AA continued

Question 1

What is Myoglobin?

Answer 1

protein that stores O2 in muscle tissue

Question 2

How are polar and non polar aa usually classified

Answer 2

NON POLAR: will be dominated by hydrocarbons

POLAR: bonds between H with O, N, sometimes S. electrons are not shared equally creating unbalanced charges.

Question 3

How can you tell if something will bond

Answer 3

look for polarized group. H-bonds are also directional, work best if donor and acceptor are in line with one another

Question 4

free amino acids are ___ due to their amino and carboxylate groups

Answer 4

weak electrolytes

Question 5

What is henderson-hasselbalch equation for aa

Answer 5

pH= pKa +log (deprotonated)/(protonated)

Question 6

the amino and carboxylate group often exist as what at pH 7

Answer 6

Coo- and NH3+

Question 7

How are amino acids linked in a peptide chain

Answer 7

alpha-amino groups and alpha-carboxylate groups are linked as UNCHARGED AMINDE BONDS

x-NH-CHR-CO-x

• note: some side chains will interact with one another

Question 8

What are the amino acids with ionizable side chains?

Answer 8

7

• aspartate and glutamate (neutral when protonated and -1 when deptotonated (at pH7))
• arginine, lysine and histidine (ionize on their side chain N atoms, +1 when protonated and neutral when deprotonated)
• cysteine: goes from SH to S- when deprotonated (neutral at pH7)
• tyrosine: Goes from OH to O-

Question 9

How can you tell where an aa undergoes deprotonation

Answer 9

pKa tells where in the pH scale, lower pKa becomes deprotonated first (acids)

• a molecule can have several ionizable groups, each with its own pKa value
• pKa changes slightly when an aa is part of a peptide chain

Question 10

How do aa become deprotonated

Answer 10

• as pH inc, [H+] dec, deprotonation is more likely to occur
• “group” undergoes this transition approx 1 unit before/after pKa value
• when pH is one or more unit higher than pKa, group is fully DEPROTONATED
• when pH=pKa ratio of protonated to deprotonated is 50-50
• when pH is one or more unit lower than pKa, group is fully PROTONATED

NOTE: pH/pKa does NOT tell if pos/neg

Question 11

Groups that ionize on O or S are ___ when protonated and ____ when deprotonated

Answer 11

neutral, negative

Question 12

Groups that ionize on N are ___ when protonated and ____ when deprotonated

Answer 12

positive, neutral

Question 13

How do you calculate the exact state of ionization at a given pH

Answer 13

• when less than 1 unit away from pKa
  pH= pKa +log (deprotonated/protonated)
• let Deprotonated =a, and protonated = 1-a
  -sub in and isolate for a