Neucleotides

• Nucleotides


  • They are the energy currency in metabolic transactions
  • The structural components of an array of enzyme cofactors and metabolic intermediates
  • They are the constituents of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), the molecular repositories of genetic information
  • The structure of every protein, and ultimately of every biomolecule and cellular component, is a product of information programmed into the nucleotide sequence of a cell's nucleic acids
  • The ability to store and transmit genetic information from one generation to the next is a fundamental condition for life

  
• Cellular Processes


  1. DNA replication

  2. RNA (mRNA) transcription

  3. Protein translation
• Central Dogma of Life

  DNA -> RNA (mRNA) -> Proteins

  
• Tautomer


  Each of two or more isomers of a compound which exist together in equilibrium, and are readily interchanged by migration of an atom or group within the molecule
• Properties of nucleotide bases

  • Free pyrimidines and purines are weakly basic compounds and are thus called bases
  • They have a variety of chemical properties that affect the structure, and ultimately the function, of nucleic acids
  • The purine and pyrimidine bases are hydrophobic and relatively insoluble in water at the near-neutral pH of the cell
  • At acidic or alkaline pH the bases become charged and their solubility in water increases

  
• Hydrophobic stacking interactions


  • Two or more bases are positioned with the planes of their rings parallel (like a stack of coins)
  • These are one of two important modes of interaction between bases in nucleic acids
  • The stacking also involves a combination of van der Waals and dipole-dipole interactions between the bases
  • Base stacking helps to minimize contact of the bases with water, and base-stacking interactions are very important in stabilizing the 3-D structure of nucleic acids
• Phosphodiester linkages


  The covalent backbone of DNA and RNA

  
• Hydrolysis of RNA under alkaline conditions
• Absorption spectra of the common nucleotides

  
• Rosa Franklin & Maurice Wilkins Contribution
• Watson & Crick model for the structure of DNA (1953)

  
• A, B, and Z forms of DNA

  • 34-36 Angstrom diameter
  • 10.5 base pairs per turn

  
• Experiments demonstrating DNA as the genetic material

  • Avery-MacLeod & McCarty Experiment
  • Alfred D.Hershey & Martha Chase Experiment
• Hoogsteen base pairs


  A single strand of DNA, typically a string of pyrimidines, hydrogen bonds in the major groove of a double-stranded DNA

  
• G tetraplex


  Four DNA strands containing a high proportion of guanosines can form a G tetraplex

  
• Unusual DNA structures


  • Rotator
  • Nurses run
• Restriction Endonucleases


  ECoR1: GAA TTC, CTT AAG
• Hairpin structure


  A single DNA strand with self complementary sequences can form a hairpin structure
• Cruciform structure


  Double stranded DNA with self complementary sequences can form a cruciform structure

  
• mRNA molecules


  Monocistronic (containing one gene) or polycistronic (containing multiple genes)

  
• In eukaryotes most mRNAs are monocistronic, in prokaryotes many mRNAs are polycistronic
• Secondary structure of RNA

  M1 RNA component of the enzyme RNase P of E. coli

  
• Denaturation and annealing (renaturation) of DNA

  Reversible process
• Melting point (Tm) of DNA

  • When half of the DNA is present as separated single strands
  • The greater the G-C content, the higher the melting point
• Electron micrograph showing partially denatured DNA

  
• Deamination


  • Spontaneous loss of an exocyclic amino group
  • Around 100 times per day in a cell
  • Every 107 cytidine residues in 24 h
  • Deamination of adenine and guanine occurs at about 1/100th this rate
• Significance of cytosine deamination in DNA
• Nitrous acid (HNO2)


  Promotes deamination reactions
• Apurinic site


  • Hydrolysis of the bond between the base and the ribose creates an apurinic site in DNA
  • Around 10,000 times per day in a cell

  
• Pyrimidine dimers


  Induced by exposure to UV light

  
• Mutation


  Alterations in DNA structure that produce permanent changes in the genetic information encoded therein
• Evidence suggests an intimate link between the accumulation of mutations in an individual organism and the process of aging and carcinogenesis
• Nucleotides found in biomolecules

  • Adenosine-containing Coenzymes
  • Regulatory Nucleotides
  • ATP as a Source of Chemical Energy

  
• Adenosine-containing Coenzymes


  • A variety of enzyme cofactors serving a wide range of chemical functions contain adenosine as part of their structure
  • They are unrelated structurally except for the presence of adenosine, and in none of these cofactors does the adenosine moiety participate directly in the coenzyme function
  • Instead, it is recognized by the enzyme as an important "handle" in the binding of the coenzyme to the enzyme

  
• Regulatory Nucleotides

  • Hormonal signal transduction systems often rely on a nucleotide for intracellular signal transmission
  • These compounds (typically called second messengers) are formed by the binding of the hormone to a cell surface receptor, and cause changes in the activities of intracellular proteins and enzymes leading to the cellular response
• ATP as a Source of Chemical Energy

  • ATP is the nucleotide that is most commonly used as a source of energy for biological processes
  • The energy released by the hydrolysis of ATP (and the other nucleoside triphosphates) is accounted for by the structure of the triphosphate group
  • The bonds between the -ß and ß-phosphates of ATP are phosphoanhydride linkages

  
• Types of RNA


  • mRNA
  • Ribosomal RNA
  • tRNA
• Genetic Code: Which nucleotide triplet codes for which amino acid