Zool 3200: Cell Biology Exam 1 1/30/15

Transcription

1 Name: TRASK Zool 3200: Cell Biology Exam 1 1/30/15 Answer each of the following short- and long- answer questions in the space provided; circle the BEST answer or answers for each of the multiple choice and True / False questions. (70 points total) The results of Stanley Miller s famous experiment in the 1950s supported the theory of chemical evolution through its production of amino acids from the simple chemicals of which the primordial earth was thought to be composed. These results conflict, however, with evolutionary scientists current hypothesis that RNA (or some derivative of it) was the first biological molecule to exist on this planet. What experimental or observational evidence supports this current hypothesis of the origin of life on Earth? (3 points) RNA can easily be replicated without the activity of other biological molecules. RNA can perform work (i.e., catalyze reactions) due to its ability to fold into 3-dimensional shapes. Ribonucleotides can be/are used as energy carriers. RNA can carry information to subsequent generations. Indicate whether the following statements about mitochondria are true or false by circling the correct answer. If you circle false, explain why you believe that the statement is false. (6 points) True / False: Mitochondria are thought to have evolved from anaerobic bacteria. Engulfed bacteria that developed into mitochondria were aerobic; they were not destroyed/digested after ingestion because they could metabolize he oxygen that was building up in the atmosphere (and was toxic to ancestral eukaryotes). True / False: Mitochondrial DNA is in the form of a single circular chromosome. True / False: Mitochondria and the nucleus are the only membrane-bound organelles to be surrounded by two lipid bilayers. True / False: Mitochondrial synthesis of ATP depends upon reduction of the enzyme ATP synthase. The proteins in the Electron Transport Chain are all reduced (in turn), but their reduction enables generation of an H+ gradient across the inner mitochondrial membrane. It is this gradient that drives ATP synthase s function. 1 P age

2 Cells that secrete large amounts of proteins also have abundant amounts of: (1 point) a.) mitochondria. b.) peroxisomes. c.) cytoplasmic ribosomes d.) rough endoplasmic reticulum. e.) smooth endoplasmic reticulum. f.) lysosomes. g.) nuclei. h.) centrosomes. From the list below, which cellular components are found in all cells? (1 point) a.) Nucleus b.) Ribosomes c.) Cytosol d.) Mitochondria e.) Chloroplasts f.) Plasma membrane g.) Endoplasmic reticulum h.) Lysosomes All proteins are synthesized: (1 point) a.) In the endoplasmic reticulum b.) At the endoplasmic reticulum c.) By ribosomes d.) In the nucleus With no additional markings, signals or tags, a protein produced at the endoplasmic reticulum ultimately can be found: (1 point) a.) In the cytoplasm b.) In the membrane c.) In the extracellular space d.) In the endoplasmic reticulum On the pentose sugar depicted below, clearly identify the carbon(s) to which a nitrogencontaining base and a tri-phosphate group would be linked. (2 points) Nitrogen-containing base Tri-phosphate 2 P age

3 What class of molecule is formed from the polymerization of the monomer shown below? What type of monomer is shown in the figure? Be specific in your answer. In addition, clearly identify the part of the molecule that is involved in polymerization by circling it. What type of chemical reaction occurs in the creation of this polymer? With what, specifically, does the end of the molecule that you circled react in the creation of a polymer? Finally, name three functions of this class of biological molecules, indicating whether monomers or polymers are responsible for each of the functions you name. (9 points) The image depicts an unsaturated fatty acid (2) that, when polymerized, will generate a lipid (1) of some sort (mono-, di- or tri-glyceride). This is because polymerization occurs via condensation reactions (1) using the circled end of the fatty acid (1) and an OH group associated with a glycerol molecule (1). Functions (3) of lipids include: communication (by monomeric steroid hormones or cholesterol, for example), containment (by polymeric phospholipids, for example), and energy production (by monomers) or energy storage (by polymers). Complete the table below. (8 points) Chemical Formula of Monomer C5H11NO2S C9H16N30O14P3 Two means by which variability occurs in polymers from the monomers in column 1 1. Which amino acids are used, the order of amino acids in a protein, 2. the number of amino acids in a protein, the shape of the protein 1.Which nucleotides are used, the order of nucleotides in a nucleic acid, 2. the number of nucleotides in a nucleic acid, shape (of RNA) C8H16O8 1. Which monosaccharides are used, how monosaccharides are linked ( or ) (C8H13O8)n 2. number of monosaccharides linked, number of OH groups linked (branching) 1.A carbohydrate is also shown here, so the same answers listed in the cell above 2. are appropriate. 3 P age

4 Chemical structures for each of the 20 amino acids that can be polymerized into proteins are shown below. After incorporation into a polypeptide chain, some of these amino acids can be modified through the covalent addition of carbohydrates. These sugars (monomers or polymers) are added to some amino acids in a protein through condensation reactions similar to those used to synthesize the protein itself. When a protein is modified in this manner sugars added via condensation reactions which of the amino acids within that protein (options shown below) is/are the most probable target(s) for sugar attachment? Circle your answer(s) (3 points) 4 P age

5 The second law of thermodynamics states that systems will change spontaneously toward arrangements with greater disorder (entropy). Cells are so intricately ordered, however, that it seems they surely violate the second law. Explain briefly, and in a way your parents could understand, how life is compatible with the laws of thermodynamics. (2 points) The disorder dictated by the 2 nd law is broken inside of the cell where cellular components are assembled and arranged in an ordered fashion to support cell function and life. But, as order is created inside the cell, heat is generated. This heat dissipates to the extracellular space where it creates disorder in the form of molecular movement. Thus, order inside of the cell is counterbalanced by disorder outside of it, thereby adhering to the 2 nd law of thermodynamics. In the following reaction, which reactant is being oxidized and which is being reduced? (2 points) 2Na + Cl2 2Na Cl - Na is oxidized to Na + ; Cl2 is reduced to Cl - Distinguish between catabolic and anabolic pathways of metabolism, and indicate (in a general way) how these pathways are related to one another (2 points) Catabolic reactions are those in which food polymers are oxidized to small biologic building blocks (monomers), producing head and useful energy as a byproduct. Anabolic reactions are those in which the monomeric building blocks produced by catabolism are reassembled via reduction to larger macromolecular polymers. What role does the chemical shown to the right play in the generation of cellular energy? If the cytoplasmic concentration of this molecule were increased ten-fold, how would ATP production be affected, if at all? (2 points) The diagram shows NAD + (note the label, oxidized form ). NAD + plays a role in energy production by accepting electrons during the oxidation of biological molecules and carrying them to the electron transport chain. ATP production may not be affected by a 10-fold increase in the cytoplasmic concentration of NAD + because the concentration of NAD + is already higher than the concentration of cytoplasmic NADH. However, if energy production were affected at all, it would likely increase. 5 P age

6 How do NADH and NADPH differ from one another? (2 points) These two reduced electron carriers differ from one another not only in their structures (NADPH has a phosphate group associated with the 2 end of the adenosine ribonucleotide portion of it), but also in both their functions and their relative ratios when compared to their respective oxidized counterparts. Specifically, NADH plays a large role in the production of ATP by mitochondria and is generally found in a much lower concentration than NAD +. NADPH, on the other hand, plays a large role in the synthesis of biological molecules and is generally found in a higher concentration than NADP +. After isolating mitochondria from eukaryotic cells, they are exposed to mild detergents. This treatment enables the isolation of three mitochondrial inner membrane proteins that are able to be reduced when incubated with NADH. First, explain how treatment with detergents is able to liberate proteins from the inner mitochondrial membrane. Second, what term best describes the collection of these three inner membrane proteins? Finally, what is/are the function(s) of these inner membrane proteins? (4 points) Like the phospholipids that make up the mitochondrial membrane, detergents are amphipathic, meaning that they have both hydrophobic and hydrophilic character within the same molecule. The hydrophobic end of the mild detergents will interact with the fatty acid portions of mitochondrial membrane phospholipid and the hydrophilic end of the detergent will interact with the polar head portion of mitochondrial membrane phospholipid, thereby disrupting the interactions between membrane phospholipids and disrupting the membrane. This liberates the membrane proteins so they can be studied further. The term that describes, collectively, the three mitochondrial inner membrane proteins that can be reduced is the electron transport chain. The function of all three of these proteins is to pump H + from the mitochondrial matrix to the mitochondrial intermembranous space. The values for G o and for G in cells have been determined for many different metabolic reactions. What information do each of these values provide about the rates of these reactions? (2 points) Both G o and G convey information about whether or not a reaction will require the input of energy (+ value) or whether it will generate energy as it proceeds (- value). These factors differ in that G o refers to the difference in free energy between reactants and products in standard conditions and at equal concentrations whereas G refers to the difference in free energy between reactants and products in variable conditions. While no direct information about reaction rates can be derived from either of these factors without additional information (e.g., the amount of activation energy required to initiate a reaction), those reactions with a more negative G o and/or G are more favorable and therefore are more likely to occur at an accelerated rate. 6 P age

7 The relationship of free energy change ( G) to the concentrations of reactants and products is important because it allows us to predict the direction of spontaneous chemical reactions. Familiarity with this relationship is essential for understanding energy production and utilization in cells. Consider, for example, the hydrolysis of ADP ADP + Pi. The free energy change for this reaction is able to be calculated using the following equation, where R is the gas constant and T is the temperature in K o (RT = 0.6 kcal/mole). In the equation, concentrations are expressed as molarities, and G o is kcal / mole. G = G o RT log [ADP] [Pi] [ATP] In a resting muscle cell, the concentrations of ATP, ADP and Pi are approximately 5mM, 1mM and 10mM respectively. What is the G for ATP hydrolysis in resting muscle? What will G equal when the hydrolysis reaction reaches equilibrium? (4 points) G = kcal/mole (0.6 kcal/mole x log (0.001) (0.010)) (0.005) G = (0.6 log 0.002) G = kcal/mole (0.6 x -2.7) G = kcal/mole (-1.62) G = kcal/mole G = While I converted the concentrations to moles (rather than the millimoles in which they were given, it was not necessary for you to do this to receive full credit. As always, G = 0 when a reaction is at equilibrium Which of the following protein pairs binds the most tightly to each other? (1 point) a.) Protein A & Protein B: kon = 55nM b.) Protein B and Protein C: kon = 4000pM c.) Protein C and Protein D: kon = 0.2 M d.) Protein C and Protein A: kon = 100 M e.) Protein D and protein A: kon = 0.6mM In the question above, briefly describe the meaning of the term, kon? (2 points) Kon is the concentration at which 50% of the proteins B and C are found independently, and 50% of the proteins are bound to one another in a BC complex. 7 P age

8 Chemical structures for each of the 20 amino acids that can be polymerized into proteins are shown below. After incorporation into a polypeptide chain, some of these amino acids can be modified through the covalent addition of phosphate (PO4 - ) groups via the activity of enzymes that transfer the terminal phosphate from ATP to amino acid side chains. This transfer results in a protein shape change that is associated with cellular work. When a protein is modified in this manner specifically the addition of a phosphate group (aka, phosphorylated ) which of the amino acids within that protein (options shown below) is/are the most probable target(s) for modification? Circle your answer(s) (3 points) 8 P age

9 In 1925, David Keilin used a simple spectroscope to observe the characteristic absorption bands of the proteins that make up the electron-transport chain in mitochondria. A spectroscope passes a very bright light through the sample of interest and then through a prism to display the spectrum from red to blue. If there are molecules in the sample that absorb light of a particular wavelength, dark bands interrupt the colors of the projected rainbow. Keilin found that tissues from a wide variety of animals all showed the spectrographic pattern shown at the top left (squared) of the images below. The different heat stabilities of the individual absorption bands (a, b and c) and their different intensities in different tissues led Keilin to conclude that the absorption pattern resulted from three different protein components. His key discovery was that the absorption bands disappeared when oxygen was introduced (A, AEROBIC, below top right) and then reappeared when the samples became anaerobic as shown (B, center right). Keilin subsequently discovered that cyanide (KCN) prevented the bands from disappearing when oxygen was introduced (C, bottom right). After reviewing the data, answer the following questions about Keilin s experiments: 1. Are the visible bands in the top image due to reduced or oxidized forms of the proteins? (2 points) The visible bands represent the reduced forms of the three electron transport chain (ETC) proteins. This is able to be determined because under anaerobic conditions (B; on the right), the bands are obviously present whereas they re absent in the presence of oxygen (A; aerobic). In the absence of the final electron acceptor oxygen, the ETC proteins are unable to get rid of their electrons and therefore remain reduced. 2. Keilin also observed that excess glucose prevented the disappearance of the absorption bands when oxygen was added. How do you think that rapid glucose oxidation to CO2 might explain this observation? (3 points) As a result of breaking down (oxidizing) the extra glucose, a lot of electrons are being generated very rapidly; the oxidation of glucose is coupled to the reduction of electron carriers. The electrons carried by NADH are being constantly delivered to and used by the ETC proteins, so the ETC proteins are nearly constantly reduced. This explains the appearance of the ETC protein bands, even in aerobic conditions. 9 P age

10 Complete the following sentence: (2 points) An enzyme facilitates the progress of a chemical reaction by: Lowering the activation energy (or by increasing the energy levels of the reactants). True / False (circle one). Linking the energetically unfavorable reaction a B to a second unfavorable reaction B C will shift the equilibrium constant for the first reaction. Explain your answer. (2 points) To shift the equilibrium of the first reaction, it would be necessary to link it to an energetically favorable second reaction. This works because a second favorable reaction would rapidly use products from the first reaction as its reactants, thereby driving the first reaction to the right (toward product). 10 P age