Midterm 1 CHEM 114C

Long answer Describe the 3-step process of topoisomerases I types.

1. One strand of DNA is nicked 2. the strand, which is not nicked, is then free to rotate and remove any supercois 3. the DNA break is resealed because tyrosine can act as a leaving group

In DNA and RNA synthesis, the new strand growth is always in the ______ direction

5' to 3'

Assay used to determine carcinogenic potential

Ames test

Who discovered DNA Polymerase I?

Arthur Kornberg

Long Answer How are breaks sealed in discontinuous DNA formed during replication?

DNA ligase is the enzyme that seals the breaks by creating a phosphodiester bond between a 3' hydroxyl group and a 5' phosphate at the end of the other piece. It can only seal a break in a double-strand piece of DNA. It normally uses the energy provided by ATP, except in bacteria, where NAD+ serves as the AMP donor.

Number of times a DNA strand winds around the helix when it is constrained

Linking (?)

Briefly describe the Meselson and Stahl experiment that indicated that DNA replication is semiconservative.

Meselson and Stahl grew bacteria in the presence of 15N, or "heavy" nitrogen (1). They rapidly replaced the 15N media with 14N, or light nitrogen (2). DNA was extracted at various time intervals during the growth of the bacteria, representing different stages of replication (generations). They examined the DNA using density-gradient equilibrium sedimentation (3) and observed that no "heavy" DNA was present in the first generation, but that the DNA was intermediate between light and heavy. After the second generation, there were equal amounts of intermediate and light. This confirmed that one strand of the parent DNA is present in each daughter strand of replicated DNA.

Long answer Why is shape complementarity so important in DNA replication?

Residues of the polymerase enzyme form hydrogen bonds with the minor-groove side of the base pair in the active site. If the shape complementarity of the bases is off, then this will effect the shape of the minor-groove, and thus effect polymerase's recognition.

Enzyme capable of synthesizing DNA from RNA template:

Reverse transcriptase

Long answer How are single-stranded regions of DNA maintained during polymerization?

Single-stranded binding proteins (SSB) bind to single stranded regions of DNA

A type of topoisomerase that does not require ATP

Type I

Aflatoxin B1 is a compound that is converted to a reactive epoxide by cytochrome P450 and causes a. a G-C to T-A transversion b. an intrastrand cross-link c. deamination of adenine d. all of the above e. none of the above

a. a G-C to T-A transversion

Photolyase functions to a. repair pyrimidine dimers b. remove damaged bases c. ligate single-strand breaks d. all of the above e. none of the above

a. repair pyrimidine dimers

How can leading and lagging strands be synthesized in a coordinated fashion? a. specific enzymes control the size of the DNA opening b. lagging-strand binding proteins inhibit leading-strand replication if the strands become disproportionate in size c. Pol III is a dimeric holoenzyme, and the looped lagging strand allows the enzyme to proceed in the same direction. d. all of the above e. none of the above

c. Pol III is a dimeric holoenzyme, and the looped lagging strand allows the enzyme to proceed in the same direction with each strand.

Technique(s) used by Franklin and Wilkins to deduce structure of DNA was a. absorbance spectrophotometry b. electron microscopy c. x-ray diffraction d. all of the above e. none of the above

c. x-ray diffraction

The feature(s) of DNA deduced by Watson and Crick included a. two antiparallel polynucleotide chains coiled in a helix around a common axis. b.the pyrimidine and purine bases lie on the inside of the helix c. the bases are nearly perpendicular to the axis d. all of the above e. none of the above

d. all of the above

One metal ion in the DNA polymerase reaction coordinates the 3'hydroxyl group of the primer and the second metal ion interacts with the ________

dNTP

mRNA of higher organisms are formed by splicing together _____ after removal of intervening sequences

exons

Proteins that use ATP to melt the DNA during replication

helicases

What the small pieces of DNA observed during DNA replication are called

okazaki fragments

Initial segment of a polymer that is to be extended

primer

The ends of chromosomes

telomeres

What DNA serves as when directing synthesis of the complementary strand of DNA or RNA

template

What the strands of DNA must be in order for replication to occur

unwound