Midterm 1 Key

Type II

A type of topoisomerase that can introduce supercoils and require ATP

Type I

A type of topoisomerase that does not require ATP

a G-C to T-A transversion

Aflatoxin B1 is a compound that is converted to a reactive epoxide by cytochrome P450 and causes

Ames test

An assay used to determine carcinogenic potential.

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.

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

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

Describe the three-step process of topoisomerases I types.

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.

How are breaks sealed in discontinuous DNA formed during replication?

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

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

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

How can the leading and lagging strands be synthesized in a coordinated fashion?

5' to 3'

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

dNTP

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

repair pyrimidine dimers

Photolyase functions to

Helicases

Proteins that use ATP to melt the DNA during replication

Telomeres

The ends of chromosomes

reverse transcriptase

The enzyme that is capable of synthesizing DNA from an RNA template

two antiparallel polynucleotide chains coiled in a helix around a common axis. the pyrimidine and purine bases lie on the inside of the helix. the bases are nearly perpendicular to the axis.

The feature(s) of DNA deduced by Watson and Crick included

Primer

The initial segment of a polymer that is to be extended.

Linking

The number of times a DNA strand winds around the helix when it is constrained.

x-ray diffraction.

The technique(s) used by Franklin and Wilkins to deduce the structure of DNA was

Template

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

Okazaki fragments

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

Unwound

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

Arthur Kornberg

Who discovered DNA Polymerase I?

Residues of the polymerase enzyme form hydrogen bonds with the minor-groove side of the base pair in the active site (0.5pt for mentioning minor-groove shape in context). 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 (0.5pt for explaining that complementarity and not hydrogen bonds between bases is what dictates the correct minor groove interaction)

Why is shape complementarity so important in DNA replication?

Splicing together exons after intervening sequences

mRNA of higher organisms are formed by