There is an enzyme “amylase” used in Bioethanol production at large scale. The enzyme has excellent Kcat and Km values but there is issue of thermostability. The enzyme cannot work beyond 50oC temperature which is not optimum for industry. We have been giving a target to increase its thermostability by using Rational Design. Can you please let us know that which region (Helix, Sheet, Loops) will be targeted to increase thermostability of enzyme and why?

We are fighting what seems to be a losing battle against antibiotic-resistant Gram negative bacteria, such as “beta-lactamase-producing Enterobacteriaeceae” (BLPE). BLPE seemed to arise all of a sudden in response to the common use of penicillin to treat infections caused by Enterobacteriaeceae.

A. BLPE are resistant to all of the following antibiotics. For each, state the antibiotic’s mode of action, and explain the most likely resistance mechanism. Ceftriaxone Tetracycline Aminoglycosides Vancomycin

B. If we only overused Penicillin, how could that lead suddenly to the development of resistance to all of these different antibiotics, especially Tetracycline and Aminoglycosides?

C. BLPE can still be treated with Polymyxins. How do Polymyxins work, and why would physicians be reluctant to use them in a patient unless absolutely necessary?

There are basically three different types of pathogen invasion “strategies” – extracellular, intracellular in non-phagocytes like epithelial cells, and intracellular in circulating phagocytes like Macrophages. That is, some bacteria try to remain outside of the host cells, while other bacteria and viruses get inside different types of host cells and survive there.

A. For EXTRACELLULAR pathogens, describe advantages and disadvantages of this strategy. How does our immune system detect and eliminate such pathogens? Explain two virulence factors that this sort of pathogen can use to survive in its chosen environment.

B. For pathogens that are INTRACELLULAR IN MACROPHAGES, explain how they gain access to macrophages. Describe advantages and disadvantages of this strategy. How does our immune system detect and eliminate such pathogens? Explain two virulence factors that this sort of pathogen can use to survive in its chosen environment.

C. For pathogens that are INTRACELLULAR IN EPITHELIAL CELLS, explain how they enter the epithelial cells. Describe advantages and disadvantages of this strategy. How does our immune system detect and eliminate such pathogens? Explain two virulence factors that this sort of pathogen can use to survive in its chosen environment.

1. What are the two manners by which prokaryotic transcription stops? How do these two manners differ? How do these differ from eukaryotic transcriptional termination?

2. What is the general process of genome expression in eukaryotes versus prokaryotes?

3. What is the Shine Delgarno sequence? What is a promoter? What is a UTRs transcriptional terminator?

4. What is Rho helicase?

5. RNA polymerase II requires a lot of other factors in order to engage in transcription. Draw out or explain what has to happen in order for transcription to start of a gene controlled by a promoter sequence that contains a TATA box. Make sure you describe the order of events and explain what each involved factor does.

For each of the following, identify the antibody or antibodies (if more than one) that meet each of the following criteria. Briefly (about one sentence or less) answer the follow-up question.

a)________ Only antibody formed in the absence of TH-B cell interaction (T-independent pathway). What types of antigen allow this mechanism of B cell activation? b)________ Able to activate the complement cascade. What are three consequences of complement activation?

c)________ Able to initiate ADCC. What happens during ADCC?

d)________ Able to opsonize a pathogen. What is another opsonin that we talked about in Bio 221?

e)________ Main antibody secreted across mucosal surfaces. How do bacteria that use this portal of entry prevent this antibody from finding them?

f)________ Used to prevent Rh- moms from being sensitized against an Rh+ baby. Briefly explain how this type of hypersensitive reaction could kill subsequent babies.

g)________ Found on the surface of a naïve B cell. What is a “naïve” B cell?

h)________ Responsible for the allergic response What happens during the two exposures required for the allergic response? (>1 sentence is OK)

i)________ Used in artificial passive immunizations What is the difference between “active” and “passive” immunity? State some examples.

5. If the external ion concentration is high, cells shrink. This happens due to
____. (Explain your answer.)
a. diffusion
b. denaturation
c. osmosis
d. facilitated diffusion

6. The process by which ATP provides energy required for muscle contraction is
a. chemical reaction.
b. mechanical work.
c. transport work.
d. chemical work.

From time to time, the CDC committee that makes recommendations about vaccines (ACIP) decides to “change their minds” about the use of a particular vaccine, even though we might have been using it for a long time. Each time they do this, there is something about the “old” vaccine they didn’t like, and something about the “new” vaccine that fixes the problem. For each of the following, explain (1) the difference between how the old and the new vaccines function, and (2) how the new vaccine avoids some problem with the old one. If the new vaccine introduces some problem of its own, describe that, too.

A. In 1983 a 23-valent pneumonia vaccine was developed using the polysaccharide capsules from 23 different Strep pneumoniae strains, and was used for elderly people. But in 2015 the ACIP recommended switching to a 13-valent polysaccharide-protein conjugate vaccine (Prevnar-13).

B. In 1997 the recommendation was made to switch from a whole-cell Pertussis vaccine, which had been in use since 1949, to an acellular subunit vaccine.

C. In 1961 we switched from an inactivated Polio vaccine (developed in 1955) to a live attenuated one. Then in 2000 we switched back to the inactivated one. Explain both ACIP decisions. D. In the near future, the decision may be made to switch from the current Flu vaccine (either the live attenuated or the inactivated one) to a DNA-based flu vaccine.

2. Match the following descriptions with the intertidal zone that exhibits the characteristic: A, B, or C: Highest risk of desiccation, highest species diversity, and shallowest area where red, green and brown algae grow.

A) lower intertidal zone B) middle intertidal zone C) upper intertidal zone

3. Which of the following does not determine an estuary's mixing pattern: A) depth of the river upstream B) water density C) nearshore currents

Scenario 2.
Normally viruses infect a host cell, replicate themselves inside it and burst the host cell so that they can go on infecting other cells. In this viral infection, the virus has stopped the normal apoptotic pathway to allow themselves to stay within the cell indefinitely – a phenomenon known as latency. Further studies on this virus has shown that the virus encodes inhibitors of caspase 8 activation.

Scenario 2 describes the development and maintenance of a latent viral infection, allowing the virus to persist in the host cell. If we assume that the infection has already developed latency in the patient (i.e. the person is already infected and the virus is persisting in the cell), which of the following methods would be the MOST APPROPRIATE method to eradicate the virus from the host cell and stop the latent infection?

Select one:
a. Develop a vaccine against the virus, which enhances apoptosis via the intrinsic pathway
b. Block viruses from inserting their nucleic acids into a host cell
c. Upregulate the expression of DISC assembly proteins
d. Promote the release of cytochrome C in all cells

Scenario 3. Parkinson’s disease is a chronic neurodegenerative disorder characterised by uncontrollable tremors and muscle rigidity. Studies have linked Parkinsons disease with mutations in several different genes, one of which is PINK1. Studies have shown that in PINK1 deficient human and mouse neurons there was an increase in cytochrome C release from the mitochondrion.

Scenario 3 describes the development of Parkinson's disease in neurons due to the accumulation of mutations in PINK1 (as well as other genes). Based on your knowledge of cell death, the function of PINK1 is most similar to that of...?

Select one:

a. Puma

b. Bcl-2

c. IAPs

d. p53

e. Bak

Why is it viral diseases are more difficult to treat compared to bacterial diseases

A biochemist replaces the DNA‐binding domain of the yeast Gal4 protein with the DNA‐binding domain of the Lac repressor and finds that the engineered protein no longer regulates transcription of the GAL genes in yeast.

A. Draw a diagram of the different functional domains you would expect to find in the Gal4 protein and in the engineered protein.

B. What might be done to the DNA‐binding site recognised by this chimeric protein to make it functional in activating transcription of the GAL genes?