Topic 3

• What is a nucleotide?

  The monomer from which nucleic acids are made
• Structure of a nucleotide

  Phosphate group, pentose monosaccharide, nitrogenous base
• Differences between DNA and RNA nucleotides

  DNA has deoxyribose whereas RNA has ribose, RNA has uracil rather than thymine
• How many carbon rings are there in purines?

  1
• How many carbon rings are there in pyrimidines?

  2
• Type of pentose sugar in DNA

  Deoxyribose
• Type of pentose sugar in RNA


  Ribose
• Type of bond in polynucleotides

  Phosphodiester bonds
• How do phosphodiester bonds form in polynucleotides?

  Condensation reactions between phosphate group on the fifth carbon of pentose sugar of a nucleotide and hydroxyl group on the third carbon of pentose sugar of the other nucleotide
• How do you break phosphodiester bonds?

  Hydrolysis reactions
• What do phosphodiester bonds form?

  Sugar-phosphate backbone
• Structure of ADP/ATP


  Phosphorylated nucleotides
• What do ADP and ATP contain?

  Ribose, adenine, phosphates (3 for ATP, 2 for ADP)
• What holds together the double helix?

  Hydrogen bonds between bases
• How is each strand organised?

  Phosphate group at one end, hydroxyl group at the other end, 5'3
• How are the strands organised with respect to each other?

  Antiparallel
• Number of hydrogen bonds between A and T

  2
• Number of hydrogen bonds between C and G

  3
• A


  Adenine
• T


  Thymine
• C


  Cytosine
• G


  Guanine
• Why is base pairing important?

  Allows DNA to be copied and transcribed, important for heredity
• Why is DNA a double helix?

  The bases are hydrophobic so the sugar-phosphate backbone chains need to stop them from coming into contact with water, the chains skew themselves to block holes between bases but this causes atoms to collide with each other, more twisting required, the twisting of the DNA produces the double-helix shape
• How to purify DNA

  Grind sample in pestle and mortar to break cell walls, mix sample with detergent to break cell membranes, add salt to break the hydrogen bonds between DNA and water molecules, add protease enzymes to break down proteins associated with DNA in the nucleus, add a layer of ethanol which causes the DNA to precipitate out of solution, white strands form between layer of sample and layer of alcohol, pick up DNA by spooling it onto a glass rod
• Process of semi-conservative replication


  DNA unwinds, hydrogen bonds between complementary bases are broken to form two separate strands, free DNA nucleotides will align with exposed bases by complementary base pairing, hydrogen bonds form between free nucleotides an exposed bases, new nucleotides join to to adjacent nucleotides with phosphodiester bonds
• Semi-conservative replication


  Two new molecules of DNA are produced, each with a strand of old DNA and another strand of new DNA
• Enzymes involved in semi-conservative replication

  DNA helicase, DNA polymerase
• Role of DNA helicase


  To travel along the DNA backbone and break hydrogen bonds between between complementary base pairs, leading to the strand unzipping
• Role of DNA polymerase

  To catalyse the formation of phosphodiester bonds between nucleotides
• What can occur in semi-conservative replication?

  Mutations
• How can mutations occur in semi-conservative replication?

  Sequences of bases not matching exactly, an incorrect sequence may occur in the newly copied strand
• Nature of the genetic code

  Triplet, non-overlapping, degenerate, universal
• Triplet nature of the genetic code

  A sequence of three bases called a codon codes for an amino acid
• Gene


  Section of DNA that contains the complete sequence to code for an entire protein
• Universal nature of the genetic code

  All organisms use the same code although the sequence of bases coding for each individual protein will be different
• Degenerate nature of the genetic code

  Many amino acids can be coded for by more than one codon.
• Non-overlapping nature of the genetic code

  A single codon signals the start of a sequence which makes sure that the codons are read in frame, meaning they start from base 1.
• Process of transcription


  The 3'5' strand is called the antisense strand and is the template strand, free RNA nucleotides will base pair with complementary bases exposed on the antisense strand when the DNA unwinds, phosphodiester bonds form between the RNA nucleotides by the enzyme RNA polymerase, mRNA produced and detaches from the DNA template and leaves the nucleus through a nuclear pore
• Process of translation


  mRNA binds to small subunit of the ribosome at its start codon, a tRNA with the complementary anticodon and a methionine binds to the mRNA start codon, amino acids continue to bind to the mRNA one at a time, first amino acid transferred to second tRNA by a peptide bond catalysed by peptidyl transferase, ribosome moves along the mRNA which releases the first tRNA and the second tRNA becomes the first