Module 1. Bio-molecules

Lesson 5


5.1 Introduction
  1. Nucleotides are building blocks of nucleic acids as the proteins are made of amino acids.
  2. They are the energy currency in metabolic transactions
  3. Nucleotides are the essential chemical links in the response of cells to hormones and other extracellular stimuli.
  4. They are structural components of an array of enzyme cofactors and metabolic intermediates.
5.2 Structure of Nucleotides

5.2.1 Nucleotides have three characteristic components
  • A nitrogenous (nitrogen-containing) base
  • a pentose sugar
  • A phosphate
The nitrogenous bases in nucleotides are derivatives of two parent compounds, pyrimidine and purine. (Fig. 5.1 Structure of nucleotides)
  • Both DNA and RNA contain two major purine bases, Adenine (A) and guanine (G),
  • Pyrimidines in DNA are cytosine (C) and thymine (T).
  • Pyrimidines in RNA are cytosine (C) and uracil
Nucleic acids have two kinds of pentoses
  • DNA contains 2’-deoxy-D-ribose,
  • RNA contains D-ribose.
The names of the four major deoxyribonucleotides (deoxyribonucleoside 5’-monophosphates)
  • Deoxyadenylate (deoxyadenosine 5’-monophosphate) Symbols : A, dA, dAMP
  • Deoxyguanylate (deoxyguanosine 5’-monophosphate) Symbols : G, dG, dGMP
  • Deoxythymidylate (deoxythymidine 5’-monophosphate) Symbols: T,dT,dTMP
  • Deoxycytidylate (deoxycytidine 5’-monophosphate) Symbols : C.dC,dCMP
The names of four major ribonucleotides (ribonucleoside 5’- monophosphates),
  • Adenylate (adenosine 5’-monophosphate) Symbols : A, AMP
  • Guanylate (guanosine 5’-monophosphate) Symbols : G, GMP
  • Uridylate (uridine 5’-monophosphate) Symbols : U,UMP
  • Cytidylate (cytidine 5’-monophosphate) Symbols : C,CMP
5.3 Nucleoside

The molecule without the phosphate group is called a nucleoside
  • Deoxyadenosine Adenosine
  • Deoxyguanosine Guanosine
  • Deoxythymidine Uridine
  • Deoxycytidine Cytosine
5.4 Phosphate “Bridges”

The successive nucleotides of both DNA and RNA are covalently linked through phosphate-group “bridges,” (Fig. 5.2)
  • The 5’-phosphate group of one nucleotide unit is joined to the 3’-hydroxyl group of the next nucleotide, creating a phosphodiester linkage.
  • Thus the covalent backbones of nucleic acids consist of alternating phosphate and pentose residues, and the nitrogenous bases may be regarded as side groups joined to the backbone at regular intervals.
  • Each linear nucleic acid strand has a specific polarity and distinct 5’ and 3’ ends.
5.5 Structure of DNA
  • In 1953 Watson and Crick postulated a three dimensional model of DNA structure.
  • In a DNA molecule, the different nucleotides are covalently joined to form a long polymer chain by covalent bonding between phosphates and sugars.
  • The phosphate attached to the hydroxyl group at the 5’postion of the sugar is attached to hydroxyl group at the on the 3’ carbon of the sugar of the next nucleotide.
  • Thus the linkage between the phosphate and hydroxyl bond is an ester linkage and is called 3’-5’posphodiester bond.
  • The DNA chain has the polarity having 5’end and 3’end because first nucleotide has a 5’ phosphate not bounded to any other nucleotide and last nucleotide has a free 3’ hydroxyl .
  • DNA consists of two helical chains of nucleotides wound around the same axis to form double helix. The two DNA strands are organized in an anti-parallel arrangement i.e. one strand is oriented 5’-3’ and other is oriented 3’-5’.
  • The hydrophilic backbones of alternating deoxyribose and phosphate groups are on the outside of the double helix, facing the surrounding water.
  • The purine and pyrimidine bases of both strands are stacked inside the double helix, with their hydrophobic and nearly planar ring structures very close together and perpendicular to the long axis.
  • Each nucleotide base of one strand is paired in the same plane with a base of the other strand. G with C and A with T, are those that fit best within the structure. This is called complementary base pairing. Three hydrogen bonds can form between G and C, but only two can form between A and T. (Fig. 5.3 Basic structure of nucleic acids) and (Fig. 5.4 The notation for nucleic acids)

5.6 Structure of RNA

Most RNA molecules are single stranded but an RNA molecule may contain regions which can form complementary base pairing where the RNA strand loops back on it. If so RNA will have some double –stranded regions. RNA molecules are of three types.
  • mRNA (messenger RNA) – carries message in the form of codons from DNA
  • rRNA (ribosomal RNA) – creates site where protein synthesis takes place
  • tRNA (transfer RNA) - specific tRNA with specific anticodon carries amino acid
Last modified: Thursday, 25 October 2012, 4:22 AM