2.1.3 nucleotides and nucleic acids

• what are nucleotides


  nucleotides are the monomers from which nucleic acids like DNA and RNA are formed
• what are the 2 types of nitrogenous bases

  purines and pyrimidines
• what are purines


  2 carbon ring structure 

  Adenine and Guanine
• what are pyrimidines


  1 carbon ring structure 

  Cytosine, Thymine and Uracil
• what are nucleotides made up of

  made up of a phosphate group, pentose sugar and a base
• how do the nitrogenous bases bond

  • Thymine (Uracil in RNA) is the complimentary base pair to adenine
  • Guanine is a complementary base pair to cytosine
  • This means a purine and pyrimidine base are always complementary to each other and complementary base pairing is important to help maintain the order of genetic code when DNA replicates
• what reaction occurs and which bonds are formed in nucleotides (strength of bond and polymer of nucleotides)

  • Both DNA and RNA nucleotides undergo condensation reactions forming phosphodiester bonds between the nucleotide monomer to create the polymer
  • A phosphodiester bond is a strong covalent bond that forms between the pentose sugar and phosphate of different nucleotides
  • The polymer of these nucleotides is called a polynucleotide.
• what is ATP and functions

  • adenosine triphosphate
  • essential for metabolism 
  • immediate source of energy for biological processes
• how is ATP made

  • Made during respiration via a condensation reaction using the enzyme ATP synthase
  • ADP+Pi -> ATP+H20
  • ATP is hydrolysed using the enzyme ATP hydrolase

  breaking one of the bonds between phosphate groups releases a small amount of energy

  • Inorganic phosphate released can bond with completely different compounds making them more reactive (phosphorylation)
• DNA structure

  • deoxyribonucleic acid codes for the sequence of amino acids in the primary structure of a protein which determines the final 3D structure and function of the protein
  • Polymer forms a double helix made of 2 antiparallel strands joined together by hydrogen bonds between bases on the 2 different strands
• how does DNA relate to its function

  • stable structure due to the sugar-phosphate backbone (covalent bonds) and the double helix
  • Double-stranded so replication can occur using both strands as a template
  • Weak hydrogen bonds between the bases for easy separation of the two strands in a double helix during replication
  • A large molecule that carries a lot of information
  • Complementary base pairing allows identical copies to be made
• DNA precipitation method

  DNA can be extracted from plant material

  1. Homogenise the cell with detergent which will break open the cells and cell membranes to release their contents

  2. Filter to remove large debris

  3. Add salt to break hydrogen bonds between the DNA and water molecules

  4. Add protease to digest the proteins associated with the DNA

  5. Add ice-cold ethanol to precipitate out the DNA from the solution so DNA appears as white strands
• what are the 3 types of RNA

  mRNA, tRNA and rRNA
• what is rRNA


  makes up the bulk of ribosomes
• mRNA

  • copy of one gene from the DNA
  • Created in the nucleus and then leaves via the nuclear pore to carry the copy of the genetic code of one gene to a ribosome in the cytoplasm
  • mRNA is much shorter than DNA
  • mRNA is single-stranded and every 3 bases in the sequence code for one specific amino acid these three bases are therefore called codons
• tRNA

  • found in the cytoplasm
  • It is single-stranded but folded to create a cloverleaf shape held in place by hydrogen bonds
  • Brings a specific amino acid to the ribosome
  • This is determined by 3 bases found on the tRNA (anticodon) which are complimentary to the 3 bases on mRNA (codon)
• why is semi-conservative DNA replication referred to as such

  • DNA replication is described as semi-conservative because in replication one strand is conserved and one new strand is created. 
  • Copying errors in DNA can occur randomly and spontaneously resulting in a change to the DNA base sequence known as a mutation
• strands of DNA (different numbers)

  • When describing the DNA double helix the top and bottom of each strand are either 3' or 5' prime end. This number refers to which carbon within the deoxyribose sugar of the nucleotide is closest to the top/bottom.
  • The enzyme that catalyses DNA replication is complementary in shape to the 3' end and can therefore only attach to the DNA at this location
• stages of DNA replication

  1. DNA helicase breaks the hydrogen bonds between the complementary bases of the two DNA polymers causing the double helix to unwind and the two strands to separate

  2. Both strands act as templates for DNA replication

  3. Free-floating DNA nucleotides align opposite their complementary base on the template strand of DNA. Hydrogen bonds will form between the base pairs

  4. DNA polymerase joins adjacent DNA nucleotides together forming a phosphodiester bond between these nucleotides to create a new polymer chain of DNA
• the genetic code

  • Degenerate - amino acids are coded for by more than one triplet of bases
  • Universal - the same triplet of bases codes for the same amino acid in all organisms
  • Non-overlapping - each base in a gene is only part of one triplet of bases that codes for one amino acid. Each codon or triplet of bases is read as a discrete unit
• protein synthesis

  Proteins are created on ribosomes of RER in two stages

  1. Transcription - where the DNA sequence for one gene is copied into mRNA

  2. Translation - where the mRNA joins with a ribosome (made of rRNA and protein) and a corresponding tRNA molecule brings the specific amino acid the codon codes for
• introns


  Introns are sequences of bases in a gene that do not code for amino acids and therefore polypeptide chains. These get removed, spliced and out of mRNA molecules after transcription
• exons

  Exons are sequences of bases in a gene that code for sequences of amino acids
• start and stop codons

  • At the start of every gene, a start codon enables the ribosome to attach.
  • At the end of every gene, 3 bases do not code for an amino acid, called the stop codon. This stop codon causes the ribosome to detach and therefore ends the translation
• transcription

  1. DNA helicase breaks the hydrogen bonds between the bases in the two strands of DNA

  2. This causes the DNA helix to unwind and one strand to act as a template

  3. Free mRNA nucleotides align opposite exposed complementary DNA bases

  4. The enzyme RNA polymerase joins together the adjacent RNA nucleotides forming phosphodiester bonds to create a new mRNA polymer chain

  5. Once one gene is copied the mRNA is then modified (splicing) and then leaves the nucleus through the nuclear envelope pores
• Translation


  1. tRNA molecule aligns opposite mRNA held in place by ribosome

  2. 2 amino acids delivered by tRNA joined by peptide bond catalysed by enzyme using ATP

  3. Ribosome moves along mRNA, next complementary tRNA attaches

  4. Continues until ribosome reaches stop codon, ribosome detaches

  5. Polypeptide chain created enters Golgi body for folding and modification