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Problem Set 4

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Updated on: October 31, 2021

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Use the structure of Molecule A, depicted below, to answer the following questions.

a) Give the names, three-letter codes, and single-letter codes of the amino acids that are covalently linked to form molecule A.
b) Circle the peptide bond(s) in molecule A.
c) Draw squares around each of the atoms that lie in the same plane as the peptide bond(s) (Hint: there should be six atoms).
d) Assign stereochemistry (D or L) below each of the chiral carbons in molecule A.
e) Calculate the isoelectric point (pI) for molecule A. In 1997, scientists in Dr. Peter Kim's laboratory at the Whitehead Institute at MIT determined the core structure of the gp41 HIV envelope glycoprotein by protein x-ray crystallography. It is shown in a ribbon diagram representation below. The first (left) view is from the side. The second (right) view has been rotated 90° about the horizontal in order to show its dimensions from the top.

a) Each of the six helices in this core structure is approximately the same length. Approximately how many amino acids make up the gp41 core structure?
b) Drawing upon your knowledge of protein secondary structure as a reference, estimate the dimensions (length, width, and height) of the HIV gp41 protein molecule in nanometers. The graph below depicts the O2 binding curves for myoglobin and hemoglobin at pH 7.4.

a) Print or draw yourself a copy of this graph then label each of the curves as Mb (myoglobin) or Hb (hemoglobin). Why do the shapes of the two curves differ?
b) Which of these curves will differ significantly as a function of pH? Draw the new curve at pH 6.8.
c) Explain the molecular mechanism of this relationship between pH and O2 binding.
d) What is the physiological significance of the relationship between pH and O2 binding? Draw a model for the structure of an Immunoglobin G (IgG) class antibody protein. Make sure that it contains each of the following labels:
a) Heavy chains
b) Light chains
c) Constant domains (Constant Heavy 1, 2, and 3 and Constant Light)
d) Variable domains (Variable Heavy and Variable Light)
e) Amino- and carboxy-terminal ends of all polypeptide chains
f) Disulfide bonds
g) Covalently attached polysaccharide (glycosylation site)
h) Antigen binding site Use the structure of Molecule A, depicted below, to answer the following questions.

a) Give the names, three-letter codes, and single-letter codes of the amino acids that are covalently linked to form molecule A.
b) Circle the peptide bond(s) in molecule A.
c) Draw squares around each of the atoms that lie in the same plane as the peptide bond(s) (Hint: there should be six atoms).
d) Assign stereochemistry (D or L) below each of the chiral carbons in molecule A.
e) Calculate the isoelectric point (pI) for molecule A.
In 1997, scientists in Dr. Peter Kim's laboratory at the Whitehead Institute at MIT determined the core structure of the gp41 HIV envelope glycoprotein by protein x-ray crystallography. It is shown in a ribbon diagram representation below. The first (left) view is from the side. The second (right) view has been rotated 90° about the horizontal in order to show its dimensions from the top.

a) Each of the six helices in this core structure is approximately the same length. Approximately how many amino acids make up the gp41 core structure?
b) Drawing upon your knowledge of protein secondary structure as a reference, estimate the dimensions (length, width, and height) of the HIV gp41 protein molecule in nanometers.
The graph below depicts the O2 binding curves for myoglobin and hemoglobin at pH 7.4.

a) Print or draw yourself a copy of this graph then label each of the curves as Mb (myoglobin) or Hb (hemoglobin). Why do the shapes of the two curves differ?
b) Which of these curves will differ significantly as a function of pH? Draw the new curve at pH 6.8.
c) Explain the molecular mechanism of this relationship between pH and O2 binding.
d) What is the physiological significance of the relationship between pH and O2 binding?
Draw a model for the structure of an Immunoglobin G (IgG) class antibody protein. Make sure that it contains each of the following labels:
a) Heavy chains
b) Light chains
c) Constant domains (Constant Heavy 1, 2, and 3 and Constant Light)
d) Variable domains (Variable Heavy and Variable Light)
e) Amino- and carboxy-terminal ends of all polypeptide chains
f) Disulfide bonds
g) Covalently attached polysaccharide (glycosylation site)
h) Antigen binding site

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