Amino acids, proteins and DNA

• General structure of an α amino acid


  NH2 - Ch - COOH

  R
• R group can be a variety of different things depending on what the amino acid is
• What does the α in amino acid mean?

  Both NH2 and COOH groups are joined to the same C
• what activity does all amino acids have?

  Optical, all are chiral, rotate in plane polarised light
• Which amino acid is the exception for having optical activity?

  Glycine ( NH2CH2COOH)
• What is a zwitterion?

  molecule with both positive and negative ions

  -only exist at isoelectric point, where overall charge = 0
• What is the structure of the species present in solid amino acid?

  a zwitterion
• Why do amino acids have higher melting points?

  -ionic bonding, stronger attraction than hydrogen bonding in another compound
• What occurs to amino acid at low pH?

  COO- accept a proton, NH3+ stays same

  -forms COOH and NH3+
• What occurs at high pH?

  NH3+ lose H+, COO- stay same,

  -forms NH3 and COO-
• Amino acids act as buffers, will only gradually change pH if small amount of acid or alkali is added to amino acid
• Amino acids are in their solid form (zwitterion) when HCl or NaOH is added to them
• Dipeptides

  2 amino acids joined together by peptide link, condensation reaction
• Amino acid + methanol + strong acid catalyst

  NH2 gains a H

  COOH -> COOCH3
• Hydrolysis of dipeptide with HCl

  -acidic

  -NH3+ and COOH
• Hydrolysis with NaOH

  -alkali

  -NH2 and COO-
• Method that mixture of amino acid can be separated from hydrolysis

  Chromatography
• Why chromatography is able to separate a mixture of compounds?

  • different solubility in solvent phase
  • different retention time in stationary phase
  • different absorption, different Rf values, amino acids travel at different speeds
• Protein

  Polymer of amino acid
• Primary structure

  single sequence of amino acids joined together by peptide links by condensation reaction
• Secondary structure

  3D structure, H bonds between peptide links in polymer chain pulls straight chains into coils, pleates
• Alpha helix

  3D arrangement of amino acid with polypeptide chain in a corkscrew shape held in place by H bonds

  -R groups point to the outside of the helix
• B pleated sheets

  Protein chain folds into parallel strand side by side, held in place by hydrogen bonds between amino acids further along chain of parallel region
• Tertiary structure

  Folding of 2nd structure into more complex shape, held into place by interactions of R groups in more distant amino acids
• How do H bonding form in amino acid?

  between highly electronegative elements O, N, H
• Disulphide bridges

  Cysteine (S-H), can lose a H ion and form disulphide bridge(S-S), which is covalent
• Enzymes

  Biological catalysts, remains unchanged, increase ROR
• Enzymes are chiral, only one enantiomer in substance will fit into active site
• Stereospecific

  Only one type of substance can fit into the active site
• Inhibitors block active site. Bind strongly so stop substrate attaching to enzyme, reduce ROR
• Why is it hard to find drugs that would fit into active site?

  Stereospecific, only one enantiomer would fit
• Development of drugs methods

  -Trial and error

  -Computer modelling
• Sugar phosphate backbone are covalently bonded, joined by phosphodiester bonds between 2 deoxyribose and phosphate group
• How does DNA being in a helix help the formation of DNA?

  twisting allow the bases to align perfectly to form hydrogen bonds
• Hydrogen bonds form between the bases
• How many bonds are in Adenine and Thymine?

  2
• How many bonds between Guanine and Cytosine?

  3 Hydrogen bonds
• Why would no other base pair form apart from (AT and GC)?

  partially charged atoms would be too close to each other and repel

  or not get close enough and hydrogen bonding can't happen
• What is Cis-platin?

  anti-cancer drug
• How does Cis-platin prevent cell division?

  -ligand replacement reaction

  -Chlorine displaced

  -dative covalent bond form between platinum and nitrogen in guanine base within DNA