FCH 530 Homework 1 1. The -carboxyl group of Glu has a pKa of 4.3. a.

What fraction of the -carboxyl groups will be unprotonated (i.e., -COO- rather than COOH) in a dilute solution of Glu at pH = 5.0? Using Henderson-Hasselbalch equation, pH = pKa + log [A-]/[HA] 5.0 = 4.3 + log [A-]/[HA] 0.7 = log [A-]/[HA] 5.0 = [A-]/[HA] = x in order to figure out the fraction of unprotonated it is equal to 5.0/6.0 = 83% at pH = 5.0 by following the fraction of protonated molecules as x/(x+1) b. At pH =3.8? At pH 3.8, 3.8 = 4.3 + log [A-]/[HA] -0.5 = log [A-]/[HA] 0.5 = log [HA]/[A-] 3.2/1 = [HA]/[A-], then reverse this to get the unprotonated fraction using x/(x+1) 1/4.2 = 24% at pH 3.8 c. explain why this -carboxyl pKa is higher than the pKa of the -carboxyl group. The electron withdrawing alpha-amino group withdraws electrons from the alpha carboxyl group and therefore carries less negative charge than does the gamma carboxyl group. Therefore, the alpha group is more stable than the gamma carboxyl group and the dissociation is more favorable for alpha-COO- and H+. This causes an increase in Ka and shift in pKa lower. 2. Calculate the pH of the following: 0.1 M HCl, 0.1 M NaOH, 3 X 10-5 M HNO3, 5 X 10-5 M HClO4, and 2 X 10-8 M KOH. Show all work. 0.1 M HCl pH=-log[H+] pH=-log[0.1] = 1

0.1 M NaOH pH=-log[H+] we know that [H+]*[OH-]=1.0 * 10-14 so, [H+]=1.0 * 10-14/[OH-] = 1.0 * 10-14/[0.1M]= 1.0 * 10-13 therefore, pH =-log[1.0 * 10-13] = 13 3 X 10-5 M HNO3 strong acid so pH = -log [H+] = -log[3 X 10-5 M] = 4.523 5 X 10-5 M HClO4 pH=4.301 2 X 10-8 M KOH This number is smaller than the concentration of OH- in water from the equation above [H+]*[OH-]=1.0 * 10-14 in water and [H+]=1.0 * 10-7 and [OH-] = 1.0 * 10-7. Because the concentration contributed by KOH is lower than concentration of [OH-] in water, we must take this into consideration. KOH = [2 * 10-8 M K+] + [2 * 10-8 M OH-] H2O= [x M H+] + [x+2 * 10-8 M OH-] (unknown) x{(2 * 10-8 +x)}= 1.0 * 10-14 x2 + 2 * 10-8x -1.0 * 10-14 = 0, solve for x using the quadratic equation

x= [-2 * 10-8 + ((2 * 10-8)2-4(1)(-1.0 * 10-14))1/2]/2(1) you will get two answers. x=9.04 * 10-8 will give you a pH of 7.04 if you plug it in.

3. Draw the structures, full names, three-letter names, and 1-letter symbols for all 20 amino acids. See Table 4-1 in Voet and Voet Biochemistry

4. Draw 4 equivalent Fischer projection formulas for L-alanine.

5. For the dipeptide Glu-Ala write out the structure and estimate the pK of all ionizable groups.
pKa~4.07 -O O O N +H OO pKa~2.10

NH3

pKa~9.47

Using your assigned pK values, determine the net charge at pH 1, 3, 5, 7, 10, 11 pKa Alpha 2.10 amino pKa Side 4.07 chain carboxy pKa Alpha 9.47 carboxy pKa Net charge Calculate the pI (2.10 + 4.07)/2=3.09 6. Write a table describing the main differences between gram-positive and gramnegative bacteria? Gram-positive Gram-negative Thick peptidoglycan layer Thin peptidoglycan layer Single membrane Inner and outer membrane No periplasm Periplasm 7. Write a table summarizing the main differences between prokaryote and eukaryote cells Prokaryotes Eukaryotes Bacteria, Archae Fungi, protests, animals, plants 1-10 m 10-100 m No nucleus Nucleus 8. The dipeptide Ala-His
N O N +H OO N

Charge pH 1 pH2 0 0 to 1/50% 0 0

pH3 -1 0

pH4 -1 0 to -1 50% +1 0

pH5 -1 -1

pH7 -1 -1

pH10 -1 -1

pH11 -1 -1

+1 +1

+1 +1

+1 0

+1 -1

+1 -1

0 -2

0 -2

NH3

alanylhistidine

9. The tripeptide Glu-Pro-Cys

OO O
-O

O
+

HN N

SH O

NH3

10. Show how an oligopeptide of Leu and Lys can be either a branched-chain or a straight-chain structure (only straight-chain structures occur in most natural proteins).
NH3+ NH3+

O N +H

H N O

O N H OO

NH3

leucinyllysinylleucinyllysine

O HN NH3+ O N +H H N O O N H OO NH3+

NH3

branch from the lysine groups