7.012 Fall 2003 17.012 Problem Set 1Question 1Bob, a student taking 7.012, looks at a long-standing puddle outside his dorm window.Curious as to what was growing in the cloudy water, he takes a sample to his TA, BradStudent. He wanted to know whether the organisms in the sample were prokaryotic oreukaryotic.a) Give an example of a prokaryotic and a eukaryotic organism.Prokaryotic: Eukaryotic:b) Using a light microscope, how could he tell the difference between a prokaryotic organismand a eukaryotic one?c) What additional differences exist between prokaryotic and eukaryotic organisms?Please print out this problem set and record your answers on the printed copy. Answers tothis problem set are to be turned in at the box by 4:10 Wednesday, September10. Problem sets will not be accepted late. Solutions will be posted on the web September 11,2003.MIT Biology Department7.012: Introductory Biology - Fall 2004Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel7.012 Fall 2003 2Question 2A new startup company hires you to help with their product development. Your task is to finda protein that interacts with a polysaccharide.a) You find a large protein that has a single binding site for the polysaccharide cellulose.Which amino acids might you expect to find in the binding pocket of the protein? What is thestrongest type of interaction possible between these amino acids and the cellulose?In the course of your research you discover a small polypeptide that is associated withcellulose. You want to design an enzyme that will bind this small polypeptide. You designthe enzyme shown below.b) In the table below please indicate which amino acid you placed in each position to give thestrongest possible interaction between your enzyme and the small polypeptide. For instance,you would choose an amino acid for position D that most strongly interacts with the carboxylgroup of the small polypeptide. Also list what interaction occurs at each position (choose from:covalent bond, ionic bond, hydrogen bond, or van der Waals forces).Amino AcidpositionAmino AcidInteractionABCDEF7.012 Fall 2003 3Question 3One of your classmates, Mike, is working on a new science fiction novel. He approaches youwith questions regarding cell membranes.a) Explain the following to Mike.i) What are lipids.ii) Why are saturated fatty acids more likely to be solid at room temperature thanunsaturated fatty acids.b) On the diagrams below label the hydrophilic and hydrophobic regions of thephospholipids.POOOO––CH2CHCH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2c) Why does the structure of the phospholipid molecule favor the formation of bilayers ormembranes?d) Mike proposes the following structure for the membranes of an alien life form. Whatconditions would need to exist to make this arrangement possible?Portion of alien membrane7.012 Fall 2003 4Question 4Prions (pronounced pree-ahns) are agents that cause a novel type of fatal brain disease. Bovinespongiform encephalopathy (BSE or mad cow disease), sheep scrapie and Creutzfeldt-Jakobdisease (CJD) of humans are examples of prion diseases. Prions enter cells and convert normalproteins found within the cells into prions just like themselves. The normal cell proteins haveall the same "parts" as the prions--specifically the same amino acid building blocks--but theyfold differently.a) What is the primary structure of a protein? What force or forces (covalent bonds, ionicbonds, hydrogen bonds, or van der Waals forces) are involved in primary structure?b) What is the secondary structure of a protein? What force or forces (covalent bonds, ionicbonds, hydrogen bonds, or van der waals forces) are involved in secondary structure?c) What is the tertiary structure of a protein? What force or forces (covalent bonds, ionic bonds,hydrogen bonds, or van der waals forces) are involved in tertiary structure?d) Do you expect both the normal and the infectious versions of a prion protein to have thesame primary structure? Why or why not.e) Do you expect both the normal and the infectious versions of a prion protein to have thesame tertiary structure? Why or why
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