01:694:301 Lecture Notes - Lecture 2: Ab Initio, Molecular Partners, Leucine

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Chapter 2 ‘Protein Composition and Structure’
KNOW the structures, names, and both 1- and 3- letter abbrev. 20 amino acids used
in protein synthesis
o Refer to pg. 29 – 31
o Refer handout Amino Acid Letter Codes
! Hydrophobic – FILL MY VW
F - phe (phenyalanine) I – ile (isoleucine) L – leu (leucine)
M – met (methionine) Y – tyr (tyrosine)
V – val (valine) W – trp (tryptophan) (double U, double ring)
! Polar – HK RED
H – his (histidine) K – lys (lysine)
R – arg (arginine) E – glu (glutamate) D – asp (aspartate (-ic acid)
! Aliphatic – PG CATS
P – pro (proline) G – gly (glycine) Ccys
A – ala (alanine) T – thr (threonine) S – ser (serotonin)
! Amides – Q & N
Q – gln (glutamine) N – asn (asparagine)
! Leftovers - JOUJOUX (ZBJOUX)
*Not used in protein synthesis; (O sometimes used for Ornithine)
KNOW the ionization shown in Table 2-1 (pg. 32); do not need to know exact pKa
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MUST be able to tell D from L amino acids
o **Biological amino acids are nearly always L.
o Identifying L & D amino acids using swap method
! Most oxidized at top (-COOH)
! Amino group to be on the left
! R-group to be on the bottom
! H to be on the right
! Even # of swaps " L
! Odd # of swaps " D
o Refer to L & D amino acids handout for other methods
Be able to draw peptides (pg. 33)
o Remember that amide formation involves the loss of water,
leaving amino acids ‘residues’ behind.
o Series of amino acids joined by peptide bonds for polypeptide
chain
! Each amino acid unit in polypeptide is residue
! Amino group is considered the ‘beginning’ of chain
! Disulfide bridges are most common bridges cross-links b/w
linear polypeptide chains (ex: cysteine " cystine)
! Mostly found in extracellular protein
! Proteins have unique amino acid sequence specified by
genes (discovery of insulin)
o Peptide Flexibility – twisting turning of bonds
! Every peptide bond is predictably planar
! Note that due to resonance double bond character of C=N,
bond inflexible; cannot rotate freely. Conformation of
peptide backbone is constraint.
Trans configuration – All most all proteins are trans (more
favorable, stable); two α-carbons are on opposite sides of peptide
bond
Cis configuration – Steric hindrance b/w groups attached to α-
carbons
! The following bonds b/w –NH2 and –COOH and α-carbon
are free to rotate; allows proteins to fold in different ways
ϕ (phi bond) " CαN ψ (psi bond) " Cα – C
A Ramachandran Plot (pg. 38) is a theoretical tool for analyzing
the structure of proteins
o Be able to reproduce Figure 2.26 & 2.29
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