Primary structure
Amino acids joined together by peptide bonds
Polypeptide chains fold into regular structural elements:
o α helixes
o β helixes
Tertiary structure:
Make up 3D structure of the protein
Quaternary structure
Some proteins consist of more than one polypeptide chain
Angstroms and Daltons
Angstroms:
Å
10-10 of a meter
Daltons:
Da
Unit of mass nearly equal to a hydrogen atom
Express mass on the atomic scale of objects
1Da= 1 atomic mass unit
1kDa = 1000Da
Typical bond lengths
Amino acids joined by peptide bonds to form polypeptides
Peptide bond is shorter than the C-N bond that exists already in the amino
acid
Peptide bonds has patrial double bond character so is stronger and less
flexible
C-N = 1.49 Å
C=N = 1.27 Å
Peptide= 1.32 Å
Peptide bond configuration
Peptide bonds are planar due to double bond character (can’t rotate
around the bond)
, Two configurations=
Trans (α carbons opposite sides of peptide bond)
Cis (α carbons same side of peptide bond)
Almost all peptide bonds are trans
R groups are on opposite sides of chain to avoid steric clashes
Proline can be Cis
Amino acid residue bonds
Free rotation occurs around single bonds within a residue (amino acid
residues joined by peptide bond)
Structure of each amino acid can be adjusted
Phi= f angle of rotation between nitrogen and α C atom
Psi= y angle of rotation between carbonyl C atom and the α C atom
f And y angles determine path of the polypeptide chain
Gopalasamudram N. Ramachandran found many combinations of angles
can't form due to steric collisions between atoms
Can be visualised on a Ramachandran plot:
There is more variation in the y angles and less variation in the f angles
Rigidity of peptide bond and restricted set of allowed y And f angles
limits the number of structures accessible to the unfolded polypeptide
chain
Secondary structure
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