FINAL 07 2020, questions and answers PDF

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Module_4_ Ch_18.1-2_and_18.4...

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6/13/2020

Module #4: Ch 18.1-2 & 18.4

Module #4: Ch 18.1-2 & 18.4 Due: 11:59pm on Thursday, July 1, 2021 You will receive no credit for items you complete after the assignment is due. Grading Policy

Activity: The lac Operon

Click here to view this animation. Then answer the questions.

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

Hint 1. Operons are arrangements of genes that are found in bacteria, but not in eukaryotic organisms.

ANSWER:

An operon is a region of RNA that consists of the coding regions of more than one gene. An operon is a region of DNA that codes for a series of functionally related genes under the control of the same promoter. An operon is a region of DNA that codes for sugar-metabolizing enzymes. An operon is a region of DNA that consists of a single gene regulated by more than one promoter.

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

Hint 1. This molecule copies DNA into RNA.

ANSWER: A nucleotide DNA polymerase DNA ligase RNA polymerase

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

Part C What is allosteric regulation?

Hint 1. Allosteric regulation is a means of altering protein function in cells.

ANSWER:

In allosteric regulation, a gene is turned on by an activator protein. In allosteric regulation, genes are expressed constitutively. In allosteric regulation, a gene is turned off by a repressor protein. In allosteric regulation, a small molecule binds to a large protein and causes it to change its shape and activity.

Correct Allosteric regulation is an important mechanism for changing enzyme activity, as well as for changing the function of some gene repressors and activators.

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

Hint 1. Remember that the lac operon is under both negative and positive control.

ANSWER:

High glucose, no lactose No glucose, no lactose High glucose, high lactose No glucose, high lactose

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

Hint 1. Recall that a portion of the lac region is affected by the presence or absence of lactose.

ANSWER:

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Module #4: Ch 18.1-2 & 18.4 The lacI gene turns on. The lacI gene turns off. The lacI gene increases its rate of transcription. There is no change—the lacI gene is constitutively expressed.

Correct 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.

Part F What is the function of the lacZ gene?

Hint 1. This gene encodes a key enzyme in lactose metabolism.

ANSWER:

This gene encodes an enzyme, b-galactosidase, that cleaves lactose into two glucose molecules. This gene encodes an enzyme, galactoside permease, which transports lactose into the cell. This gene encodes an enzyme, b-galactosidase, which cleaves lactose into glucose and galactose. This gene encodes the repressor of the lac operon.

Correct 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.

Part G Which of the following enzymes converts ATP to cAMP? ANSWER:

Adenylyl cyclase b-galactosidase ATP synthase Galactoside permease

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

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.

Hint 1. Think about the effects of glucose and lactose on the lac operon.

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ANSWER: True False

Correct 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.

Regulation of Gene Expression in Eukaryotes In all organisms, certain genes are expressed at any given time while other genes are not. Both prokaryotes and eukaryotes regulate gene expression at the transcription stage. However, the greater complexity of eukaryotic cells makes it possible for gene expression to be regulated at many other stages as well. The diagram below shows different stages at which gene expression may be regulated in eukaryotes.

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

Hint 1. Chromatin structure Eukaryotic DNA is packaged with proteins in a complex known as chromatin. Most of the proteins in chromatin are called histones. The attraction between DNA and histones is partially due to the charges of the molecules: DNA is negatively charged, whereas histones are positively charged because they contain positively charged amino acid residues, such as lysine. The basic structural unit of chromatin is the nucleosome, which consists of DNA wound twice around a cluster of eight histones. The amino end, or “tail,” of each histone extends from the nucleosome. Chromatin may exist in either a condensed or a decondensed form, as shown below. Chemical modifications of the chromatin determine which form it has.

Hint 2. Do you understand acetylation and methylation of histones?

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Sort the following phrases based on whether they pertain to acetylation of histone tails, methylation of histone tails, or both. Drag each phrase to the appropriate bin. ANSWER:

Reset

addition of acetyl group

catalyzed by enzymes

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can be reversed

addition of methyl group neutralizes positive charge on lysine

alters chromatin structure

Hint 3. Epigenetic inheritance Epigenetic inheritance is the inheritance of traits transmitted by mechanisms that do not directly involve differences in the genome sequence. Chromatin modifications, such as acetylation and methylation of histone tails, may be passed on to future generations of cells. Whereas mutations in the nucleotide sequence of DNA are permanent, modifications to chromatin structure may be reversed.

ANSWER:

Some forms of chromatin modification can be passed on to future generations of cells. Methylation of histone tails in chromatin can promote condensation of the chromatin. DNA is not transcribed when chromatin is packaged tightly in a condensed form. Acetylation of histone tails is a reversible process. Acetylation of histone tails in chromatin allows access to DNA for transcription. Deacetylation of histone tails in chromatin loosens the association between nucleosomes and DNA.

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Module #4: Ch 18.1-2 & 18.4

Correct 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 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.

Hint 1. Can you define terms related to transcription initiation? Drag the terms on the left to the appropriate blanks on the right to complete the sentences. ANSWER:

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Module #4: Ch 18.1-2 & 18.4

Reset

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1. A(n) proximal control element is a regulatory sequence of noncoding DNA located near the promoter of a gene. 2. A(n) distal control element is a regulatory sequence of noncoding DNA located far from the promoter of a gene. 3. A grouping of several regulatory DNA sequences located far from the promoter of a gene is called a(n) enhancer .

4. A(n) general transcription factor is a regulatory protein that is required for the transcription of all protein-coding genes. 5. A regulatory protein that interacts with control elements of particular genes is called a(n) specific transcription factor .

Hint 2. Activators and repressors Specific transcription factors are proteins that either promote or inhibit the transcription of particular genes. Those that promote transcription are called activators. Many activators work by interacting with a specific distal control element and with one or more other proteins involved in transcription. These interactions are required for particular genes to be transcribed at high levels. Specific transcription factors that inhibit transcription are called repressors. Many repressors work by preventing activators from interacting with control elements or with other proteins.

ANSWER: 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. Control elements C, D, and E are distal control elements for the imaginin gene. The imaginin gene will be transcribed at a high level when repressors specific for the imaginin gene are present in the cell. 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 whenever general transcription factors are present in the cell. Control elements A, B, and C are proximal control elements for the fantasin gene. The fantasin gene and the imaginin gene have identical enhancers.

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All attempts used; correct answer displayed 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 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.

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.

Hint 1. Exons and introns Eukaryotic genes are composed of regions called exons and introns. Exons are regions of a gene that can be expressed because they can be part of a final mRNA molecule. Introns are intervening regions of a gene that are not expressed because they are never part of a final mRNA molecule. A cell can produce different final mRNA molecules from the same gene by controlling which of the gene’s exons are included in each mRNA molecule. Hint 2. Can you describe the process of alternative RNA splicing? Which choice(s) accurately describe(s) the process of alternative RNA splicing? Select all that apply. ANSWER:

Some exons of the primary RNA transcript may be removed. Some introns of the primary RNA transcript are removed. All introns of the primary RNA transcript are removed. All exons of the primary RNA transcript are removed.

ANSWER:

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Correct 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.

Activity: Control of Transcription

Click here to complete this activity. Then answer the questions.

Part A _____ bind(s) to DNA enhancer regions. ANSWER: RNA polymerase Promoters Introns Activators Exons

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

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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. ANSWER: unbending of the DNA and the release of RNA polymerase from the promoter binding of the activators to enhancers transcription binding of mRNA to the smaller ribosomal subunit binding of RNA polymerase to the promoter

Correct The bending of the DNA allows for the interaction of transcription factors and RNA polymerase.

Part C Which of these indicates an enhancer region?

ANSWER: A B C D C and D

Correct This is an enhancer region.

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

ANSWER:

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Module #4: Ch 18.1-2 & 18.4 A B C D C and D

Correct Both RNA polymerase and transcription factors bind with the promoter.

Activity: Transcription Initiation in Eukaryotes

Click here to view this animation. Then answer the questions.

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

Hint 1. How are these DNA–protein complexes structured?

ANSWER: 30-nanometer fiber Nucleosome Chromatin Histones

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

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

Hint 1. What regulatory elements are found in DNA?

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ANSWER: Activators Promoter-proximal elements Silencers Enhancers

Correct Activators are proteins that are involved in transcription initiation.

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

Hint 1. How do regulatory and basal transcription factors control transcription?

ANSWER: True False

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

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

Hint 1. When tissue-specific regulatory transcription factors bind to these sites, transcription is stimulated.

ANSWER:

Promoter Enhancer TATA box Promoter-proximal element

Correct Enhancers can function thousands of nucleotides away from the promoter and transcription start site.

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

Hint 1. Consider how an RNA molecule is made during transcription.

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ANSWER: RNA polymerase binds to the promoter of the gene. Basal transcription factors form a basal transcription complex. Regulatory transcription factors bind to enhancers. TBP is recruited to the promoter.

Correct RNA polymerase is recruited only when other transcription factors, including TBP, are assembled at the promoter.

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.

Hint 1. Think about the association of histones and DNA in chromat...