Lecture 10 - Amino Acids and Peptide Synthesis

Question 1

What are the steps in the synthesis of amides from carboxylic acids?

Answer 1

• Convert acid into activated form (i.e. acid chloride by treating with PCl5 or ester by treating with p-nitro phenyl ester)
• Add amine to activated form (acid chloride/ester) to form amide

Question 2

What are the steps in the synthesis of amides from nitriles/cyanides? Can the reaction go further?

Answer 2

• Acidic/basic conditions
• RCN + H2O/H+ –> RCONH2
• Reaction can be stopped at this stage or further treatment gives corresponding carb. acid (RCOOH)

Question 3

Why are amides chemically inert and what does this mean for amide reactions? Why is its chemical inertness important?

Answer 3

• Inert because LP on N atom delocalised into carbonyl group (means N isn’t basic, amides are planar, high energy barrier to rotation about C-N bond)
• Means carbonyl doesn’t readily undergo nucleophilic attack (like other carb. derivatives e.g. aldehydes, ketones, esters, acid chlorides etc) as this disrupts stabilisation
• Important as amide bonds hold together amino acids in proteins

Question 4

What shape are secondary amides and why?

Answer 4

• Secondary amides have transoid conformation to reduce steric hindrance (R groups are trans to each other)

Question 5

Give examples of important peptides, their no. of residues and their biological properties (9 examples)

Answer 5

• GABA, 1, neurotransmitter (controls nerve impulses)
• Monosodium Glutamate, 1, Meaty flavoured food additive
• Aspartame, 2, artificial sweetener (1000x sweeter than sugar)
• Penicillin, 3, powerful antibiotic formed in certain fungal moulds
• TRH, 3, hormone that controls release of another hormone (thyrotrophin)
• Enkephalins, 5, control sensation of pain (found in brain)
• Phalloin, 7, extremely poisonous (found in Deathcap toadstool)
• Angiotensin II, 8, increases blood pressure (hypertensive agent)
• Cyclosporin A, 10, treats organ rejection after transplants

Question 6

What is the issue with selectively reacting amine group of 1 amino acid with carboxylic acid group of another amino acid? What can be done to prevent this?

Answer 6

• If 2 different amino acids reacted, two different dipeptides will form
• Protecting groups used to prevent mixture of products (only single product)

Question 7

What do protecting groups do? What properties do they need?

Answer 7

• Group that blocks/suppresses reactivity of reactive functional group (either sterically or electronically)
• Must be:
• Put on in high yield
• Stable to subsequent reaction
• Removed in high yield

Question 8

What are the 2 most commonly used protecting groups? How are they each removed after use (what is used?)

Answer 8

• Benzyloxycarbonyl (Z) and fluorenylmethoxycarbonyl (Fmoc)
• Z removed by catalytic hydrogenation
• Fmoc removed by treatment with weak base (piperidine)

Question 9

What are the steps in selective coupling of 2-amino acids?

Answer 9

1. Protect amine group of 1st amino acid (use Z-Cl or Fmoc)
2. Activate carboxylic group of 1st amino acid: OH group attacks DCC then pentafluorophenyl attacks carbonyl group and kicks out DCC derivative (urea)
   OR
3. OH group attacks DCC then other amino acid’s N LP attacks carbonyl group and kicks out DCC derivative/urea
4. Protect carboxylic acid group of 2nd amino acid (MeOH/HCl)
5. Couple 1st and 2nd amino acid together to form amide bond (only 1 possible product)
6. Remove Z group with H2, Pd/C
7. Hydrolyse ester with LiOH

Question 10

How are peptides cleaved (separated into 2 parts)?

Answer 10

• Cysteine protease enzymes (Enzyme-SH) used to catalyse cleavage via nucleophilic attack of thiol on amide bond (carbonyl) of target peptide
• Enzyme irreversibly inhibited