Mastering Biology Chp. 15 HW

PART E Which of the following events in transcription initiation likely occurs last?

RNA polymerase binds to the promoter of the gene. [RNA polymerase is recruited only when other transcription factors, including TBP, are assembled at the promoter.]

PART F What is the function of the lacZ gene?

This gene encodes an enzyme, b-galactosidase, which cleaves lactose into glucose and galactose. [The lacZ gene encodes b-galactosidase, a key enzyme in lactose metabolism. When lactose is present in the cell, the cell expresses lacZ and metabolizes lactose.]

A gene on human chromosome 15 is expressed throughout the body. However, in the brain, only the maternal copy of the gene is expressed, whereas the paternal copy of the gene is silent and not transcribed. What accounts for this pattern of expression this gene displays in the brain?

Through genomic imprinting, methylation regulates expression of the paternal copy of the gene in the brain. [Imprinting of the paternal copy of the gene by DNA methylation inactivates it and prevents its expression in brain cells. Read about DNA methylation and genomic imprinting.]

PART F If deletion of a control element causes a reduction in gene expression, what must be the normal role of that control element?

To activate gene expression; without the control element, activators are not able to bind to the enhancer, and the level of gene expression decreases. [If a repressor cannot bind, wouldn't you expect the expression to increase instead of decrease?]

PART H If deletion of a control element causes an increase in gene expression, what must be the normal role of that control element?

To repress gene expression; without the control element, repressors are not able to bind to the enhancer, and the level of gene expression increases.

miRNAs can control gene expression by what action?

binding to mRNAs and degrading them or blocking their translation [miRNAs can effectively "silence" genes by binding to mRNA transcripts. The mRNAs are either broken down by enzymes or are unable to physically interact with the ribosomes to complete translation.]

PART B What was the dependent variable in this experiment?

the relative level of reporter gene mRNA [The dependent variable was the relative level of reporter gene mRNA because that was the response that was measured in the experiment.]

PART D Which of these directly bind(s) to the promoter?

C and D [Both RNA polymerase and transcription factors bind with the promoter.]

Which statement(s) about repressible operons is/are correct?

-A repressible operon is on unless a corepressor is present. -Repressible operons usually contain genes that code for anabolic enzymes. [A repressible operon is usually on but can be turned off when a corepressor interacts with and activates the repressor. The enzymes in an inducible operon generally function in anabolic pathways. Read about repressible operons.]

PART C True or false? Regulatory and basal transcription factors regulate transcription by binding to the promoter.

False [Basal transcription factors do indeed bind to the promoter, but regulatory transcription factors bind to promoter-proximal elements and enhancers.]

PART F True or false? One possible way to alter chromatin structure such that genes could be transcribed would be to make histone proteins more positively charged.

False [The positive charge on histone proteins allows them to interact tightly with negatively charged DNA, thus inhibiting transcription. To disrupt this interaction, the histone proteins would have to be made more negatively charged.]

PART A _____ bind(s) to DNA enhancer regions.

Activators [Activators are a type of transcription factor that bind to enhancer regions.]

PART D Which of the following regulatory DNA sequences might be located thousands of nucleotides away from the transcription start site of a gene?

Enhancer [Enhancers can function thousands of nucleotides away from the promoter and transcription start site. This sequence is located within the promoter region of the gene, just upstream of the transcription start site.]

PART H True or false? The mechanism by which glucose inhibits expression of the lac structural genes is known as catabolite stimulation, whereas the mechanism by which lactose stimulates expression of the lac structural genes is known as allosteric regulation.

False [The process by which lactose binds to the lac repressor and inactivates it by causing it to change shape is known as allosteric regulation. However, the process by which glucose causes cAMP levels in the cell to drop, thereby preventing CAP from stimulating expression of the lac structural genes, is known as catabolite repression.]

PART B What is the event that IMMEDIATELY follows the last event of this animation? To view the animation, click here. Then click on the image to start the animation.

binding of RNA polymerase to the promoter [The bending of the DNA allows for the interaction of transcription factors and RNA polymerase.]

PART G Which of the following enzymes converts ATP to cAMP?

Adenylyl cyclase [Adenylyl cyclase converts ATP to cAMP, which helps CAP bind and facilitates binding of RNA polymerase to the lac promoter.]

Which statement(s) about inducible operons is/are correct?

-In an inducible operon, an inducer inactivates the repressor. -In an inducible operon, the repressor is synthesized in an active form. [An inducible operon is usually off but can be turned on when an inducer interacts with and inactivates the repressor. The enzymes in an inducible operon generally function in catabolic pathways. Read about inducible operons.]

PART C Which of these indicates an enhancer region?

A [This is an enhancer region.]

Promoters

Promoters are DNA sequences.

PART E What happens to the expression of the lacI gene if lactose is not available in the cell?

There is no change—the lacI gene is constitutively expressed. [The lacI gene is expressed regardless of the presence of lactose. Only the structural genes of the lac operon are affected by the presence or absence of lactose.]

How are genes coordinately controlled in eukaryotic cells?

-Coordinately controlled genes in eukaryotic cells are activated by the same chemical signals. -Coordinately controlled genes in eukaryotic cells share a set of control elements. [In eukaryotes, specific transcription factors bind to control elements, promoting transcription of coordinately controlled genes, even if the genes are on separate chromosomes. Read about coordinately controlled genes in eukaryotes.]

PART C What is allosteric regulation?

In allosteric regulation, a small molecule binds to a large protein and causes it to change its shape and activity. [Allosteric regulation is an important mechanism for changing enzyme activity, as well as for changing the function of some gene repressors and activators. First, genes that are expressed constitutively are not regulated—they are transcribed all the time. Second, allosteric regulation relates to more than the phenomenon of gene expression.]

PART C What was the control treatment in this experiment?

the construct that had no DNA deleted from the enhancer [The control treatment was the construct that had no DNA deleted from the enhancer. All the other treatment groups were compared to that control group.]

PART D Under which conditions are the lac structural genes expressed most efficiently?

No glucose, high lactose [When glucose is absent and lactose levels are high, the lac structural genes are expressed the most efficiently. Without glucose, cAMP is produced and CAP can stimulate transcription of the structural genes. In the presence of lactose, the repressor does not bind to the operator and therefore does not block transcription.]

PART B What molecule binds to promoters in bacteria and transcribes the coding regions of the genes?

RNA polymerase [RNA polymerase is the enzyme that binds to promoters and transcribes the coding regions of genes into RNA.]

PART C - Alternative RNA splicing The diagram below shows a segment of DNA containing an imaginary gene (Z) and the primary RNA transcript that results from the transcription of gene Z. Exons are represented in green and introns are represented in blue. The figure shows a segment of DNA containing an imaginary gene Z and the primary RNA transcript that results from the transcription of gene Z. Exons are represented in green and introns are represented in blue. They are labeled with letters as well. So, the exons are A, C, E, G, and I. Introns are B, D, F, and H. Both DNA and primary RNA transcript contain all the mentioned exons and introns. Which of the following choices represent mRNA molecules that could be produced from the primary RNA transcript by alternative RNA splicing? (In each choice, the yellow part on the left represents the 5' cap, and the yellow part on the right represents the poly-A tail.) Select all that apply.

[Alternative RNA splicing produces different mRNA molecules from the same primary RNA transcript. During alternative RNA splicing, all introns are removed, and some exons may also be removed. The removal of different exons produces different mRNA molecules, which are then translated into different proteins. Alternative RNA splicing can greatly expand the number of proteins produced from the same gene.]

PART B Which of the following regulatory elements is not composed of DNA sequences?

Activators [Activators are proteins that are involved in transcription initiation.]

PART D - Interpreting the graph Do the data suggest that any of these possible control elements are actual control elements?

All three appear to be control elements. [All three elements appear to be control elements because when they were deleted, the levels of reporter mRNA differed from the level produced by the intact enhancer construct. For each of the three treatment groups, look at how the level of reporter mRNA changes relative to the intact enhancer construct (top). What do those differences indicate?]

Why is the lac operon said to be an inducible operon?

When allolactose is present, it induces the inactivation of the lac repressor. [The lac repressor keeps the production of lactose-digesting enzymes turned off. When allolactose is present, the lac repressor is inactivated, allowing the expression of lactose-digesting enzymes.]

PART A Which of the following terms describes the DNA-protein complexes that look like beads on a string?

Nucleosome [The "beads on a string" appearance of nucleosomes comes from the wrapping of DNA around a core of eight histone proteins.]

It is possible for a cell to make proteins that last for months; hemoglobin in red blood cells is a good example. However, many proteins are not this long-lasting; they may be degraded in days, hours, or even minutes. What is the advantage of short-lived proteins?

Short-lived proteins enable the cells to control their activities precisely and efficiently. [Some proteins are needed only for short-term use.]

DNA methylation is a mechanism used by eukaryotes to do what?

inactivate genes [DNA methylation, involving the attachment of methyl groups to certain bases, is a mechanism for the long-term inactivation of genes during development.]

PART A Which of the following statements best defines the term operon?

An operon is a region of DNA that codes for a series of functionally related genes under the control of the same promoter. [This arrangement of genes is common in bacteria. For example, genes involved in lactose metabolism are clustered in the lac operon of E. coli, and genes involved in tryptophan metabolism are in the trp operon.]

PART G Did deletion of any of the possible control elements cause an increase in reporter gene expression? How can you tell?

Deletion of control element #1 or #2 caused an increase in reporter gene expression; both constructs resulted in over 100% of the control level of mRNA. [For cells incubated with the DNA constructs in which element #1 or #2 was deleted, the amount of reporter mRNA made was over 100% of the amount of reporter mRNA made by the cells in the control group. This result indicates that the deletion of control element #1 or #2 causes an increase in reporter gene expression.]

PART B - Regulation of transcription initiation The diagram below shows two stretches of DNA in the genome of an imaginary eukaryotic cell. The top stretch of DNA includes the fantasin gene, along with its promoter and one of its enhancers. The bottom stretch of DNA includes the imaginin gene, its promoter, and one of its enhancers. The slash marks (//) indicate that more than 1,000 nucleotides separate the promoter and enhancer of each gene. Which statements about the regulation of transcription initiation in these genes are true? Select all that apply.

-Control elements C, D, and E are distal control elements for the imaginin gene. -The fantasin gene will be transcribed at a high level when activators specific for control elements A, B, and C are present in the cell. -Both the fantasin gene and the imaginin gene will be transcribed at high levels when activators specific for control elements A, B, C, D, and E are present in the cell. [Only certain genes are transcribed in a eukaryotic cell at any particular time. The regulation of transcription initiation depends on the interaction of specific transcription factors with specific control elements in enhancers. In the imaginary eukaryotic cell used as an example here, the enhancers for the fantasin gene and imaginin gene are unique because they contain different sets of control elements (A, B, and C for the fantasin gene; C, D, and E for the imaginin gene). Each gene will be transcribed at a high level when activators specific for all of the control elements in its enhancer are present in the cell.]

PART A - Operon vocabulary Can you match terms related to operons to their definitions? Drag the terms on the left to the appropriate blanks on the right to complete the sentences.

1. A(n) OPERON is a stretch of DNA consisting of an operator, a promoter, and genes for a related set of proteins, usually making up an entire metabolic pathway. 2. The GENES OF AN OPERON is/are arranged sequentially after the promoter. 3. A(n) PROMOTOR is a specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place. 4. A(n) REGULATORY GENE codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes. 5. Regulatory proteins bind to the OPERATOR to control expression of the operon. 6. A(n) REPRESSOR is a protein that inhibits gene transcription. In prokaryotes, this protein binds to the DNA in or near the promoter. 7. A(n) INDUCER is a specific small molecule that binds to a bacterial regulatory protein and changes its shape so that it cannot bind to an operator, thus switching an operon on. [An operon is made up of a promoter and the genes of the operon. The promoter, which includes an operator, is the stretch of DNA where RNA polymerase binds. Regulatory proteins bind to the operator. The genes of the operon code for a related set of proteins. A regulatory gene located away from the operon codes for a protein that controls the operon.]

In humans, the hormone testosterone enters cells and binds to specific proteins, which in turn bind to specific sites on the cells' DNA. These proteins probably act to do what?

help RNA polymerase transcribe certain genes [Testosterone stimulates the expression of genes involved in male sexual characteristics; it follows that the proteins that it interacts with and which bind to DNA will promote transcription.]

PART A - Understanding the experimental design The diagrams show the intact DNA sequence (top) and the three experimental DNA sequences. A red X indicates the possible control element (1, 2, or 3) that was deleted in each experimental DNA sequence. The area between the slashes represents the approximately 8 kilobases of DNA located between the promoter and the enhancer region. The horizontal bar graph shows the amount of reporter gene mRNA that was present in each cell culture after 48 hours relative to the amount that was in the culture containing the intact enhancer region (top bar = 100%). What was the independent variable in this experiment?

the possible control element that was deleted [The independent variable was the possible control element that was deleted from the experimental sequences because the researchers manipulated that variable in each treatment.]

PART C - Regulation of a hypothetical operon You are studying a bacterium that utilizes a sugar called athelose. This sugar can be used as an energy source when necessary. Metabolism of athelose is controlled by the ath operon. The genes of the ath operon code for the enzymes necessary to use athelose as an energy source. You have found the following: -The genes of the ath operon are expressed only when the concentration of athelose in the bacterium is high. -When glucose is absent, the bacterium needs to metabolize athelose as an energy source as much as possible. -The same catabolite activator protein (CAP) involved with the lac operon interacts with the ath operon. Based on this information, how is the ath operon most likely controlled? Drag the labels onto the diagram to identify the small molecules and the states of the regulatory proteins. Not all labels will be used.

[Metabolism of the sugar athelose in this hypothetical system is controlled by an operon that exhibits both positive control and negative control. Transcription of the ath operon is turned on when athelose is present (negative control), and sped up when the bacterium runs out of glucose and must rely on athelose for energy (positive control).]

Which noncoding RNAs are correctly matched with their function?

-Piwi-associated RNAs (piRNAs) reestablish appropriate methylation patterns in the genome during gamete formation. -Small interfering RNAs (siRNAs) bind to complementary sequences in mRNA and block its translation. -MicroRNAs (miRNAs) bind to complementary sequences in mRNA and block its translation. [Read about the multiple roles of noncoding RNAs.]

PART A - Modification of chromatin structure Which statements about the modification of chromatin structure in eukaryotes are true? Select all that apply.

-Some forms of chromatin modification can be passed on to future generations of cells. -Acetylation of histone tails in chromatin allows access to DNA for transcription. -DNA is not transcribed when chromatin is packaged tightly in a condensed form. -Acetylation of histone tails is a reversible process. -Methylation of histone tails in chromatin can promote condensation of the chromatin. [One of the mechanisms by which eukaryotes regulate gene expression is through modifications to chromatin structure. When chromatin is condensed, DNA is not accessible for transcription. Acetylation of histone tails reduces the attraction between neighboring nucleosomes, causing chromatin to assume a looser structure and allowing access to the DNA for transcription. If the histone tails undergo deacetylation, chromatin can recondense, once again making DNA inaccessible for transcription. Recent evidence suggests that methylation of histone tails can promote either the condensation or the decondensation of chromatin, depending on where the methyl groups are located on the histones. Thus, methylation can either inactivate or activate transcription, and demethylation can reverse the effect of methylation. Changes in chromatin structure may be passed on to future generations of cells in a type of inheritance called epigenetic inheritance.]

PART E Did deletion of any of the possible control elements cause a reduction in reporter gene expression? How can you tell?

Deletion of element #3 caused a reduction in reporter gene expression; that construct resulted in less than 50% of the control level of mRNA. [For cells incubated with the DNA construct in which element #3 was deleted, the amount of reporter mRNA made was less than 50% of the amount of reporter mRNA made by the cells in the control group. This result indicates that the deletion of control element #3 causes a reduction in reporter gene expression.]

PART B - Regulation of model operons The trp and lac operons are regulated in various ways. How do bacteria regulate transcription of these operons? Sort the statements into the appropriate bins depending on whether or not each operon would be transcribed under the stated conditions.

operon is not transcribed -trp operon: tryptophan present -lac operon: lactose absent operon is transcribed, but not sped up through positive control -lac operon: lactose present, glucose present -trp operon: tryptophan absent operon is transcribed quickly through positive control -lac operon: lactose present, glucose absent [The trp operon is regulated through negative control only. When tryptophan is present, the operon genes are not transcribed. The lac operon is regulated through both negative control and positive control. Negative control: -When lactose is absent, the repressor protein is active, and transcription is turned off. -When lactose is present, the repressor protein is inactivated, and transcription is turned on. Positive control: -When glucose is absent, another regulatory protein (CAP) binds to the promoter of the lac operon, increasing the rate of transcription if lactose is present.]