Problem Set 1

Which of the following statement about hydrogen bonds is TRUE? Please
select the single best answer and explain why other answers are wrong?
A. Hydrogen bonds only occur among water molecules
B. Hydrogen bonds involve sharing of electron pairs
C. Hydrogen bonds refer to any non-covalent bonds involving a
hydrogen atom
D. Hydrogen bonds are the primary reason for the cohesiveness of water
E. It takes more energy to break a hydrogen bond than to break an
O-H bond

The correct answer is D.
A is wrong b/c hydrogen bonds involve the sharing of electron pairs.
B is wrong b/c hydrogen bonds are a kind of non-covalent
interaction as only the sharing of electron pairs involves covalent interactions.
C is wrong b/c hydrogen bonds involve bonds between other
hydrogen, N, O, and F.
E is wrong b/c an O-H covalent bond requires more energy to break
than a hydrogen bond.

Draw a water molecule:
(a) Label the bond angle and localize partial charges (?- and ?+)
of the two dipoles
(b) Explain briefly why these dipoles occur.
(c) Do the two dipole of water cancel each other? Why?
(d) Draw a second water molecule participating in a hydrogen bond
with the first.

Dipoles occur b/c w/n O-H bond, O is much more electronegative than
the H, therefore the shared electron pair is pulled closer to O,
making H partially positive, O partially negative, and forming a
dipole. Two O-H bonds of water are separated by a bond
angle of 104.5�which gives water a bent formation. These two dipoles
of water do not cancel each other but rather they form a net dipole.

For each of the following parts, pick the best answer out of the
choices: covalent bonds, hydrogen bonds, ionic interaction, van der
Waals interaction and hydrophobic interaction. What kinds of
interactions hold together?
A. The one oxygen and two hydrogens in one water molecule
B. Molecules of water with each other in a glass of water
C. A lipid micelle in water
D. Two cysteines in a disulfide bond
E. Hydration of sodium cation
F. Two neighboring hydrocarbon molecules in an oil tank with no water

A. Covalent bonds
B. Hydrogen bonds
C. Hydrophobic interaction
D. Covalent bond
E. Ionic interaction
F. van der Waals interaction

Will the following pair of molecules interact via hydrogen bonding?
If not, state why. If yes, show how this interaction can occur.
A. Isopropanol and isopropanol
B. Propane and propane
C. Propane and isopropanol

A. Yes a hydrogen bond would form between the alcohol OH.
B. The two propane molecules would not be able to interact with
each other as it only has nonpolar C-C and C-H bonds. In addition,
the electronegativity of the carbons is too low to form any hydrogen bonds.
C. The isopropanol and propane will not interact via hydrogen
bonding. Isopropanol has a hydrogen atom bound to a highly
electronegative atom but propane doesn�t have another highly
electronegative atom to interact with the hydrogen atom in isopropanol.

See the two scenarios depicted below:
A) Which weak intermolecular interaction is driving the
transition from A to B?
B) Which condition has more ordered water and why?
C) Which condition has higher entropy and why?

A. Hydrophobic interactions
B. Condition A has more ordered water as more water is exposed to
the nonpolar surface area in which the water commences to align into
an ordered cage. In B the nonpolar surface regions are packed against
each other so the amount of area that is exposed to water is greatly decreased.
C. Condition B has higher entropy as the ordered water in A is
released into the bulk solution which in turn would increase the
overall randomness of the system.

Are the following statements true or false? Explain why.
A. van der Waals interactions are weaker than hydrogen bonds.
B. van der Waals interactions can occur between non-polar molecules.
C. Individual hydrogen bonds are long-lived interactions.


A. Yes, van der Waals interactions are weaker than
hydrogen bonds because van der Waals are transient, induced dipoles
while hydrogen bonds are permanent dipoles.
B. Yes, van der Waals interactions can occur between any atoms
with the only two considerations in mind being their polarities and
their proximity to one another.
C. This statement is false as hydrogen bonds can be transient
like those in water molecules. Despite O-H dipoles are permanent,
both hydrogen and oxygen in a water molecule can switch hydrogen
bonding partners easily when present in an aqueous solution. Hydrogen
bonds can also be disrupted by thermal energy.

Among the 20 common amino acids:
i.) Which one is highly reactive at physiological pH? Explain why.
ii.) Draw the zwitterion form of this amino acid.

i.) Histidine. It has a side chain pKa of 6.0 which is close in
proximity to physiological pH of 7.4. Small fluctuations of pH in
cells make the side chain of Histidine donate or accept a proton.
ii.)

For the following eight types of amino acids:
(i) Match the one letter code to the correct amino acid (0.8 pt):
(ii) Which of these two absorb UV light at 280 nm? (0.2 pt).
(iii) Which of these can be glycosylated?
Tryrosine
Glutamine
Lysine
Tryptophan
Glutamate
Phenylalanine
Asparagine
Asparatate

i. ) Y, Q, K, W, E, F, N, D
ii.) Tryptophan and tyrosine can absorb 280 nm UV light.
iii.) Asparagine can be glycosylated

Your lab needs to use several amino acids for a key experiment. You
find a drawer in your lab storing several vials of amino acid powders.
Unfortunately, the labels are worn out. While the lab manager would
like to purchase a new set of amino acids, you suggest to find out the
identities of these powders using the knowledge you learned in BIBC
100. You first dissolve the powder in HCl, and then measured the pH
value as you titrated OH- to the solution, and you obtained a
titration curve as shown in green below.
(i) How many ionizable groups does this AA have? What is its side
chain pKa?
(ii) Which AA is this one? Why?
(iii) Can you estimate the isoelectric point of this AA based on the
pKa values?


i.) There are three ionizable groups which is
indicated by the three buffer zones in the titration curve. The pKa
values of the three ionizable groups are 2, 9, 12.5. The side chain
pKa is 12.5 which can be deduced by the values of the NH3+ and COOH
which are respectively 2 and 10.
ii.) It is my belief that this amino acid is Arg because the pKa
value of the side chain of Arg is approximately 12.5.
iii.) Yes, it is possible to estimate the isoelectric point of the
amino acid based on the pKa values. This can be calculated by
averaging the two pKa values that flank the zwitterion form (COO- +
side chain) divided if half. The values would be (9+12.5)/2 which
would result in an isoelectric point of 10.8.

You accidentally mixed 2 precious proteins. Protein A is a large,
positively-charged molecule while Protein B is a small,
negatively-charged molecule at physiological pH. (i) Propose 2 methods
to separate these proteins. Be sure to explain the order in which
these proteins elute.
(ii) Is it possible for protein B to contain Lysines or Arginine?
Explain why.
(iii) If you were to convert protein A to a zwitterion, would you
increase or decrease pH. Why?


i.)Ion exchange chromatography, two ways to do it:
first way=cation chromatography where the beads are (-) charged so
they bind to + charged Protein A; means Protein B would elute first.
Second way= anion chromatography where beads are + charged so that
they bind to (-) charged Protein B; Protein A would elute first. Size
exclusion chromatography Protein B would go through column�s beads
since it's smaller thus traveling all the way through the column to
the bottom. Since Protein A is much larger it would be too large to
enter the pores in b/w beads so it would go around the beads thus
being the one to elute faster.
ii.) It is possible for protein B to contain Lys or Arg as Protein B
is (-) charged at physiological pH. This means Protein B can have
basic and acidic residues.
iii.) Since Protein A is currently a + charged molecule, the
transition to a zwitterion would cause it to increase in pH as it
would release a proton. Hence, it would become less acidic.