Describe the role of cancer associated fibroblasts in the development of cancer. By keeping in mind that cancers are named as wounds that do not heal.

After death, metabolism shuts down and ATP runs out. As a result, calcium pumps at the sarcoplasmic reticulum stop, so Ca⁺² ions diffuse out into the sarcoplasm.   Produce a diagram describing the contraction cycle and use it to explain what will be the consequence of a sudden calcium increase in the absence of ATP for the muscles of this person’s body?

During elongation of translation, each new amino acid is added to the growing chain by this chemical bond. (multiple choice)

a. hydrogen

b. peptide

c. phosphodiester

d. covalent

e. ionic

what kind of concentration effects can be seen in the self assembly of amino acids?

11. What are the functions of the 5’ cap? How is it added on the RNA?

12.Explain how a poly-A tail is produced; (CPSF and CstF, Poly APolymerase, Poly A Binding Protein (PABP)).

13.What are the two hypotheses for eukaryotic transcription termination?

14.How does splicing of pre-mRNA occur?

15.Compare and contrast splicing of group I introns, group II introns and spliceosome-mediated splicing of mRNA.

6. What is the basic difference between general transcription factors and specific transcription factors?

7. How is DNA opened up along a prokaryotic promoter. How does this occur along a eukaryotic promoter?

8. Describe the functions of Transcription factors: TFIID(TBP,TAFs),TFIIA, TFIIB, TFIIE, TFIIF, TFIIH.

9. What is ELL(negativeelongationfactor) and pTEFb?

10.What is the CTD tail? What are some of the functions of it? What are the phosphorylation states and what do they signify?

Describe what is epithelial to mesenchymal transition (EMT). Is the process of EMT essential for metastatic spread? Please give evidences that support your answer.

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.