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Identify amino acids which when being part of a protein structure have side chains that can participate in the hydrogen bond formation. Draw the structure of each amino acid and indicate how it can form the hydrogen bonding.

2. Identify amino acids which when being part of a protein structure have side chains that can participate in chemical reactions. Explain why and how. For instance which residues are used for post-translational modifications, for regulation of protein activity, how are glycans and lipids attached to proteins?

3. Identify amino acids which when being part of a protein structure have side chains that can ionize or are charged at pH 7. Based on the pKR values of the free amino acids estimate/calculate what percentage of the amino acid is in the charged form.

Explain why some amino acids, like serine in serine proteases, can ionize/lose proton at neutral pH while their pKR values suggest that this should not be possible.

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Deanna Hettinger
Deanna HettingerLv2
29 Sep 2019

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Related questions

1. Amino acid changes in the primary structure of the protein arenot capable of causing changes in the
overall shape of a protein.
a.) True
b.) False

2. An alpha helix:
a.) is destabilized by the amino acid alanine
b.) can only form by hydrogen bonding between different polypeptidechains
c.) can only form when cysteines form disulfide bridges within thisstructure
d.) all of the above
e.) none of the above

3. What will likely happen if two aspartates at pH 5 are next toeach other in a polypeptide chain?
a.) The side chains of these amino acids will be uncharged andthere will be no effect.
b.) The side chains of these amino acids will be charged and theywill attract each other.
c.) The side chains of these amino acids will be charged and theywill repel each other.
d.) Not enough information is given to determine the effect.

4. Consider the amino acid phenylalanine. Which of the followingbest describes where you predict this
amino acid would be found?
a.) This amino acid is hydrophobic and would be on the surface of aprotein that is in the middle
of a membrane.
b.) This amino acid is hydrophilic and would be on the surface of aprotein that is in the middle
of a membrane.
c.) This amino acid is hydrophobic and would be in the interior ofa protein that is in the middle
of a membrane.
d.) This amino acid is hydrophilic and would be in the interior ofa protein that is in the middle of
a membrane.
e.) Not enough information is given to determine.

5. The difference between fetal and adult hemoglobin with regard tooxygen binding occurs because fetal
hemoglobin has an amino acid substitution in one of its chains thatresults in a histidine being replaced by a
serine.
a.) True
b.) False

1. The side chain of tyrosine is considered to be polar because even though it is reminiscent of phenylalanine it also has two types of atoms that have large differences in electronegativity with asymmetry at the terminus.

a.) True

b.) False

2. Which of these changes in primary structure will be certain to cause a loss of protein activity?

a.) Asp to Glu

b.) His to Lys

c.) Trp to Ser

d.) Gly to Pro

e.) Not enough information is given since any one of these changes could be severe depending on the context of the situation

3.The difference between fetal and adult hemoglobin with regard to oxygen binding occurs because fetal hemoglobin has an amino acid substitution in one of its chains that results in a histidine (adult version) being replaced by a serine (fetal version).

a.) True

b.) False

4. What will likely happen if the side chains of aspartate and histidine at pH 5 are next to each other in a polypeptide chain?

a.) The side chains of these amino acids will be uncharged and there will be no electrostatic effect.

b.) The side chains of these amino acids will be charged and they will attract each other.

c.) The side chains of these amino acids will be charged and they will repel each other.

d.) Not enough information is given to determine the effect.

5. A beta pleated sheet:

a.) can occur between two different polypeptide chains
b.) can be formed by either intramolecular or intermolecular hydrogen bonds
c.) can only form when cysteines form disulfide bridges within this structure
d.) forms when side chains of D and E attract each other
e.) both a and b

You wish to design a new serine protease that will cleave polypeptide chains to create a series of fragments that contain either cysteine or serine residues at their C-termini. Which of the following characteristics of the new protease is most important to achieve this result?

A.

The protease should have an oxyanion hole that is capable of binding only to cysteine side chains.
B.

The protease should have a specificity pocket that can accommodate only small, uncharged polar side chains.
C.

The protease should have a specificity pocket that can accommodate only small negatively charged side chains.
D.

The protease should be able to form hydrogen bonds to the side chains of the cysteine residues in the substrate polypeptide that do not form with other amino acids.
E.

The protease should be able to form irreversible disulfide bonds to the cysteine residues in the substrate polypeptide.

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