Nucleotides and nucleic acids

Department of Biochemistry, KMC, DuwakotThursday,
February 4, 2016
Rajesh Chaudhary 1

Nucleotide and Nucleic acids
Thursday, February 4, 2016
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Nucleoside
Sugar BasePhosphate
DNA RNA
Nucleotides
Nucleic acid

Nucleic acids
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 Information flow
 DNA  RNA 
PROTEIN
 DNA: storage of
genetic information
 RNA: expression of
genetic information
 PROTEIN:
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Ribose and Deoxyribose |sugar within gene
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DNA vs RNA
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DNA vs RNA
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With exception of few
viruses that contain single-
stranded (ss) DNA, DNA
exists as dsDNA.
The two strands of DNA are
coiled around a common
axis forming helical
structure known as “AXIS
OF SYMMETRY”.
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Nucleic acid
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 DNA contains 4
deoxynucleotides:
 1. deoxyadenylate (A)
 2. deoxyguanylate (G)
 3. deoxycytidylate (C)
 4. thymidylate (T)
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Thursday, February 4, 20168 Rajesh Chaudhary

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DNA chain with nucleotide sequence
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Phosphodiester bond
Phosphodiester bonds in DNA or RNA
are cleaved hydrolytically by
chemicals or enzymes such as
nucleases: deoxyribonucleases for
DNA and ribonucleases for RNA.

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Major grooves Vs Minor grooves
Anticancer drug, for example, “Actinomycin D” exerts its cytotoxic effect by
intercalating into the narrow groove of DNA double helical structure.

Structure of DNA
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Base pairing
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1. Hydrogen bond
2. Van der Waals force
3. Hydrophobic interaction
4. 3’,5’-phosphodiester bond
What are the stabilizing forces in
DNA?
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Chargaff’s rule
Thursday, February 4, 2016Rajesh Chaudhary
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 1. The base composition of DNA generally varies from
one species to another.
 2. DNA specimens isolated from different tissues of the
same species have the same base composition.
 3. The base composition of DNA in a given species does
not change with an organism’s age, nutritional state or
changing environment.
 4. In all cellular DNAs, regardless of the species, the total
number of purines is equal to total no. of pyrimidine.

“In any sample of dsDNA, the amount of
Adenine equal the amount of Thymine, the
amount of Guanine equals the amount of
Cytosine, and the total amount of Purines
equals the total amount of Pyrimidines.”
Chargaff Rule
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-- Lippincott’s Illustrated Review, Biochemistry
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The simpler representation of
nucleotide sequence
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Forms of DNA
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Forms: A – E and Z-form
B-form: found under low
salt, high degree of
hydration

DNA exists in relaxed & supercoiled
form
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 Circular DNA
 Mitochondrial & bacterial
 Torsional stress of DNA
 Negative supercoiling
 Topoisomerase (coils or relaxes)
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Melting temperature (Tm)
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Factors influencing
melting temperature:
1. The GC-content of
DNA.
2. Non-covalent cations
3. Formamide

Denaturation of DNA to analyze its
structure
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 How?
 Increasing temperature (Tm)
 Decreasing salt concentration
 10-fold increase in monovalent cation concentration increases Tm by
16.6 0C
 Denaturation  Increased optical absorbance
 Hyperchromicity
 Addition of FORMAMIDE
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Renaturation of DNA
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Differences between DNA and RNA
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DNA RNA
1. Sugar moiety: deoxiribose 1. Sugar moiety: Ribose
2. Usually double stranded 2. Usually single stranded
3. Bases: Adenine, Guanine, Cytosine,
Thymine
3. Bases: Adenine, Guanine, Cytosine,
Uracil
4. DNA is comparatively more stable
then RNA
4. RNA is comparitively less stable then
DNA
5. Follows Chargaff’s rule 5. Do not follow Chargaff’s rule
6. DNA is bigger in size compared to
RNA
6. RNA is comparatively smaller in size
than DNA
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Chemical nature of RNA
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 Sugar moiety: ribose rather than 2’-deoxyribose of
DNA
 ss rather than ds
 Doesn’t follow Chargaff's rule
 Alkaline treatment: RNA can be hydrolyzed while
DNA can’t
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RNA types
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 1. Messenger RNA (mRNA)  acts as a template
 2. Transfer RNA (tRNA)  carries AA for protein
synthesis
 3. Ribosomal RNA (rRNA)  structural component of
ribosomes
 4. Small nuclear RNA (snRNA)  helps in RNA
processing
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RNA
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mRNA
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 Heterogeneous in abundance, size and stability
 Have unique chemical characteristics

7-methylguanosine triphosphate
Cap prevents from 5’-exonuclease as
well as 3’-exonuclease digestion,
stability, recognition by protein
synthesis complex
Poly A tail residue (20-250 nucleotide long)
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tRNA
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 Length = 74 – 95 nucleotides
 Adaptor for the translation of information
 20 species of RNA in each cell to carry 20 AA.
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What is common in all tRNA?

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• (CpCpAoH) terminal
• Added post transcriptionally
• By Nucleotidyl transferase
enzyme
Define specific RNA
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tRNA

rRNA
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 Protein synthesis (RNA + Protein) = Polysomes.
 MW = 4.6×106
 Sedimentation velocity = 80S (60S vs 40S)
 Mammalian cells = 2 mitochondria rRNA and 4
Cytoplasmic

Ribosomal RNA
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Small stable RNA
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 Complexed with protein  ribonucleoprotein
 Size = 90 – 300 nucleotides
 Copies = 100,000 – 1,000,000 per cell
 sRNA (mRNA processing and gene regulation)
 sRNA = U1, U2, U4, U5, U6 (intron removal and hnRNA to
mRNA)
Rajesh Chaudhary

References35

Nucleotides and nucleic acids

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