Lecture 7 Peptides – Structure and Function

Plan the synthesis of a target dipeptide from two amino acids, including the use of protecting groups.
Recognize that amino acids and peptides are drawn/represented with the N-terminus at the left-hand side of the page.
Understand why amide bonds have restricted rotation and the implications of this on peptide shape.
Recognize that hydrogen bonds and disulfide bridges both influence peptide shape and recap thiol oxidation from Lecture 1.

Amino acids join together to make peptides via amide bonds (called peptide bonds in a peptide).
A carboxylic acid reacts with an amine to form an amide bond. This is a type of nucleophilic acyl substitution, but a coupling reagent is required.
The general reaction is: $OOH + H2N \rightarrow OHN + H2O$ with a coupling reagent facilitating the reaction.

A peptide coupling reagent is needed because:
- The carboxylic acid is not a great electrophile.
- Combining an amine and carboxylic acid results in an acid-base reaction instead: $OOH + H2N \rightarrow OONH3$
Adding an acid ( $H^+$ ) won't help because it protonates the amine, eliminating its nucleophilic character: $H2N + H^+ \rightarrow H3N$ .
Coupling reagents turn the carboxylic acid into something more reactive, such as an acid chloride: $OOH + Cl \rightarrow OCl$ .
The acid chloride easily reacts with amines: $OCl + H2N \rightarrow OHN + H2O$

If two unprotected amino acids are reacted, four dipeptide products are possible (e.g., A-A, A-G, G-A, G-G).
Peptides are always written with the N-terminus on the left-hand side.
A-G is a different compound from G-A.
To make only one target product, protect the functional groups that you don't want to react by temporarily blocking the reactivity in that position.
For example, to target ala-gly, use protecting groups P1 and P2:
- $H2NOOH (Alanine) + H2NOOH (Glycine) \rightarrow P1H2NOOH + P2H2NOOH$
- $P1$ and $P2$ = “protecting groups”.

The lone pair of electrons of the amide nitrogen is in resonance, delocalized towards the carbonyl group oxygen.
Peptide bonds in peptides are:
- Relatively unreactive towards nucleophiles, and chemically quite stable.
- Rigid and planar, due to the delocalized electrons and restricted rotation of the O-C-N bonds.

Peptides are polymers of amino acids.
They are named according to the number of monomers:
- 2 amino acids: dipeptide
- 3 amino acids: tripeptide
- Many amino acids: polypeptide
Peptides have a directional sense; always write them with the N terminus on the left.
The word ‘protein’ is generally used to describe peptides that are greater than 50 amino acids long.

Peptide properties are governed by the sequence of amino acid units, which is called the primary structure.
Different amino acids have different side chains, and the properties of these side chain groups (e.g., ionization at certain pHs, hydrogen-bonding) influence peptide properties.
Bond rotation is not easily possible about the amide bonds. Sequential α-carbons are usually in a trans relationship.

Primary structure: sequence of amino acids.
Secondary structure: segments of structure along the peptide chain (e.g., α-helix, turns, β-sheet).
Tertiary structure: how secondary structural elements fit together.
Quaternary structure: how proteins or independent peptide chains come together.
In an aqueous environment, the chain will adopt a conformation to expose the polar side chains (hydrophilic groups) and bury the non-polar side chains (hydrophobic groups) i.e. maximize favorable non-covalent interactions.
Hydrogen bonding between different amide bonds also stabilizes secondary structural structures.

The NH from an amide hydrogen bonds with the CO of a different amide four amino acids along the chain.
This same pattern of hydrogen bonds repeated along the peptide gives the stabilized helical secondary structure.
$i, i+4$ H-bond

Sickle-cell anemia is a genetic disease where one glutamic acid in the protein hemoglobin is replaced with the amino acid valine.
The change from the hydrophilic glutamic acid ( $CO_2$ - at pH 7.4) to the non-polar, more hydrophobic valine causes the protein to aggregate.

Depending on the protein, disulfide bonds (or bridges) can be defined as stabilizing both secondary or tertiary peptide/protein secondary structures.
The amino acid cysteine contains a thiol functional group on its side chain.
Even under just mild air oxidation conditions, two cysteines can react in an oxidation reaction to give a disulfide bond.

If a disulfide bridge forms, this can even link/bring together otherwise remote ends of the peptide.

Disulfide bridges can even join together separate peptides into a single molecule.
Insulin is two peptide chains connected/stabilized by three disulfide bonds, one intrachain and two interchain.