
iii. D-arm/ DHU arm: it contains unusual base dihydrouracil,
it has 3 to 4 base pairs,
serves as recognition site for the enzyme which adds amino acids

50. iv. Pseudo uridine arm: opposite to D-arm contains unusual base
Pseudo uridine.
▪it has 5 base pairs,
▪Involved in binding of tRNA to ribosomes
v. Variable arm: extra arm present between anti-codon and
Pseudouridine arm, it is most variable region and it forms the basis for
classification of tRNA.
▪Type I tRNA consisting of 3 base pairs and Type II tRNA 13 to 20 base
pairs
Functions of tRNA:
•Helps in transfer of amino acids from cytoplasm to ribosomes.
•Each rRNA is specific for an amino acids, but some amino acids are
carried by more than on tRNA

51. Differences between m-RNA & t-RNA
m- RNA t-RNA
1Acts as a template for protein
synthesis
Acts as carrier of amino acid
2Carries codon Carries anticodon
3Shape and size is not constantShape and size constant for all t-RNAs clover leaf
4Most heterogenous Only about 20 different forms - less heterogenous
55’ cap is present at 5’OH end No such structure
6Poly A tail is present at 3’OH end 3’OH end carries CCA sequence which accept
specific amino acid
7Precursor is hn-RNA No such precursor
8Unusual bases not found Unusual bases such as pseudouridine, thymine,
etc. are found
9Large molecular weight Low molecular weight
10Stem and loop structure is not foundStem and loop structure is found

52. rRNA (Ribosomal RNA)
▪Ribosomal RNA constitute 80% cellular RNA.
▪These ribosomal RNAs are extremely methylated
▪Most of the rRNA combines with proteins and
exists as ribosomes. Thus ribosomes are
nucleoproteins.
▪Ribosomes have 2 subunit a large subunit and small
subunit.
▪Prokaryotic ribosomes are 70S ribosomes made up
of larger 50 S and smaller 30 S subunits,
▪Eukaryotic ribosomes are 80S ribosomes made up
of larger 60 S and smaller 40 S subunits
▪40S sub unit consisting of 18 S RNA with 30
protein complex where as 60S subunit consisting of
5S RNA, 5.8S RNA and 23S RNA with more
protein content.

53. Functions of rRNA:
▪Ribosome is a cytoplasmic nucleoprotein acts as machinery for
protein biosynthesis.
▪mRNA and tRNA interact with each other on the ribosomes to
translate the codons present in mRNA to specific sequence of
amino acids in the polypeptide chain
Heteronuclear RNA (hn-RNA)-
▪hn-RNA is longer than mRNA and it acts as precursor for
synthesis of mRNA which are subsequently modified for
attachment of long poly A tail at 3’ end and 7-methyl guanosine
cap structure at 5’ end.

54. Small nuclear RNA (Sn-RNA)- These are types of RNA present
in nucleus with small size consisting of about 300 nucleotides.
These Sn-RNA are associated with specific proteins to form
complex called as Snurps.
Functions: These snRNA’s are required for splicing. Splicing
means removal of introns from hnRNA’s. splicing is one of the
event in post transcriptional processing of mRNA.
Spliceosomes- Small nuclear RNA’s forms a complex called
spliceosomes composed of snRNA, proteins and precursor of
mRNA containing introns and exons.

55. NUCLEOTIDE AND NUCLEIC ACID CHEMISTRY
Short Essays (5 Marks)
1.Define Nucleotides give examples, write the functions of nucleotides./ Biologically
important nucleotides
2.Describe the Watson and crick model of DNA with neat labelled diagram.
3.Write the structure of t-RNA with suitable diagram and mention it functions.
4.Structure and functions of m-RNA with suitable diagram.
5.Write the difference between DNA & RNA
6.Write the difference between t-RNA & m-RNA
Short Answers (3 Marks)
1.Define Nucleosides and give examples.
2.Name the purines & pyrimidines bases present in nucleic acids
3.Chargaff’s rule
4.Denaturation of DNA
5.Different types of RNA and their functions
6.Functions of DNA
7.Write rRNA structure and functions

56. REFERENCES:
▪Vasudevan DM, Sreekumari S, Vaidyanathan K. Textbook of
biochemistry for medical students. JP medical ltd; 2013.
▪Satyanarayana U. Biochemistry. Elsevier health sciences; 2013 jun15.
▪Krishnananda prabhu. Jeevan K shetty. Quick review of biochemistry
for undergraduates. Jaypee brothers medical; 2014.
Thank you