Practice set 2 lecs 1-7

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Practice set 2: Covers lectures 1-7 Complete each set of questions as we advance through the course material. Every question in this exam is connected! You will sometimes have to go back to read information presented here at the beginning or in a previous question. The entirety of this exam regards Malathion. Come back to this information regularly. Malathion is a common insecticide used to kill pests such as wasps, ants, and mosquitos. It can also be toxic for other animals. Malathion exposure causes malfunction of the nervous system because it binds to the active site of the important nervous system enzyme acetylcholinesterase (ACHE). Normally, ACHE is produced inside nerve cells. After production, the enzyme leaves the nerve cell and acts outside the nerve to break down acetylcholine (a neurotransmitter) into choline and acetic acid. This serves two important functions: 1. By breaking down acetylcholine, muscles can relax after contraction. 2. By producing choline, nerve cells (and others) can take up the choline (a required nutrient) through the choline co-transporter protein. Questions 1-11 cover lectures 1-3: 1. Marisol discovers a nest of fire ants in her backyard. Through a google search, she learns that malathion can be used to kill ants. However, Marisol has two dogs and a frog pond on her property. She is worried about the potential for malathion poisoning of her dogs and frogs. Which of the following sources will provide Marisol with the most accurate information regarding malathion toxicity? a) The Agency for Toxic Substances and/or Poison Control and/or US. Environmental Protection Agency. b) The website for Cheminova, the company that manufactures malathion. ¢) A blog post by Dr. Oz which summarizes the affects of malathion poisoning. 2. Marisol also searches the peer reviewed literature and finds two recent papers. Both papers aim to uncover if malathion exposure effects non target organisms (organisms that malathion is not intended to harm). The first paper tests the effect of three low concentrations of malathion exposure to 50 mice. The second paper tests the effect of four high concentrations of malathion to 200 honeybees. The different approaches in these papers reveals what feature of the scientific process? a) Conclusions change based on new evidence. b) Scientists use each other’s work. ¢) Hypotheses are tested multiple times using different methods. d) Scientists often collaborate.

3. Marisol continues to search and finds a third scientific paper which has a red RETRACTED stamp on all its pages. Upon further searching, Marisol learns that the paper was retracted because one of the authors intentionally manipulated the data. How does this demonstrate that science is trustworthy? a) The peer review process prevents incorrect papers from being published. b) Scientists identify problems in newly published papers. ¢) The news media often interviews the authors directly about their work. At the local state university Celeste Avery PhD is doing new research on malathion. She is interested in how indirect exposure of malathion might affect organisms. Think about the difference between hypothesis and prediction. Which of the following statements are hypotheses? (Select all) a) Frogs that are fed insects that developed in media contaminated with malathion will show symptoms of nervous system distress. b) Green frogs that are daily fed fruit flies that developed in media contaminated with 2 ppM (parts per million) of malathion will have a significantly higher mortality rate within 30 days. c) Bull frogs that are daily fed crickets that developed in media contaminated with 4 ppM (parts per million) of malathion will eat significantly fewer crickets within 15 days. d) Exposing insects to low doses of malathion will negatively impact frogs. Celeste designs her experiment such that some fruit fly larvae are reared in media that contains 2 ppM malathion and some fruit fly larvae are reared in media that contains 4 ppM malathion. Once hatched as adults, the flies are kept in vials that contain the same concentration of malathion as their larva environment. Meanwhile there are three tanks, each of which contain 20 female bull frogs. Two of the tanks are assigned to be given 10 flies from one of the experimental groups each day. The most robust negative control protocol for the third tank of frogs would be for the frogs to be given a) Another type of insect reared in a pet store. b) Fruit flies from both experimental groups. ¢) Another type of insect reared on the same media with a different pesticide. d) Fruit flies reared on the same media just without the malathion. On day 6, 12 and 24 of her experiment, Celeste’s research assistants remove each frog from its tank and performs a reflex test to measure the health of their nervous systems. The research assistants do not know which tank is assigned to which treatment, thus removing bias from the data collection process. Celeste uses a statistical test to compare the treatments. She is most interested in potential differences at 3 microseconds, as seen in the figures below for days 6 and 24.

10. 11. Day 6 Day 24 SN DA 1 2 3 4 Microseconds ' 2 3 4 Reflex (uv) =80 Malathion == 20pM Malathion =#=4ppm Malathion =80 Malathion == 20pM Malathion =—=4ppm Malathion Based on these results, Celeste a) rejects the null hypothesis b) fails to reject the null hypothesis Before beginning the experiment, Celeste had predicted that bull frogs fed fruit flies that had been reared in 2ppM and 4ppM would show reduced reflex action compared to the control. Based on the statistical results of this experiment, her prediction a) was correct b) was not correct On both days shown, standard error was highest in which treatment? a) 0 malathion b) 2ppM malathion ¢) 4ppM malathion The high standard error in the treatment mentioned in the previous question is directly due to variation in (select all) a) the sample size of each vial of fruit flies. b) the sample size of each cage of frogs. ¢) the measurements of each fruit fly’s contamination level. d) the measurements of each frog’s reflexes. Celeste is intrigued by these results and immediately makes plans to perform the experiment again to see if they are repeatable. Based on the standard error measurements for this experiment, should Celeste increase the number of frogs in each treatment group? a) Yes, because standard deviation of frogs exposed to 4ppm malathion is narrow. b) Yes, because standard deviation of frogs exposed to 4ppm malathion is wide. ¢) No, because standard deviation of frogs exposed to 4ppm malathion is narrow. d) No, because standard deviation of frogs exposed to 4ppm malathion is wide. Celeste tells a colleague about her preliminary results. Her colleague is interested in ‘whether bull frogs can evolve resistance to the effect of malathion on the nervous system.

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What features must be present in her experimental design for her to capture evolution by natural selection occurring? a) Frogs must be genetically identical. b) Frogs that show minimal affects from malathion exposure should be removed from the experiment. ¢) Only include either males or females but not both. d) Track multiple generations of frogs from the same original population. Questions 12-15 cover lectures 4-5: 12. Celeste’s colleague performs the evolution experiment and eventually finds that the frogs do evolve resistance to malathion. She proceeds with a genetic analysis and identifies the genetic mutation that confers resistance. Which of the following is true of that initial genetic mutation? a) It arose because the frogs needed to survive despite the malathion contaminated food. b) It could only arise in frogs that were being exposed to malathion and not frogs that were unexposed. c) It arose by chance. 13. The bull frogs used in Celeste’s and her colleague’s experiments originate from a temperate (cool) climate. Xenopus laevis is another type of frog often used in laboratory research. It originates from tropical Africa. Which frog species likely has a greater percentage of unsaturated phospholipids in their cell membranes? a) Xenopus laevis b) Bull frogs 14. When Xenopus laevis individuals are removed from their natural habitat and placed in cool laboratory conditions, what is the effect on their cell membrane’s permeability to oxygen? a) It increases permeability. b) It reduces permeability. ¢) It has no effect on permeability. 15. Below is a diagram of malathion’s chemical structure. ) HiC ) 0" cH ] H P o_ _CH Cso-iiNs ~ 8 o What kind of bond(s) will be made by P and O?

Pauling scale of electronegativity; Electronegativitics of the Elements 1998 Dr Mchoet Baber . NUNIPIEN ™ T [F Ei & E 3040 2502838 an 6 6n B~ B~ 15 2n 5 _REE 0 o B 2020 Y b B 11 A [ 2 Rl S 7 [ 2 [0 1519 15 Lol Cr [ [ a [ 5t [ 5 i Fluorine is the most electronegative clement followed by O and N, Cl are. equal third. Cs s least. Electronegativity increases from left to right along the Periodic Table. a) The P and O will form a bond other than a covalent bond because O has an almost-filled valence shell. b) The P and O will form a bond other than a covalent bond because O has more valence electrons than P. ¢) The P and O will share electrons unevenly because the O has a higher electronegativity. Questions 16-20 cover lectures 6-7: 16. Malathion exposure causes malfunction of the nervous system because it binds to the active site of the important nervous system enzyme acetylcholinesterase (ACHE). What does this binding cause? a) Competitive inhibition, which is reversible if the concentration of the substrate increases. b) Competitive inhibition, which is not reversible because the primary structure has been altered. ¢) Allosteric inhibition, which is reversible if the concentration of the inhibitor decreases. d) Allosteric inhibition, which is irreversible because the inhibitor has induced fit. 17. ACHE is an enzyme that is present in all animals, however the specific form of ACHE in different animals performs optimally in the conditions of which the animal evolved. A figure demonstrating this is shown below:

18. ACHE in 100- o Xenopus ACHE in laevis g ® bullfrogs . \ . z s Z 0 . . 8 1 . £ w . . & : . 20 . . ° e o 30 40 50 60 70 80 [ETN— Temperature If Celeste decides to use Xenopus laevis in a different set of experiments that directly measures ACHE activity with and without exposure to malathion, at which temperature should she keep the enzyme? a) 50C b) 65C ¢ 80C Remember that one function of ACHE is to break down acetylcholine (a neurotransmitter) into choline and acetic acid. Below is a simplified diagram of the choline metabolism pathway. It shows that ACHE breaks down acetylcholine to yield choline and acetic acid. Choline is then combined with fatty acids to create phosphatidylcholines. VAN A oetylcholin\ csterase ( (ACHE).)‘ ~~ Acetic acid Acetylcholi:#i + Cho‘line — | Enzymes are Indcated by (_J i his metabol . ) it Fayuids simplified for this l (- Phosphatidylcholines When ACHE activity is eliminated because of malathion binding what would be the immediate result on the DGPE enzyme? What immediate affect would it have on the concentration of phosphatidylcholines? a) The rate of DGPE activity would slow down. The concentration of phosphatidylcholines would decrease.

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b) The rate of DGPE activity would slow down. The concentration of phosphatidylcholines would increase. ¢) The rate of DGPE activity would speed up. The concentration of phosphatidylcholines would decrease. d) The rate of DGPE activity would speed up. The concentration of phosphatidylcholines would increase. e) The rate of DGPE activity and the concentration of phosphatidylcholines would remain the same. 19. Remember that once choline is produced by ACHE, choline can be absorbed by nearby cells (who then proceed to perform the rest of choline metabolism shown above). The choline co-transporter moves choline from outside the cell to inside the cell against its concentration gradient. It accomplishes this by also moving Ca*" across the cell membrane from a high concentration to a low concentration. What kind of transport does this describe? a) Simple diffusion b) Facilitated diffusion ¢) Primary active transport d) Secondary active transport 20. A researcher wants to improve the understanding of how choline movement affects water movement between cells and blood. She constructs a choline co-transporter such that it is partially inhibited. It can only transport Ca2+ and not choline. She embeds this augmented choline co-transporter (and aquaporins) into an artificial cell that is floating in a flask of water.The water contains 0.3 umol/L choline and 1 umol/L Ca2+. She injects the inside of the cell with 0.2 umol/L choline and 0.4 umol/L Ca2+. Immediately, where will water move (in relation to solute movement)? a) Water won’t move because if choline cannot move through the co-transporter, Ca2+ can’t either. b) Most of the water will move from outside the cell to inside. A little will move out. ¢) Most of the water will move from outside the cell to inside. None will move out. d) Most of the water will move from inside to outside the cell. A little will move in. e) Most of the water will move from inside to outside the cell. None will move in. Key: 1. Answer: A. These are organizations which summarize the primary, peer reviewed literature, so they are the best source of information. The company itself may be biased. Dr. Oz is just a single doctor and so he is not the best source. He also may have biased motives since he promotes products on TV.

10. 11. Answer: C. This scenario directly describes how the same hypothesis is tested in different ways. The hypothesis itself is implied in the second sentence. The scenario does not describe any conclusions. It does not directly describe one scientist using another’s work. And it does not state that the authors of the papers collaborated. . Answer: B. Since this paper has been retracted, we know it was published. The manipulated data must have been found out by scientists who scrutinized the work after publication. We can trust that science is trustworthy, because incorrect information always gets found out, even if its after publication. Answer: A & D. A and D are broad statements that could generate many predictions and thus be tested many different ways. Both B and C are specific and measurable. They provide precise dosages and imply methodology. So, B and C are predictions. Answer: D. The negative control should have the exact same conditions as the experimental groups except for the one variable being tested, in this case, the presence of malathion in the diet/environment of the fruit flies. Answer: A. On day 6, there is a significant statistical difference between 0 malathion and 4ppm malathion. On day 24, there is a significant statistical difference between 0 malathion and 2ppm, and a significant statistical difference between 0 malathion and 4ppm. Therefore, she rejects the null (there will be no differences...) Answer: A. Rejecting the null means that the prediction was correct. Answer: C. Standard error is depicted on a graph using standard error bars. On both graphs, the standard error bar is tallest for 4ppM malathion. Answer: B and D. Standard error is a measurement of whether sample size is sufficient for the width of the standard deviation. In this case, what is being measured is frog refluxes so the sample size of the frogs would affect standard error. Differences/variability in the measurement of the frogs reflexes will drive the large standard error calculation that we see. Answer: B. We know standard deviation is wide because standard error is high but sample size is the same as the other treatments. So, to capture all the variation in that wide standard deviation, Celeste should increase the sample size. Answer: D. A is wrong. Frogs should actually be genetically varied. This is one of the requirements of evolution by natural selection. B is wrong, to mimic natural selection frogs that show high effects from malathion exposure should be killed or removed from the experiment. C is wrong, evolution can only occur over multiple generations, so both males and females must be included in the experiment.

12. 13. 14. 15. 16. 17. 18. 19 20. Answer: C. Genetic mutations arise by chance. They sweep through populations if individuals with the mutation survive and reproduce more than individuals that don’t have it. The initial gene that conferred resistance to malathion arose by chance, but swept through the population because it provided an advantage in that specific environment. Thus, the population evolved resistance. Answer: B. Unsaturated phospholipids increase permeability. So frog populations that are already dealing with reduced permeability because of the cold will evolve more unsaturated phospholipids in their cell membranes to bring permeability back up. Answer: B. Xenopus laevis evolved in a warm climate so they have more saturated phospholipids in their cell membranes to reduce permeability. When they are removed from their natural habitat and placed in the cold, permeability is reduced even more. Answer: C. P and O have different electronegativities so they will share electrons unevenly. They will make a polar covalent bond. Answer: A. Malathion binds to the active site. So this is competitive inhibition. It is reversible as long as the concentration of the substrate increases significantly because once a substate is bound to the active site, the malathion will have no where else to bind. Answer: B. ACHE performs optimally in about 65 degrees Celsius. Thus, when performing an experiment that directly measures that ACHE activity, it would be best to provide the optimal environment uniformly for all frogs. Answer: A. ACHE produces one of the substrates for DGPE. Since ACHE activity is eliminated, the substate (choline) for DGPE is reduced so DGPR activity will slow down. Subsequently, fewer phosphatidylcholines will be produced. . Answer: D. This is secondary active transport. Ca moving from high to low, with its concentration gradient, is powering the co transporter to move choline from low to high. Answer: D. The choline cotransporter is using secondary active transport. When working correctly, choline moves into the cell against its gradient and ca moves into the cell with its gradient. You know that ca is moving in the same direction as choline because that is how secondary active transport works. In this case, the cotransporter is adjusted so that choline can’t move at all. But Ca still can, because its moving from high concentration outside the cell to a low concentration inside the cell. Initially, there are more total

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solutes outside the cell, so most of the water will move out. But a little bit of water will move in because Ca is moving in so some water will follow that solute movement.

Practice set 2 lecs 1-7

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