Nucleotides And Nucleic Acid

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Nucleotide consist of

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Nitrogenous base (purine pyramidine) , pentose sugar and phosphate group. Normally linked to the furanose via the 5-OH.

Front 2

Nucleoside consist of

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Base and the sugar without the phosphate linked by glycosidic bond. Nucleoside more water soluble than the corresponding nitrogenous base.

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RNA

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The pentose sugar is D-ribose

Presense of 2'-OH in RNA

Rapidly hydrolyse in dilute alkali

Soluble in dilute NaCl

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DNA

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The pentose sugar is 2-deoxy-D-ribose

Presence of 2'-H in DNA

Stable in dilute alkali

Insoluble in NaCl

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Pyrimidines are

Back 5

Six membered rings

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Purine

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Five-membered ring (imidazole) fused to a pyrimidine

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Any shift in pH may affect H-bonding between nitrogenous bases

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True, particularly in DNA which the structure is stabilize by hydrogen bond

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Cylic nucleotide (cAMP) formed when

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the phosphate moiety is linked to two furanose hydroxyls, usually 3' and 5' hydroxyls. Play essential role in regulating cellular processes.

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Nucleic acids form from

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Polymerization of nucleotides, being linked via phosphodiester bonds. Has hydrophilic backbone of alternating phosphate and pentose units. Sequence of bases is always listed in 5

to 3' direction

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Deoxyribonucleic acid (DNA) stabilised by

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Hydrogen bonding betwenn complementary base pairs.

Van der Waal's forces between the stacked bases.

Hydrophobic effects as helix formation shields base pair from the external solvent.

Electrostatic interactions between negatively charged phosphate groups and positively charged histone proteins and metal ions.

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B-DNA

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1. Can be bent, twisted and supercoiled enable it to become more compacts.

2. Helix type : B-DNA is right handed double helix.

3. The strands run anti-parallel to one another with hydrogen bonding between bases.

5. Number of residue = 10.4

6.

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A-DNA

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1. Alternative configuration.

2. Helix type : Right handed double helix but wider and shorter.

3. Orientation of base pairs : tilted

4. Wider and shorter than B-helix

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Z-DNA

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Helix type : Left-handed

No of residues : 12

Orientation of base pairs : slightly tilted

Other features : longer and narrower than B-helix

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Supercoiling

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Coiling of a coil. Makes DNA molecules become more compacts. Only possible for circular DNA or for linear DNA. Attachment of protein prevents free rotation of the ends of the DNA molecule and allows supercoils to be introduce.

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Denaturation of DNA can occur by

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1. Extremes pH

2. Extremes temperature

3. Exposure to agent such as formamide or urea

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Denaturation disturp

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Hydrogen bonding between base pairs in the double helix and causes the DNA molecules to seperate into two single strands.

Denaturation is accompanied by a decrease in solution viscosity.

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Denaturation can be monitored

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1. Increase in A260 (hyperchromic effect) due to unstacking of the bases.

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Melting point of DNA increase when

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Percentage of GC increases.

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Rate of renaturation is affected by

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1. Degree of denaturation

2. Length of the DNA molecule : Longer DNA molecules, takes longer to reanneal

3. Complexity of the DNA sequence : Complex sequence take longer to reanneal

4. Double bond

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Chromosomal DNA (eukaryotes)

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1. Located in the cell nucleus.

2. Linear double stranded DNA.

3. Stabilised by electrostatic interactions with basic histone protein.

4. Contains both regulatory sequences and structural genes that encode RNA molecules or more often polypeptides .

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Nucleosome

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Basic unit of DNA packaging in Eukaryote. Consist of segment of DNA wound in sequence around 8 histone protein.

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Satallite DNA

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Comprises about 10% of the genome.

Consist of short base sequence repeated hundreds of thousands of times.

Highly repetitive DNA is clustered into tandem repeats, in which the same sequences is repeated over and over without interruption.

Basis detection of DNA fingerprint.

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Extrachoromosomal DNA

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Required fro the transcription and translation of organelles genes.