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Exam 16: Control of Gene Expression in Prokaryotes

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Question 21

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Which of the following facts about riboswitches is INCORRECT?

A) Binding of certain molecules to the riboswitches results in the formation of specific secondary structures of mRNA.
B) Certain molecules that bind to riboswitches may act as repressors or inducers of transcription.
C) Riboswitches are not only found in bacterial cells but also in archaeal, fungal, or plant cells.
D) Riboswitches are typically found in the 3'UTR of the mRNA structure.
E) The secondary structure that forms riboswitches typically contains a base stem and several branching hairpins.

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Question 22

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The _____ is a type of regulator protein that binds to a region of DNA in the promoter of a gene called the operator and prevents transcription from taking place.

A) inducer
B) repressor
C) activator
D) inactivator
E) terminator

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Question 23

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In the absence of tryptophan, what happens to the genes within the trp operon?

A lac operon of genotype lacI⁺ lacP⁺ lacO⁺ lacZ⁺ lacY^- will produce $\beta$ -galactosidase but not permease when:

The trp operon in E. coli contains a 5' UTR sequence that is translated into a small polypeptide of 14 amino acids, which includes two tryptophans. If the two trp codons in the 5' UTR of the RNA are changed to serine codons and the resulting cells are starved for tryptophan but not for any other amino acid, what will be the effect of the mutant codons on the operation of the trp operon?

Fill in the blanks in the following table with "yes" or "no" for each condition of trp operon regulation. The strain is wild type, with no partial diploidy. $\begin{array}{|lr|c|c|c|}\hlineModerate &t r p ~repressor &\text { trp repressor } & \text { Antiterminator } & \text { Transcription } \\&bound~ to~ trp?&\text { bound to } & \text { hairpin formed in } & \text { attenuated? }\\&&\text { operator? } & \text { mRNA? }\\high ~tryptophan&& \\low ~tryptophan&& &\\\hline\end{array}$

E. coli lac operon control by lacI is:

Explain why glucose-dependent catabolite repression in E.coli is important and how it is possible to achieve this repression without influencing glucose metabolism.

There are enzymes called aminoacyl-tRNA synthetases that attach tRNAs to the appropriate amino acid. Assume that the aminoacyl-tRNA synthetase that attaches tryptophan to its tRNA in an E. coli mutant strain is only partially active. It is active enough for the strain that carries it to be viable but is much less active than that of wild-type cells. What would be the expected effect of this mutation on attenuation in the trp operon?

An operon is controlled by a repressor. When the repressor binds to a small molecule, it binds to DNA near the operon. The operon is constitutively expressed if a mutation prevents the repressor from binding to the small molecule. The type of control illustrated is:

Assume that a mutation occurs in the promoter for the lacI regulatory gene and this mutation results in a tenfold increase in the transcription of lacI. What would be the expected consequences of such a mutation?

A lac operon of genotype lacI^- lacP⁺ lacO⁺ lacZ⁺ lacY⁺ will produce $\beta$ -galactosidase and permease when:

A mutant E. coli strain, grown under conditions that normally induce the lac operon, produces particularly high amounts of ß-galactosidase. What is a possible genotype of the cells?

Fill in the blanks in the "level of transcription" column of this table with (+) for high levels of transcription, (+/-) for Moderate levels of transcription, and (-) for minimal levels of transcription of the lac operon. Consider regulation by both the lac repressor and CAP (catabolite activator protein). The strain is wild type with no partial diploidy. The first line is filled in for reference. $\begin{array}{|lc|}\hline Moderate ~conditions & Level ~of ~transcription\\\hline ~ high~ glucose, ~no~ lactose&-\\\hline no ~glucose, ~high ~lactose\\\hline high ~glucose, ~high~ lactose\\\hline no ~glucose, ~no~ lactose\\\hline\end{array}$

Imagine the following scenario: You take the regulatory region of the trp operon (including the promoter, operator, and 5' UTR) and attach it upstream of the structural genes of the lac operon. You then introduce this artificial construct into a mutant strain in which its own lac operon is completely nonfunctional. Indicate the level of ß-galactosidase activity in each of the following cases and explain why you expect that level of activity: a. No tryptophan, no lactose b. High tryptophan, high lactose

Which of the following is generally constitutively transcribed?

Suppose that you perform an experiment where you construct a plasmid that carries a copy of the lac operator region (lacO) but no other part of the lac operon. (The lac repressor can bind to single operator regions.) This plasmid is placed in an E. coli cell, which has a normal copy of the lac operon in its chromosome. When this strain is grown, the number of plasmids reaches about 50 copies per bacterial cell. What is the expected phenotype of such a strain in the absence of glucose?

An example of a gene product encoded by a regulatory gene is:

The bacterium Bacillus subtilis can grow on minimal media with a variety of sugars as a carbon source. One such sugar is mannose, metabolized by the products of the man operon. Expression of the operon is controlled by a regulatory protein encoded in a separate gene, manR. Depending on conditions, the regulatory protein may bind at one of two sites in the operon, as follows: (i) When mannose is absent from the cell, the regulatory protein is in a conformation called R1. R1 can bind specifically at an operator site manO. Binding of R1 at manO reduces transcription of the operon fourfold from a basal level of 20 units. (ii) When mannose is present in the cell, it binds to the regulatory protein, causing it to undergo an allosteric transition from conformation R1 to a new conformation, called R2. R2 cannot bind at manO. However, R2 can bind specifically at a different site called the initiator, manI. Binding of R2 at manI increases transcription of the operon twofold from the basal level. Mutations m1-m3, which affect expression of this operon, were identified. Each mutation affects only a single component of the operon. Levels of operon activity were measured in haploids. They were also measured in partial diploids with an F' carrying the wild-type alleles of all genes and regulatory elements described above. $\quad\quad\quad\quad\quad\quad\quad\quad\quad\quad\quad\quad\text { Operon activity }$ $\quad\quad\quad\quad\quad\quad\quad\quad\quad$ Haploids $\quad\quad\quad\quad\quad\quad\quad$ Partial Diploids $\begin{array}{lcccc}&(-) \text { mannose }&(+) \text { mannose } &(-) \text { mannose }&(+) \text { mannose }\\\text { wild type } & 5 & 40 & 10 & 80 \\\mathrm{~m} 1 & 20 & 20 & 10 & 80 \\\mathrm{~m} 2 & 5 & 20 & 10 & 60 \\\mathrm{~m} 3 & 20 & 40 & 25 & 80\end{array}$ For each mutation, describe which component is affected. In addition, explain the observed activity in the haploid and partial diploid in each case.

What is the function of allolactose in regulation of the lac operon?