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section3_ak - MIT Department of Biology 7.014 Introductory...

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MIT Department of Biology 7.014 Introductory Biology, Spring 2005 Recitation Section 3 Answer Key February 9-10, 2005 Biochemistry—Proteins A. CBS proteins, 3D representation The protein we will consider today and periodically throughout the term is the yeast cystathionine beta synthase (CBS) protein. Today we will see gels visualizing wild-type and mutants versions of the yeast CBS protein. Yeast that lack CBS protein can not synthesize the amino acid cysteine. Mutant versions of the human CBS protein can lead to a very serious disease called homocystinuria. Some symptoms include mental retardation, early strokes and heart disease. First consider a crystallographic model of a form of CBS protein. Open the CBS structure html file in Internet Explorer. Rotate the molecule and get an idea of the three dimensional structure of CBS. The true 3-dimensional structure of CBS can be observed using the “Show Spacefill” button, and a trace of the peptide backbone can be observed using the “Show Ribbon” button. 1. What is the primary structure of a protein? What information does the modeling program provide us about the primary structure of CBS? The primary structure of a protein is the linear sequence of amino acids. It is impossible to determine this for CBS with the representation that has been provided. We could look up the sequence in the Protein Data Bank and it would read something like (…Trp-Ile-Arg-Pro-Asp-Ala-Pro-Ser…) through all 430 amino acids. 2. What is the secondary structure of a protein? What information does the modeling program provide us about the secondary structure of CBS? The secondary structure is described as α -helical or β -sheet. Remember that secondary structure is controlled by backbone hydrogen bonds between amino acids. CBS contains both types of secondary structure. The majority of the secondary structure elements are -helices. There are 4 -sheets. 3. What is the tertiary structure of a protein? What information does the modeling program provide us about the tertiary structure of CBS? The tertiary structure is determined by the side-chain interactions between amino acids in adjacent secondary structures. Although it is hard to resolve the desired interactions from this view, it is clear that amino acids in both the -helices and -sheets are interacting with amino acids in other secondary structure elements to contribute to the overall tertiary structure. 4. What is the quaternary structure of a protein? What information does the modeling program provide us about the quaternary structure of CBS? (Hint: Use the “Color Ribbon by Protein Subunit” button) The quaternary structure of a protein is created by a number of distinct interacting amino acid chains. If we color CBS by chain we find that there are two amino acid strands indicating that the protein is a homodimer.
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B. Protein gels 1. Yeast cells produce enough CBS to fulfill their needs depending on the conditions in which they are growing. In order to procure large quantities of the enzyme, we created special
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This note was uploaded on 05/02/2009 for the course BIOL 7.014 taught by Professor Walker during the Spring '05 term at MIT.

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section3_ak - MIT Department of Biology 7.014 Introductory...

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