1. Genomics is the study of:
a. The structure and function of mutations and how they alter genetic traits.
b. Genes and the DNA sequences between genes and how they determine development.
c. The information provided by computer programs which analyzes mRNA.
d. The human genome as compared to other vertebrate genomes.
2. Microarrays are a very useful tool in genomics because they:
a. Help scientists examine intergenetic DNA by separating it from genes.
b. Provide a unique promoter region for polymerase chain reactions.
c. Allow scientists to examine thousands of genes all at once.
d. Decrease the time it takes for scientists to make copies of DNA.
3. Generally, every cell in our body contains the same 20,000 (or so) genes.  However, cells  in our body are different from each other because they:
a. Have different genes turned “on” or “off” to support different functions.
b. Contain different copies of genes for different functions.
c. Provide different nucleotide bases for each developmental function.
d. Function differently based on varying proteomics.

4. How can scientists determine the function of or differences between cell types?  They can examine the:
a. Number of nucleotide bases in genes versus intergenetic sequences.
b. Amount of mRNA expressed for each gene in a cell type, and then compare that information between cell types.
c. Amount of mutations between genes in the intergenetic spaces.
d. Number of tRNA copies for a particular cell type.

5. How is a microarray constructed?  In each spot, there are:
a. Copies of all the genes for an organism.
b. Multiple copies of one gene; each spot has copies for a different gene.
c. Multiple copies of intergenetic sequences, which bind to genes in the samples.
d. Copies of intergenetic sequences, which promote the replication of DNA in a sample.

6. The experiment that begins in Chapter 3 of the simulation seeks to answer the question:
a. What is the difference between intergenetic spaces in cancer cells versus healthy cells?
b. Why do different cell types express different amounts of mRNA?
c. How do different cancer cells produce different mutations?
d. What is the difference between healthy cells and cancer cells?

7. Why can’t doctors use cell appearance to diagnose cancer?
a. Not all cancer cells look different from healthy cells.
b. Cancer cells are too small to examine using cell appearance.
c. Not all cancer cells are able to be biopsied from the body.
d. Cancer cells change appearance when taken out of the body.

8. In the experiment, a solvent is added to each cell type (healthy cells and cancer cells).  After the sample tube containing each cell type is mixed on the vortex, the RNA is separated from the rest of the sample in a centrifuge.  Why does DNA settle to the bottom of the tube and RNA doesn’t?
a. RNA is much longer than DNA.
b. RNA is attached to proteins that help it stay in solution.
c. DNA is attached to biomolecules that weigh it down and help it settle to the bottom.
d. DNA is much longer than RNA.

9. What feature does mRNA have that tRNA and rRNA do not? mRNA always:
a. Contains a GABA box.
b. Contains a TATA sequence.
c. Ends with a G tail.
d. Ends with a poly-A tail.

10. How do the beads in the column separate mRNA from all other RNA?  The beads contain:
a. Sequences that magnetically separate the mRNA.
b. A glue-like substance derived from spider webs.
c. Poly-T’s.
d. A sequence of uracil’s that bind to the Poly-A tail.

11. After you isolate mRNA, you have to make a DNA copy.  Why can’t we just use mRNA?
a. DNA is much more stable than mRNA.
b. We have to add a fluorescent label that will allow us to see the sample.
c. mRNA will eventually transform into tRNA making it unusable.
d. A and B

12. Scientists call hybridization the key to microarrays.  Hybridization occurs when:
a. Two complimentary strands of DNA from different sources bind to each other.
b. Poly-A tails bind to Poly-Ts.
c. Different species interbreed and create new DNA base pairings.
d. Two strands of identical DNA bind without using the traditional nucleotide pairs.

13. When you scan the microarray in the scanner, the data show some dark spots.  What do these represent?
a. The DNA that has been replicated in healthy cells.
b. The mRNA that was washed away in the washing solution.
c. The DNA that was not transcribed and expressed in healthy cells.
d. The mRNA that was not bound by Oligo-d-tails in the beads.

14. When you scan the microarray in the scanner, some spots are yellow and represent places where the gene was expressed in both healthy and cancer cells.  These spots tell us:
a. Where to look for mutations.
b. Where DNA hybridized in cancer cells.
c. That DNA expression didn’t change in these genes when cancer occurred.
d. That the microarray didn’t work in these genes.

15. In our example, gene 6219 mRNA is made in both healthy and cancerous cells; however proteins are only translated from that mRNA in healthy cells.  Microarray analysis:
a. Shows us this defect by making yellow spots.
b. Cannot show us this defect, which is a limitation of this type of analysis.
c. Show us this defect by making red spots.
d. Cannot show us this defect, which is a benefit of this type of analysis.