Homework 2 KEY BCH2333 Winter 2017

Topics covered: pH, pKa, H-H equation, amino acids, nucleic acids

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?
b. At pH =3.8?
c. explain why this -carboxyl pKa is higher than the pKa of the -carboxyl group.

a. at pH =5.0

5.0 = 4.3 + log [A-]/[HA]

0.7 = log [A-]/[HA]

5.0 = [A-]/[HA]

in order to figure out the fraction of unprotonated you need [A-]/([HA]+[A-]).

If 5.0 = [A-]/[HA] then [HA] = [A-]/5
Therefore the fraction of unprotonated = [A-]/(1/5*[A-]+[A-]) = 1/(0.2+1) = 0.83 or
83%

b. At pH =3.8?

At pH 3.8, 3.8 = 4.3 + log [A-]/[HA]

-0.5 = log [A-]/[HA]

0.316 = [A-]/[HA]

[HA] = 3.16[A-]

Therefore the fraction of unprotonated = [A-]/(3.16*[A-]+[A-]) = 1/(3.16+1) = 0.24

or 24%

c.
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; HCl fully dissociates so it makes 0.1M [H+]

pH=-log[H+]
Homework 2 KEY BCH2333 Winter 2017

pH=-log[0.1] = 1

0.1 M NaOH
pH=-log[H+]
we know that [H+]*[OH-]=1.0 x 10-14
so, [H+]=1.0 x 10-14/[OH-] = 1.0 x 10-14/[0.1M]= 1.0 x 10-13
therefore, pH =-log[1.0 x 10-13] = 13

3 X 10-5 M HNO3
strong acid so it fully dissociates making 3 x 10-5 M H+
pH = -log [H+] = -log[3 X 10-5 M] = 4.523

5 X 10-5 M HClO4
Strong acid.
pH=4.301

2 x 10-8 M KOH
This number is smaller than the concentration of OH- in neutral water
[H+]*[OH-]=1.0 * 10-14 in neutral 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.

From the KOH we have [K+] = 2 10-8 M and [OH-] = 2 10-8 M

From water we have [H+] = x M and [OH-] = x + 2 10-8 M (add the OH- from
KOH to the water self ionization)

Kw = [H+][OH-] = 1.0 10-14

x(x + 2 10-8)}= 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. A hospital lab has 10 ml of stomach juice (hours after a meal, so no food is there as a
buffer) and it was titrated to neutrality with 7.2 mL of 0.1 M NaOH. What is the pH of
stomach juice (HCl)?

Amount of OH- used = 7.2 mL x 0.1 mmol/mL = 0.72 mmol

This means there was 0.72 mmol of acid in the 10 mL of stomach juice.
[H+] = 0.072 M in stomach juice. pH = 1.14
Homework 2 KEY BCH2333 Winter 2017

4. You have 100 mL of 0.08 M phosphate buffer at pH 6.0. By accident, 3.2 mL of 6 M

HCl was added. What is the resulting pH? The pkas of phosphate are 2.14, 6.86, 12.4.

First calculate the moles of total acid.

19.2 mmol of HCl
Use HH eqn to calculate [HPO42-]/[H2PO4-] ratio (these are the conj base and acid
for the pKa = 6.86)
[HPO42-]/[H2PO4-]=0.13
[HPO42-] + [H2PO4-] = 0.08M
[H2PO4-] = 0.0708M
[HPO42-] = 0.0092M
With 100mL of buffer there is 0.92 mmol of [HPO42-] and 7.08 mmol of [H2PO4-]
HCl will protonate the HPO42- to make H2PO4- leaving 19.2 mmol 0.92 mmol =
18.3 mmol of H+
HCl will now protonate the 8 mmol of H2PO4- leaving 18.3 mmol - 8 mmol = 10.3
mmol of HCl.
10.3 mmol/103.2mL = 0.1 M HCl
pH = 1

5. Draw the structures, full names, three-letter names, and 1-letter symbols for all 20
amino acids. Indicate the pKas for each of the functional groups on each amino acid.

See course notes.

6. Draw the Fischer projection formula for L-alanine. Rotate L-alanine and draw 4 other
rotation states of the molecule where at least two bonds are in the plane of the page.

CO2 CO2 CO2 CO2

H
NH3 H3N H
H3N H = H3N H CH3 CO2 CO2
H3N H NH3
CH3 CH3 H CH3 CH3 H3C

Fisher
Here are a few, CH3 H
projection
there are many H H3N CO2
H3N CO2
CH3

These two are good to remeber

They are easy to connect to make a
polypeptide chain.
Homework 2 KEY BCH2333 Winter 2017

7. For the dipeptide Glu-Ala write out the structure and estimate the pK of all ionizable
groups.

O O
pKa~4.07
-O O- pKa~2.10
N
NH3 +H O

pKa~9.47

Using your assigned pK values, determine the net charge at pH 1, 3, 5, 7, 10, 11

Charge
pKa pH 1 pH2 pH3 pH4 pH5 pH7 pH10 pH11
Alpha 2.10 0 Partial -1 -1 -1 -1 -1 -1
Carboxy negative
pKa
Side 4.07 0 0 0 Partial -1 -1 -1 -1
chain negative
carboxy
pKa
Alpha 9.47 +1 +1 +1 +1 +1 +1 0 0
amino
pKa
Net +1 between 0 Between -1 -1 -2 -2
charge +1 and 0 0 and -1

8. Draw the following amino acid or oligopeptide structures:

a. The dipeptide Ala-His

O
H
N
H3N O
O N

N
H
Ala His
at pH 7.0
b. The tripeptide Glu-Pro-Cys
Homework 2 KEY BCH2333 Winter 2017

O O

Pro
N
H3N
O NH SH
Glu O
O Cys
O

at pH = 7
c. 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).
Lys
O Branched chain amide bond
H3N (to the epsilon amino of lysine)
O O
H
N
H3N O
O Lys
Leu Leu
straight chain amide bond HN
NH3
(to aplha amino of lysine)
NH3 O

9. What amino acid has a methyl alcohol attached to the -carbon? Draw it as a fisher
projection with the correct stereochemistry and with two bonds to the -carbon in the
plane of the page.

CO2 OH
H3N H H O
CH2OH H3N
O
Ser
Homework 2 KEY BCH2333 Winter 2017

10. What amino acid has a guanidinium ion at pH 7? Draw the Fisher projection of this
amino acid with the correct stereochemistry and with two bonds to the -carbon in the
plane of the page.

CO2
H2N NH2
H3N H
CH2 NH
CH2
CH2
NH H O
H3N
H2N NH2 O
Arg R

11. What is the net charge of the peptide DRAMA at pH 8? Draw the structure of this
pentapeptide.

O O O
H H
N N O
H3N N N
H H
O O O

S
NH

H2N NH2 pH = 8, net charge = 0

12. Draw the structure of the artificial sweetener aspartame (L-aspartyl-L-phenylalanyl-

methyl ester) at pH 6. What is the charge on the peptide at pH 6?
O
Phe
O O
H
N
H3N O
O
Asp
neutral at pH 6.

13. Draw the structures of the 4 DNA nucleosides.

NH2 O
NH2 O
N N N NH
N NH
N N N O N O
N N NH2
HO HO HO HO
O O O O

OH OH OH OH
A G C T
Homework 2 KEY BCH2333 Winter 2017

14. Draw the structure of the 4 RNA nucleotides.

NH2 O NH2 O
N N N NH N NH

O N N O N N NH2 O N O O N O
-O P O O -O P O O -O P O -O P O
O O
O- O- O- O-
OH OH OH OH OH OH OH OH
A G C U

15. What is the difference between a nucleoside and nucleotide?

Nucleoside is base plus sugar. Nucleotide is base plus sugar plus phosphate

16. Show the base pairing for G with C, A with T, and A with U. What non-covalent
forces are involved in these base pairings? Of these three base pair interactions, which
has the strongest non-covalent attraction and why?

Hydrogen bonds. GC since it has 3 H-bonds.

17. Show the acid-base equilibrium reaction for adding the acid HA to water. Give the
equilibrium equation. Show the equation that defines the Ka of the acid. How do these
two equations differ?

HA + H2O H3O + A

[H3O+][A-] [H3O+][A-]
Keq = Ka =
[HA][H2O] [HA]

Keq = Ka/[H2O]

18. Define the following and give an example of each as it relates to biochemistry:
Hydrophobic interaction
Hydrogen bonds
Disulfide bond
London Forces
Ionic interactions

See any text for these answers.

Homework 2 KEY BCH2333 Winter 2017

19. Draw all the tautomers you can for the bases cytosine and uracil.

NH2 NH2 NH NH

N N NH NH

N O N OH N OH N O
H H

O O OH OH

NH NH N N

N O N OH N OH N O
H H

20. Draw the DNA sequence 5-GTACC-3.

O
N NH

O N N NH2
O P O O O
O
NH
O
N O
O P O O NH2
O N N
O
N N
O P O O NH2
O
N
O
N O
O P O O NH2
O
N
O
N O
O P O O
O
OH