primary structure - peptide bonds and cis-trans isomers

how is a peptide bond formed?

what type of reaction is a peptide bond formation?

condensation reaction

what direction are peptides drawn?

N terminus (amino group) ——> C terminus (carboxyl group)

what is a peptide bond?

carboxyl group of one amino acid links with the amino group of another

what is an isopeptide bond?

bond between a side chain carboxyl group and ⍺-amino group OR

bond between a side chain amino group and ⍺-carboxyl group

peptides have a resonance structure, draw this

what properties does the partial C=N bond give peptides?

planar and rigid

rotation around peptide bond is restricted

results in trans/cis isomerism

what is trans/cis isomerism?

• molecules that share the exact same chemical formula but feature different 3D shapes

• occurs in molecules with rigid structures e.g. double bond which prevent rotation

• requires two non-identical groups attached to each atom in double bond and at least one identical group

what is a cis isomer?

what is a trans isomer?

what isomer are peptide bonds usually?

trans configuration

• preferred because there are no steric clashes/hindrance between groups attached to the C_⍺ atoms

how are proteins named?

• names are derived from the amino acid residues in the primary structure

• 1 letter/3 letter code is used

• written from left (N terminus) to right (C terminus)

• Cys(1)-xyz-Cys(1) — the (1) indicates there is a disulfide bridge

how do you calculate the molecular weight (Mw) of a peptide and what are the units?

• calculate by adding the isotpic masses of amino acids + isotopic mass of one water molecule

• measured in Daltons (Da)