Problem set 1: Amino acid and peptides (to accompany module 1)

o Please note: You MUST practice drawing NEAT, legible titration curves ON graph paper, which
has been provided for you at the end of this problem set packet. Please print out the desired
number of copies as needed.

Practicing the basics

1. Practice learning how to recognize and name (full name, three–letter code and one–letter code)
the 20 protein amino acids. Please use your module packet. Do NOT use any other source.
2. Practice drawing the 20 protein amino acids. Learn both the skeletal and the atomic
representations.
3. Learn the pKa values of the amino acids with ionizable side chains.
4. Learn the pKa values of the –amino functional group and the –carboxylate functional group of
a free amino acid
5. Learn the pKa values of the –amino end and the –carboxylate end of a peptide or protein
6. Using your module packet, please practice assigning charges to fully protonated and fully–
deprotonated amino acids.
7. Using your module packet, please practice assigning charges to fully protonated and fully-
deprotonated amino acid side chains.

Problems

8. Which amino acids are considered aliphatic? Please provide their complete names.
9. Which amino acids are considered aromatic? Please provide their complete names.
10. Which amino acids are considered hydrophilic? Please provide their complete names.
11. Which amino acids are able to engage in hydrogen bonding? Please provide their complete
names.
12. Which amino acids (please provide complete names) exhibit resonance as part of their side chain
structures?
13. At a pH of 7.40, which amino acid is able to function ONLY as a hydrogen bond donor?
14. At a pH of 7.40, which amino acids are able to function ONLY as hydrogen bond acceptors?
15. At a pH of 7.40, which amino acid has the ability to donate one hydrogen bond and accept one
hydrogen bond?

16. Calculating the charges of fully-protonated amino acids

a. Please calculate the charge on a fully-protonated free amino acid with the one–letter code, K.
b. Please calculate the charge on a fully–protonated free amino acid with the one–letter code, D.
c. Please calculate the charge on a fully-protonated free amino acid from the GAV LIM FWP NQ
category

17. Calculating the charges of fully-deprotonated amino acids

a. Please calculate the charge on a fully-deprotonated free amino acid with the one–letter code, H.
b. Please calculate the charge on a fully–deprotonated free amino acid with the one-letter code, Y.
c. Please calculate the charge on a fully-deprotonated free amino acid from the GAV LIM FWP NQ
category

18. Calculate the isoelectric point of the amino acid that comprise the GAV LIM FWP NQ group.
Please note: you do NOT need to calculate the isoelectric point of each and every one. You need
to follow the method we used during the class lecture.

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19. Calculating isoelectric points of free amino acids
Calculate the isoelectric points for the following free amino acids:
C, D, H, K and R

20.
a. How many protein amino acids are considered to be zwitterionic at a pH of 7.40, which is the
approximate pH in mammalian cells?
b. Which amino acids are not considered to be zwitterionic at a pH of 7.40.

21.
a. How many amino acids have one chiral center?
b. Which amino acid has no chiral center?
c. Which amino acids have two chiral centers?

22. How many atoms comprise a repeating unit of a peptide backbone?

23.
a. What is the minimum number of ionizable functional groups that can be present in a peptide or a
free amino acid?
b. What are these functional groups? Please provide their names.

24. Calculating peptide charge

a. Please calculate the charge of the hypothetical peptide H3N+1 –A Q L T K C R–COO–1 at a pH of

7.40
b. Please calculate the charge of the hypothetical peptide H3N+1 –R N K D H E F–COO–1 at a pH of
7.40
c. Please calculate the charge of the hypothetical peptide H3N+1 –L S R E K D H–COO–1 at a pH of
7.40

25. Calculating the isoelectric point of a peptide

a. Please calculate the isoelectric point of the hypothetical peptide H3N+1– V D N Y R H–COO –1
b. Please calculate the isoelectric point of the hypothetical peptide H 3N+1– K Q E S R H C–COO –1
c. Please calculate the isoelectric point of the hypothetical peptide H 3N+1– T D N L Y Q–COO –1

26.
a. Draw a representative titration curve for the GAV LIM FWP NQ group of amino acids. Assume
that each amino acid is solubilized in a solution at a pH of 1.00.
b. Neatly indicate the buffering regions and the pH range

27.
a. Draw the titration curve for the free amino acid with the one-letter code, R. Assume that each
amino acid is solubilized in a solution at a pH of 1.00.
b. Neatly indicate the buffering regions and the pH range

28.
a. Draw the titration curve for the free amino acid with the one-letter code, D. Assume that each
amino acid is solubilized in a solution at a pH of 1.00.
b. Neatly indicate the buffering regions and the pH range

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29.
a. Draw a titration curve for the hypothetical peptide H3N+1–L D R Q–COO–1. Assume that the
peptide is solubilized in a solution at a pH of 1.00.
b. Neatly indicate the buffering regions and the pH range
c. How many total ionizable groups are in this peptide?

30.
a. Draw a titration curve for the hypothetical peptide H3N+1–H V S N–COO–1. Assume that the
peptide is solubilized in a solution at a pH of 1.00.
b. Neatly indicate the buffering regions and the pH range
c. How many total ionizable groups are in this peptide?

31.
a. Draw a titration curve for the hypothetical peptide H3N+1–D H C Q L–COO–1. Assume that the
peptide is solubilized at a pH of 1.00.
b. Neatly indicate the buffering regions and the pH range
c. How many total ionizable groups are in this peptide?

32. Which amino acids have an ionizable side chain?

33. What is the meaning of the isoelectric point?

34. Drawing peptide structures. Please assume a pH of 7.40. Please show all of the backbone atoms
and please use SKELETAL representations for the side chains of the amino acids.

a. Please draw out the structure of the hypothetical peptide H3N+1–M N V D Y–COO–1

b. Please draw out the structure of the hypothetical peptide H3N+1–L S K Q F–COO–1

c. Please draw out the structure of the hypothetical peptide H3N+1–I R T P E–COO–1

35. Calculating the isoelectric points of peptides

a. Calculate the isoelectric point of the hypothetical peptide H 3N+1–R K F–COO–1

b. Calculate the isoelectric point of the hypothetical peptide H3N+1–H C S–COO–1

c. Calculate the isoelectric point of the hypothetical peptide H 3N+1–D N K–COO–1

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 36.

a. Determining estimated and precise protonated: deprotonated ratios of ionizable functional groups.

Please determine the estimated and precise protonated: deprotonated functional groups at a pH value of
7.40 and round to whole number values.

Ionizable functional Estimated protonated: deprotonated Precise protonated: deprotonated ratio

group ratio
Carboxylate group
of a free amino acid
Amino group of a
free amino acid
Carboxylate end of a
peptide or protein
Amino end of a
peptide or protein

b. Please determine both the estimated and precise protonated: deprotonated ratios at a pH of 7.40
and round to whole number values.

Name of ionizable functional group Estimated protonated: Precise protonated: deprotonated

deprotonated ratio ratio
R group of the amino acids D and E

Thiol

R groups of the amino acids, S and T

Phenol

Imidazole

–amino

Guanidinium

37.

a. Determine the number of amino acids in a protein that has 535 peptide bonds.

b. A peptide has 29 residues. How many peptide bonds does it contain?

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 38.

An octapeptide is composed of Asp, His, Trp., Tyr, Arg., Lys, Pro and Met. To determine its
sequence, the following experiments were done:

o One cycle of Edman degradation resulted in the formation of PTH–Tyr.

o When trypsin was used, it resulted in the formation of a pentapeptide composed of Met, Trp.,
Lys, Pro and Tyr and the remaining residues. It also resulted in the formation of a dipeptide
consisting of His and Arg., and a free amino acid, Asp.
o Using cyanogen bromide results in the formation of a tetrapeptide composed of homoserine,
Trp., Pro and Tyr and the remaining residues.
o When chymotrypsin was used, it resulted in the formation of a tripeptide composed of Pro,
Tyr and Trp. and the remaining residues.
Based on this information, please determine the sequence of this peptide in the box below. Make sure to
indicate the ends of the peptide and use dashes to connect amino acids in sequence.

39. Please consider the hypothetical peptide: H3N+1– G F P H L R V K S D–COO–1

a. If we were to use trypsin on this peptide, how many cuts would be made by trypsin? How many
fragments would we see?

b. If we were to use chymotrypsin on this peptide, how many cuts would be made by chymotrypsin?
How many fragments would we be able to see?

40. Please consider the peptide hormone glucagon whose sequence is shown below.

H3N+1–H S Q G T F T S D Y S K Y L D S R R A Q D F V Q W L M N T–COO–1

a. What would be the sizes of the peptide fragments if someone decides to do a cyanogen bromide
treatment on glucagon?

b. How many fragments would be generated if we were to use chymotrypsin?

c. How many cuts would be made by trypsin?

41. Consider the peptide hormone, ghrelin whose sequence is shown below.

H3N+1–G S S F L S P E H Q R V Q Q R K E S K K P P A K L Q P R–COO–1

a. Please determine the number of cuts and the resulting number of fragments that are generated of
someone cleaves ghrelin with trypsin.
b. Please determine the number of cuts and the resulting number of fragments that are generated of
someone cleaves ghrelin with chymotrypsin.
c. What would be the resultant amino acid if someone performs exactly one cycle of Edman
degradation on ghrelin?
d. Would it be useful to perform a cyanogen bromide cleavage on ghrelin?

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 42. Consider the side chains of the ionizable amino acids. Determine the charge on the SIDE CHAIN
in their protonated and deprotonated form

Side chain Protonated charge on Deprotonated charge on side chain

side chain
Thiol
Carboxylate side chain of D and E
Hydroxyl group of S and T
Phenol
Imidazole
–amino
Guanidinium

43. Please consider the hypothetical peptide sequence: H3N+1–V S L Q G R–COO–1

a. In this peptide, how many amino acids are capable of participating in hydrogen bonding

b. In this peptide, how many amino acids would be considered hydrophobic?

c. How many total ionizable groups are there in this peptide?

44. Learning to perform categorical amino acid analysis using naturally occurring long/large peptide
and protein sequences

The sequence shown below is from a Chilean Rose Tarantula toxin. Please use the sequence to answer
the questions that follow. The sequence has been reproduced for you in each part of the question.
Please note that this problem requires you to use what is known as redundant counting for a given amino
acid category. In other words, you need to count a given categorical amino acid more than once.

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

a. How many amino acids are zwitterionic? Please do a redundant count!

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

b. How many amino acids are non-zwitterionic? Please do a redundant count!

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

c. How many amino acids are hydrophobic? Please do a redundant count.

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

d. How many amino acids exhibit resonance? Please do a redundant count.

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

e. How many amino acids are aliphatic? Please do a redundant count.

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

f. How many aromatic amino acids are there? Please include both hydrophilic and hydrophobic
aromatic amino acid residues in your response and please do a redundant count

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

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 g. How many amino acid residues can exhibit hydrogen bonding? Please use a redundant count.

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

h. How many ionizable functional groups are there? Please use a redundant counting method.

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

i. Are there any amino acid residues that contain two chiral centers within this sequence?

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

j. If we were to use chymotrypsin, how many cuts and fragments would we generate?

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

k. If we were to use trypsin, how many cuts and fragments would we generate?

H3N+1–E C G K F M W K C K N S N D C C K D L V C S S R W K W C V L A S P F–COO–1

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