From Biolk483

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



  • 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
  • Ala, Leu, Val, (Pro), Ile
  • no catalysis but they fold the chain because of the hydrophobic effect
  • Phe, Trp
  • Terrible H20 solubility
Contain Sulphur
  • Met
  • disulphide bonds
  • hold protein in position
  • mostly found on outside of protein
  • mostly found on outside of protein
  • 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).
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