Lecture 2

Question 1

1) Explain protonation and deprotonation in the context of amino acid pKa and pH.

Answer 1

When pH is decreased, we increase the amount of protons, if the pH is LESS THAN the pKa of the amino acid, then it becomes PROTONATED. If the pH is GREATER THAN the pKa of the amino acid, it becomes deprotonated.

Question 2

2) What do the L and D prefixes on amino acid names stand for and which are most common?

Answer 2

L means left handed and all of our natural amino acids are L, the placement of the amino group determines this. Amino group must be on the left

Question 3

3) Based on hydrophilic and hydrophobic properties, what amino acids would you typically find within the internal part of the protein and what would you find on the outer side? Will charge make any difference? What is this term called?

Answer 3

• Nonpolar allypathic, aromatic (Phe especially) on the inside. Polar and charged ones on the outside due to ability to H-bond (mainly).
• AA with a large + charge are considered hydrophobic to they would be internal and vice versa.
• Hydropathy? The relative hydrophobicity

Question 4

4) Name 5 ways that amino acid derivatives can be made.

Answer 4

Proline to hyroxyproline
Glycosylation
Phosphorelation of Ser, Thr, Tyr
Cysteine to Cystine
Met to N-formylmethionine in bacterium

Question 5

5) AA’s have varying ionization values, why are these important?

Answer 5

• Each AA has atleast 2 pka values, so they have different overall charges are different pH values, important for determining the 3D structure and active sites of enzymes

Question 6

5) Titration curves:
What does pI stand for and how is it calculated?
What is the zwitterion form of an amino acid?
What can titration curves tell us about pKa?

Answer 6

pI: isoelectric point of the amino acid (where the net charge is 0), calculated pI=(pK1+pK2)/2
Zwitterion is when the net charge is 0 (when the amine group is protonated and the carboxyl group is deprotonated)
Titration curves can give us the pKa value of an amino acid based on the pH they are exposed to.

Question 7

6) Why does pKa of amino acids vary in proteins that in solution?

Answer 7

• Repulsion of charges from the ammonium or carboxyl group
• induction effect
• electronegative atoms pulling electron density will lower pKA