Peptides and Protein Chemistry 1; Amino Acids, Peptides, Proteins. Flashcards
What is the difference in molecular weight for peptides and proteins?
- Peptides: usually less than 50 AA residues linked by peptide bonds
- Proteins: more than 50 AA residues (large proteins can contain thousands)
What are the characteristic groups of an amino acid?
- Chiral carbon centre
- Amino group (NH2)
- Carboxyl group (COOH)
- Rando hydrogen (H)
- Characterising R-group side chain
How can amino acids be classified?
According to their side chains:
- Charged (positive/negative)
- Polar uncharged (hydroxide/amide group)
- Non-polar/hydrophobic (aliphatic/aromatic)
- ‘Special cases’ w/unique properties (Cys/Gly/Pro)
How are peptides defined/is there any overlap with proteins?
- Small molecules
- Usually less than 50 AA residues
- Do not possess well-defined 3D structures
- Distinction between peptides and proteins sometimes unclear, particularly with medium-sized molecules (15-50 residues)
What is responsible for the main properties of a peptide bond?
The mesomeric effect of the N lone pair with the electronegative O; resonance giving rise to partial double bond character C = N+.
What are the two consequences of resonance stabilisation of the amide group?
- The peptide bond is chemically inert
- The amide group is planar; has double bond character
> Electrons delocalised into π orbital (via P)
What are the potential issues with synthetic peptide synthesis (not see in nature) e.g. making a dipeptide?
- There is no way of distinguishing between the two amino/carboxyl groups; 3 other dipeptides formed
- Many amino acids possess side chains with reactive functional groups e.g. NH2 of Lys, COOH of Glu, OH of Ser.
What is the solution to the issues of synthetic peptide synthesis?
- Protection of amino acid residues (the NH2, R-side chains and -COOH not desired to be reacted) with protecting groups that prevent unwanted reactions
- Condensation (H2O leaves) with now-protected amino acids form peptide bond
- Removal of protecting groups in mild conditions
What is chemical activation of amino acids and why is it necessary?
- Attachment of a leaving group (X instead of -OH) of -COOH to facilitate attack by amino component (of other AA)
- Otherwise at ambient temperatures an amine will form a salt with a carboxylic acid instead; NH3+/COO-
What does chemical activation do to the carbon of -COOH to facilitate a reaction with an amino group?
Replacing the -OH for -X (e.g. Cl) means the carboxylic C is more delta positive (Cδ+) thus more likely to react; HX is leaving group instead of H2O in the OG
What does chemical activation mean for peptide bond formation?
- Rapid and quantitative reaction
- Under mild conditions
- Avoids side-reactions
- Doesn’t affect chirality
- Produces easily removable co-products (HX)
What are good leaving groups to chemically activate an amino acid (replace the -OH) with?
Conjugate base of a strong acid (e.g. HCl w/o the H):
- acyl halides
- active esters
- carbodiimide reagents
What comprises the backbone of a protein?
The primary amino acid sequence; the peptide bonds and C-alpha atoms.
What is a torsion angle?
The angle between the plane of atoms of stuff
What two torsion angles define the conformation of the peptide chain and why?
- Angle about the Cα-N bond; phi φ
- Angle about the C α-C bond; psi ψ
- Peptide bond has partial double bond character thus is planar; main chain rotations are thus restricted to the above two torsion angles.
How do steric factors influence the conformation of the peptide chain; is there one preferred?
- Cis conformation is unfavourable (e.g. R-groups on the same side = bulky and interfere)
- Thus most peptide bonds are of the trans conformation; R-groups etc. on different sides
What is hydrogen bonding and what role does it play in protein structure?
- Hydrogen bound to electronegative atom (e.g. N, O, F) experience electrostatic attraction with another electronegative atom
- Key to formation of secondary structure; alpha helices and beta sheets
How does hydrogen bonding feature in alpha helices?
How does it contribute to stability?
- Oxygen of C = O (carbonyl) of residue ‘i’ forms H-bond with H of amide residue ‘i+4’; there are 3.6 amino acid residues per turn of the helix
- Relatively weak in isolation, but summation of H-bonds in helix = stable
How are the amino acid side chains arranged in an alpha helices?
They point outwards and towards the N-terminus of the chain; ‘up like a tree’.
How does hydrogen bonding feature in beta-pleated sheets?
- C=O and N-H groups form H-bonds between neighbouring strands; may be parallel or antiparallel
- Sheets pleat to maintain correct H-bond stereochemistry
How are the amino acid side chains arranged in a beta pleated sheet?
Side chains point alternatatively on opposite sides of the sheet
What are β-turns in relation to proteins?
β-turns allow the protein backbone to make abrupt turns; more rare.
When is it possible that the same protein/primary sequence can adopt different structures?
E.g. in Mad Cow Disease; native proteins re-fold into a different stable conformation, with fatal consequences.
What is Glycine’s unique property as an AA and how does this influence protein structure?
- Simply hydrogen as side chain R; thus no chiral centre either
- Lack of bulky side chain (R) means less steric hindrance; Gly renders a polypeptide more flexible
What is Proline’s unique property as an AA and how does this influence protein structure?
- Forms a cyclical secondary amine w/side chain
- The tertiary amide bond formation means that proline restricts the torsion angles in a polypeptide chain
What is Cysteine unique property as an AA and how does it influence protein structure?
- Thiol group (R-SH)
- Disulfide bond formation (covalent-type) can occur within same polypeptide chain or between different chains (of Cys)
Where proteins w/disulfide bridges normally found?
Often seen in proteins excreted into the extracellular environment; intracellular environment is reducing and therefore these proteins due not generally contain disulfide bridges
Define: structural motif
Groupings of secondary structure elements e.g. beta-hairpin (antiparallel strands connected by tight turns)
Define: protein domains
Globular-type units that are connected by linker regions, often fulfilling different roles and bind to different binding parameters (bringing together different functionalities)
