amino acids, proteins & DNA

• α amino acid


  General structure: NH2-CH-CO2H, where R group can be a variety of different things depending on the amino acid
• Glycine


  Simplest amino acid, where R group is H
• Optical activity

  • All amino acids, except glycine, are chiral because there are four different groups around the C
  • They rotate plane polarised light
• Acidic/basic amino acids


  Have an extra carboxylic acid or amine group on the R group
• Zwitterion


  The ionic form of an amino acid, where the amine group is protonated and the carboxylic acid group is deprotonated
• Amine group is basic

  Carboxylic acid group is acidic
• Amino acids as buffers

  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
• Esterification reaction


  Amino acid + alcohol -> ester + water
• Hydrolysis of di-peptides/proteins


  Splitting back into constituent amino acids using concentrated HCl or NaOH
• Thin-layer chromatography (TLC) of amino acids

  • Wear gloves, draw pencil line, use capillary tube for tiny drops, use solvent chamber with lid, spray with ninhydrin, calculate Rf values
• Protein can be split into amino acids by reacting with concentrated hydrochloric acid</b>
• Primary structure of proteins

  Sequence of 20 different naturally occurring amino acids joined by peptide links
• Secondary structure: α-helix


  • R-groups pointed to outside of helix, held by hydrogen bonds

  
• Secondary structure: β-pleated sheet


  • Protein chain folds into parallel strands side by side, held by hydrogen bonds

  
• Tertiary structure of proteins

  Folding of secondary structure into more complex shapes, held by interactions between R-groups

  
• 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
  • 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
  • Interactions include hydrogen bonding, sulfur-sulfur bonds and ionic interactions

  
• Enzyme active site

  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

  
• Enzyme-substrate complex


  • When the enzyme bonds to the active site
• Stereospecific active site

  If the substrate is chiral then its likely that only one enantiomer will have the correct stereochemistry to fit in the active site of the enzyme and so only one isomer will be catalysed
• Enzyme inhibitors

  • Many drugs act as an enzyme inhibitor by blocking the active site
  • The inhibitor will often bind to the active site strongly so stopping the substrate attaching to the enzyme
• Nucleotide


  Made up from a phosphate ion bonded to 2-deoxyribose which is in turn bonded to one of the four bases adenine, cytosine, guanine and thymine

  
• Sugar-phosphate chain

  A single strand of DNA is a polymer of nucleotides linked by covalent bonds between the phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide

  
• DNA double helix

  • DNA exists as two complementary strands of the sugar phosphate polymer chain arranged in the form of a double helix
  • Hydrogen bonding between base pairs leads to the two complementary strands of DNA
  • Guanine pairs with cytosine by 3 hydrogen bonds
  • Adenine pairs with thymine by 2 hydrogen bonds

  
• Cisplatin

  • A Pt(II) complex used as an anticancer drug
  • Cisplatin can prevent the replication of healthy cells by bonding on to healthy DNA which may lead to unwanted side effects like hair loss
• Cisplatin prevents DNA replication in cancer cells

  By a ligand replacement reaction with DNA in which a dative covalent bond is formed between platinum and a nitrogen atom on guanine