Energy/Length Scales in Biology
Amino Acids Review
Non-polar side groups: Glycine (gly), Alanine (ala), Valine (val), Leucine (leu), Isoleucine (ile), Methionine (met),
Phenylalaline (phe), Proline (pro), Tryptophan (trp)
Uncharged polar side groups: Serine (ser), Threonine (thr), Asparagine (asn), Cysteine (cys), Glutamine (gln), Tyrosine
Acidic side groups: Aspartic Acid (asp), Glutamic Acid (glu)
Basic side groups: Lysine (lys), Arginine (arg), Histidine (his)
Useful amino acids:
Cys (not very reactive and rare – 1.7% abundant), Gly (small, mobile, 7% abundant), Leu (most
abundant – 9%), Tryptophan (least abundant – 1.3%, best for spectroscopy)
Primary structure – the sequence of the amino acids.
Secondary structure – local 3D structure formed due to H-bonds.
The most common are alpha helices and beta sheets.
Alpha helix – 3.6 residues/turn, 1.5A/residue, linear distance = 3.6n A
Beta sheet – 3.4A/residue
Tertiary structure – the 3D structure of the entire protein
Quarternary structure – arrangement of multiple polymer subunits
Covalent: shared electrons.
Need to know the wave function to treat properly.
= electron charge = 1.6 x 10
= separation distance
= relative permittivity (=80 for water)
= vacuum permittivity = 8.85 x 10