chapter 12 homework genetics

The wild mustard Arabidopsis thaliana is used as a model organism in genetic studies of plants. Which statements explain why Arabidopsis is an excellent model organism? (a) Arabidopsis is able to self‑fertilize and cross‑fertilize. (b) Arabidopsis produces a few, large seeds in each generation. (c) Arabidopsis has a life cycle that is short compared to other plants. (d) Arabidopsis has a large, polyploid genome. (e) Arabidopsis is small and requires very few laboratory resources to grow.

a, c, e,

A DNA sequence located near the start of a gene where RNA polymerase binds to initiate transcription is called _____

promoter.

Select the post‑translational modifications of histones that are most commonly associated with changes in transcription levels in eukaryotes. (a) methylation and carboxylation (b) acetylation and lipidation (c) methylation and acetylation (d) glycosylation and ubiquitination

c

A gene that controls the expression of one or more genes by promoting or inhibiting transcription are called ________.

regulatory gene

An operon is a group of genes under the control of a single promoter. Match each type of operon with the descriptions below. 1)Inducible2)Repressible3)Constitutive

1)Under default conditions, transcription is inhibited2) Transcription stops when the repressor gene product is activated. Sufficient amounts of the gene product inhibit further transcription3) Amount of gene product is constant

Suppose a scientist identified two E. coli mutants, called huh1 and huh2. The mutants have constitutive expression of the nopoperon, which includes the genes nop1 and nop2. One of the mutants is a point mutation in a DNA‑binding site, and the other mutant is a deletion of the gene that encodes the DNA‑binding protein. Which term describes the regulatory function of the DNA‑binding protein? (a) not a regulator (b) negative regulator (c) positive regulator

b

Which statement describes an operon?

a gene cluster controlled by a single promoter that transcribes to a single mRNA strand.

How many genes are in a 300‑kilobase DNA sequence with four H3K4me3 modifications? four genes zero genes four or fewer genes four or more genes eight genes

d

An operon is made up of 3 basic DNA components:

Promoter - a nucleotide sequence that enables a gene to be transcribed. ... Operator - a segment of DNA to which a repressor binds. ... Structural genes - the genes that are co-regulated by the operon.

A small molecule that activates transcription by inhibiting the action of a repressor protein is _____

inducer.

A transcriptional element that blocks signal between promoter and enhancer is ____.

insulator

In E. coli, three structural genes, A, D, and E, encode enzymes A, D, and E, respectively. Gene O is an operator. The genes are in the order O‑A‑D‑E on the chromosome and might form an operon. These enzymes catalyze the biosynthesis of valine. Mutations were isolated at the A, D, E, and O genes to study the production of enzymes A, D, and E when cellular levels of valine were low (T. Ramakrishnan and E. A. Adelberg, 1965). Levels of the enzymes produced by partial‑diploid E. coli with various combinations of mutations are shown in the table. The wild type is indicated with a (+), and the mutant is indicated with a (−). What type of regulator protein is binding to the operator in this possible operon? a repressor a coactivator an attenuator an inducer an activator Are genes A, D, and E all under control of the operator O? a.Yes, because when the operator is nonfunctional the genes E, D, and A expression levels are high. b. Yes, because when the operator is functional the genes E, D, and A expression levels are high. c. No, because genotype 4 shows that gene A is controlled separately from genes E and D. d. No, because genotype 5 shows that gene E is controlled separately from genes A and D

1) The regulator protein is a repressor. → When the operator is defective or nonfunctioning (O-), then the expression of enzymes encoded by the A, D, and E loci is significantly increased over the wild type operator genotype. → This suggests that the regulator protein cannot bind the O- region and repress TXN. 2) Yes, all the genes are under control of the operator. → When operator (O+) and repressor are both functional, then the levels of expression are low. → When the operator is nonfunctional the enzyme levels generally increase.

Classify each of the characteristics as pertaining to gene regulation in either prokaryotes or eukaryotes.

Prokaryotic Gene Regulation. genes are located on one chromosome some genes are organized into operons and mRNA transcripts often specifiy more than one protein. transcription and translation occur in the cytoplasm Eukaryotic Gene Regulation. gene are located on different chromosomes mRNA splicing must occur to remove introns transcription occurs in the nucleus, whereas translation occurs in the cytoplasm Eukaryotic Gene Regulation.

U937D cells express high levels of creatine kinase (CK‑B) mRNA but do not translate the mRNA into protein. Ribosomes bind the 5' end of the CK‑B mRNA; however, translation into protein is repressed in these cells. U937D cells synthesize the CK‑B enzyme when researchers introduce numerous short segments of RNA containing 3' UTR consensus sequences into the cells. The total amount of CK‑B mRNA does not change after adding RNA containing 3' UTR sequences. Introducing short RNA segments without the 3' UTR consensus sequences does not stimulate CK‑B synthesis. Which of the statements explains how the introduction of short RNA containing 3' UTR sequences allows CK‑B translation in U937D cells? (a) Translational repressor proteins inhibit CK‑B translation by binding 3' UTR sequences in the CK‑B mRNA. These repressors bind the 3' UTR sequences in the introduced RNA instead of the CK‑B mRNA, allowing the ribosomes to freely translate CK‑B mRNA. (b) The CK‑B mRNA molecule is too short for efficient translation. The added 3' UTR RNA sequences recombine with the existing CK‑B mRNA, creating a longer transcript that increases translation rates. (c) The introduced RNA increases the intracellular RNA concentration, which triggers an increase in the number of ribosomes and accessory factors and improves translation efficiency. (d) Ribosomes stall when the cell does not contain enough free nucleotides as substrate. Degradation of the additional 3' UTR RNAs provides nucleotides to increase translation rates.

a

The mmm operon, which has sequences A, B, C, and D, encodes enzymes 1 and 2. Sequences A, B, C, and D may be structural genes or regulatory sequencies. Mutations in sequences A, B, C, and D have the effects, where a plus sign (+) indicates that the enzyme is synthesized and a minus sign (−) indicates that the enzyme is not synthesized. mm absent and then mm present No mutation: (+,+) (-,-) A: (-,+) (-,-) B: (+,+) (+,+) C: (+,-) (-,-) D: (-,-) (-,-) Is the mmm operon inducible or repressible?(a) The operon is inducible because a mutation in B results in the production of both enzymes. (b) The operon is inducible because neither enzyme is made when mmm is present. (c) The operon is repressible because both enzymes are made when mmm is absent. (d) The operon is repressible because a mutation in D results in a lack of production of both enzymes. Is the mm operon inducible or repressible?Which sequence is part of the following components of the operon? a. Regulator gene b. Promoter c. Strucutral gene for enzyme 1 d. Structural gene for enzyme 2

c a. B b. D c. A d. C

Tryptophan is an amino acid necessary for E. coli survival and growth. E. coli contain genes coding for enzymes that synthesize tryptophan. These genes are grouped together on a segment of DNA called the tryptophan (trp) operon. Cells can use these enzymes to synthesize tryptophan when it is not present in the environment. However, when tryptophan is already present in the environment, cellular resources are shifted away from manufacturing the enzymes for tryptophan synthesis. Tryptophan binds with and activates the trp repressor, which then binds to the trp promoter and blocks RNA polymerase. Blocking RNA polymerase decreases the normal transcription rate of the operon. What type of regulation does the trp operon exhibit?

negative regulation

The scientist then performs an experiment adding a plasmid to the bacterial cell to determine which mutation is in the DNA‑binding protein and which is in the DNA‑binding site. The experimental setup is listed in the table, wherein a minus indicates a loss‑of‑function mutation, and a plus indicates the wild‑type allele. Experiment |Bacterial cell | Plasmid How will nop1 and nop2 be expressed if huh1 encodes the DNA‑binding protein and huh2 is a mutation in the binding site? How will nop1 and nop2 be expressed if huh2 encodes the DNA‑binding protein and huh1 is a mutation in the binding site?

part 2: Experiment 1 Experiment 2 nop1 not con not con nop2 con not con

A regulatory protein that blocks transcription by binding to the operator site is called____

repressor

A mutant strain of E. coli produces β‑galactosidase in the presence and in the absence of lactose. Where in the operon might the mutation in this strain occur, and why? (a) in the operator region, which leads to increased binding of the lac repressor to the operator (b) in the CAP binding site, where the mutation leads to the inefficiency of RNA polymerase activity (c) in the operator region, where the mutation leads to the failure of the operator to normally bind the repressor (d) near the lacI gene, where the mutation leads to increased levels of lac repressor being made (e) in the lacI gene, which leads to an inactive lac repressor (f) in the promoter region of the operon, where the mutation leads to the failure of the RNA polymerase to bind to the promoter

(c) (e)

Arrange the steps of the regulation of the trp operon in order of occurrence. Levels of tryptophan in the cell are low ... ... ... ... Transcription of the gene stops

1. Levels of tryptophan in the cell are low 2.RNA polymerase binds to the promoter, allowing transcription of trp genes to proceed. 3. Products of the trp genes synthesize tryptophan. 4. Levels of tryptophan rise, and no more is required. 5. Tryptophan binds to the trp repressor protein and induces a conformational change. 6. The trp repressor protein binds to the operator. 7. The trp repressor protein blocks RNA polymerase from binding to the promoter 8. Transcription of trp gene stops

Which of the post‑translational modifications generally targets a protein for degradation in eukaryotes? (a) lipidation (b) nitrosylation (c) ubiquitination (d) acetylation (e) methylation

c

Histone proteins (a) increase the transcription rate for a particular gene. (b) regulate transcription by changing their associations with DNA. (c) stabilize condensed chromosomal DNA during transcription. (d) bind tightly to DNA and strengthen hydrogen bonds between bases

(b)

Enhancer I can stimulate the transcription of gene A, but the insulator blocks its effect on gene B. Enhancer II can stimulate the transcription of gene B, but the insulator blocks its effect on gene A. What would be the effect of moving the insulator to a position between enhancer II and the promoter for gene B? (a) The newly positioned insulator allows enhancer II to hyperactivate gene B transcription. (b) The new positioning of the insulator prevents gene A expression. (c) The newly positioned insulator allows enhancer I to activate gene B transcription. (d) The newly positioned insulator prevents enhancer II from stimulating the transcription of gene B.

d

How do cells regulate gene expression using alternative RNA splicing? a. Alternative RNA splicing determines which genes are underexpressed. b. Alternative RNA splicing determines which genes are transcribed to mRNA. c. Alternative RNA splicing determines how fast certain proteins are translated. d. Alternative RNA splicing determines which proteins are produced from each gene.

d.

The trp operon contains five genes: trpE, trpD, trpC, trpB, and trpA. These five genes code for components that produce three enzymes that catalyze the biosynthesis of tryptophan. The trpL region is the leader region, which helps regulate transcription once RNA polymerase has initiated transcription. The trp operon also undergoes negative regulation by a repressor. Tryptophan is the signal molecule (effector molecule) that binds to the repressor. Determine which events lead to an increase in transcription. The trp operon is transcribed when: (a) the trp repressor dissociates from DNA (b) tryptophan is present at high concentrations inside the cell. (c) tryptophan binds to the repressor. (d) the trp repressor is inactive. (e) the trp repressor is bound to the operator

(d) and (a)

A mutation at the operator site of an operon prevents the repressor from binding. What effect will this mutation have on transcription in a repressible operon? (a) There will be no change in the operon's activity. (b) It will be impossible to turn on transcription of the structural genes. (c) The operon will always be transcriptionally active. (d) There will be a significant decrease in the operon's activity. What effect will this mutation have on transcription in an inducible operon? (a) There will be a significant decrease in the operon's activity. (b) There will be no change in the operon's activity. (c) It will be impossible to turn on transcription of the structural genes. (d) The operon will always be transcriptionally active.

c d

Suppose Jim isolated four E. coli mutants, mut1 to mut4, that showed abnormal expression of the Lac permease protein. To identify the defect in each mutant, he determined the relative levels of Lac permease protein in each mutant. He also generated F' plasmids that contained the wild‑type (wt) lac operon or the lac operon from each of the four mutants. He determined lac permease protein levels in partial diploids of wild‑type cells containing F' lac from each mutant and mutant cells containing wild‑type F' lac. All measurements were carried out in cultures grown in the presence ( + ) or the absence (-) of lactose and glucose, as shown in the table in cell genotype / F' plasmid genotype format. Identify the defect in each mutant. Not all defects will be placed.

mutant 1: election of operator mutant 2: dilection of repressor gene mutant 3:super-repressor mutant 4: deletion of the CAP gene

The GAL gene system in yeast is a eukaryotic gene regulation model system. In this gene system, GAL1 is a structural gene. The regulatory gene GAL4 is required for transcription of GAL genes. Additionally, GAL80 is a negative regulator of GAL4,and GAL3 is required to disrupt the interference of GAL80 with GAL4 so transcription can proceed. In the figure, 80 represents Gal80p, which is the protein produced by GAL80, and 4 represents Gal4p, which is the protein produced by GAL4. Refer to the figure to determine what would inhibit transcription of GAL1 by preventing contact of the Gal4p activating domain and other proteins. (a) GAL3 mutation that prevents interaction with Gal80p (b) GAL4 mutation that prevents encoding of amino acids 148‑768 (c) GAL80 mutation that prevents disruption of the Gal80p-Gal4p complex (d) GAL80 deletion

a and c

Growth in nutrient‑rich medium represses expression of the yeast serine biosynthesis gene SER3. Martens, Laprade, and Winston repressed SER3 expression and found a highly transcribed region of DNA upstream of the SER3 gene. This upstream region contains a non‑protein‑coding gene called SRG1. An RNA polymerase binds the SRG1 promoter and transcribes the SRG1 gene through the adjacent SER3 promoter, which leads to the repression of SER3. Mutations in the SRG1 promoter remove the repression of SER3. Which of the statements explains how SRG1 transcription represses SER3 transcription? (a) The SRG1 transcription process occurs at such a high rate that it titrates basal transcription factors away from other initiation sites. (b) Transcription machinery on the SRG1 gene prevents binding of transcription factors on the SER3 promoter, blocking SER3 transcription. (c) SRG1 RNA modifies the histones in the region of the SER3 promoter, creating a heterochromatic region around the SER3 gene. (d) The protein product of the SRG1 gene binds to the SER3 promoter and prevents its transcription.

b.

A short sequence of DNA located near the promoter region that is recognized by a repressor protein is called _______.

operator