1. Which is the mRNA complement of the DNA sequence 5’ ACGGTCGGAT 3’

1. 5’ ACGGTCGGAT 3’
2. 5’ AUCCGACCGU 3’
3. 5’ TGCCAGCCTA 3’
4. 5’ UGCCAGCCUA 3’

2. Answer question a in the first row (with a number).

For statements b-k, enter an X to indicate if it is associated with DNA replication, transcription or translation. A statement may apply to more than one.

3. The start codon to begin translation is 5’ AUG 3’. Which of the following is the complementary DNA sequence on the template strand?

1. 3’ AUG 5’
2. 3’ TAC 5’
3. 5’ AUG 3’
4. 5’ ATG 3’
5. 5’ TAC 3’

4. Examine this segment of double stranded DNA. Which is the template strand for transcription?

Strand 1: 5’ A T C T C C T G C C C C T C A T A A 3’

Strand 2: 3’ T A G A G G A C G G G G A G T A T T 5’

5. What molecule is produced through the process of transcription?

6. What molecule is produced through the process of translation?

7,Translate the following mRNA strand using the codon chart below:

mRNA:           5’ C C A U G U C C C A A C G U C C C G G A A A C U A A 3’

peptide:

4. In your studies with mice, you have sequenced a piece of wild-type DNA and it clearly contains a gene, but you do not know what this gene does. Therefore, to investigate further, you would like to create a transgenic mouse to learn more about the phenotypic qualities this gene confers. What kind of transgenic mouse would allow you to correctly determine any phenotypes that depend on this gene’s function? How would you go about making such a mouse?

The partial pressure of oxygen in the lung alveoli is a bit lower than in ambient air, being about 100 mm of mercury, or 0.13 Atm (it is lower than the partial pressure in air mainly because oxygen is continually taken up by the alveolar capillaries and carbon dioxide is continually released into the alveoli).  In cell-free blood plasma (or a saline solution formulated to match key characteristics of blood plasma), which lacks red blood cells and therefore lacks hemoglobin, the concentration of oxygen will equilibrate at 37° C at about 0.3 ml O₂/100 ml plasma. For whole blood (with hemoglobin), however, the O₂ concentration is around 20 ml O₂/100 ml whole blood.

By what factor does the presence of hemoglobin increase the oxygen content of blood?

B.  Given the above, imagine that you are an emergency room physician treating a patient who lost a quarter of his blood in an accident. A paramedic replaced this lost blood with saline solution to keep his blood pressure up. The saline solution contains no hemoglobin since it contains no red blood cells. The patient is short of breath and oxygen levels in his blood are dangerously low. If for some reason you must choose between administering pure (100%) oxygen or giving a transfusion of whole blood to restore the red blood cell count, which would you expect to be more helpful? Address this decision by answering the questions below. Show your work and be as quantitatively explicit as possible.

1. Under normal conditions, what percentage of blood oxygen content is accounted for by oxygen dissolved in the plasma and what percentage is bound to hemoglobin? By how much do these percentages change after the patient has a quarter of his blood volume replaced with saline solution?
2. a) By what percentage could total blood oxygen content be increased by delivering pure (100%) oxygen instead of allowing the patient to simply breathe ambient air? Assume that Henry’s Law applies.

b) One obviously can’t deliver oxygen at a concentration higher than 100%, but how else might the partial pressure of the oxygen being delivered be modified to increase the amount diffusing into the blood?

3. By what percentage could blood oxygen content be increased by transfusing whole blood to restore the red blood cell count? Relative to delivering pure oxygen, is this a more promising or less promising approach for restoring normal blood oxygen levels? Explain.

Taxol is a drug used in chemotherapy that interrupts the function of the mitotic spindle and prevents chromosomes from aligning properly. A cell treated with Taxol would:

A) arrest at the G1 checkpoint B) arrest at the S phase checkpoint C) arrest at the G2 checkpoint D) arrest at the M phase checkpoint E) go into the ‘resting’ G0 phase

Which of the following would you predict to find in an individual after 15 years of persistent opioid use? A) Increased gene expression of the gene encoding the dopamine re-uptake receptor protein, leading to higher amounts of dopamine in the synapse B) Reduced gene expression of the gene encoding the dopamine re-uptake receptor protein, leading to fewer dopamine re-uptake receptors in pre-synaptic neurons C) Increased gene expression of the gene encoding the dopamine receptor protein, leading to higher dopamine receptor levels in post-synaptic neurons D) Decreased gene expression of the gene encoding the dopamine receptor protein, leading to fewer dopamine receptor levels in post-synaptic neurons E) Reduced gene expression of the gene encoding dopamine

Super enhancers have been shown to regulate the expression of oncogenes like Myc. These super enhancers can be targeted by small molecule inhibitors to histone readers like BRD4. Inhibiting histone readers like BRD4 has been leveraged as a therapeutic strategy to repress oncogene expression (i.e. Myc) in specific tumor types. Can you further explain the rationale behind this approach by addressing the following questions? A.) Does BRD4 occupy super enhancers to a different extent than regular enhancers? If so, why does BRD4 bind to super enhancers differently? B.) Would BRD4 inhibition affect normal enhancers in the patient’s body to the same extent as the active super enhancers in the patient’s tumor? If yes or no why? C.) Would BRD4 inhibition in tumors of different origin (lymphoma vs neuroblastoma) affect the expression of the same oncogenes? If yes or no why?

Question 1:

1. You have been studying various oncogenes and tumor suppressor genes in tumor cell lines in vitro, but would now like to address certain questions in mouse models in vivo. For each of the questions below, briefly describe the type of mouse model you would use.
   • For xenograft/allograft experiments, briefly describe the type of cell lines you might use and the experimental end points you would be looking at.
   • For GEMs, briefly describe the type of mouse you would make (you don’t need to go into details about how the mouse is generated), and the experimental end points you would be looking at.

Note: there is no single right answer. However, try to select the model that would be most straight-forward way to initially address your question.

3. You are studying a (hypothetical) newly-described member of a family of protein kinases (XYK6), which you suspect may function as an oncogene, based upon the observation that specific point mutations (especially Thr489Asp) are sometimes seen in human breast tumors.You’ve queried the TCGA database and found that this mutation, when present, seems to be an “early” mutation, since it is seen as frequently in early-stage lesions as in later-stage tumors.You therefore hypothesize that it may be a driver mutation that contributes to the process of breast cancer initiation.Describe a mouse model that would allow you to test this hypothesis.
4. Oncogenic mutations of the (hypothetical) PRO gene are present in many tumor types, and are associated with high rates of tumor cell proliferation. Several drug companies are therefore trying to develop agents that specifically inhibit the mutant PRO gene product without affecting the normal protein. One company has approached you to assist with in vivo studies to test the efficacy of this agent and its specificity for tumors with PRO mutations. What type of mouse model would you propose to use?

QUESTION 3

1. Describe the normal cellular functions of tumor suppressor genes and explain their roles in cancer. List all possible mechanisms by which tumor suppressor genes are inactivated and explain. Explain why loss-of-heterozygosity of a particular chromosome/chromosomal region in tumor DNA suggests the existence of a tumor suppressor gene in that region.

2. Why is pRB function compromised in human tumors through mutations of its encoding gene while the genes encoding its two cousins, p170 and p130, have virtually never been found to suffer mutations in the genomes of cancer cells?

What are examples of how corporations are responding to the effects of deforestation for palm plantations?

Describe the state of chromosomes (e.g., position in cell, attachments, condensation), spindle, and nuclear envelope at each stage of mitosis. Similarly, name the stage of mitosis corresponding to a description of a cell’s chromosomes, spindle, and nuclear envelope.

1. Temperature-sensitive mutations (ts) in E. coli are a type of conditional lethal mutation. A conditional lethal means that the mutation is only deadly under certain growth conditions, in this case when the temperature is increased to the restrictive temperature. The proteins are fully functional at the lower temperature (permissive). This type of mutation has been indispensable for studying the essential process of DNA replication. Mutants in proteins that are necessary for DNA replication can be classified into either quick-stop or slow-stop. Quick-stop mutants arrest DNA replication immediately, but slow-stop mutants halt after several minutes. Fill in the chart below to indicate which mutations will be slow and which quick when shifted to the higher, restrictive temperature. Assume that the E. coli have already started replication. Explain your answers. (6pts total: 1.5pts each)

What were Mendell’s experiments? Explain the F0, F1, and F2 generations. What postulates did he form from these experiments?

Which of the following is NOT a potential benefit of using transgenic plants?

List, describe (IN DETAIL), and provide examples for the four types of mutations.

1. A recent article predicts that the population of orcas (killer whales) in the ocean will drop by about one half over the next ten years because the whales have high PCB levels in their tissues. These highly intelligent mammals are top predators and their absence would cause widespread distortions of ocean food webs, although the population sizes of edible fish species would not change. Followers of which kind of ethics will find this news distressing? [Note that orcas are no longer held in captivity by marine mammal entertainment facilities (e.g., seaworld).]

• A. Anthropocentric ethics.
• B. The branch of biocentric ethics that concentrates its efforts only on animals with self-awareness.
• C. The branch of biocentric ethics which posits that all living things have equal intrinsic value.
• D. Eco-centric ethics
• E. Three of the above

2. Which of the following companies comes closest to operating in a sustainable manner, paying the "true costs" of its operations, and uses the triple bottom line philosophy?

• A. Pulp and Paper, Inc. owns pine plantations in western Michigan. Every day, pines are cut down to provide pulp that is made into paper. Michigan law prohibits bleaching of paper because this releases dioxin into the environment. The company immediately replaces each tree it has cut down with a new sapling. It takes care to cause minimum damage to the ecosystem in which the pines grow. It puts the highest priority on worker safety and follows EEOC guidelines in hiring and promotions. Its workers are paid well, have good health insurance, retirement benefits, and other important benefits. Pulp and Paper, Inc. reimburses the state for damage to roads caused by its trucks. To compensate for the CO2 emissions produced by the machines it uses, the company donates trees to surrounding cities that have agreed to plant the trees in parks and on parkways and and to replace these trees when they die.
• B. This company mines Helium, fills balloons with the Helium, and sells millions of Helium balloons around the world. Helium is an element and is made in stars; it cannot be made on Earth. Millions of people enjoy their Helium balloons, but the Helium eventually leaks out of the balloons, rises into the atmosphere, and disappears into space. The company has excellent pay and benefits. It also devotes considerable funds to exploration of new sources of Helium and, over the years, has found more Helium than it has used up. It makes the balloon material from recycled plastic.
• C. Coke industries extracts bitumen from tar-like deposits in eastern Alberta, processes the bitumen into an oil substance, and sends this oily substance by pipeline to Houston, TX where it is refined into various usable products. Coke pays taxes to the Canadian government and pays for the land it uses, but does not pay for contamination of surface waters, death of wildlife, loss of natural beauty, or its contribution to climate change with CO2 emissions during the mining process and when the petroleum products are burned by consumers. Its workers have average salaries, but no retirement plan.
• D. WVC, Inc. mines coal in West Virginia by blowing off the tops of mountains and strip mining the newly exposed surfaces. The coal company pays for use of the land and provides good pay and health care for workers who develop silicosis, suffer copperhead bites, or die in avalanches caused by the explosions. Coal trucks weigh about 90,000 pounds and require special roads with thick roadbeds. The taxpayers living in the state pay for the roads. The company does not pay for aesthetic damage to the West Virginia scenery, contamination of ground water, the damage done by dumping debris in stream beds, or CO2 emissions produced during the mining process and when the coal is eventually burned.

3.

Below is a list of examples of benefits that ecosystems provide to people. Match each benefit with the correct category of ecosystem services.

4.

Both energy and matter move into and out of nearly all ecosystems on Earth.