Chapter 19

A protein kinase activating many other protein kinases is an example of _____. a cellular response mutualism amplification deactivation sensitization

amplification By activating many other molecules the initial signal is amplified.

Calcium ions that act as second messengers are stored in _____. chloroplasts endoplasmic reticula lysosomes mitochondria peroxisomes

endoplasmic reticula The ER stores calcium ions

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

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

The presence of a DNA template (e.g., a product from PCR), general transcription factors, and RNA polymerase II allows for the initiation of transcription in vitro. Explain why the initiation of transcription is not possible with only general transcription factors and RNA polymerase II using the genomic DNA as a template. Genomic DNA is wrapped in nucleosomes, while template DNA from PCR is not. For remodeling or removing nucleosomes additional proteins are required. Template DNA from PCR is wrapped in nucleosomes, while genomic DNA is not. The nucleosomes are required for initiation of transcription. None of the above.

Genomic DNA is wrapped in nucleosomes, while template DNA from PCR is not. For remodeling or removing nucleosomes additional proteins are required.

****Repressors in eukaryotic cells work by four mechanisms. List and describe how the mechanisms work.

1) Competition: Repressor binds at site on DNA overlapping binding site of activator and inhibits activator from binding to gene and thus activation of that gene. 2) Inhibition: Repressor binds at site on DNA beside activator and interacts with activator, obstructing its activating region. 3) Direct repression: Repressor binds at site on DNA upstream of gene and by interacting with transcriptional machinery at promoter in specific way, inhibits transcription initiation. 4) Indirect repression: Repression caused by recruiting histone modifiers that alter nucleosomes in ways that inhibit transcription, eg deacetylation or methylation.

Which of the following regulatory DNA sequences might be located thousands of nucleotides away from the transcription start site of a gene? Promoter-proximal element Promoter Enhancer TATA box

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

Which of these acts as a second messenger? adenylyl kinase protein kinase G-protein-linked receptor G protein cyclic AMP

cyclic AMP Cyclic AMP can act as second messengers.

A signal molecule is also known as a(n) _____. receptor ligand protein initiator key

ligand

The most common type of regulation of gene expression occurs at the level of transcription. Select other types of regulation for gene expression in eukaryotic cells. Check all that apply. protein transport post-translational modifications of proteins splicing transcript stability initiation of translation RNA stability protein stability (half-life) RNA transport

post-translational modifications of proteins splicing transcript stability initiation of translation RNA stability protein stability (half-life) RNA transport

A signal transduction pathway is initiated when a _____ binds to a receptor. G protein calmodulin signal molecule cyclic AMP tyrosine kinase

signal molecule

A signal transduction pathway is initiated when a _____ binds to a receptor. G protein tyrosine kinase calmodulin signal molecule cyclic AMP

signal molecule The binding of a signal molecule to a receptor initiates a signal transduction pathway.

Which of these is responsible for initiating a signal transduction pathway?

signal molecule This is a signal molecule. The attachment of a signal molecule to a plasma membrane receptor initiates a signal transduction pathway.

Which of the following best describes the purpose of the yeast two-hybrid system? It allows identification of proteins that can act as activators of Gal1. It provides visual detection of protein-protein interactions. It allows the expression of foreign genes in a yeast culture. It allows observation of the effects of protein-protein interactions that would not otherwise occur.

It provides visual detection of protein-protein interactions. The yeast two-hybrid system allows detection of genes that code for proteins that interact with a known protein.

Recall the use of combinatorial control in regulation of the S. cerevisiae mating type specific gene expression. Describe how Mcm1 serves to repress and activate transcription of target genes in haploid MAT α cells.

Mcm1 is a site-specific DNA-binding transcription factor that forms repressor or activator complexes. A dimer of α2 binds cooperatively with Mcm1 upstream of a-specific genes to REPRESS the transcription of those genes in haploid alpha cells. At the same time, Mcm1 binds cooperatively with α1 upstream of alpha-specific genes to ACTIVATE transcription of those genes in haploid α cells.

_____ catalyzes the production of _____, which then opens an ion channel that releases _____ into the cell's cytoplasm. Phospholipase C ... cyclic AMP ... Ca2+ Phospholipase C ... IP3 .... Ca2+ Protein kinase ... PIP2 ... Na+ Adenylyl cyclase ... cyclic AMP ... Ca2+ Adenylyl cyclase ... IP3 .... Ca2+

Phospholipase C ... IP3 .... Ca2+ Phospholipase C cleaves IP3 from a membrane protein, and IP3 then binds to a calcium channel on the ER.

A eukaryotic gene is most likely to be transcribed if it is located where? in a region of the genome in which the histones are deacetylated in a heterochromatic region of the genome in the telomeric region of a chromosome in a euchromatic region of the genome

in a euchromatic region of the genome Euchromatin is less packed than heterochromatin and is usually associated with active transcription.

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. DNA: A-B-C-D-E-F-G-H-I Primary RNA transcript: A-B-C-D-E-F-G-H-I 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.)

A-C-E-G-I A-C-E-I A-C-G-I 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.

Which of the following regulatory elements is not composed of DNA sequences? Silencers Promoter-proximal elements Activators Enhancers

Activators Activators are proteins that are involved in transcription initiation.

Compare and contrast the DNA sequence elements involved in regulating transcription in bacterial cells and eukaryotic cells.

Bacterial and eukaryotic cells: Include promoter sequences within the DNA upstream of the coding sequence of a gene Include DNA-binding sites for regulatory proteins like repressors or activators Bacterial cells: Genes are typically controlled by one activator and/or one repressor protein The regulatory elements are mostly located close to the gene they regulate Eukaryotic cells: genes are typically controlled by multiple activator and repressor proteins the regulatory elements may be located at great distances from the gene they regulate

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. 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 and the imaginin gene have identical enhancers. Control elements A, B, and C are proximal control elements for the fantasin 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 whenever general transcription factors 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. 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. 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.

What role does a transcription factor play in a signal transduction pathway? By binding to a plasma membrane receptor it initiates a cascade. It relays a signal from the cytoplasm to the plasma membrane. It activates relay proteins. By binding to DNA it triggers the transcription of a specific gene. It is a plasma membrane protein that binds signal molecules.

By binding to DNA it triggers the transcription of a specific gene. This is the function of a transcription factor.

You discover a novel DNA-binding protein. What would be the best technique to define the identity of the specific DNA sequence to which this protein can bind? reporter gene assay two-hybrid assay ChIP-Seq assay ChIP assay

ChIP-Seq assay ChIP-Seq is an improvement over the general ChIP (chromatin immunoprecipitation) assay. In ChIP-Seq, the DNA fragment bound by the novel DNA-binding protein is liberated and directly sequenced using next-generation sequencing methods. This allows one to know the precise identity of the DNA sequence to which the protein of interest is bound.

Which of the following best describes the role of chaperone proteins in the regulation of gene expression by steroid hormones? Chaperone proteins directly enhance transcription. Chaperone proteins maintain functionality of the receptor. Chaperone proteins enter the cell and bind receptor molecules. Chaperone proteins activate receptor proteins.

Chaperone proteins maintain functionality of the receptor. Chaperone proteins maintain the functionality of the receptor prior to binding of the steroid hormone to the receptor.

Which statements about the modification of chromatin structure in eukaryotes are true? Select all that apply. DNA is not transcribed when chromatin is packaged tightly in a condensed form. Some forms of chromatin modification can be passed on to future generations of cells. 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. 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. Some forms of chromatin modification can be passed on to future generations of cells. Acetylation of histone tails is a reversible process. Acetylation of histone tails in chromatin allows access to DNA for transcription. 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.

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. True False

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.

Which of the following terms describes the DNA-protein complexes that look like beads on a string? Histones Chromatin 30-nanometer fiber Nucleosome

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

Which of the following events in transcription initiation likely occurs last? Basal transcription factors form a basal transcription complex. RNA polymerase binds to the promoter of the gene. Regulatory transcription factors bind to enhancers. TBP is recruited to the promoter.

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.

What is the function of a spliceosome? protein activation translation protein degradation regulating the transport of mRNA to the cytoplasm RNA processing

RNA processing

Which one of the following gene families is not under the control of a group of regulatory elements called a locus control region (LCR) or a global control region (GCR)? S. cerevisiae mating-type genes human globin genes mouse globin genes mouse HoxD gene cluster

S. cerevisiae mating-type genes The mating-type genes in yeast are under combinatorial control and do not utilize an LCR or a GCR. The three cells types of yeast (haploid a, haploid α, and diploid a/α) are determined by gene expression within the mating-type locus. Various combinations of different regulatory proteins (a1, α1, α2, and Mcm1) work together to regulate the cell type. These regulatory proteins function as activators or repressors, depending on the various combinations bound at the MAT locus.

Which of the following best describes the mechanism by which steroid hormones control gene expression? Steroid hormones enter a cell, bind directly to hormone response elements (HREs), and enhance transcription. Chaperone proteins transport steroid hormones into the cell and guide them to their target genes. Steroid hormones that enter the cell activate receptors. These hormone-receptor complexes then bind HREs and influence gene expression. Steroid hormones transport mRNA from the nucleus into the cytoplasm, where it is translated into protein.

Steroid hormones that enter the cell activate receptors. These hormone-receptor complexes then bind HREs and influence gene expression.

All of the following are necessary conditions of the yeast two-hybrid system except _______. a single yeast cell can harbor two different plasmids simultaneously both the binding domain and the activating domain of Gal4 retain their individual functions after being separated by recombinant DNA methods UASG must be situated between the Gal1 and Gal10 gene sequences β-galactosidase synthesis is under the control of UASG

UASG must be situated between the Gal1 and Gal10 gene sequences Although this is the native configuration of UASG , the configuration is not a necessary feature of the yeast two-hybrid system as the Gal10 gene is not used in this system.

Are there any types of regulation unique to eukaryotic cells versus prokaryotic cells? Yes, initiation of translation and control of transport of RNA or proteins to specific organelles. Yes, splicing and control of transport of RNA or proteins to specific organelles. Yes, initiation of translation and splicing. No.

Yes, splicing and control of transport of RNA or proteins to specific organelles.

Each of the expression vectors used in the yeast two-hybrid system contains a different selectable marker. It is important that two different markers be used so that _______. the Gal4 binding domain cannot interact with the Gal4 activation domain none of the recovered colonies will contain the Gal4 activation domain all recovered colonies will contain the Gal4 binding domain all recovered colonies will contain the Gal4 activation domain AND the Gal4 binding domain

all recovered colonies will contain the Gal4 activation domain AND the Gal4 binding domain It is important that all surviving colonies contain both the Gal4 activation domain AND the Gal4 binding domain as BOTH are required for the detection of interaction The growth medium is formulated so that any cells not meeting this condition fail to grow.

Enzyme complexes that break down protein are called _____. lipases ubiquitins amylase proteasomes nucleases

proteasomes Proteasomes are enzyme complexes that break down proteins.

Protein-phosphorylating enzymes' role in the regulation of gene expression involves _____. protein activation translation protein degradation regulating the transport of mRNA to the cytoplasm RNA processing

protein activation

The nuclear membrane's role in the regulation of gene expression involves _____. protein activation translation protein degradation regulating the transport of mRNA to the cytoplasm RNA processing

regulating the transport of mRNA to the cytoplasm This is the role of the nuclear membrane in the regulation of gene expression.

Which of the following mechanisms illustrates a form of transcriptional repression that is unique to eukaryotes? repressors recruiting enzymes to modify groups on histones to compact chromatin repressors binding to a site near an activator binding site where they interact with and inhibit the activator repressors blocking RNA polymerase by binding an operator site within the promoter repressors recruiting enzymes to modify groups on histones to loosen chromatin

repressors recruiting enzymes to modify groups on histones to compact chromatin Bacterial DNA is not wrapped around nucleosomes. Eukaryotes use this mechanism of repression often. An example of this mechanism is seen in the recruitment of deacetylases that remove acetyl groups from histones, resulting in tighter winding of the DNA around the histone core.

Players in a signal transduction pathway can be classified into the following categories: signal, receptor, relay molecule, and output. Classify each component of the STAT pathway pictured in the Figure as signal, receptor, relay molecule, and output. You can use a term more than once.

signal: cytokine receptor: cytokine receptor relay molecule: JAK, STAT output: Transcriptional expression of specific genes

The reason some cells respond to the presence of a steroid hormone while others do not is that _______. the receptors necessary for regulation differ among cells of various types the specific HRE is present only in certain cells only certain cells contain the gene that is targeted by a given steroid hormone chaperone proteins block the hormone response elements (HREs) in some cells

the receptors necessary for regulation differ among cells of various types The specificity of steroid hormone regulation is due to the presence or absence of the receptor in different cell types.

In this animation, which of the following, when activated by a signal transduction pathway, moved from the cytoplasm to the nucleus of a cell? relay protein DNA plasma membrane receptor protein signal molecule transcription factor

transcription factor Activated transcription factors trigger transcription.

Which of these is the second of the three stages of cell signaling? gene activation reception binding of a neurotransmitter to a plasma membrane receptor transduction cell response

transduction Transduction is the second of the three stages of cell signaling.