09/13/06

From Biolk483

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

Contents 1 pKa 1.1 Isoelectric Point 1.2 Relative Abundance of Amino Acid Forms 2 The 20 Common Amino Acids 2.1 Categories of Amino Acids 2.1.1 Non-polar (Hydrophobic) 2.1.2 Neutral, Polar 2.1.2.1 Aliphatic 2.1.2.2 Aromatic 2.1.2.3 Contain Sulphur 2.1.3 Anionic 2.1.4 Cationic 2.1.5 Aromatic 2.2 Protein Shape

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

• don't worry about this group.
• 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).