Concept explainers
For each element in the list that follows, indicate what kind of molecule it is (DNA, RNA, protein, small molecule), whether it acts as a positive or negative regulator, what stage of gene expression it affects, and whether it acts in cis or in trans. (In its most general sense, the term cis describes elements that affect the function of the molecule of which it is a part, while trans describes elements on one molecule that affect the function of a different molecule.)
a. Lac repressor |
b. lac operator |
c. CRP |
d. CRP-binding site |
e. Trp repressor |
f. charged tRNATrp (in terms of its function at the Trp trp operon) |
g. the antiterminator at the trp operon |
h. a terminator in the expression platform of a riboswitch |
i. an sRNA that blocks mRNA translatio |
a.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of Lac repressor.
Introduction:
Lac repressor is involved in inhibiting the transcription of the lac operon. In unavailability of lactose, the lac repressor binds to the operator tightly and inhibits transcription.
Explanation of Solution
Lac repressor is a protein molecule, and it acts as a trans element. Lac repressor acts as a negative regulator of genes. The repressor protein that is synthesized by the gene i of lac operon binds to the operator to inhibit transcription. When lactose is present in high concentration in the cell, it binds to the repressor and makes it unfit for binding. In this case, the RNA polymerase transcribes the structural genes.
b.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of lac operator.
Introduction:
The operator is basically a small region of DNA that is partially present within the promoter. It interacts with the regulatory protein and controls the transcription of the lac operon.
Explanation of Solution
The lac operator is a DNA molecule, and it acts as a cis element. It is considered to be a positive regulator. The gene O of the lac operon is the site of the operator, where the repressor protein tends to bind.
c.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of CRP.
Introduction:
CRP or cAMP Receptor Protein consists of cAMP. It is involved in binding next to the promoter region and then helps the RNA polymerase to bind to the promoter. CRP protein plays a role in upregulating the transcription of the lac operon.
Explanation of Solution
CRP is a protein molecule, and it acts as a trans element. It is known as the positive regulator. As the bacteria utilize glucose more as compared to the lactose, the attachment of RNA polymerase to the promoter needs the presence of CAP (catabolite gene activator protein) or CRP (cAMP receptor protein) bound to the cyclic AMP. The presence of glucose lowers the concentration of cAMP, which, as a result, lowers the formation of CAP-cAMP. As a result RNA polymerase does not bind to DNA in the presence of glucose. As a result, after the addition of glucose, the transcription of the lac operon is decreased.
d.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of CRP-binding site.
Introduction:
The CRP binding site is the site present on the lac operon, where the CRP protein binds. The CRP protein is involved in upregulating the process of transcription of lac genes
Explanation of Solution
The CRP binding site is a type of DNA molecule, and it acts as a cis element. It is known to act as a positive regulator. The CRP-binding site is the DNA region, where the CRP binds.
e.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of Trp repressor.
Introduction:
The trp repressor is a type of transcription factor that is involved in controlling the metabolism of tryptophan. When trp repressor is bound to tryptophan, the complex attaches to the operator and blocks the RNA polymerase from binding to the promoter and preventing the transcription of the operon.
Explanation of Solution
The trp repressor is a protein molecule, and it acts as a cis element. This protein is known to act as a negative regulator. The trp repressor is produced by trpR gene, which is present in upstream to the promoter. In the presence of tryptophan, the trpR protein binds to the operator and prevents the RNA polymerase from binding and transcribing the operon. As a result, tryptophan is not synthesized from the precursor. In the absence of tryptophan, the repressor gets unable to bind to the operator, and the transcription is continued.
f.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of charged tRNATrp.
Introduction:
When tryptophan is present in limiting concentration, the tRNATrp will also be present in insufficient amount. As a result, the translation will pause at the tryptophan codon.
Explanation of Solution
The charged tRNATrp is a type of protein molecule, and it acts as a trans element. It is considered as a positive regulator. The ribosomes bind to mRNA and recruit the tRNA molecules bound with tRNA specific amino acids. This tRNA contains anticodons that are complementary to the codon sequence of mRNA.
g.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of the antiterminator at the trp operon.
Introduction:
When the charged tryptophanyl tRNA is present in a deficient concentration, the ribosome that is involved in translating the leader peptide sequence stalls and the antiterminator structure forms.
Explanation of Solution
The antiterminator at the trp operon is a RNA molecule, and it acts as a trans element. It acts as a positive regulator. The Trp operon is known to be regulated by a process known as attenuation. The occurrence of this process is only possible in the presence of a leader sequence coding for a leader peptide. The peptide consists of two trp codons lying adjacent to each other. The attenuator RNA, which is also known as antiterminator structure, consists of four short sequences, which form three distinct secondary structures. This formation of stem-loop structure functions as an antiterminator.
h.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of a terminator in the expression platform of a riboswitch.
Introduction:
The riboswitches are known as the regulatory segment present in the mRNA molecule that has the tendency to bind to a small molecule. This binding results in the change in the production of proteins that are coded by mRNA.
Explanation of Solution
A riboswitch is a protein molecule, and it acts as a cis-element. Riboswitches act as a negative regulator. These riboswitches are located in the untranslated regions of mRNA. The metabolites that bind to riboswitches send a feedback signal to regulate the transcription of RNA or the initiation of translation.
h.
To determine:
The type of molecule (DNA, RNA, protein, small molecule), type of regulation (Positive or negative), the stage of gene expression affected, and the mode of action (cis or trans) of an sRNA that blocks mRNA translation.
Introduction:
The sRNA are the small bacterial RNA that are 50-500 nucleotides long non-coding RNA molecules.
Explanation of Solution
sRNA is an RNA molecule, which acts as either cis and trans molecule depending on the target mRNA. It is considered as a negative regulator. The sRNA are known as the posttranscriptional regulators because they regulate gene expression on base pairing to target mRNAs.
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Chapter 16 Solutions
Genetics: From Genes to Genomes
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