Name _______________ID_____________
Chem 153A – Homework 1 due Tuesday 1/13 @ 11:59 pm
1. [Exploratory] The Van der Waals radius of a carbon atom is 170 pm. How much larger
are the following? (Notes: Estimate end-to-end; feel free to use google for this question)
a. The length of the average amino acid residue (from amine to amine)
(average amino acid residue is 3.2 Å long*) roughly 2x larger
*my estimate
b. The average alpha helix (length)
(average alpha helix is roughly 15 Å long) 9x larger
c. Eukaryotic ribosome (radius)
(eukaryotic ribosome radius is 140 Å long) 82x larger
d. E. Coli cell size
(E. Coli has a length of 2 μm) 11,760x larger
e. The average human skin cell
(average human skin cell has diameter of 30 μm) 175,000x larger
f. The length of the tip of your thumb (measured from first knuckle to the edge of
your nail)
(the tip of my thumb is 2.5 cm) 1.5 x 108x larger
2. Consider two molecules, X and Y.
a. X is able to dissolve in water. What does this imply about the favorability of
interactions between molecules of X versus interactions between X and water?
Given this, you know the following about X: 1) It is hydrophilic, and can form
beneficial intermolecular interactions with water (which will based on
permanent dipoles/charges) 2) Addressing the specific question, it prefers to
form interactions with water rather than forming interactions with itself – i.e.
interacting with water is thermodynamically favorable
b. Y is unable to dissolve in water. What does this imply about the favorability of
interactions between molecules of Y versus interactions between Y and water?
Draw what happens to Y in water.
This tells us that: 1) Y is hydrophobic and likely can’t form
beneficial intermolecular interactions with water (because
Y is nonpolar) 2) Due to the un-favorability of interactions
with water, Y will prefer to interact with itself, making it
aggregate in solution (this property is called immiscibility).
(Representation of clathrate
cages collapsing also works)
1
, Name _______________ ID _____________
3. [Exploratory] Vitamins are an interesting class of organic molecule because they aren’t,
in any way, distinguished by specific functional groups; their only common denominator
is that they’re essential nutrients. Make an educated guess as to whether the following
vitamins are water or fat soluble. (best method to make this determination is looking at
water soluble the predominance of polar functional groups!)
fat soluble
water soluble
fat soluble
4. Given two acids, HA and HB, with pKas of 4 and 6 respectively, answer the following.
a. Which has the higher proton affinity?
HB has a higher affinity
b. When deprotonated, which has a less stable negative charge?
HB has a less stable negative charge
c. Which will dissociate more when added to water?
HA will dissociate more when added to water
d. For each, what is the major (predominant) protonation state at pH 3, pH 4, and
pH 7?
HA: (pH = 3, HA), (pH = 4, A- and HA), (pH = 7, A-)
HB: (pH = 3, HB), (pH = 4, HB), (pH = 7, B-)
e. For each, at what pH is the ratio of protonated to deprotonated 3:1?
HA: pH = 4 + log(1/3) = 4-0.48 = 3.52
HB: pH = 6 + log(1/3) = 6-0.48 = 5.52
2
, Name _______________ ID _____________
5. Consider the intermolecular interactions occurring within a group of methanol
molecules. List the types of interactions that can occur, then draw these interactions
individually, labeling any partial charges.
6. You are handed a solution containing 0.125 M acetic acid and 0.25 M sodium acetate.
The pKa of acetic acid is 4.75. Using this information, answer the following.
a. What is the Ka of acetic acid?
Ka = 10-4.75 = 1.78 x 10-5
b. Is this a buffer system? How do you know?
It is a buffer system. We know this because there are significant amounts of both
conjugate acid and base (ratio of 1:2)
c. Using the Henderson-Hasselbach equation, determine the pH of this system.
pH = 4.75 + log(2/1) = 4.75+0.3 = 5.05
7. You are given a solution of alanine at pH 4.5:
a. What is the ratio of to in the solution?
1:1000 1:100 1:10 Ratio is around 1:300, so closest to
1:1 10:1 100:1 1:100, but within these two ratios
1000:1
b. Is alanine a good buffer at pH 4.5? Briefly explain why or why not. If you
answered no, include the pH range(s) at which alanine would be a good buffer.
No it’s not a good buffer at pH 4.5, it’s outside of the two buffer ranges (which
are ±1 of each pKa)
pH ranges of alanine buffer systems: 1.34-3.34, 8.69-10.69
3
Chem 153A – Homework 1 due Tuesday 1/13 @ 11:59 pm
1. [Exploratory] The Van der Waals radius of a carbon atom is 170 pm. How much larger
are the following? (Notes: Estimate end-to-end; feel free to use google for this question)
a. The length of the average amino acid residue (from amine to amine)
(average amino acid residue is 3.2 Å long*) roughly 2x larger
*my estimate
b. The average alpha helix (length)
(average alpha helix is roughly 15 Å long) 9x larger
c. Eukaryotic ribosome (radius)
(eukaryotic ribosome radius is 140 Å long) 82x larger
d. E. Coli cell size
(E. Coli has a length of 2 μm) 11,760x larger
e. The average human skin cell
(average human skin cell has diameter of 30 μm) 175,000x larger
f. The length of the tip of your thumb (measured from first knuckle to the edge of
your nail)
(the tip of my thumb is 2.5 cm) 1.5 x 108x larger
2. Consider two molecules, X and Y.
a. X is able to dissolve in water. What does this imply about the favorability of
interactions between molecules of X versus interactions between X and water?
Given this, you know the following about X: 1) It is hydrophilic, and can form
beneficial intermolecular interactions with water (which will based on
permanent dipoles/charges) 2) Addressing the specific question, it prefers to
form interactions with water rather than forming interactions with itself – i.e.
interacting with water is thermodynamically favorable
b. Y is unable to dissolve in water. What does this imply about the favorability of
interactions between molecules of Y versus interactions between Y and water?
Draw what happens to Y in water.
This tells us that: 1) Y is hydrophobic and likely can’t form
beneficial intermolecular interactions with water (because
Y is nonpolar) 2) Due to the un-favorability of interactions
with water, Y will prefer to interact with itself, making it
aggregate in solution (this property is called immiscibility).
(Representation of clathrate
cages collapsing also works)
1
, Name _______________ ID _____________
3. [Exploratory] Vitamins are an interesting class of organic molecule because they aren’t,
in any way, distinguished by specific functional groups; their only common denominator
is that they’re essential nutrients. Make an educated guess as to whether the following
vitamins are water or fat soluble. (best method to make this determination is looking at
water soluble the predominance of polar functional groups!)
fat soluble
water soluble
fat soluble
4. Given two acids, HA and HB, with pKas of 4 and 6 respectively, answer the following.
a. Which has the higher proton affinity?
HB has a higher affinity
b. When deprotonated, which has a less stable negative charge?
HB has a less stable negative charge
c. Which will dissociate more when added to water?
HA will dissociate more when added to water
d. For each, what is the major (predominant) protonation state at pH 3, pH 4, and
pH 7?
HA: (pH = 3, HA), (pH = 4, A- and HA), (pH = 7, A-)
HB: (pH = 3, HB), (pH = 4, HB), (pH = 7, B-)
e. For each, at what pH is the ratio of protonated to deprotonated 3:1?
HA: pH = 4 + log(1/3) = 4-0.48 = 3.52
HB: pH = 6 + log(1/3) = 6-0.48 = 5.52
2
, Name _______________ ID _____________
5. Consider the intermolecular interactions occurring within a group of methanol
molecules. List the types of interactions that can occur, then draw these interactions
individually, labeling any partial charges.
6. You are handed a solution containing 0.125 M acetic acid and 0.25 M sodium acetate.
The pKa of acetic acid is 4.75. Using this information, answer the following.
a. What is the Ka of acetic acid?
Ka = 10-4.75 = 1.78 x 10-5
b. Is this a buffer system? How do you know?
It is a buffer system. We know this because there are significant amounts of both
conjugate acid and base (ratio of 1:2)
c. Using the Henderson-Hasselbach equation, determine the pH of this system.
pH = 4.75 + log(2/1) = 4.75+0.3 = 5.05
7. You are given a solution of alanine at pH 4.5:
a. What is the ratio of to in the solution?
1:1000 1:100 1:10 Ratio is around 1:300, so closest to
1:1 10:1 100:1 1:100, but within these two ratios
1000:1
b. Is alanine a good buffer at pH 4.5? Briefly explain why or why not. If you
answered no, include the pH range(s) at which alanine would be a good buffer.
No it’s not a good buffer at pH 4.5, it’s outside of the two buffer ranges (which
are ±1 of each pKa)
pH ranges of alanine buffer systems: 1.34-3.34, 8.69-10.69
3
