Which of the following pairs are orthologs? Which are paralogs? Which are neither?

Human Trypsin and horse Trypsin

Human Trypsin and horse chymotrypsin

Human Trypsin and human elastase

Bacillus subtilis subtilisin and horse chymotrypsin

1. What are the official names of the genes that code for the C.bo two-component proteins that control toxin expression?

2. What does a protease do? A nuclease? A kinase? A DNA polymerase? An RNA polymerase?

3. What is the function of the wHTH effector protein? Of the BotR protein? Of the HA70 (hemagglutinin) protein (or any hemagglutinin protein)? Of the botA protein?

4. You have a 5kb linear fragment of DNA and you cut it with a Hind III restriction enzyme that has a recognition site at 500 bp from the left end and 1500 bp from the right end. Then you run the digested DNA on an agarose gel. Drae a picture placing the expected sizes of DNA on the gel.

5. You have the same DNA fragment as above but it is circular and not linear. You cut it with the same restriction enzyme (Hind III) and the restriction recognition sites are in the same places. What would this look like on an agarose gel?

6. You have a 4.5 kb linear fragment of DNA and you cut it with Pst I restriction enzyme that has a recognition site at 1500bp from the left end and 1500bp from the right end. What would this look like on an agarose gel?

7. You did a restriction digest on a linear DNA fragment 3000bp long. You ran it on the gel and discovered that the DNA was not cut. What reasons could yield this result?

8. If you want to cut a fragment of DNA with a restriction enzyme and you know that the DNA sequence has an EcoRI restriction site in it. (You use a computer to identify the EcoRI restriction site.) You look in your freezer for restriction enzymes and find that you only have Hind III and have no EcoRI. Could you substitute HInd III and have it cut the DNA at the same place as EcoRI?

How are glycolysis and gluconeogenesis are reciprocally regulated in the liver? Answer this question by providing explanations on all levels of pathway regulation. Discuss the reciprocal/opposite regulation in the categories shown in the following sections. However, this is not just a listing of the regulated enzymes and conditions or substances which are effectors of those reactions; you need to address types of regulation which are examples of reciprocal or opposite regulation of the two pathways.

Identify the most highly regulated steps of these pathways. Give the full reactions including reactants, produces and enzymes. For each identify the most highly regulated step AND other reactions which are regulated.  

What does “opposite” or “reciprocal” regulation of opposite pathways mean?

Discuss how reciprocal/opposite “allosteric” regulation of the most highly regulated steps of these two pathways.

Discuss the reciprocal/opposite “hormonal” regulation of the most highly regulated steps of these two pathways.

Discuss the reciprocal/opposite “reversible covalent modification” of these two pathways.

Discuss any other recipocal/opposite type of regulation that occurs in the regulation of these two pathways of glucose metabolism.

1a. You are researching a gene involved in the process of glycolysis. Which of the following would you expect to see in terms of regulation of this gene?  Select all that apply.

1b.

If you are genetically engineering a protein that you want to accumulate in the endoplasmic reticulum of a eukaryotic cell, what is the best answer for what you should do?

1c. Which of the following can be considered final products of a gene? Select all that apply.

1d. Indicate at least two possible reasons that eukaryotes have introns, and what benefits they may provide

Calculate the amount of energy released in the liver upon the complete oxidation of a triacylglycerol containing three 6-carbon saturated fatty acids. Compare that to 3 molecules of glucose. Which one is a better energy source? Show your calculations.

Find the pH of each of the following solutions of mixtures of acids.​

Part A

0.190 M in HCHO2 and 0.23 M in HC2H3O2​

Part B

6.0×10⁻² M in acetic acid and 6.0×10⁻² M in hydrocyanic acid

Excess production of ketone bodies can occur in a diabetic liver cell when the level of

a-NADH is very low

b- fatty acids are very low

c-oxaloacetate is very low

d-acetyl Co-A is very low

Which of the following acids would be most suitable for preparing a buffer of pH 3.10 and why: hydrogen peroxide (pKa= 11.65), propanoic acid (pKa=4.874), cyanoacetic acid (pKa= 2.472), and 4-aminobenzenesulfonic acid (pKa=3.232)?

Some scientists believe that fructose is particularly bad for human health because it promote fat synthesis, contributing to development of type II diabetes and fatty liver disease. You are a scientist working for a lab attempting to develop a drug to help with such diseases called fructono. The idea is that fructono could be added to the diet to reduce fructose absorption; even though fructono would be absorbed, it would not be metabolized, and would be excreted by the kidney. The hypothesis is that fructono binds to the fructose transporter, competitively displacing fructose. This cannot be easily studied in humans, so you are investigating this hypothesis with a mouse small intestine, which is known to transport fructose using a transporter that is quite similar in amino acid sequence and structure to the human protein. For your research, you set up a perfused intestine prep. You cut out about 1 cm of small intestine, and put it in a dish containing saline. You insert a tube into the intestinal section, and use a pump to push any fluid you want through the lumen of the intestine. You have radio-labeled fructono, so you can measure its appearance in the saline outside the intestine. How can you measure the rate of transport of fructono? 1 pt Describe experiments that would test whether the absorption of fructono is protein-mediated vs. passive (just leaking through cracks, or diffusing through membranes). What results will you get if the transport is protein-mediated vs. passive? 2 pts. Describe experiments that would test whether the absorption of fructono is active, and the predicted results if transport is active or not. 2 pts. Describe experiments that will test whether the active transport of fructono requires luminal Na+, and the predicted result if transport is Na+-dependent or not. 1 pt. Describe experiments that will test whether fructono can reduce the transport of fructose in a dose-dependent manner. 2 pts What side-effects might fructono have? 2 pts