Proteins
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23 common amino acids, these can also have modified residues
There are also peptides not synthesized on ribosomes, synthesized by nonribosomal
peptide synthetases
 For pI, average pka of +1 structure and -1 structure
Protein Structure
 Primary, secondary, tertiary, quaternary
 When wavelength is even number (constructive), bright lines appear on the surface
 Most effective diffraction occurs when wavelength of light and width of slits are similar
in magnitude
 Right-handed alpha helix is most common
 Antiparallel beta sheets have more hydrogen bonds than parallel
 Most beta sheets are twisted rather than parallel
 Different turns involving 3-6 residues
 Beta Turn: the structure is a 180 turn involving four amino acids, with the carbonyl
oxygen of the first residue forming a hydrogen bond
 There is no repetitive structure to random coils
 Proteins used to be crystalized in order to view their structures, though electron
microscopy changed it so that crystallization, which could take weeks/months, is
unnecessary
 James Dubochet started freezing the proteins for cryo-EM
 NMR Spectroscopy
o TOCSY: coupling of nuclear spins in atoms connected by covalent bonds
o NOESY: coupling of nuclear spins in nearby atoms through space
Subunits, Domains, and Motives
 Subunit: every amino acid chain is a separate subunit of a protein
 Tertiary structure is assembled from smaller substructures, motives, and larger
substructures, domains
 In many cases, a domain from a large protein will retain its correct 3-d structure even
when its separated from the remainder of the polypeptide chain