a. i - VCE - SSCE Chemistry - Question 5 - 2007 - Paper 1

One possible dipeptide formed from the condensation reaction of two 2-amino acids can be represented as follows:

     H   O      H   O
     |   ||      |   ||
H₂N-C-C-N-C-C-OH
     |   |      |   |
     H   H      H   H

In this structural formula, the peptide bond (-C-N-) forms between the carboxyl group of one amino acid and the amino group of another amino acid, with the loss of a water molecule.

In the given primary structure of the protein chain, a complete peptide link should be circled. This can be visualized by identifying the bond occurring between the carboxyl group of one amino acid and the amino group of the next amino acid.

[---C(=O)N---] 

This indicates the formation of a peptide bond.

At pH 2, the side chain group Z₂, represented as -CH₂CH₂CH₂NH₂, would be positively charged. This is because the amino group can accept a proton, thus making it positively charged in an acidic environment.

The side chain group Z₁, represented as -CH₂SH, is involved in the formation of covalent cross links due to the presence of the sulfhydryl (-SH) group. This group can undergo oxidation to form disulfide bonds, which are critical for stabilizing the tertiary structure of proteins.

Carboxypeptidase functions optimally at a higher pH (around 8) because its active site likely requires a certain ionization state, which is facilitated in more basic conditions. At the low pH of the stomach, the enzyme may undergo denaturation or have its active site altered, preventing it from catalyzing the digestion of food proteins.

The full structural formula of urea (NH₂)₂CO can be represented as follows:

      O
      ||
H₂N-C-NH₂

All bonds, including the double bond to oxygen and the single bonds to nitrogen, are clearly shown.