Download Exam 1 v6 Win2014 Bio200

Name: TA Name: Lab section: .
Biology 200 Winter Quarter 2014 Exam 1, Version A 100 points Honor Code Agreement -­‐ Signature: ________________________________ Date: ____________ (You agree to not accept or provide assistance to anyone else during this exam.) *************************************************************************************** DO NOT OPEN EXAM UNTIL DIRECTED TO DO SO • Make sure you have 6 pages, including this one. Print your name and information on ALL pages. • Please use a pen. Pen is much easier to read, even with extensive crossing-­‐out. Pencil-­‐written exams are acceptable, but may not receive full credit to penciled answers on regrades. • When asked, provide concise and clearly written answers. We may deduct points if you do not fully answer the question or if your answer is too vague or too confusing for us to follow. Extra information, if incorrect, will lose points. • When finished, please hand to your TA if possible. For Question 5: These structures are shown at pH = 7.0 Arginine (Arg): Glutamate (Glu): Bio200 Exam 1 Version A Page 1 of 6 Name: TA Name: Lab section: .
1. (23 pts) Flesh-­‐eating bacteria are a growing problem due to climate change. These bacteria have an enzyme that dissolves a particular flesh protein. Your research team believes that the flesh-­‐
dissolving enzymes can be stopped by a competitive inhibitor. a) (3 points) You don’t know anything about specific structures below, but you understand scale. Put an “L” next to the 3 most likely competitive inhibitors: ____ Long branched carbohydrate polymer ____ Carbohydrate monomer ____ A carbon atom ____ A single fatty acid ____ A golgi apparatus ____ A eukaryotic cell ____ A 3-­‐amino-­‐acid protein ____ An entire 930-­‐amino-­‐acid protein ____ a water molecule b) (5 pts) To test potential competitive inhibitor candidates, you attach a “Tst” molecule to each of them. The candidate-­‐Tst complex is colorless, while the Tst alone has a bright red color. You test the enzyme, the candidate-­‐Tst, and flesh protein all together. Will tubes with good competitive inhibitors be red or colorless? Why? Circle one: Red Colorless Explain your reasoning in 1-­‐2 sentences, max: c) (5 pts) You find a miracle drug called ‘Ukb’: Ukb completely and permanently inactivates 92% of all flesh-­‐dissolving enzymes in live human infections. Why are patients that take this drug still experiencing the same amount of flesh protein loss? Explain your reasoning in 1-­‐2 sentences, max: d) (5 pts) A different drug (‘Dhj’) will destroy all hydrogen and ionic bonds of the flesh-­‐dissolving enzyme. You see this effect in laboratory tests with only the Dhj, the enzyme, and the flesh protein substrate. Do you think this is a good thing to use to treat patients with flesh-­‐eating infections? Why or why not? Explain your reasoning in 1-­‐2 sentences, max: e) (5 pts) The active site of the flesh-­‐dissolving enzyme has eight R-­‐groups that contact the substrate. Six of these R-­‐groups are acidic or highly polar. What does this tell you about the mechanism of action of this enzyme? Explain at the molecular level in 1-­‐2 sentences, max: Bio200 Exam 1 Version A Page 2 of 6 Name: TA Name: Lab section: .
2. a) (8 pts) Fill out the following table. Put an ‘R’ in each box that is True about that molecule. This molecule could form a This molecule is (or is This molecule is hydrogen bond with water made of) amino-­‐acids clearly amphipathic b) (2 pts) Draw a small star on a high-­‐redox-­‐energy bond on one of the structures in the table above. 3. (5 pts) a) Imagine an ocean planet covered by a liquid that is made primarily of the last molecule in the chart above. This ocean planet has no phospholipids, but it does have a replacement molecule that fills the same role. Draw several of these replacement molecules interacting in solution. Your molecule should be identifiable as a carbohydrate, lipid, protein, or nucleic acid. Be sure to show the chemical structure of at least one molecule of your new molecules. Also, indicate which parts of your membrane contact the liquid and which are protected from the liquid. b) (5 pts) Organisms on this planet use ~20 different carbohydrate monomers and hundreds of different polymer structures within their cells. However, every single carbohydrate monomer has the chemical formula C5H10O5. Explain this diversity of carbohydrate structures in 1-­‐2 sentences, max. Bio200 Exam 1 Version A Page 3 of 6 Name: TA Name: Lab section: .
4. (18 pts) Phospholipid Dynamics: Inside the plasma membrane shown below are several integral membrane proteins labeled with the type of molecule that they can help to move across the membrane. You can assume that the molecules shown are the only molecules around this membrane and that they are found in large numbers in the ratios shown here. Li+ a) (3 pts) This cell is impermeable to the poisonous carbohydrate animose. What transport mode is needed to m ove m ore animose out of the cell? Cl-­‐ Circle one: Active transport Facilitated Diffusion Passive Diffusion Cy5 & Li+ How do you know? Explain in 1 sentence or less. Br-­‐ K+ H2C=CH2 Li+ b) (4 pts) Would any of these be highly permeable? Cy5 Animose Circle one: Cl-­‐ HCN through a b ilayer with very long phospholipid tails Li+ C16H15N through a bilayer with very saturated phospholipid tails Lithium ion (Li+) through a bilayer at high temperature Br-­‐ C2H6 through a bilayer at high temperature Why or why not? Explain in 1-­‐2 sentences. Br-­‐ animose K+ Br K+ Inside of the Cell c) (4 pts) What types of amino acid R-­‐groups would you expect to find on Br-­‐ the inside of the animose transporter protein? Explain in 1-­‐2 sentences. d) (3 pts) The animose carrier protein was built: Circle one: In the Smooth ER In the Rough ER In the Golgi e) (4 pts) Cy5 is an important nutrient. To import as many Cy5 molecules as possible, this cell uses system of transport that moves Li+ across the membrane at the same time. Why does this double-­‐transport help the cell? Explain in 1-­‐2 sentences, max. Bio200 Exam 1 Version A Li+ animose Cy5 Cy5 Br-­‐ Br-­‐ H2C=CH2 Br-­‐ animose Br-­‐ Cy5 Outside of the Cell Page 4 of 6 animose Name: TA Name: Lab section: .
5a) (4 points) (True or False) 'There is an extremely huge number of possible protein sequences that could be either found in nature or synthesized'. Is this sentence true or false? Explain in 2 sentences of less. b) (10 points) You work for a biotech company that asked you to purify a particular fully functional protein (protein A) out of a soup of several proteins (cell lysate). One of your colleagues suggested that you try to boil the solution, cool it down and centrifuge it in a tube to separate soluble and insoluble parts. You were skeptical about boiling proteins, but you gave it a try and indeed it worked! In the end, protein A was in the soluble part, purified, fully functional. Explain succinctly: What properties of protein A made this procedure possible and successful? Why did boiling work in this case? Explain your answers in a paragraph or less. c) (11 points) Consider the following 4 amino acid sequence (from N-­‐terminus to C-­‐terminus) for the nuclear localization signal of a hypothetical protein called 'Husky': Lys -­‐ Arg -­‐ (any amino acid) -­‐ Lys Husky is imported to the nucleus to perform an important cellular function. i) (6 pts) Predict whether Husky will be imported into the nucleus if the second amino acid (Arg) is substituted by Glu. Explain your answer in one sentence, max. ii) (5 pts) What type of interactions are likely to occur between the nuclear localization signal and importin? Explain your answer in one sentence. Bio200 Exam 1 Version A Page 5 of 6 Name: TA Name: Lab section: .
Energy 6) (6 pts) Think of a specific reaction needed for an immune cell to crawl towards a target bacterial cell. On the graph below, draw a diagram of the chemical reaction. Show this with ATP being used to power the coupled reaction. Be sure to label all needed reactants and products in a way that makes it clear what reaction you are diagramming. Reaction Progress  7. Organelles a) (3 pts) Imagine a eukaryotic cell that has lost the ability to partition the microenvironment of the Rough ER. What will happen to this cell? Be as specific as possible in 1 sentence. b) (2 pts) If you used one of your Bio200 lab microscopes, could you see the nucleus in a eukaryotic cell? Circle one: Yes, visible to the naked eye in most cells
Yes, it is visible in some cells
This is never visible using Bio200 microscopes c) (3 pts) Imagine a cell that has many chloroplasts. Besides these chloroplasts, the cell has a large supply of ATP and enough DNA to code for needed proteins. Would this cell be useful? If so, propose a specific role for this cell. If not, explain why not. Answer in 1-­‐2 sentences, max. You could see it but need a stronger microscope
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