BIOL 114  Test 3

November 10, 2006

Name ________________________________

Scores:

45-50 A- to A+
40-44 B- to B+
35-39 C- to C+
<35 D

1. (6 pts)  Draw a chart of the evolutionary divergence of these five species.  The table shows percent relatedness between pairs of species.  Assume that these species mutate and diverge at 1.5% / million years.

 

 

A

B

C

D

E

A

100

90

85

85

80

B

90

100

85

85

80

C

85

85

100

95

80

D

85

85

95

100

80

E

80

80

80

80

100

 

 

 

Sample calculation: C-D divergence = (100-95%)/1.5% per million years = 3.3 million years

 

2. (6 pts)  In evolution of genes, explain what is meant by orthologs versus paralogs.

       Explain an example of a pair of orthologs, and a pair of paralogs.


Orthologs are genes in different species that share the same ancestral gene, and retain equivalent function in each species. An example is the globin gene in mammals. Another example is the rhodopsin pigment gene.

 

Paralogs are genes in the same species that share the same ancestral gene, but have evolved different functions in the same species. The Hox genes, for example, serve different key roles in development, although all evolved from a common ancestor.

3. (4 pts) For a restriction enzyme of sequence AA(Pur)(Pyr)TT, about how many cut sites would you expect in a genome of size  6 x 109 bp?

 

Average spacing of sites = (4)(4)(2)(2)(4)(4) = 1024
Total number of cut sites = 6 x 109 bp/1024 bp= approximately 5.9 x 106

 

4. (8 pts) Explain how the processes of gene cloning and PCR amplification are based on naturally occurring enzymatic processes in microbial genetics.

 

Gene cloning involves cutting a plasmid and target DNA with a restriction endonuclease, a type of enzyme made by bacteria in order to cleave foreign DNA (such as from a phage) that endangers their survival. The plasmid DNA incorporates the cleaved target DNA into its sequence by annealing (hybridization) of its staggered ends, regenerating the restriction site sequences. Completion of the recombinant plasmid requires use of ligase to seal the phosphodiester backbone. Ligase is an enzyme used by bacteria to seal the nicks between portions of the lagging strand of DNA replication.

PCR amplification involves the use of a single enzyme, thermostable DNA polymerase, which can withstand the heating and cooling cycles of repeated amplification and denaturation of a small DNA molecule. The DNA polymerase is obtained from thermophilic bacteria or archaea.

 

5.  (6 pts)  Sketch the structure of a recombinant plasmid, of the type found in the Plasmid program. The restriction enzyme data are shown:

 

EcoRI -- 3 kb, 9 kb

PstI -- 1.5 kb, 10.5 kb

BamHI -- 4 kb, 8 kb

EcoRI + PstI -- 1.5 kb, 3 kb, 7.5 kb

EcoRI + BamHI -- 1 kb, 3 kb, 8 kb

PstI + BamHI -- 1.5 kb, 4 kb, 6.5 kb

6.  (6 pts) Explain the structure of a drug-resistance transposon, including its essential genetic features.

 

A drug-resistance transposon makes its host bacterium resistant to an antibiotic drug. The transposon consists of a DNA sequence flanked by two inverted repeat ends, which pair up for recombination in a "stem-loop" during excision of the transposon. The DNA sequence must include a gene encoding a transposase enzyme to catalyze excision or copying of the transposon sequence; and a gene encoding an enzyme that deactivaes or exports the antibiotic drug.

 

7.  (6 pts) For each partial-diploid for the lac operon, explain whether B-galactosidase is expressed, and whether lactose is needed as inducer, and why:

 

A.
p- o+ lacZ+

p+ oc lacZ+

 


lacI-

lacI+

B.
p+ o+ lacZ+

p- o+ lacZ-

 


lacI-

lacI+

 A. The lacZ gene (lower operon) expresses B-galactosidase constitutively (without requiring lactose inducer), because the operator fails to bind repressor (expressed by lacI+).

B. The lacZ gene (upper operon) expresses B-galactosidase, only when lactose is present to bind the repressor (expressed by lacI+ in the upper operon).


8. (8 pts) Explain with a diagram the comprehensive model of eukaryotic transcription regulation.

Regulation of eukaryotic transcription requires: basal factors, protein complexes vthat enable RNA polymerase to transcribe from the core promoter; coactivators, protein complexes that connect the basal factors to the protein-binding domains of the activators; transcription factors (activators) that contain protein-binding domains to bind the coactivators, and DNA-binding domains to bind the enhancer sequences on DNA. Transcription can be repressed by repressors binding to silencer sequences.