I.         
Signaling cascades (4 pts)

1.     Which of
the following is an example of a signaling cascade?

                          
A.          Binding of
lactose to the lac repressor

                          
B.          Binding of
the lac repressor to the lac operon

                         
C.          The series
of proteolytic digests that occur during clotting

                         
D.          The
Collins Toggle Switch

2.     Why is it
important that signaling cascades have negative feedback loops?

II.         
Metabolism (4 pts)

1.     What is a
benefit of a negative feedback allosteric regulator?

                          
A.          It
prevents starting materials from being unnecessarily consumed.

                          
B.          It
regulated metabolism without requiring new protein synthesis.

                         
C.          It can be
rapidly reversed as conditions change.

                         
D.          All of the
above.

2.     How is a
metabolic cycle, like the citric cycle, distinct from a
metabolic pathway, like glycolysis?

III.         
Transcription (4 pts)

1.    
Transcription factors, repressors, and activators are examples of
proteins that _________.

                          
A.          randomly
activate RNA polymerases.

                          
B.          bind
specific DNA sequences.

                         
C.          bind
specific rRNA sequences.

                         
D.          are found
in the lysosome.

2.     The
trp operon is attenuated by a stem-loop structure that can
form near RNA polymerase. The RNA sequencing encoding the stem loop
is:

5’-AUACCCAGCCCGCCUAAUGAGCGGGCUU-3’

The stem loop is composed of 7
nucleotides which perfectly base pair. Indicate the two halves of
the stem loop on the sequence above.

IV.         
DNA replication/repair/genome editing (4 pts)

1.     What is a
consequence of the need for RNA primers during DNA replication?

                          
A.          Linear
chromosomes gradually shorten each cell division.

                          
B.         
Transcription factors often trigger DNA replication.

                         
C.          RNA
primers are not actually needed for DNA replication.

                         
D.          Lagging
strands can be avoided.

2.    
CRISPR-mediated genome editing has gene-specific components: an
sgRNA, and a double-stranded repair template. Describe the role of
the sgRNA in directing genome editing.

V.         
Genetic circuits (4 pts)

1.     Which
statement best describes the mechanism of the toggle switch?

                          
A.          Inducers
must be continuously applied to maintain one of two states.

                          
B.          Competing
repressors keep the cell in one of two transcriptional states.

                         
C.          An
activator and a repressor keep the cell in one of two states.

                         
D.          A pair of
repressors cause the cell to oscillate between two states without
input.

2.     How is
bistability achieved by the Collins toggle switch?