® Comprehensive Exam Part 1- June 2015, Section A. 9AM—1PM Instructions: You must pass SIX of the following questions Aim to attempt at least eight questions é Do not spend more than 30 minutes on each question Begin the answer to each question on a fresh page aC resistance to herbivory is obviously beneficial to a plant, why don’t plants always invest “mally in defense? Describe three constraints that limit how well plants can defend themselves from the suite of vertebrate herbivores trying to consume them, >) 1 Drosophila hindgut has a higher regenerative capacity than other parts of the digestive sfem, suggesting the presence of stem cells in this region. Most cells in the hindgut fall into two ‘groups, one expressing the protein Dela and the other the protein Wingless. It is hypothesized that one of these groups might be the stem cell population, while the other is a progenitor cell type (ic. it is more specialized than a stem cell) Propose a confirmative experiment to prove that the hindgut region of the intestine has stem cells. ii, Define an experimental strategy to identify the difference between Delia and Wingless positive cell types. That is, explain how you would determine which of these two proteins marks the stem cell, and which marks the progenitor cell type. )3,) Some of the most exciting biological questions emerge from studying animals that live in the ig biological qi Bt | (értidal zones of stony beaches (the area above water at low tide and under water at high tide). i, Why is life in the intertidal zone so difficult (and hence so interesting!)? ii, Name at least five types of animals that live in the intertidal zone. For each, what are the main challenges they face on a day-to-day basis? Of the above, in at least three cases, explain the adaptations that have enabled these animals to overcome the challenges of staying in the intertidal zone. \jos ‘You are provided a mixture of four proteins whose pl values are known (pl is the isoelectric point, the pH at which the protein has no net clectrical charge). You can use exchange chromatography to separate your protein of interest X from the mixture. Protein A iB [fe x pl 4 33 7 9 i, What should be the charge on the ion-exchange resin you use, and why? ii, How will the chosen buffer (with a different pH than the resin) affect your choice of resin? ili, Describe two ways to elute your bound protein from ion-exchange resin. Briefly explain the mechanisms underlying these strategies iv, Can you provide an alternative method to separate these proteins? What additional information would you need to do so?(QS. A conserved family of bacterial nucleotide transporters shows an upstream intergenic space of ~200 nucleotides in E. coli, You guess that this region is responsible for sensing intracellular levels of the nucleotide, and regulating the expression of the transporter in response. i, Suggest experiments to test if this intergenic space harbours a non-coding RNA which can bind the nucleotide. ii, How would you test if this RNA controls the levels of the nucleotide transporter protein? ili, How would you test if this RNA functions by controlling the transcription or translation of the nucleotide transporters? (ee Hes Working on the nervous systems of primitive animals sometimes have a hard time Arining, whether or not an observed cell type should be called a “neuron” Outline five distinct eriteria you would use to determine ia cell should be ealled a ‘neuron’ Definitions can’t be perfect, Think about the Metazoan (animal) cell types you know of. For each criterion, list a non-neuronal cell which satisfies the criterion (if any), and a neuron which does not satisfy the criterion (if any), _ @ terial cells have an inner membrane (IM) and an outer membrane (OM). These barriers create > % distinct regions: the extracellular medium, the intracellular cytoplasm, and the periplasmic space in between. Large nutrient molecules like polypeptides must be broken down into small molecules like amino acids by bacterial enzymes, before they can be used by the cell. A lot of this happens in the periplasmic space. Thinking like an engineer, what could be the reason for the two-membrane design? Hint: Think about which types of molecules can cross the IM and the OM, either freely, or via channels and specialized pumps or transporters. (emo: Vertebrate embryos have a unique developmental cell type: the neural crest. X diomically, they are located in the border of the developing central nervous system. The trunk neural crest arises from the level of developing spinal cord, while the head neural ctest arises from developing brain. The trunk neural crest is multipotent but pales in comparison to the extraordinary ‘mult lineage differentiation potential of head neural crest. Hypothesis: The basis of the difference between the differentiation potential of the head and trunk neural crest is non-cell autonomous (determined by environmental cues) and not duc to cell intrinsic differences. Propose an experiment to test the hypothesis ‘ou observe that a particular species of butterfly on our campus is always attracted to the same pskies of flower. i. What cues could the butterfly be using to identify this flower (identify at least 6)? ii, How would the butterfly detect each of these cues? iii. Design a simple field experiment to test if one or more of your proposed cues might be used by the butterfly to identify the flower. Q10. Dr. X wants to study the stability of proteins. He takes his protein of interest, and using a dialysis kit, changes the pH of the protein’s buffer from pH 6 to pH 2. i. Which type of amino acids in the protein will be altered due to the change in buffer pH? ii, Which interactions will be affected most by this change? iii If the buffer had been shifted from pH 6 to pH 12, what would be the answers to (i) and (ii)? iv. How would these results change depending on the location of the amino acid in the protein?Jou In your favorite organism, you observe a strong intracellular response to a stress hormone. You nd that the early part of this response involves the activation of a kinase that potentially controls downstream responses. You suspect that this might be a second-messenger mediated event (second messengers are small molecules that relay signals intracellularly). i, What criteria would you use to determine if a second messenger is indeed activated? ii, You subsequently rule out known second messengers such as CAMP, cGMP, Calcium, and IP3. and therefore suspect a novel second messenger. How would you identify such a molecule? Paid squid giant axon has a diameter of up to half a millimetre. This enables the neuron to (duct nerve impulses relatively quickly, and is important for the escape response of the squid. Consider how the following quantities vary with diameter. Write a sentence in each case explaining the likely impact on action potential conduction velocity. i. Lambda, ie., the passive electrotonic length constant of the axon. ~ ji, tn ie., the membrane resistance per unit length of axon, qs ie, the membrane capacitance per unit length of axon. the axial resistance per unit length of axon, v. Ep, ie. the leak potential. vi. Gating properties of ion channels. Finally, put these together with what you know about ion channels to explain how propagation of action potentials (as opposed to passive signals) would be expected to vary with diameter. 13) Answer both of the following questions about standard deviations. K student discovers a new type of cellular organelle present in multiple copies per cell. These copies are distributed in two distinct pools on the apical (A) and basal (B) side of the cell. She counts the numbers in each pool across 25 cells, and reports values per cell as 200 + 20 for pool A and 100 + 20 for pool B (values are average + standard deviation from 25 cells). The reviewer of the manuscript asks the student to plot a histogram of A+B. The student finds that this histogram has a mean of 300 and a standard deviation of 35. What can she conclude based on this observation? Hint: Calculate ‘what you believe the standard deviation should be under some set of assumptions. Does it equal the observed value? If not, which assumption is probably violated? ii, The student then measures the average radius of the 25 cylindrical cells as 10 jum with a standard deviation of + 5 um. Assuming the cell cross section to be perfectly circular, think about the average cross-sectional area of the cells. Do you expect the average area to be to be less than, equal to, or greater than 100z jum? ? Explain your answer. Hint: Think of the formula which defines the standard deviation, 14. In_an experimental tomato farm, researchers found a new plant similar to tomato but significantly larger, with large fruits and extra plant vigor. Its seeds were sterile, All these characters are hallmarks of polyploids that are usually lethal in animals, but very common among plants. i, How will you show that this plant is indeed a polyp! sterility? ii, Propose a strategy to correet the sterility. and pinpoint the reasons for itsky ky ks ky E+S)+8: 2 ES) +S: = ESS; = EP = E+P ka ka ks ky a. At which step(s) is there entropy decrease? b. At which step(s) is there entropy increase? c. At which step would chemical bonds be broken and formed? d. At which step would general acid catalysis or general base catalysis occur? Will a high dielectric constant increase or decrease reaction rate? Justify in one sentence. For answers to (a-d), merely list the step(s), by using the microscopic rate constant for the step (backward or forward). ‘Now consider the following diagrams which describe ester hydrolysis £ Which diagram shows product dissociation to be rate limiting 8. Which diagram shows the uncatalyzed reaction? h Which diagram depicts the most efficient catalysis? i Which diagram describes the reactions with a poor substrate? j. Which diagram describes the least efficient catalysis?