Biology exercise Discussion Paper
a) Draw the amino acid L-tyrosine in its fully protonated form. What are the three-letter and single-letter codes for tyrosine? Show the proper stereochemistry in your drawing. Sketch a titration curve for tyrosine (Hint: plot pH on the y-axis and equivalents of strong base on the x-axis). What is the charge on the prevailing species of tyrosine at pH 12? Calculate the isoelectric point (pI) of tyrosine.
b) Draw the amino acid L-histidine in its fully protonated form. What are the three-letter and single-letter codes for histidine? Show the proper stereochemistry. Sketch a titration curve for histidine. What is the charge on the prevailing species of histidine at pH 12? Calculate the isoelectric point (pI) of histidine
The chemical structures of four amino acids are depicted below and labeled as I, II, III, and IV. Use your knowledge of amino acid nomenclature, structure, and chemistry to answer the questions that follow.
Chemical structures of four amino acids.
a) What is the single letter code of amino acid I?
b) Which of these does not carry a neutral charge at pH 7?
c) Which amino acid is classified as aromatic?
d) Which is shown above as a D-amino acid
e) What is the three letter code of amino acid III?
f) What is the isoelectric point (pI) of I?
g) Which has a chiral center within its side group?
h) Which amino acid contains the indole side group?
i) Which cannot form hydrogen bonds through its side group?
j) Which will elute last from (or bind most tightly to) an anion exchange column at pH = 7?
k) Which has a polar uncharged side group?
l) Between amino acid II and amino acid III, which would you more expect to see buried at the core of a globular protein?
The enzyme gyrase is a tetramer composed of two subunits of molecular weight 110,000 and two subunits of molecular weight 90,000. A sample of the pure gyrase is run on a size exclusion column under physiological conditions (i.e., neutral pH, normal saline). A single peak corresponding to molecular weight 400,000 is detected. A separate sample of gyrase is electrophoresed on an SDS polyacrylamide gel under reducing conditions. What is the expected outcome of the SDS PAGE? Explain your answer.
Use the structure of Molecule A, depicted below, to answer the following questions.
Molecular structure of biomolecule.
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.
Ribbon diagram of HIV gp41 protein.
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.