# 09/13/06

• note: much of the notes on pKa here is omitted as it is very difficult to put into web-text

## pKa

• there are about 8 pKas that we'll need to know
• pKa of H on N of amino acid is 9.1
• pKa of H on OH of Carboxy group of amino acid is 2.1
• pKa of H on OH of Glutamic acid's r-group is 4.0
• we limit our study of pKa to labeling charges as +1, +1/2, and 0 for N and 0, -1/2, and -1 for O
• so:
• if the pH is above 2.1, then the O (with the H removed because the pH is high so there are lots of H+ floating around) will have a charge of -1.
• if the pH is exactly 2.1, then the O with the H removed will have a charge of -1/2 (because approximately half of the Os have their H and half do not)
• if the pH is below 2.1, then the O with the H removed will have a charge of 0.
• these rules are true also for the OH group of the R-group of Glutamic acid (using a 4.0 pH)
• and:
• if the pH is above 9.1 the N will have a charge of 0 because the H+ has been removed from the N
• if the pH is exactly 9.1, then we say N has a charge of +1/2 because half have lost their H and half have not.
• if the pH is below 9.1, then we say the N has a charge of +1 because it has all its H
• so, we add up all the charges on all the dissociable groups to get the entire chain's charge
• all this is to show that pKa never changes, but the charge of the chain can be changed by changing the pH in which it resides
• Here are all the pKas we need to know:
 GROUP Amino Acid pKA alpha-COOH all 2.1 r-group COOH Asp, Glu 4.0 imidazole His 6.1 alpha-amine all 9.1 -SH group Cys 8.3 phenalic group Tyr 10.1 r-group Epslion Lys 10.8 adeno group Arg 12.5
##### Isoelectric Point
• this is the pH at which the net charge on the polypeptide is 0
• this is the minimum water solubility a polypeptide can have because there is zero charge (and charge helps make things water soluble)
• at the Isoelectric point, a polypeptide will not move in an electric field, therefore, this phenom can be used to separate out one's desired polypeptide from others because each has a very specific isoelectric point.
##### Relative Abundance of Amino Acid Forms
• we use glycine as a generalization of all amino acids:
• 99.58% of glycine in the world is in the zwitterion form: it has formal charges but no net charge.
• 0.41% is anionic: having the H from the Carboxyl group removed
• 0.00019% is cationic: having an extra H on the amine group
• 0.0000037% is neutral
• how do we know?
• we compare the dipole moment of water and glycine
• water's dipole moment is 1.8 and glycine's is 11.2, so we know that LOTS of the glycines in the bottle must have formal charges

## The 20 Common Amino Acids

• remember that common is not the same as abundant: there are tons of other amino acids, often in greater abundance than the twenty our genetic code includes
• amino acids in proteins that are non-common are the result of post-translation modification of common amino acids
• essential amino acids are those that must be consumed via diet because our bodies cannot make them
• there are 10 of these
• Argenine we actually learn how to make as we become adults.
• we have 19 amino acids and 1 imino acid: proline
• the ring structure of proline makes it very restrained
• we can identify proline easily because it shines a brilliant yellow while all the others shine bluish-reddish.

### Categories of Amino Acids

• amino acids are categorized based on r-group
• we can divide the amino acids into four groups based on whether they prefer a water or lipid environment.
##### Non-polar (Hydrophobic)
• Inert. Can't form H-bonds.
• about 50% of all amino acids fall in this group
• have hydrophobic side chains, don't have dissociable groups, often have CH2s and Aromatic groups
• mostly found on inside of proteins
• these guys are responsible for folding the protein
##### Neutral, Polar
• neutral side chains that are polar, they like water
• mostly found on outside of protein
###### Aliphatic
• Ala, Leu, Val, (Pro), Ile
• no catalysis but they fold the chain because of the hydrophobic effect
###### Aromatic
• Phe, Trp
• Terrible H20 solubility
###### Contain Sulphur
• Met
• disulphide bonds
• hold protein in position
##### Anionic
• mostly found on outside of protein
##### Cationic
• mostly found on outside of protein
##### Aromatic
• there are only three, and we could classify them in the other groups

### Protein Shape

1. Chain: all amino acids are involved in the chain
2. Folding: some amino acids are involved in folding because of hydrophobic effect, some because of disulfide bonds (see Non-polar amino acids)
3. Function: some amino acids cause function because theya re dynamic.
• Proline's involvment in shape
• not flexible (because of ring)
• no enzymatic activity on alpha-helix
• if proline is present, alpha helix won't work so we call it an alpha helix terminator
• this is an exmaple of an unique function
• Phenylalanine
• a great binding site for the helper prophin which also has Pi electrons with a metal in the middle toggline between 2+ and 3+
• so these two (phenylalanine and porphin) are planar molecules
• prophin must be protected on one side of porphin's plane (this keeps H20 from oxidizing the metal and is useful in biochemical reactions).