Nucleic Acid Chemistry

Nucleotides
 Def :
 The building block of DNA & RNA.
 Present in body as poly-nucleotide (DNA,RNA) or free nucleotides.
 Structure :
1. Nitrogenous base :
Purines Pyrimidine

 Adenine. (A)
 Cytosine. (C)
 Guanine. (G)
 Uracil . (U)
 Hypoxanthine
 Thymine. (T)
 Xanthine

2. Pentose sugar :
 D-ribose in RNA.
 2-deoxy-D-ribose in DNA.
3. Phosphate (phosphoric acid).

NB:
 Nucleoside = nitrogenous base + pentose sugar

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 Types :
Base Nucleoside Nucleotide
 Adenosine. AMP , ADP,ATP ,
Adenine
 Deoxy adenosine d. AMP, d. ADP , d. ATP
 Guanosine. GMP , GDP, GTP ,
Guanine
 Deoxy guanosine. d. GMP, d. GDP , d. GTP

Hypoxanthine  Inosine IMP

Xanthine  Xanthosine XMP

 Cytidine. CMP , CDP, CTP ,

Cytosine
 Deoxy cytidine. d. CMP, d. CDP , d. CTP

Thymine  Deoxy thymidine d. TMP, d. TDP , d. TT

Uracil  Uridine UMP, UDP, UTP

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 Functions : written Q
1. Building blocks of RNA and DNA
2. Source of energy: ATP, GTP act as source of energy.
3. Mediate action of hormone: c.AMP & c.GMP are 2nd messenger. MCQ
4. Co-enzymes: as NAD, FAD, Co-enzyme A.

5. Activation of chemical compounds :

UDP- glucose → synthesis of glycogen.
6. Chemical group donors :
 PAPS is a sulfate donor → synthesis of sulfolipids
 SAM is a methyl donor → trans-methylation reactions.

7. Synthetic Analogue: they are prepared by altering the base ring or sugar
part :

5 flurouracil Allopurinol
Nucleotide  Thymine (pyrimidine) analogue  Hypo-xanthine (purine) analogue
analogue :
 Anti-cancer because it decrease
thymine and DNA synthesis
Use :  Anti-gout .
leading to decreasing growth
of cancer cell

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 DNA Structure
A. Primary structure :

 DNA is 2 strands.
 In each strand nucleotides are linked by 3`,5` phosphodiester bond ( ) 3`-hydroxyl
group of one nucleotide & 5`phosphate group of next nucleotide.

 Characters of poly nucleotides chain :

1. Alternating sugar-phosphate units form asymmetrical backbone of each
strand.
2. Nitrogenous bases are projecting to the inside of the 2 stands at right angle
3. Sequence of bases determines genetic information.
4. Sequence of bases are written in the 5` to 3`
5. Polarity: each strand has 2 terminals
 One end (5`end) has free phosphate group.
 Other end (3`end) has free hydroxyl group.

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 B. Secondary structure (B-form of DNA) :

 Waston and crick proposed structure for DNA in the form of double helix which is
the common physiological form.

 Characters :
1. Right handed helix (its diameter =2 nm).
2. The 2 strands are anti-parallel: they run in opposite direction
(one runs in the 5` to 3` direction while the other strand runs in the
3` to 5` direction).
3. Complementary base pairing: 2 strands are held together by
complementary base pairing through hydrogen bonds : MCQ
 Adenine pairs with thymine though 2 hydrogen bonds (A=T).
 Guanine pairs with cytosine through 3 hydrogen bonds (GΞC).

Melting temperature (Tm) (Written Q)

 Def :
 Temperature at which 50 % of helical structure is lost.
 Factors affecting :
Types of bases  Tm decrease if DNA contains higher proportion of AT bases
p.H of medium  Tm Decreases if the medium is more alkaline.
Salt  Tm decreases if salt concentration is decrease.
concentration (salts is stabilizing agent ).

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 RNA structure

 Structure :
 All RNA molecules are formed in the nucleus form DNA by RNA polymerase ,
then most of RNA is transported to cytoplasm.
 They contain 4 types of nucleotides (AMP, GMP, CMP, UMP) which are inter
connected by phosphodiester bonds.
 Types :
Ribosomal RNA (r.RNA) 80%
Transfer RNA (t.RNA) 15%
Messenger RNA (mRNA) 5%
Small nuclear RNA (snRNA) ˂ 1%

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 1. Ribosomal RNA ( r.RNA) :

 Percentage: 80% of total RNA.

 Function :
 It is broken into few pieces that bind with several proteins to form ribosome.
 Mammalian ribosome consist of 2 subunits :
 Large subunit (60S).
 Small subunit (40S).
The 2 together form 80 S ribosome.

2. Transfer RNA (t.RNA) :

 Percentage: 15% of total RNA.
 Common features :
1. Clover-leaf appearance, stabilized by hydrogen bonds ( ) complementary
bases (A=U), (GΞC). MCQ

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2. It has 4 arms :
 Has base paired stem of 3 or 4 bp
D arm
 Ends in loop that contains di-hydro-uracil.
 Has base paired stem of 5 bp
TΨC
 Ends in loop contains sequence : thymine , pseudo-uridine &
arm
cytosine.

Anti-  has base paired of 5 bp

codon  ends in loop that contains 7 bases , three of 7 bases in middle of
arm loop constitute the anti-codon.
 It has base paired stem of 7 bp.
Acceptor  It doesn’t end in loop.
arm  It ends in sequence CCA (5’ →3’), the 3’ end is site of attachment
for amino acid .

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 3. Messenger RNA ( m.RNA ) :

 Percentage: 5% of total RNA.

 Functions :
 Carries message from DNA to ribosome for protein synthesis.
 Each protein has specific m.RNA
 Common features: In 5’ to 3’ direction, m.RNA is divided to 3 regions :
5’ untranslated leading  Not translated.
sequence :  Ends by cap.
Translated coding  Responsible for arranging amino acids in proper
sequence : order in protein.
3’ untranslated tailing  Not translated.
sequence:  Ends in poly (A) tail.

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 Compare between DNA & RNA : written Q
DNA RNA
Occurrence Nucleus, Mitochondria Cytoplasm
Storage & transfer of genetic Protein synthesis
Functions
information
Bases A,G,C,T A,G,C,U
Structure

Sugar Deoxy-ribose Ribose

Strands 2 strands forms double helix One strand only
One type 4 Types
Types
mRNA, tRNA, rRNA, snRNA
Shape Double helix Variable

 Compare between different types of RNA : written Q

m.RNA t.RNA r.RNA
More than 105 50-60 different
Types 28S ,18S, 5S, 5.8S
different species species

Abundance 5% 15 % 80 %

Stability Unstable to very stable Very stable Very stable

Carries message from

Carries amino acids Constitutes ribosome ,
Functions DNA to ribosome to
for protein synthesis site of protein synthesis
direct protein synthesis
Type of RNA polymerase I
polymerase (18S,5.8S.28S)
RNA polymerase II RNA polymerase III
responsible for RNA polymerase III
synthesis (5S)

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