Chapter 16 Chapter Questions
In E. coli, the trp operon is on by default, while the lac operon is off. Why do you think that this is the case?
5 Tryptophan is an amino acid essential for making proteins, so the cell always needs to have some on hand. However, if plenty of tryptophan is present, it is wasteful to make more, and the expression of the trp receptor is repressed. Lactose, a sugar found in milk, is not always available. It makes no sense to make the enzymes necessary to digest an energy source that is not available, so the lac operon is only turned on when lactose is present.
A mutation within the promoter region can alter transcription of a gene. Describe how this can happen.
A mutation in the promoter region can change the binding site for a transcription factor that normally binds to increase transcription. The mutation could either decrease the ability of the transcription factor to bind, thereby decreasing transcription, or it can increase the ability of the transcription factor to bind, thus increasing transcription.
What is the difference between a repressible and an inducible operon?
A repressible operon uses a protein bound to the promoter region of a gene to keep the gene repressed or silent. This repressor must be actively removed in order to transcribe the gene. An inducible operon is either activated or repressed depending on the needs of the cell and what is available in the local environment.
Protein modification can alter gene expression in many ways. Describe how phosphorylation of proteins can alter gene expression.
Because proteins are involved in every stage of gene regulation, phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering the transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications).
Describe how transcription in prokaryotic cells can be altered by external stimulation such as excess lactose in the environment.
Environmental stimuli can increase or induce transcription in prokaryotic cells. In this example, lactose in the environment will induce the
Changes in epigenetic modifications alter the accessibility and transcription of DNA. Describe how environmental stimuli, such as ultraviolet light exposure, could modify gene expression.
Environmental stimuli, like ultraviolet light exposure, can alter the modifications to the histone proteins or DNA. Such stimuli may change an actively transcribed gene into a silenced gene by removing acetyl groups from histone proteins or by adding methyl groups to DNA.
Name two differences between prokaryotic and eukaryotic cells and how these differences benefit multicellular organisms.
Eukaryotic cells have a nucleus, whereas prokaryotic cells do not. In eukaryotic cells, DNA is confined with in the nuclear region. Because of this, transcription and translation are physically separated. This creates a more complex mechanism for the control of gene expression that benefits multicellular organisms because it compartmentalizes gene regulation. Gene expression occurs at many stages in eukaryotic cells, whereas in prokaryotic cells, control of gene expression only occurs at the transcriptional level. This allows for greater control of gene expression in eukaryotes and more complex systems to be developed. Because of this, different cell types can arise in an individual organism.
How can external stimuli alter post-transcriptional control of gene expression?
External stimuli can modify RNA-binding proteins (i.e., through phosphorylation of proteins) to alter their activity.
Alternative forms of a protein can be beneficial or harmful to a cell. What do you think would happen if too much of an alternative protein bound to the 3' UTR of an RNA and caused it to degrade?
If the RNA degraded, then less of the protein that the RNA encodes would be translated. This could have dramatic implications for the cell.
An increase in phosphorylation levels of eIF-2 has been observed in patients with neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's. What impact do you think this might have on protein synthesis?
Protein synthesis would be inhibited.
Describe how RBPs can prevent miRNAs from degrading an RNA molecule.
RNA binding proteins (RBP) bind to the RNA and can either increase or decrease the stability of the RNA. If they increase the stability of the RNA molecule, the RNA will remain intact in the cell for a longer period of time than normal. Since both RBPs and miRNAs bind to the RNA molecule, RBP can potentially bind first to the RNA and prevent the binding of the miRNA that will degrade it.
Describe how controlling gene expression will alter the overall protein levels in the cell.
The cell controls which proteins are expressed and to what level each protein is expressed in the cell. Prokaryotic cells alter the transcription rate to turn genes on or off. This method will increase or decrease protein levels in response to what is needed by the cell. Eukaryotic cells change the accessibility (epigenetic), transcription, or translation of a gene. This will alter the amount of RNA and the lifespan of the RNA to alter the amount of protein that exists. Eukaryotic cells also control protein translation to increase or decrease the overall levels. Eukaryotic organisms are much more complex and can manipulate protein levels by changing many stages in the process.
in females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes would have on nucleosome packing?
The nucleosomes would pack more tightly together.
New drugs are being developed that decrease DNA methylation and prevent the removal of acetyl groups from histone proteins. Explain how these drugs could affect gene expression to help kill tumor cells.
These drugs will keep the histone proteins and the DNA methylation patterns in the open chromosomal configuration so that transcription is feasible. If a gene is silenced, these drugs could reverse the epigenetic configuration to re-express the gene.
How can understanding the gene expression pattern in a cancer cell tell you something about that specific form of cancer?
Understanding which genes are expressed in a cancer cell can help diagnose the specific form of cancer. It can also help identify treatment options for that patient. For example, if a breast cancer tumor expresses the EGFR in high numbers, it might respond to specific anti-EGFR therapy. If that receptor is not expressed, it would not respond to that therapy.
In cancer cells, alteration to epigenetic modifications turns off genes that are normally expressed. Hypothetically, how could you reverse this process to turn these genes back on?
You can create medications that reverse the epigenetic processes (to add histone acetylation marks or to remove DNA methylation) and create an open chromosomal configuration.
Post-translational modifications of proteins can affect which of the following? a. protein function b. transcriptional regulation c. chromatin modification d. all of the above
a
What are epigenetic modifications? a. the addition of reversible changes to histone proteins and DNA b. the removal of nucleosomes from the DNA c. the addition of more nucleosomes to the DNA d. mutation of the DNA sequence
a
If glucose is absent, but so is lactose, the lac operon will be ________. a. activated b. repressed c. activated, but only partially d. mutated
b
Post-translational control refers to: a. regulation of gene expression after transcription b. regulation of gene expression after translation c. control of epigenetic activation d. period between transcription and translation
b
What will result from the binding of a transcription factor to an enhancer region? a. decreased transcription of an adjacent gene b. increased transcription of a distant gene c. alteration of the translation of an adjacent gene d. initiation of the recruitment of RNA polymerase
b
Cancer causing genes are called ________. a. transformation genes b. tumor suppressor genes c. oncogenes d. mutated genes
c
Targeted therapies are used in patients with a set gene expression pattern. A targeted therapy that prevents the activation of the estrogen receptor in breast cancer would be beneficial to which type of patient? a. patients who express the EGFR receptor in normal cells b. patients with a mutation that inactivates the estrogen receptor c. patients with lots of the estrogen receptor expressed in their tumor d. patients that have no estrogen receptor expressed in their tumor
c
The binding of ________ is required for transcription to start. a. a protein b. DNA polymerase c. RNA polymerase d. a transcription factor
c
Binding of an RNA binding protein will ________ the stability of the RNA molecule. a. increase b. decrease c. neither increase nor decrease d. either increase or decrease
d
Control of gene expression in eukaryotic cells occurs at which level(s)? a. only the transcriptional level b. epigenetic and transcriptional levels c. epigenetic, transcriptional, and translational levels d. epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels
d
Prokaryotic cells lack a nucleus. Therefore, the genes in prokaryotic cells are: a. all expressed, all of the time b. transcribed and translated almost simultaneously c. transcriptionally controlled because translation begins before transcription ends d. b and c are both true
d
Which of the following are involved in post- transcriptional control? a. control of RNA splicing b. control of RNA shuttling c. control of RNA stability d. all of the above
d
Which of the following are true of epigenetic changes? a. allow DNA to be transcribed b. move histones to open or close a chromosomal region c. are temporary d. all of the above
d
What could happen if a cell had too much of an activating transcription factor present?
if too much of an activating transcription factor were present, then transcription would be increased in the cell. This could lead to dramatic alterations in cell function.
