3. 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. 4. Use the structure of Molecule A, depicted below, to answer the following questions. , +H3N H H N. H Molecule A O 0 NH 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 (pl) for molecule A. 5. 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. in Jul 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. 3. 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. 4. Use the structure of Molecule A, depicted below, to answer the following questions. , +H3N H H N. H Molecule A O 0 NH 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 (pl) for molecule A. 5. 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. in Jul 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.