The Nitrogen containing bases are aromatic, heterocyclic bases and belong to two families of compounds: The Purines and The Pyrimidines. Their six-atom rings are numbered in opposite direction from each other.They can exist in two forms --- keto form and enol form depending on the positioning of the oxo and amino groups.
If a phosphate group is added to a nucleoside, forming an ester linkage with the hydroxyl group of the pentose sugar, a mononucleotide is formed.
In case of ribose there are three such places at carbon atoms number 2,3 and 5 where an ester linkage can be formed which are written as nucleoside 2´-monophosphate,nucleoside 3´-monophosphate and nucleoside 5´-monophosphate respectively.
The first phosphate group is attached to the 5´-OH of the pentose and is called nucleoside 5´-monophosphate (NMP) or 5´-nucleotide e.g Adenosine monophosphate (AMP), also called adenylate.
In contrast to ribose which has three OH groups and thus three points for phosphate group attachment, deoxyribose has two such places(3´ and 5´) as C2 lacks an oxygen atom and thus named as deoxyribose.
Thus a nucleotide can be RIBONUCLEOTIDE or DEOXYRIBONUCLEOTIDE.The letter d is placed before the name of the nucleotide containing deoxyribose e.g dAMP.
6-MERCAPTOPURINE, 6-AZAURIDINE are widely used by oncologists. These drugs get incorporated into DNA before cell division.
ALLOPURINOL is a purine analog, used in the treatment of hyperuricemia and gout. It acts by inhibiting purine biosynthesis and it inhibits the enzyme xanthine oxidase which acts for uric acid synthesis.
CYTARABINE used in cancer chemotherapy and in viral infections.
AZATHIOPRINE ,catabolized to 6-MARCAPTOPURINE, used in organ transplantation to suppress immunological rejection.
When two or more nucleotides are joined together by internucleotide bonds, polynucleotides are formed.
The bond between the nucleotides is the “phosphodiester bond”. This bond is formed mainly between the 3´OH group of sugar of one nucleotide and 5´OH group of sugar of another nucleotide. This forms a Dinucleotide.
This 3´-5´ linkage is the backbone of DNA and RNA.
This is made up of a double stranded helix formed by two polydeoxyribonucleotide strands around a central axis called the axis of symmetry.
The chains are paired in anti-parallel manner,that is, the 5´ end of one strand is paired with 3´ end of the other strand.
The deoxyribose-phosphate backbone is hydrophilic and thus in each chain it is on the outside of the molecule.
The bases are hydrophobic and thus located towards the inside of the molecule.
The overall structure resembles a twisted ladder.
The phosphodiester bonds in the two interwoven strands run in opposite directions. Therefore the strands are called Antiparallel. The 3´-5´strand is called Coding or Template strand while 5´-3´ strand is called non-coding strand.
The spatial relationship between the two strands in the helix creates a major ( wide ) groove and a minor narrow groove. These grooves are used by the regulatory proteins to bind to their specific recognition sequences along the DNA chain.
BASE PAIRING: The bases of one strand of DNA are paired with the bases of the other strand. ADENINE IS ALWAYS PAIRED WITH A THYMINE AND A CYTOSINE IS ALWAYS PAIRED WITH A GUANINE.
Therefore one strand of the double stranded DNA is always the complement of the other strand….. Given the sequence of bases on one chain, the sequence of bases on the other chain can be determined.
This base pairing leads to CHARGAFF RULE: in any sample of dsDNA, the amount of adenine equals the amount of thymine, the amount of guanine equals amount of cytosine, and the total number of purines is equal to total number of pyrimidines.
The base pairs are held together by hydrogen bonds--- two between A and T and three between G and C. They stabilize the structure of the helix.
B-DNA – the most common type. Described by Watson and Crick. Usually found under physiologic conditions( low salt, well hydrated ).
A right handed helix.
Contains ten residues per 360 degree turn of the helix.
The planes of the bases is perpendicular to the helical axis.
A-DNA – It is formed by moderately dehydrating the B form. It is also a right handed helix but contains eleven base pairs per turn. The planes of the bases are tilted 20 degrees away from the perpendicular to the axis of helix.
Z-DNA- left handed helix.
twelve base pairs per turn
found in regions of DNA which has alternating purines and pyrimidines.
Special structural characteristics of eukaryotic messenger RNA:-
It contains a long sequence of adenine nucleotides (20-250) on the 3´ end of the RNA chain and is called “poly-A tail”. It is thought to play role in stability of mRNA against 3´ exonucleases.
There is a “cap” on the 5´ end consisting of a molecule of 7-methylguanosine. The cap is involved in the recognition of mRNA by the translation machinery and also helps to stabilize mRNA against 5´ exonucleases.
In mammalian cells, the messenger RNA that comes to cytoplasm is the product of processing of a precursor called, HATEROGENOUS NUCLEAR RNA (hnRNA). It is synthesized in the nucleus and is much bigger than mRNA. Most of it is degraded in the nucleus and only 25% of it forms a precursor of mRNA called pre-mRNA which is then converted to mRNA.
tRNA is the smallest of the three major species of RNA.
Single stranded globular molecules.
Remain largely in cytoplasm.
Functions; The t RNA molecules serve as ADAPTERS for the translation of information in the sequence of nucleotides of the mRNA into specific amino acids.
T here is at least one specific type of tRNA molecule for each of the amino acids commonly found in proteins.
Each tRNA carries its specific amino acid to the site of protein synthesis. There it recognizes the genetic code word on mRNA and this specifies the addition of its amino acids to the growing peptide chain.
Primary structure; tRNA molecules consist of 74-95 nucleotides in a particular sequence.
The tRNA molecules contain not only the usual bases like adenine, guanine, cytosine, uracil but also contain unusual bases like dihydrouracil , pseudouridine, thymine.
Secondary structure: each single stranded tRNA is folded extensively and extensive intrachain base pairing which leads to a characteristic CLOVER-LEAF structure. These folds are stabilized by hydrogen bonds between complementary bases of the same strand. This leads to the formation of double stranded structures.
Arms or loops of tRNA: All tRNA molecules contain 4 main arms or loops.
1-Acceptor arm; This is made up of unpaired sequences of cytosine-cytosine-adenine at the 3´end. The 3´OH terminal of adenine binds with the carboxylic group of a specific amino acid and carries it to ribosomes for protein synthesis.
2-Anticodon arm: it is in the form of a loop and carries specific sequences of three bases which constitute the anticodon. The bases of anticodon are bonded with three comlementary bases of codon of mRNA.
3-D arm: it contains the base dihydrouridine.
4-T Ψ C arm: contains thymine, pseudouridine and cytosine.
The extra arm and the T Ψ C arms help define a specific tRNA.
rRNA is found as a component of ribososmes--- a cytoplasmic nucleoprotein structure that acts as the machinery for the synthesis of proteins from the mRNA template. The rRNA forms 80% of the total cellular RNA.
The ribosomal subunits are defined according to their sedimentation velocity in Svedberg units. The mammalian ribosomes has a sedimentation velocity of 80S . It contains two major subunits- a larger one with 60S and a smaller one with 40S. The 60S subunit carries 60% of rRNA .
There are four distinct species of rRNA in eukaryotic cells--- 28S, 18S, 5.8S and 5S.
The bases in rRNA are mainly adenine, guanine, cytosine and uracil and a few pseudouridine.
Small nuclear RNA (SnRNA) are large number of small stable RNA species found in eukaryotic cells. Most of them are complexed with proteins to form ribonucleoproteins. They are distributed in the nucleus, in the cytoplasm or in both. They are significantly involved in mRNA processing and gene regulation.
PABA analogs ---- Sulfonamides are structural analogs of PABA and thus competitively inhibit folic acid synthesis in bacteria. Human beings get folic acid from external sources and thus are not affected by the drug.
Folic acid analogs---- methotrexate is one such drug. It inhibits the reduction of dihydrofolate into tetrahydrofolate and thus no purines synthesis. This slows down DNA replication . Used for the treatment of cancer. Harmful to all the cells.