Nucleic Acids

• Nucleic acids


  DNA and RNA
• DNA


  A polynucleotide, the repeating unit is the nucleotide
• Nucleotide


  • Consists of a sugar, a base, and a phosphate
• Sugar in DNA


  Deoxyribose [C5H10O4]
• Sugar in RNA


  Ribose [C5H10O5]
• Phosphate


  From phosphoric acid
• Bases in DNA


  • Cytosine
  • Guanine
  • Adenine
  • Thymine
• Thymine does not occur in RNA, Uracil is present instead
• Numbering atoms in nucleotides


  To avoid confusing the carbon atoms in the sugar and those in the base, the carbons in the sugar are given a dash (called a prime)
• Formation of a nucleotide


  Several nucleotides are joined together to form a polynucleotide
• DNA structure


  • Two polynucleotide strands held together by hydrogen bonds
  • Strands coil around each other forming a right handed spiral (the double helix)
  • Chains run in opposite directions (anti-parallel)
  • Hydrogen bonds form between the bases
  • Adenine always pairs with Thymine (2 hydrogen bonds)
  • Cytosine always pairs with Guanine (3 hydrogen bonds)
• One complete turn of the double helix

  • 10 base pairs and is 3.4nm long
  • Distance between bases is 0.34nm
• Comparing DNA and RNA


  • DNA: Bases A, T, G, C; Sugar deoxyribose; Double stranded; Larger molecule
  • RNA: Bases A, U, G, C; Sugar ribose; Single stranded; Smaller molecule; 3 types: mRNA, rRNA, tRNA
• DNA Replication


  1. DNA helicase unwinds the two strands

  2. Strands act as templates for formation of new strands

  3. Replication is semi-conservative

  4. DNA polymerase catalyses formation of new strands

  5. Nucleotides supplied as triphosphates (ATP, GTP, TTP, CTP)
• DNA polymerase


  • Only catalyses addition of nucleotides in 5' to 3' direction
  • Continuously synthesises one new strand (leading strand)
  • Other strand synthesised as Okazaki fragments (lagging strand)
  • Okazaki fragments joined by DNA ligase
• Unwinding of DNA


  • Causes supercoiling reduced by DNA topoisomerase and DNA binding proteins
• Mechanisms of DNA replication

  • Conservative replication
  • Semi-conservative model
  • Dispersive model
• Evidence that DNA replicates semi-conservatively was provided by Meselson and Stahl's experiment with E. coli
• Gene


  A sequence of nucleotides on DNA that codes for the synthesis of a polypeptide (protein molecule)
• Genetic code


  Triplets of bases that code for amino acids
• Features of the genetic code

  • A triplet of bases codes for one amino acid
  • Universal - same triplet codes for same amino acid in all living systems
  • Degenerate - more than one triplet can code for the same amino acid
  • Non-overlapping
• Protein synthesis
• Nucleic acids


  Long chains (polymers) of lots of nucleotide monomers joined together by phosphodiester bonds

  
• Nucleotide


  • Made up of 3 components: Pentose sugar, Nitrogenous base, Phosphate

  
• DNA


  Consists of two nucleic acid strands bonded together by complementary base pairing, twisted around each other to form a double helix
• Base pairing in DNA

  Guanine always pairs with cytosine with three hydrogen bonds, Adenine always bonds with thymine (in DNA) or uracil (in RNA) with two hydrogen bonds

  
• Purines and pyrimidines


  • Adenine and guanine are purines (large double ring structure), Cytosine and thymine are pyrimidines (single ring structure)

  
• Differences between DNA and RNA

  • DNA contains deoxyribose sugar, RNA contains ribose sugar
  • RNA contains uracil instead of thymine
  • DNA is double-stranded, RNA is single-stranded
  • DNA has hydrogen bonds between the two complementary strands

  
• DNA and RNA synthesis

  1. Nucleotides connected through phosphodiester bonds

  2. Condensation reaction catalysed by DNA polymerase or RNA polymerase

  
• Hydrolysis of phosphodiester bonds

  Requires the addition of a water molecule
• ATP


  A phosphorylated nucleotide, consisting of a ribose sugar, adenine, and three phosphate groups

  
• ATP hydrolysis


  1. Converted into ADP and inorganic phosphate, releasing energy

  2. Phosphate can be attached to other molecules to make them more reactive

  3. ATP re-synthesised in a condensation reaction catalysed by ATP synthase
• Purifying DNA


  1. Blend fruit to break cells apart

  2. Mix with detergent, salt, and water

  3. Heat at 60°C to denature enzymes

  4. Cool, filter, add proteases

  5. Precipitate DNA with cold ethanol
• Semi-conservative DNA replication


  New DNA molecule made up of one strand of original DNA and one newly synthesised strand

  
• DNA replication process


  1. DNA helicase unwinds double helix

  2. Complementary nucleotides attach to template strand

  3. DNA polymerase catalyses phosphodiester bond formation

  4. Two daughter DNA molecules formed

  
• DNA polymerase


  • Proofreads complementary strand, can replace mismatched nucleotides
  • Accuracy rate of about 99%

  
• DNA mutations can have detrimental effects, as they can change the sequence of amino acids in a protein
• Types of RNA


  • Messenger RNA (mRNA)
  • Transfer RNA (tRNA)
  • Ribosomal RNA (rRNA)
• mRNA


  Carries genetic code from nucleus to cytoplasm, provides instructions for protein synthesis on ribosome

  
• tRNA


  Carries amino acids to ribosome, contains amino acid binding site and anticodon