Amino acids and proteins and DNA

• α amino acid


  General structure: NH2-CH-CO2H-R
• Glycine


  Simplest amino acid, R group is H
• Amino acids


  • Except glycine, they are chiral because there are four different groups around the C
  • They rotate plane polarized light
• Acidic/basic amino acids


  Have an extra carboxylic acid or amine group on the R group
• You do not need to know any common names for the 20 essential amino acids
• You should be able to name given amino acids using IUPAC organic naming
• Zwitterion


  The no charge form of an amino acid never occurs. The amino acid exists as a dipolar zwitterion.
• Amine group is basic

  Carboxylic acid group is acidic
• Amino acids as buffers


  They act as weak buffers and will only gradually change pH if small amounts of acid or alkali are added
• Dipeptide


  Simple combination molecule of two amino acids with one amide (peptide) link
• For any two different amino acids there are two possible combinations of the amino acids in the dipeptide
• Hydrolysis of di-peptides/proteins


  If proteins are heated with concentrated hydrochloric acid or concentrated strong alkalis they can be hydrolysed and split back into their constituent amino acids
• Chromatography of amino acids

  • Thin-layer chromatography method
  • Calculate Rf values to identify amino acids
• A protein can be split into amino acids by reacting with concentrated hydrochloric acid
• Primary structure of proteins

  The sequence of the 20 different naturally occurring amino acids joined together by condensation reactions with peptide links
• Secondary structure: α-helix


  • The R-groups on the amino acids are all pointed to the outside of the helix
• Secondary structure: β-pleated sheet


  • The protein chain folds into parallel strands side by side, held in place by hydrogen bonds
• Tertiary structure of proteins

  The folding of the secondary structure into more complex shapes, held in place by interactions between the R-side groups
• Secondary structure: α-helix


  • The R-groups on the amino acids are all pointed to the outside of the helix
• Secondary structure: β-pleated sheet


  • The protein chain folds into parallel strands side by side
  • The protein chain is held into the pleated shape by hydrogen bonds between the H of –N-H group and the –O of C=O of the amino acid much further along the chain in the parallel region
• Tertiary structure of proteins

  • The folding of the secondary structure into more complex shapes
  • Held in place by interactions between the R- side groups in more distant amino acids including hydrogen bonding, sulfur-sulfur bonds and ionic interactions
• Enzyme


  Proteins that increase the rate of chemical reactions
• Active site of an enzyme

  • A hollow in the globular protein structure into which a substrate molecule can bond to the amino acid side chains through hydrogen bonding, van der waals forces, permanent dipole-dipole forces, and ionic interactions
• Lock and key hypothesis

  Only substrate molecules with the right shape and correct positions of functional groups will fit and bind to the active site
• Enzyme-substrate complex


  When the enzyme bonds to the active site
• Enzyme inhibitor


  A drug that blocks the active site of an enzyme, often by binding strongly to it
• DNA


  A polymer of nucleotides linked by covalent bonds between the phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide
• DNA structure


  • Exists as two complementary strands arranged in a double helix
  • Hydrogen bonding between base pairs (A-T, C-G) holds the two strands together
• Cisplatin


  A Pt(II) complex used as an anticancer drug that prevents DNA replication in cancer cells by forming a dative covalent bond between platinum and a nitrogen atom on guanine
• Cisplatin can also prevent the replication of healthy cells, leading to unwanted side effects like hair loss
• Unwanted side effects of cisplatin can be minimised by giving it in small doses
• Society needs to assess the balance between the benefits and the adverse effects of drugs, such as the anticancer drug cisplatin