Amino acids, proteins & DNA

• Why are amino acids amphoteric?

  Have acidic & basic properties. Can act as acids as carboxyl group is acidic (can donate proton). Can act as bases as amino group can accept proton (is basic).
• What are zwitterions?


  Dipolar ion- has both positive & negative charge in different parts of molecule. Amino acids can exist as zwitterions. Zwitterions only exist near amino acid's isoelectric point- pH where overall charge on amino acid is 0. It's different for different amino acids-depends on R' group.
• When does an amino acid become a zwitterion?


  When its amino group is protonated to NH3+ & its COOH group is deprotonated to COO-. In conditions more acidic than isoelectric point, -NH2 group likely to be protonated but -COOH will be unchanged-amino acid carries positive charge but not negative. In conditions more basic than isoelectric point, -COOH likely to lose its proton but -NH2 unchanged-amino acid carries negative charge but not positive. Only at or near isoelectric point both carboxyl & amino group likely to be ionised, forming zwitterion.
• How could you separate mixtures of amino acids?

  Thin-layer chromatography. (Different amino acids have different R' groups so have different solubilities in the same solvent).
• How can you make amino acids visible?

  Spray ninhydrin solution on TLC plate- amino acids turn purple. Could also use special plate with fluorescent dye added to it. Dye glows when UV light shines on it. When there's spots of chemical on plate, they cover fluorescent dye so spots appear dark. Put plate under UV lamp & draw around dark patches to show where spots are.
• How do you hydrolyse proteins into amino acids?

  Add aqueous 6 mol dm-3 HCl & heat under reflux for 24 hours.
• What is the primary structure of a protein?

  Sequence of amino acids in long polypeptide chain that makes protein.
• What is the secondary structure of a protein?

  Peptide links can form hydrogen bonds with eachother- chain not straight line. Shape of chain=secondary structure. Alpha helix spiral & beta pleated sheet (layer of protein folded like a concertina).
• What is the tertiary structure of a protein?

  Chain of amino acids itself often coiled & folded in characteristic way that identifies protein. Extra bonds can form between different parts of polypeptide chain-gives protein 3D shape.
• How are secondary & tertiary structures formed in proteins?

  Intermolecular forces causing amino acid chains to fold or twist. Forces important as 3D shape vital to function. Hydrogen & disulfide bonds hold proteins in shape.
• How does hydrogen bonding work in proteins?

  Can only exist between polar groups. These groups contain electronegative atoms which induce a partial positive charge on H atom. H then attracted to lone pairs of electrons on adjacent polar groups & a hydrogen bond is formed.
• What is a residue?


  An amino acid that's part of a protein.
• How does disulfide bonding work in proteins?

  (Sulfur-sulfur bonding) occurs between residues of amino acid cysteine. Cysteine contains a thiol group (-SH) & this can lose its H atom & join together to form a disulfide -s-s- bond with another thiol group. Bonds link together different parts of protein chain & help stabilise tertiary structure.
• What can affect hydrogen bonding & formation of disulfide bonds?

  Temperature & pH. This can change protein shape.
• Specificity of enzymes:


  Enzymes only work with specific substrates. Active sites are stereospecific- only work on 1 enantiomer of a substrate.
• Why is the phosphate group in DNA an ion?

  Due to negative charge on 1 of the oxygens.
• How does a polynucleotide chain form?

  Covalent phosphodiester bonds form between phosphate group of 1 nucleotide & sugar of another. Formed by condensation reaction.
• Why does complementary base pairing work?

  Due to arrangement of atoms in base molecules that are capable of forming hydrogen bonds. 2 atoms have to be right distance apart to bond. DNA double helix twists so bases are in right alignment & at right distance apart for complementary base pairs to form. Any other base pairings would put partially charged atoms too close (repel) or too far or bonding atoms wouldn't line up.
• What is cisplatin?


  Anti-cancer drug. Complex of platinum(II) with 2 Cl ligands & 2 ammonia ligands in square planar shape. (2 Cl next to eachother).
• What does cisplatin do?

  Cancer= cells dividing uncontrollably. For cell to divide it has to replicate DNA. 2 strands of DNA unwind. Cisplatin stops this happening properly so tumour cells stop reproducing.
• How does cisplatin work?

  Nitrogen atom on G base in DNA forms co-ordinate bond with cisplatin's Pt ion, replacing 1 of Cl ion ligands. 2nd N atom from nearby G either on same or opposite DNA strand can bond to Pt & replace 2nd Cl ion ligand too. Presence of cisplatin complex bound to DNA strands causes strands to kink-can't unwind & be copied properly so cell can't replicate properly. Damage to DNA also triggers mechanisms that lead to cell death.
• Adverse effects of cisplatin:

  Can bind to DNA in normal cells as well as cancer cells. Can cause hair loss & suppress immune system (controlled by WBC). Can also cause kidney damage. Side effects lessened by low doses of cisplatin. Can also be reduced by targeting tumour directly (deliver drug to cancer cells so healthy ones not attacked).