Amino acid side chain charge calculation (approximation) 1. Write out ionic form
ID: 473664 • Letter: A
Question
Amino acid side chain charge calculation (approximation)
1. Write out ionic forms of the amino acids and determine acid and base charge forms. 2. Use the Henderson-Hasselbach equation to calculate ratio
3. Assigncharge(approximation):
If 10%, assign plus/minus 0.9 or 0.10 values. If 99% assign whole number (or 1% of whole and 99% of whole). If at pKa assign half value 0.5 (plus/minus)
a) The amino acid sequence of sea lamprey adrenocorticotropic hormone is given below. Given the sequence, identify each ionizing amino acid residue and indicate its charge (-1, 0, or +1) in the completely protonated amino acid form of the polypeptide hormone.
S-V-S-S-P-K-Y-A-M-G-H-F-R-W-G-S-P-D-K-A-T-I
b)
Given the same sequence above, indicate the charge (-1, 0, or +1) on each amino acid residue in
the completely proton dissociated form of the polypeptide hormone.
Explanation / Answer
1.
Amino acids are molecules which contain both a carboxylic acid and an amine group.
Charged Amino Acids (at physiological pH)
Acidic : aspartic acid, glutamic acid
Basic : histidine, lysine, arginine
2.
The formula for the Henderson–Hasselbalch equation is: pH=pKa+log(A-HA).
Where pH is the concentration of [ H+],pKa is the acid dissociation constant, and [A-]and [HA] are concentrations of the conjugate base and starting acid.
The equation can be used to determine the amount of acid and conjugate base needed to blood of a certain pH.
example: Use the Henderson-Hasselbalch equation to calculate the ratio of H2CO3 to HCO3- in blood having a pH of 7.40.[H2CO3]/[HCO3-]=?
pKa = 6.37
7.40 - 6.37=1.03
10^1.03 =10.7 = [HCO3-]/ [H2CO3]
[H2CO3]/ [HCO3-]= 1 / 10.7=0.0933
3.
a) The third peptide, with an apparent molecular weight of 15 kDa, was tentatively designated lamprey ACTH, based on a structural feature: the N-terminal 22-residue-MSH (SVSSPKYAMGHFRWGSPDKATI) is followed by four consecutive basic amino acids (RKRR) and a ACTH-like sequence (PVRPNTSDSPEIPDYAF--). MSH-B is 10 and 100 times more potent than alpha-MSH and MSH-A, respectively, in a frog skin assay in vitro, whereas the lamprey ACTH showed no melanotropic activity.
b) Amino Acid
charge at pH 2
charge at pH 7
charge at pH 12
Glutamtic acid
0
-1
-1
Aspartic acid
0
-1
-1
Lysine
+1
+1
0
Arginine
+1
+1
+1 (50%)
Histidine
+1
+1 (25%)
0
Tyrosine
0
0
-1
Cysteine
0
0
-1
b) Amino Acid
charge at pH 2
charge at pH 7
charge at pH 12
Glutamtic acid
0
-1
-1
Aspartic acid
0
-1
-1
Lysine
+1
+1
0
Arginine
+1
+1
+1 (50%)
Histidine
+1
+1 (25%)
0
Tyrosine
0
0
-1
Cysteine
0
0
-1
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