Dr. Reichler’s Bio 212  12-1pm        Print Name:_______   KEY  _______  _______
In-class Exam #1  September 23, 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.  Why does DNA have a very regular 3-dimensional shape while RNA has a varied 3-D shape?
RNA is single-stranded so areas with complementary bases form loops and bend the RNA.  DNA is double stranded, and the regularity of its structure only allows one 3-D structure, a double helix.

b. Why does the high heat used during PCR not effect the information stored in DNA?
Heat can not break the covalent bonds holding the two strands together.  The information stored in DNA is the order of nucleotides.

2. Why does DNA need to be packaged, and at what level of packaging would you expect to find DNA during DNA replication?
The total length of DNA is huge, and it must fit into a cell and/or nucleus.  During replication, the DNA would be packaged in chromatin fiber or nucleosomes.

3. a.  Why does DNA need to be replicated?
When a cell divides, it must have 2 copies of the DNA to pass on to the 2 new cells.

b. Below is a short sequence of DNA.  Complete the complementary strand and then draw this sequence after is has been replicated.  Include all 5’ and 3’ ends labeled, as well as which are the original strands and which are the replicated strands.

Original  5’-ACTGGGTCAACG-3’            5’-ACTGGGTCAACG-3’  Copy
Copy       3’-  TGACCCAGTTGC-5’           3’- TGACCCAGTTGC-5’  Original

c. How is the 5’ end of DNA different from the 3’ end?
Phosphate or tri-phosphate is present.  OR  Only 3’ end can have nucleotides added.

d. Given a much longer sequence, millions or billions of bases long, would you expect that the copy would be exactly like the original?  Why or why not?
Either answer of:  No, replication errors would cause the copies to be slightly different than the original.  No, there would be gaps at the ends due the last lagging strand primer not being replaced by DNA.

4. a.  DNA is a double-stranded molecule.  RNA is involved in the replication process, but not present in the DNA after replication.  Why is RNA needed, and why is it not present at the end of replication?
DNA polymerase can only begin copying the DNA when there is a double stranded part with a single stranded part attached.  Primase adds an RNA primer to achieve this situation.  The RNA primer is eventually removed and replaced with DNA by DNA polymerase I.  

b. What are three differences between the leading and lagging strand of DNA replication?
Any three of:
Leading:  DNA poly follows helicase, continuous replication, only one RNA primer needed, can replicate to end of DNA
Lagging:  DNA poly moves away from helicase, replicated in spurts (Okazaki fragments), many primers needed, leaves gap at end

c. What are two instances in which ligase is needed?  Why is it needed in these instances?
When RNA primer replaced, and during error repair.  DNA poly can only add to 3’end of DNA.  It cannot make the connection between a 3’ end and a already present DNA strand.

5. a. What is the minimum number of origins of replication that would be needed to copy a circular piece of DNA?  Explain.
One.  Replication could start and continue around until all of the DNA has been copied.

b. Does circular DNA need telomeres?  Why or why not?
No, there are no ends, so no gaps are left.

c.  What does telomerase do?  Describe what it specifically does and why it is needed.
It adds nucleotides to the 3’ end of a DNA strand where a gap has been left.  The DNA must be extended because of the gap left where the lagging strand RNA primer cannot be replaced with DNA so the DNA gets shorter each time it is replicated.

6. What are three differences between PCR and DNA replication?
Any three of:
PCR:  Uses heat to separate strands, copies a portion of the DNA, DNA primer, many cycles to produce a lot of DNA, both strands copied the same
DNA rep.:  helicase separates strands, copies all of the DNA, RNA primer, only copies DNA prior to cell division, leading and lagging strand synthesis

7. Why is RNA a good candidate for the first biological macromolecule?
It is a nucleotide and can be replicated, and it has enzymatic activities so it could have been self-replicating.

8. Using rules 1 and 2 of Strong Inference (the parts prior to actually doing any experiments), answer the following question…What is the function of DNA in living systems?
(10 pts)
This answer must include multiple hypotheses, and an experiment designed to eliminate one of the hypotheses.
Example:  Hypo’s-  DNA contains information.  DNA performs enzymatic reactions.  DNA gives structural support to a cell.  Expt-  Remove DNA from a cell, see what the cell cannot do.