20 Amino Acids

http://wbiomed.curtin.edu.au/teach/biochem/tutorials/aaquiz/index.html
http://www.tamu.edu/classes/eharris/410/Tutorials/Amino%20Acids%20tutorial%20.ppt

http://www.le.ac.uk/by/teach/biochemweb/tutorials/aminoacidstruct.html
Strictly speaking, aliphatic implies that the protein side chain contains only carbon or hydrogen atoms. eg Alanine but not Cysteine (because it contains a Sulfur)

A hydrophobic molecule is repelled by water; literally, hydrophobe means something with a fear of water. eg aromatics (6 carbon ring)? like Tyrosine, aliphatics (neutral), NOT histidine (charged+), usually neutral charged are hydrophobic and don't have OH group (non-polar) (except for Tyrosine), when in doubt, put hydrophilic
* neutral and non-polar
* aliphatics
Interestingly, exactly half (10) of the amino acids are hydrophobic.
Usually it goes, Polar Yes, Hydrophobic No (except Cys and Tyr which are both Polar Yes and Hydrophobic Yes so polar residues tend to be hydrophilic), Glycine is Polar No and Hydrophobic No

Hydrophobic Residues (10 amino acids):
* Cys and Met (all the thiol containing groups)
* all the aliphatics (ala, val, leu, ile)
* all ring containing (tyr, trp, pro, phe) except His because it has strong polarity?
For properties - the only trick I ever learned was FAMILY VW (family volkswagon) for the 8 hydrophobic amino acids: Phe, Ala, Met, Ile, Leu, Tyr, Val, and Trp.

Polar if it has a charge or a free hanging NH, OH or SH that can do hydrogen bonding (but not Met) (11 amino acids):
* acids(-charged): asp, glu
* basic(+charged): lys, arg, his
* amides: asn, gln
* tyr (has OH) and cys (has free SH) (NOT Met because it has C-S-C)
* ser, thr (OH containing)

Mistakes when doing the quiz:
* hydrophobicity
* AspArtate not Aspertate
* Glutamate (E as in gluE) not Q
* Asparagine molecule is wrong, mixed with Glutamine (Gln, Q, Qlutamine) -- has CD (c-delta)
* Asparagine 1 letter code is N (asparagiNNNNNe) not A (A is alanine), neutral amide version of Asp
* Arginine 1 letter code is R (aRRRRginine) not N, basic
* Histidine, although a 5 carbon ring is still aromatic because of N lone pairs
* Proline is NOT aromatic

Group Names:
* Imidazole ring - His
* Pyrolidine ring - Pro
* Phenyl ring - Phe
* Phenol ring - Tyr
* Indole ring - Trp
* Guanidinium - Arg
* Ethyl - Ile

Atom naming
* alpha (A), beta (B), gamma (G), delta (D), epsilon (E), zeta (Z), eta (H)
* when picking 1 or 2, the precedence is S(16 heaviest), O(8), then N(7), then C(6)
* In proline, you count it in a circle
* In Trp, there's a point where you branch (CE2 - closer to NE1 and CE3) from a branch (branchpoint CD2)
* Asp (D) and amide sister (Asn N) only goes up to atom D
* Glu (E) and amide brother (Gln Q) only goes up to atom E
* Lys goes up to NZ (N-epsilon group), longest straight chain
* Arg is longer than Lys, goes up to NE-CZ-NH1 and NH2
* Only Thr and Ile branches early at atom B, like Thr, CB-OG1 and CG2 and Ile, CB-CG2 and CG1-CD1
* Met goes like CB-CG-SD-CE (Met has an E so it ends at E)


Dihedral Angles
* psi - CA-C bond (-60 degrees for right handed helix) (N-CA-C-N in N+1)
* phi - N-CA bond (-50 degrees for right handed helix) (C in N-1 - N-CA-C)
* omega - C-N bond (peptide bond, planar, 180 degrees, 1.33A in length)
* chi1 - CA-CB bond (4 atoms are N-CA-CB-CG)
note: Lys only has chi1, chi2, chi3 and chi4, NO chi5 (need 4 atoms) and Ala has no chi1
* Every angle needs 4 atoms, creating two planes
* In the Mage program, you hold look down the two atoms (so in psi, CA-C bonds are on top of each other), then a 90 degree psi angle will mean that N is 90 degrees away from N(n+1)
* rotamers are energetically staggered sidechain angle conformations

Amino Acid Covalent Bond Lengths. Peptide bond (C-N) is 1.33A long and has a partial double bond character due to the adjacent carbonyl.
ph, pKa, Henderson-Hasselbach Equation
http://www.le.ac.uk/by/teach/biochemweb/tutorials/hendhassel1.html
pH = pKa + log([a-]/[ha])

so if pKa > pH, equilibrium shifts to the left and you get more protonated ions than neutral
pKa = pH @ equilibrium

pI = pH = no charge = zwitterion NH3+ and COO- (normally at pH ~ 7)

explain why alanine has a +1 charge at pI=9.74 at neutral pH
pI=9.74=pH, so at this pH, there's the zwitterion form, no net charge, at pH=7, more acidic, then equilibrium shifts left, so we get protonation of nh2 to nh3+ (NOT coo- to cooh) and so we get a +1 net charge

Zwitterionic (net charge = 0) form in the middle
pka1 (coo-) on avg ~ 2
pka2 (nh3+) on avg ~ 9
pKa3 r-group

pI=(pka1+pka2)/2 for alanine, no charge, so (2+9)/2 ~ 5.5
but for aspartic acid, has a net charge, pkI=(pKa1+pKa3)=(2+4)/2 ~ 3
http://en.wikipedia.org/wiki/List_of_standard_amino_acids

Protonated His