Dr. Reichler’s Bio 212  1-2pm        Print Name:_______KEY_____________
In-class Exam #2  October 21, 2002

    Answer each question as succinctly as possible in the space provided.  If needed, continue on the back.  If you use a drawing as part of your answer, be sure to also include a written explanation.  Read each question carefully and don’t hesitate to ask if a question seems unclear.  These questions have specific answers, although for some, more than one answer is possible.  To receive full credit you must clearly and fully answer the question being asked.  Each question is worth 6 pts, unless otherwise noted, for a total of 100 points possible for this exam.

1. a.  What are three differences between gene expression in bacteria and eukaryotic cells?
Any three of:
Bact- have operons, transcription/translation simultaneous, no introns, transcription occurs without other factors, gene express controlled at level of transcription
Euk- no operons, transcription/translation separate, have introns, transcription requires transcription factors, gene express has many levels of control

b. Based on information from various organisms, what is the relationship between the quantity of DNA and the number of genes?
There is a general trend between very simple organisms that have few genes and little DNA, as compared to complex organisms with many genes and much DNA.  But within more complex organisms, there is little or no correlation between quantity of DNA and number of genes.

2. What are all of the parts of a gene, and what information is stored in each part?
These are the primary three:  Promoter- tells where gene starts and when it will be transcribed.  Coding region- the nucleotides that will code for the protein/amino acids.  Terminator- marks the end of the gene/transcription.  May also include:  (the coding region may be divided into)Exons- nucleotides coding for protein/amino acids.  Introns- will be removed before translation.  UTR’s- will determine mRNA stability.

3. a.  Based on the bacterial DNA sequence given below, show the mRNA and protein sequence (label 5’ and 3’ ends as appropriate; the genetic code is on page 4): (10 pts)
    RNA polymerase oriented    5’-T GGATGCTTT ATGTAGAAGGGCATTAACAGC-3’
    towards the right        3’-ACCT ACGAAATACATC TTCCC GTAATTGTCG-5’

                    protein Met-Leu-Tyr-Val-Glu-Gly-His
5 pts for mRNA sequence, 1 pt for correct 3’/5’ label, 4 pts for correct amino acid sequence, (-1 pt if add either start or stop as part of protein)

b. What would be the final protein sequence if the first three amino acids are the signal sequence for transport to the nucleus? (5 pts)
Same as above, no change.

c. What would be the final protein sequence if the first three amino acids are a signal sequence for a secreted protein? (5 pts)

4. a.  If an mRNA was transported before the introns were removed, what effect would that have on the protein?
There would be extra amino acids translated likely resulting in an non-functional protein.  OR There could also be a stop codon in the intron, causing the protein to end prematurely.

b. In a eukaryotic cell, does an mRNA that exists in the cytoplasm for a long period of time always lead to a high quantity of that protein being produced?  Why or why not?
No, if translation is blocked, or repressed, then the mRNA will not be translated and the protein will not be produced.

5. How could a mutation in a gene (a change of the nucleotides) cause the following effects:
a.  Production of a non-functional protein?
Any of:  Code for different amino acid, add a stop codon, delete or change start codon, (4 of 6pts) change promoter so no transcription

b. No change in the protein?
Any of:  could be in intron, could be in third codon position which would not change the amino acid coded for (wobble)

c. A protein to be produced in greater quantity than normal?
Any of:  Change to promoter so that more transcription occurs, Change to UTR so that mRNA is more stable, change protein sequence so protein is not degraded

6. a.  What are operons, and how do eukaryotic cells perform a similar function?
Operons are several functionally related genes (proteins that are part of a pathway) that are controlled by one promoter.  In Euk functionally related proteins have similar promoters that will be bound by the same transcription factor.

b. The trp operon is used to produce the amino acid tryptophan.  It is controlled by a repressor that inhibits transcription.  When there is no tryptophan in the environment, will the repressor be present?  Explain.
The repressor will not bind to the DNA/promoter so that the genes can be expressed and tryptophan can be produced.

7. a.  What would happen if the proteins in a cell were never degraded?
Any of:  The cell would not be able to react to changes in the environment.  OR  Faulty, non-functional proteins would not be recycled.  OR  The cell would run out of amino acids and not be able to make more proteins.

b.  How can DNA sequences relatively far away from the gene have an effect on the expression of the gene?
Any of:  Enhancers are DNA sequences far away from the gene that bend and the enhancer protein/transcription activators interact with other transcription factors at the promoter to encourage transcription.  OR  A transcription factor gene far away can be expressed and the gene product, a transcription factor, can initiate transcription.

8. Using rules 1 and 2 of Strong Inference (the parts prior to actually doing any experiments), answer the following question…What is the infectious agent for Mad Cow disease (Bovine Spongiform Encephalopathy)? (8 pts)
Use Strong Inference.  Make multi hypos, design experiments to eliminate hypos.  Example:  Hypos- Infectious proteins are the infectious agent.  Viruses are the infectious agent.  Bacteria are the infectious agent.  Expt- Destroy DNA/RNA from infected material and test whether it can infect other animal.  Bacteria and viruses use DNA or RNA as genetic material.