exam1_review

exam1_review - Energy/Length Scales in Biology: Amino Acids...

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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 (tyr) 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) Protein Review : 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 Interactions Covalent: shared electrons. Need to know the wave function to treat properly. Electrostatic: E = 1 ( q 1 q 2 ) 4 πε r q = electron charge = 1.6 x 10 -19 C r = separation distance ε = relative permittivity (=80 for water) 0 = vacuum permittivity = 8.85 x 10 -12 C 2 /Jm
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exam1_review - Energy/Length Scales in Biology: Amino Acids...

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