3.3.13 Amino acids, proteins and DNA

• Why is the melting point of 2-aminoethanoic acid is much higher than that of hydroxyethanoic acid?

  2-aminoethanoic acid exists as a zwitterion in their normal state so they have ionic bonding.

  Whereas hydroxyethanoic acid has hydrogen bonding

  Ionic bonding is stronger than hydrogen bonding
• polypeptides are hydrolysed to amino acids by refluxing with conc HCl so the NH2 groups will get protonated
• Primary structure of a protein is the order of amino acids in the chain

  The chain folds and forms hydrogen bonds producing secondary structure. There are two types of secondary structures

  > Alpha - helix

  > B - pleated sheet

  Tertiary structure is the folding of the secondary structure into more complex shapes. It is held in place by interactions between the R - groups of amino acids
• Tertiary Structure:

  The 4 types of interactions are:

  > Ionic - lysine and aspartic acid has charged R groups

  > Hydrogen bonding - Serine and lysine

  > Disulfide bridge - only cysteine

  > Van der Waals - alanine and phenylalanine
• Sulfur-Sulfur bonds are stronger than hydrogen bonding as sulfur-sulfur bonds are covalent bonds. Whereas hydrogen bonding is a force of attraction.
• If the substrate is chiral then it's likely one enantiomer will fit the active site.

  > The substrate molecule must have the right shape and correct position of functional groups to fit and bind to the active site.

  > Enzyme active sites are stereospecific and will only bind to one enantiomer
• Complementary means that the base sequences match e.g. (A and T) and (C and G)
• Amino acids exist in their zwitterion form, which is when both functional groups are charged
• If an amino acid is placed in acidic conditions (low pH)

  because the RNH2 is a good proton acceptor it accepts a protons and become +RNH3

  If an amino acid is placed in basic conditions (High pH) because the carboxylic group is acidic the COOH group looses a proton and becomes COO-
• Amino Acids form crystals at room temp and have high melting points because amino acids exist as zwitterions in their normal state and there is ionic bonding due to the electrostatic attraction.
• When 2 amino acids react together they form a dipeptide and water
• Condensation reaction:

  Amino acids -> polypeptide + water

  Hydrolysis reaction:

  Reagent: reflux , conc HCl

  Polypeptide + Water -> Amino acids
• Nucleotide: phosphate ion bonded to 2-deoxyribose which is in turn bonded to one of the four bases adenine, cytosine, guanine and thymine

  A) Phosphate

  B) Sugar

  C) Base

  
• How hydrogen bonding between base pairs leads to 2 complementary DNA strands

  There's is a hydrogen atom attached to an electronegative N atom which creates an electron deficient hydrogen atom. There is a force of attraction between the lone pair of electrons on the oxygen of the C=O and the H of the N-H bond, this is called a hydrogen bond.
• Cisplatin

  formula : [PtCl2(NH3)2]

  Name: Diamminechloroplatinum

  shape: square planar

  The Pt(Il) complex cisplatin is used as an anticancer drug. The cisplatin version only works as two chloride ions are displaced and the molecule joins on to the DNA. In doing this it stops the replication in cancer cells by a ligand substitution reaction with DNA in which a coordinate bond is formed between platinum and a nitrogen atom on guanine

  Side effect

  > Kills healthy cells by attaching to the DNA

  > Limited dosage and target specific site will limit the effects of the side effects
• Drugs as 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. Computers can be used to help design such drugs.