Genetics ch.15 1WORD

List three general ways this can occur.

1)effector molecule 2)protein-protein interactions 3) covalent modifications.

Arrange the following in the proper order in which they occur during glucocorticoid hormone action. 1. Binding of hormone to receptor 2. Release of HSP90 proteins 3. Entry of hormone into the nucleus

1,2,3

Transcription factors usually contain one or more motifs that play key roles in their function. What is the function of the following motifs? A. Helix-turn-helix

DNA binding.

Transcription factors usually contain one or more motifs that play key roles in their function. What is the function of the following motifs? B. Zinc finger

DNA binding.

Is each of the following statements true or false? D. An enhancer may cause the down regulation of transcription.

False

Is each of the following statements true or false? B. A core promoter is a type of regulatory element.

False

Nucleosome-free regions (NFRs) are found in many eukaryotic genes. Select the statement that is not true about NFRs.

NFR=gene activation.

A particular drug inhibits the protein kinase that is responsible for phosphorylating the CREB protein. How would this drug affect the following events? D. The ability of the CREB protein to dimerize

No effect.

A particular drug inhibits the protein kinase that is responsible for phosphorylating the CREB protein. How would this drug affect the following events? A. The ability of the CREB protein to bind to CREs

No effect.

A particular drug inhibits the protein kinase that is responsible for phosphorylating the CREB protein. How would this drug affect the following events? B. The ability of extracellular hormones to enhance cAMP levels

No effect.

Which of the following is not a process mediated by histone variants?

Phosphorylation

Transcription factors such as the glucocorticoid receptor and the CREB protein form homodimers and activate transcription. Other transcription factors form heterodimers. For example, a transcription factor known as myogenic bHLH forms a heterodimer with a protein called the E protein. This heterodimer activates the transcription of genes that promote muscle cell differentiation. However, when myogenic bHLH forms a heterodimer with a protein called the Id protein, transcriptional activation does not occur. Which of the following possibilities best explains this observation? Only one possibility is correct.

Possibility 2

Transcription factors usually contain one or more motifs that play key roles in their function. What is the function of the following motifs? C. Leucine zipper

Protein dimerization.

The gene that encodes the enzyme called tyrosine hydroxylase is known to be activated by the CREB protein. Tyrosine hydroxylase is expressed in nerve cells and is involved in the synthesis of catecholamine, a neurotransmitter. The exposure of cells to adrenaline normally up-regulates the transcription of the tyrosine hydroxylase gene. A mutant cell was identified in which the tyrosine hydroxylase gene was not up-regulated when exposed to adrenaline. List all the possible mutations that could explain this defect. How would you explain the defect if only the tyrosine hydroxylase gene was not up-regulated by the CREB protein, whereas other genes having CREs were properly up-regulated in response to adrenaline in the mutant cell?

The mutation could cause a defect in the following: 1. Adrenaline receptor 2. G protein 3. Adenylyl cyclase 4. Protein kinase A 5. CREB protein 6. CREs of the tyrosine hydroxylase gene

Is each of the following statements true or false? C. Regulatory transcription factors bind to regulatory elements.

True

Describe two different ways that insulators may exert their effects.

a barrier to changes in chromatin structure block the effects of a neighboring enhancer.

What is a histone variant?

a histone with an amino acid sequence that is slightly different

What is an insulator?

a segment of DNA that functions as a boundary between two adjacent genes.

What is a CpG island?

a stretch of 1,000 to 2,000 base pairs that contains a high number of CpG sites.

How are nucleosome-free regions thought to be functionally important?

activated & termination

What are the functions of transcriptional activator proteins ? Explain how they work at the molecular level.

activates transcription. 1)interact with transcription factors 2)alter the structure of chromatin to gain access to the promoter

Where are they located relative to the core promoter?

anywhere

Where are such regions typically found in a genome?

beginning and ends of genes.

Explain how phosphorylation affects the function of the CREB protein.

causes it to act as a transcriptional activator.

Briefly describe three ways that ATP-dependent chromatin-remodeling complexes may change chromatin structure.

change the positions of nucleosomes, evict histones, or replace histones with histone variants.

The binding of a small effector molecule, protein-protein interactions, and covalent modifications are three common ways to modulate the activities of transcription factors. Which of these three mechanisms are used by the CREB protein?

covalent modification and protein-protein interactions.

Explain how the acetylation of core histones may loosen chromatin packing.

decreases the positive charge decrease the binding of the DNA

The DNA-binding domain of each CREB protein subunit recognizes the sequence 5′-TGACGTCA-3′. Due to random chance, how often would you expect this sequence to occur in the human genome, which contains approximately 3 billion base pairs?

it should occur every 4^8 bp, 65,536 bp. 3/65,536 = 45,776 times. This is much greater than a few dozen.

Where would you expect one to be located?

near promoters.

What is a nucleosome-free region?

nucleosomes are missing.

What is the difference between an miRNA and an siRNA. How do these ncRNAs affect mRNAs?

one type of miRNA inhibits the translation of several different mRNAs. siRNAs are not normally made by cells. promote mRNA degradation.

How does the methylation of CpG islands affect gene expression?

promote a closed conformation.

Examine Table 15.1. Why might all histone variants not be expressed by all cells?

some histones not needed in cells

Glucocorticoids are ________ hormones secreted by ________ glands.

steroid ; endocrine

.In ChIP-Seq, how does the DNA in the supernatant and the DNA in the pellet differ?

supernatant no histones pellet histones

What is DNA methylation?

the attachment of a methyl group

The glucocorticoid receptor and the CREB protein are two examples of transcriptional activators. These proteins bind to response elements and activate transcription. A. How could the function of the glucocorticoid receptor be shut off?

the glucocorticoid hormone will be degraded by the cell

What is meant by the term histone code? With regard to gene regulation, what is the proposed role of the histone code?

the pattern of covalent modifications of histones gene regulation.

The binding of a small effector molecule, protein-protein interactions, and covalent modifications are three common ways to modulate the activities of transcription factors. Which of these three mechanisms are used by steroid receptors

1)Steroid receptors 2)binding of an effector molecule 3)protein-protein interactions

Describe the steps that need to occur for the glucocorticoid receptor to bind to a GRE.

1)enter the cell. 2)hormone then binds to release HSP90. 3)HSP90 exposes a NLS then enters the nucleus. 4)dimer binds to a GRE, which activates transcription

Discuss the structure and function of regulatory elements.

1)short genetic sequences recognized by regulatory transcription factors. 2)affects the rate of transcription.

Let's suppose a mutation in the glucocorticoid receptor does not prevent the binding of the glucocorticoid hormone to the protein but prevents the ability of the receptor to activate transcription. Make a list of all the possible defects that may explain why transcription cannot be activated.

1. DNA-binding domain 2.HSP90 domain 3. dimerization domain 4. nuclear localization domain 5. domain that activates RNA polymerase

Which of the following proteins does NOT directly interact with TFIID?

Histone deacetylase

A particular drug inhibits the protein kinase that is responsible for phosphorylating the CREB protein. How would this drug affect the following events? C. The ability of the CREB protein to stimulate transcription

It would be inhibited.

Variant histones are very prevalent in eukaryotes. The Barr body, the inactive X in eukaryotic females, is associated with which variant histone?

MacroH2A

Researchers can isolate a sample of cells, such as skin fibroblasts, and grow them in the laboratory. This procedure is called a cell culture. A cell culture can be exposed to a sample of DNA. If the Page 386 cells are treated with agents that make their membranes permeable to DNA, the cells may take up the DNA and incorporate it into their chromosomes. This process is called transformation or transfection. Scientists have transformed human skin fibroblasts with methylated DNA and then allowed the fibroblasts to divide for several cellular generations. The DNA in the daughter cells was then isolated, and the segment that corresponded to the transformed DNA was examined. This DNA segment in the daughter cells was also found to be methylated. However, if the original skin fibroblasts were transformed with unmethylated DNA, the DNA found in the daughter cells was also unmethylated. With regard to the transformed DNA, do fibroblasts perform de novo methylation, maintenance methylation, or both? Explain your answer.

maintenance methylation because they can replicate and methylate DNA if it has already been methylated

Briefly describe the method of chromatin immunoprecipitation sequencing (ChIP-Seq).

only DNA fragments that are bound to nucleosomes are precipitated and sequenced

The glucocorticoid receptor and the CREB protein are two examples of transcriptional activators. These proteins bind to response elements and activate transcription. B. What type of enzyme would be needed to shut off the activation of transcription by the CREB protein?

phosphatase

If the number of random occurrences of the sequence in the human genome is much higher than a few dozen, provide at least one explanation why the CREB protein is not activating more than a few dozen genes.

1. two of these sequences close together, 2. CREs might not be near a gene. 3. conformation of chromatin not

An enhancer, located upstream from a gene, has the following sequence: 5′-GTAG-3′ 3′-CATC-5′ This enhancer is orientation-independent. Which of the following sequences also works as an enhancer? A. 5′-CTAC-3′ 3′-GATG-5′ B. 5′-GATG-3′ 3′-CTAC-5′ C. 5′-CATC-3′ 3′-GTAG-5′

A

When we say that DNA methylation is heritable, what do we mean? How is it passed from a mother to a daughter cell?

After de novo methylation has occurred, it is passed from mother to daughter cell. DNA replication is semiconservative

How is it used to determine nucleosome positions within a genome?

By comparing these sequences with the entire genome sequence

Is each of the following statements true or false? A. An enhancer is a type of regulatory element.

True

Glucocorticoid hormones activate genes that are involved in which of the following processes?

glucose,fats,proteins

What is meant by the term transcription factor modulation?

how transcription factors are regulated.

Describe how the binding of iron regulatory protein to an IRE affects the mRNAs for ferritin and the transferrin receptor. How does iron (Fe3+) influence this process?

inhibits the translation of ferritin mRNA and enhances the stability of the transferrin receptor mRNA When the iron concentration is high, more ferritin protein is translated, and less transferrin receptor is made.

A segment of DNA that serves as a boundary between two genes is called a(n)

insulator

What would be the consequence if an individual was homozygous for an IRP that could not bind iron but could bind to the IRE?

iron toxicity

Let's suppose that a vertebrate organism carries a mutation that causes some cells that normally differentiate into nerve cells to differentiate into muscle cells. A molecular analysis reveals that this mutation is in a gene that encodes a DNA methyltransferase. Explain how an alteration in a DNA methyltransferase could produce this phenotype.

the methyltransferase is responsible for methylating and inhibiting a gene that causes a cell to become a muscle cell. The methyltransferase is inactivated by the mutation.

.A transcriptional repressor that controls the transcription of gene A is not normally active unless bound by an effector molecule X. In a certain cell, the domain of the repressor that binds to the silencer of gene A is mutated. With all other factors being the same, what effect do you predict on the transcription of gene A?

transcription increase

A transcriptional repressor that controls the transcription of gene A is not normally active unless bound by an effector molecule X. In a certain cell, the domain of the repressor that binds X is mutated. With all other factors being the same, what effect do you predict on the transcription of gene A?

transcription increase.

Discuss the common points of control in eukaryotic gene regulation.

transcriptional regulation, energy-efficient

Which of the following is true with regards to enhancer sequences?

upstream or downstream of promoter.

Histones are thought to be displaced as RNA polymerase is transcribing a gene. What would be the potentially harmful consequences if histones were not put back onto a gene after RNA polymerase had passed?

waste of energy.