Exam 9: Tools for Analyzing Gene Expression

A nonscientist friend of yours asks how findings in a worm or fly can be relevant to human biology. Explain to your friend the importance of model organisms in molecular biology research.

During the process of two-dimensional PAGE

Which of the following is not a property of green fluorescent protein (GFP)?

At its isoelectric point

What kinds of information can be obtained from a Northern blot? Compare this with the information obtained from a Southern blot.

In a yeast two-hybrid assay that uses lacZ as a reporter gene, what does the production of a blue product signify?

Describe the structure of green fluorescent protein and discuss how this structure relates to the function of the protein.

Double-stranded RNAs are processed by the enzyme _______ to form small interfering RNAs (siRNAs). One strand of the siRNA is loaded into a silencing complex named _________. The siRNAs target mRNA for ___________ .

You have purified a protein. When you subject it to SDS-PAGE, two bands are seen. Provide a possible explanation and describe how you could test your hypothesis.

Which of the following has not been used as a model organism in molecular biology research?

Which component is not required for in vitro translation of a recombinant protein?

Explain the molecular basis for protein separation by isoelectric focusing (the first step of 2D-PAGE).

Morpholino oligonucleotides have proved useful for

Explain the information gained from an in situ analysis differs from that gained from an in vitro analysis, using protein or RNA expression as an example to illustrate your answer.

Southern blotting is the process that is used to identify

Which method would best help you to identify specific amino acid residues that are critical for the function of a protein?

In an indirect immunofluorescence assay, which component is fluorescently labeled?

Consider a cotransfection assay with expression vectors for two putative transcription factors that you suspect work together to activate transcription, and with a regulatory region of interest attached to a CAT reporter gene. You also test two deletion () mutants of the regulatory region. (a) How could you confirm that the transcription factors are transcribed and translated in the transfected cells? (b) Interpret the results of the CAT assay below. The plus and minus symbols indicate that presence or absence of expression vectors for the listed components in the transfection assay. (c) How would you demonstrate protein-protein interaction between the two transcription factors in vivo and in vitro? Show sample positive results. (d) Describe protocols to further characterize direct binding of the proteins to DNA in vitro and in vivo. Show sample results.

Diagram the key steps in a GST pull-down assay. Is the GST-tagged protein the "bait" or the "prey"?

Compare and contrast the type of information that can be obtained from X-ray crystallography with nuclear magnetic resonance (NMR) spectroscopy.