amino acids, proteins and DNA (3.3.13)
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what do amino acids have?
acidic and basic properties
what happens when amino acids are in acidic conditions?
• the lone pair on the amine group is protonated • a positively charged ammonium group forms (add + charge and extra H to amine group)
what happens when amino acids are in alkaline conditions?
• the carboxyl group is deprotonated to COO- • the molecule has a negative charge (remove H from carboxyl group and add lone pair and - charge to O)
what is the structure of a zwitterion?
an amino acid where the amine group has been protonated (as if in acidic conditions) and the carboxyl group has been deprotonated (as if in alkaline conditions)
when do amino acid molecules exist as zwitterions?
when they are at an intermediate pH eg. dissolved in water or in solid form
what are proteins?
sequences of amino acids joined by peptide links
how do hydrogen bonds form in proteins?
a lone pair on an electronegative oxygen atom from a polar C=O bond on one part of the polymer chain attracts the partially positive hydrogen atom from a polar N-H bond on another part of the polymer chain
how do disulphide bridges form in proteins?
they form between sulfur atoms on the R groups of two amino acids (H+ and e- are removed)
what is the primary structure of a protein?
the sequence of amino acids in the polypeptide chain
what is the secondary structure of a protein?
when intermolecular forces in the primary structure cause the amino acids to fold into an alpha helix or beta-pleated sheet
what type of interaction is found in the secondary structure of proteins?
hydrogen bonds
what is the tertiary structure of a protein?
the unique 3D structure of a polypeptide
what type of interaction is found in the tertiary structure of proteins?
disulphide bridges
what is the quarternary structure of a protein?
when two or more polypeptides join together to form the protein (the interaction of the tertiary structure)
how can ionic bonds form in a protein?
they form between acidic amino acids eg. aspartic acid and basic amino acids eg. lysine - a hydrogen ion is transferred from the COOH group to the NH2 group forming a zwitterion
what does hydrolysis of the peptide bond in a protein do?
produce the constituent amino acids (remember to show protonated amine group)
what reagent is required to hydrolyse a peptide link?
hot concentrated HCl solution
how can amino acids be separated and identified?
by thin-layer chromatography
how can amino acids be located on a chromatogram?
using developing agents like ninhydrin or UV light
how can amino acids be identified on a chromatogram?
by their Rf values (distance moved by amino acid/distance moved by solvent)
what are enzymes?
proteins
how do enzymes act as catalysts?
they have a stereospecific active site which is complementary and binds to a substrate molecule forming an enyme-substrate complex - the reaction is then catalysed and the products are released
why can a stereospecific active site only bind to one enantiomeric form of a substrate or drug?
if the substrate is chiral, it is likely that only one enantiomer will have the correct stereochemistry to fit into the active site of the enzyme by forming appropriate bonds
how can a drug act as an enzyme inhibitor?
they have a similar shape to the substrate and bind irreversibly to the active site which blocks it so the substrate can’t bind