Download Exam 2 Full v3 Bio200 Win16

Biology 200, Winter 2016
Exam 2
Name: ________________________________________
Student ID#: ______________ TA: ________________
DO NOT OPEN EXAM UNTIL DIRECTED TO DO SO
• Make sure you have 4 pages of questions and six pages total. Print your
name and information on all pages.
• Please use a pen. Pen is much easier to read, even with extensive
crossing-out. Pencil-written exams are acceptable, but may not receive
full credit to penciled answers on regrades.
• When asked, provide concise and clearly written answers. We may
deduct points if you do not fully answer the question or if your answer is
too vague or too confusing for us to follow.
• Extra information, if incorrect, will lose points.
• Limit your answers to the space provided. If you need extra space, you
can use the bottom of this first page. Indicate “on first page” where
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Page
Points Awarded
2 ______ out of 20 points
3 ______ out of 20 points
4 ______ out of 20 points
5 ______ out of 20 points
Total ______ out of 80 points
Exam 2
Name:_____________________________
[20 points] Transcription and Translation
In the diagram, a snapshot of a single chromosome is shown along with RNA
polymerase and ribosomes. There are RNAs of various sequences, as well as three
different proteins. Use this diagram to answer the questions on pages 2-3.
/5 1a) At the moment of this snapshot shown to the right, which of the following
are likely to be True? Mark all correct answers.
_____ Proteins are binding to different nucleic acid sequence locations.
_____ This chromosome contains at least three different genes.
_____ This species is prokaryotic.
_____ The hexagonal molecules are likely to move relative to DNA.
_____ Every RNA is currently being used to encode a protein.
/5 1b) Imagine that all tRNAs with the anticodon 5’-CAU-3’ are instantly destroyed.
How many new proteins can be made after this instant?
Explain your answer in 1-2 sentences, max.
/4 1c) All sigma protein molecules are destroyed instantly. How many new proteins
can be made after this instant? Choose the single best answer.
______ An infinite number
______ A very large number
______ A small number (less than 10)
______ None
______ A negative number
Explain your answer in 1-2 sentences, max.
/6
1d) On the diagram:
• Indicate with an arrow a place where hydrogen bonds are both made and broken
• Indicate with a star the N-terminus of a protein
• Indicate with a triangle the 5’ end of a single mRNA
Total: _____
Page 2 of 6
Exam 2
Name:_____________________________
[20 points] Transcription and translation, continued
/6 1e) Which of the following are changes that happen to a ribosome during termination?
_____ A protein binds within the ribosome.
_____ A mutation occurs in the ribosome.
_____ Subunits of the ribosome form new bonds with each other.
_____ An anticodon or codon is broken.
_____ A protein is released from the ribosome.
_____ A bond between an RNA and an amino acid is broken.
/6 1f) How would you do an experiment to determine which promoters are stronger and which are
weaker? Explain (in general terms) in 2-3 sentences, max.
/8 1g) You’ve isolated four mutant bacteria in the lab. Based on the descriptions below, judge these
mutants in terms of their likely fitness. Fitnesses should be on a scale from zero to ten, with 7
equaling wild-type fitness and 10 being much more fit than wild-type. A fitness of 0 is instantly and
comprehensively dead. The fitnesses you note should all be relative to each other.
Fitness:
______ The gene that encodes Protein
codon.
has a mutation that changed the stop codon into a different
______ A mutation in every promoter moves the -10 and -35 sequences closer to each other in the
DNA, but does not change the sequence of -10 or -35.
______ A mutation in the amino-acyl tRNA synthetase enzyme that increases its rate of reaction.
______ Mutant J: A mutation in the transcription termination signal of 10 different protein-encoding
genes that moves this sequence 20 bases farther downstream in the gene.
Total: _____
Page 3 of 6
Exam 2
Name:_____________________________
[20 points] Replication and Information Flow
Note: For the full version of the exam, the sequence will be filled in and other diagram details may change.
Below is a portion of double stranded DNA from a bacterial chromosome.
The promoter region and the +1 base pair are indicated, as well as the polarity of the two DNA strands.
+1
-10
-35
...5’..CCTTATGGCAAAAGCATAGCGCGCAAACGCTGATAACCGTATGCGCAAATATGCCA..3’....
...3’..GGAATACCGTTTTCGTATCGCGCGTTTGCGACTATTGGCATACGCGTTTATACGGT..5’....
/10 2) What is the translated protein sequence from this gene? Be sure to include the N- and C-termini. You can
abbreviate amino acids using the 3-letter code.
You’ve been hired by a bioengineering firm to create specific gene structures by mutating bacterial
DNA. For each, pick the mutation that is most likely to consistently create the specific structural
feature that is desired.
Example: Every chromosome has sporadic single breaks between nucleotides in the phosphodiester backbone.
____ Mutation in the gene encoding the helicase enzyme
__X_ Mutation in the start codon of the open reading frame encoding the ligase enzyme
____ Mutation in the origin sequences on a single chromosome
____ Mutation in the promoter regions of all genes encoding DNA polymerase enzymes
5/ 3a) Short chromosomes are copied well. Longer chromosomes are either delayed, or the interior
regions of the DNA are never completely replicated.
_____ Synonymous mutation in the gene encoding the helicase enzyme
_____ Mutation in the promoter regions of all genes encoding DNA polymerase enzymes
_____ Deletion mutation in the area of the chromosome between the genes for ligase and helicase
_____ Mutation in the start codon of the topoisomerase enzyme
_____ Missense mutation in the open reading frame of the primase enzymes
5/ 3b) Absolutely no DNA is replicated, but when a single-stranded DNA molecule is inserted into
the cell it is replicated.
_____ Synonymous mutation in the gene encoding the topoisomerase enzyme
_____ Missense mutation in the gene encoding the helicase enzyme
_____ Premature stop mutation in the gene encoding a DNA polymerase enzyme
_____ Frameshift mutation in the gene encoding ssBP
_____ Large deletion in the promoter region of the gene encoding primase
_____ Large insertion mutation in the gene encoding the topoisomerase enzyme
Explain your answer to 3b in 1-2 sentences, maximum.
Total: _____
Page 4 of 6
Exam 2
[20 points] Bacterial genetic forensics
Name:_____________________________
Researchers at the NIH are trying to use probiotics (helpful bacteria) to cure symptoms in patients suffering
from chronic bowel conditions. A set of four artificial genes is bioengineered into a non-coding region of the
bacterial chromosome as shown in Figure 2 (on Page 6). The problem is that several mutations are decreasing
the effectiveness of that four-gene cluster, and the researchers are having trouble figuring out the cause of
these mutations. They’ve asked you to consult on the problem and try to determine the simplest possible
mechanisms that may have caused these mutations.
/5
4a) There is a mutation in the open reading frame of W. This mutation does not change the
expression or function of W, but it does change the expression of Gene H. Describe the most likely
mutation in 2-3 sentences, maximum.
/5
4b) Protein analysis suggests that a few bacteria have a strange ‘combo’ protein. Protein
analysis suggests that the protein has a region that is similar to Protein H and another region that is
similar to protein B. What is the smallest possible mutation that would produce this phenotype?
Choose the single best answer.
______ A loss of a stop codon at the end of Gene H.
______ A loss of a transcription termination signal at the end of Gene H.
______ A loss of a transcription termination signal AND a stop codon at the end of Gene H.
______ None of the combinations of mutations might produce this ‘combo’ phenotype.
/5
4c) A mutation occurred that changes the expression of all four genes.
______ This is likely to be a point mutation
______ This is likely to be a large-scale chromosomal inversion
______ This is likely to be a large-scale chromosomal deletion
______ This is likely to be a polymerase making many errors
Draw a simple diagram to indicate clearly what has happened.
/5
4d) Imagine that the region of the chromosome shown in Fig 2 was inserted into the protein
encoding region of a gene for DNA polymerase. Describe the amount of mutations that would result.
Explain your answer in 2-3 sentences, maximum.
Total: _____
Page 5 of 6
Exam 2
Name:_____________________________
Fig 2: Use this reaction diagram for Q4.
Gene W
Gene B
Promoter
for Gene H
om
Pr
Promoter
for Gene F
ote
r fo
en
rG
Promot
e
r for Ge
ne B
eW
Gene H
Gene F
Total: _____
Page 6 of 6