BIOL 114  Test 1

September 22, 2006

Name ________________________________

Total possible:      50

1. (6 pts) Sketch the structure of one deoxyribose-phosphate unit of a DNA backbone.  Indicate the link to the nitrogenous base.

3. (10 pts) Outline all the steps of DNA replication in detail.

Include one diagram showing two replicating forks.

See DNA Replication.

1. Helicase enzyme unwinds DNA. This reaction needs ATP. At each replicating fork, the exposed single-stranded DNA is protected by single-strand binding proteins (ssb). Primase enzyme binds, preparing to make RNA primers.

2. Primase enzyme makes RNA primer molecules. Each primer hybridizes (base pairs) with DNA, at the origin of replication. The 3' OH end will attach new deoxy nucleotides (dNTPs). The primers will each start a leading strand,

3. DNA polymerase III (Pol III) attaches new dNTPs to the 3' OH end of the growing chain of the leading strand, which elongates toward the replicating fork, 5' to 3'. (For each origin, there are TWO leading strands; why?) For each NTP, a pyrophosphate (PP) is released, providing the necessary energy.

4. More primers hybridize to the opposite strand of DNA. Pol III starts elongating 5' to 3' but it keeps running into the back of an RNA primer. This is the lagging strand. There are TWO lagging strands (why?)

5. DNA polymerase I (Pol I) starts at “nicks” in the growing strands. It edits the strand by removing bases ahead of it (5' end), including RNA and mismatched bases, while elongating the strand "behind" 5' to 3'. It replaces all RNA nucleotides with dNTPs.

6. Ligase seals the phosphate bonds at all “nicks” in the DNA.

7. Editing endonucleases excise mismatched nucleotides, replacing with the proper match. How do they know which is old DNA vs. new DNA? The old DNA contains methyl groups on some of its cytosine bases.

8. Gyrase restores negative superturns in DNA. ATP is needed.

9. Methylases add methyl groups to the new DNA, at the same positions as the original strands. Now the two daughter helices are indistinguishable from each other, and from the original helix.

4. (6 pts) Explain what is Z-DNA, and what is its main role in living systems.

Z-DNA is a form in which the helix is unwound so far as to twist in the opposite direction (left-handed) from B-DNA (right-handed). Z-DNA has its own distinctive shape and conformation of the base pairs. Z-DNA forms transiently behind the RNA polymerase as it plows through the helix, leaving extreme negative supercoils transiently behind it. Certain RNA editing enzymes recognize Z-DNA as a place where new RNA is being made, and may need editing. Also, at other places the DNA sequence of base pairs causes more long-term Z-DNA forms which are recognized by regulatory proteins that bind to regulate gene expression.