Genetics ch.15 tb 1WORD
List three general ways this can occur.
1)effector molecule 2)protein-protein interactions 3) covalent modifications.
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?
A potentially harmful consequence would be that transcription may be initiated at multiple points within a gene, thereby producing many nonfunctional transcripts. The result would be waste of energy.
What is an insulator?
An insulator is a segment of DNA that functions as a boundary between two adjacent genes.
Where would you expect one to be located?
CpG islands are often located near promoters.
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.
What is DNA methylation?
DNA methylation is the attachment of a methyl group to a base within the DNA
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
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.
Explain how phosphorylation affects the function of the CREB protein.
Phosphorylation of the CREB protein causes it to act as a transcriptional activator. Unphosphorylated CREB protein can still bind to CREs, but it does not stimulate transcription.
Explain how the acetylation of core histones may loosen chromatin packing.
The attraction between DNA and histones occurs because the histones are positively charged and the DNA is negatively charged. The covalent attachment of acetyl groups decreases the amount of positive charge on the histone proteins and thereby may decrease the binding of the DNA. In addition, histone acetylation may attract proteins to the region that loosen chromatin compaction.
What is meant by the term histone code? With regard to gene regulation, what is the proposed role of the histone code?
The histone code is the pattern of covalent modifications of histones that acts much like a language in specifying alterations in chromatin structure and function. In this way, the modification of histones plays a role in gene regulation.
Where are such regions typically found in a genome?
They are typically found at the beginning and ends of genes.
Is each of the following statements true or false? C. Regulatory transcription factors bind to regulatory elements.
True
How does the methylation of CpG islands affect gene expression?
When an island is methylated, this inhibits transcription. This inhibition may be the result of the inability of the transcriptional activators to recognize the methylated promoter and the effects of methyl-CpG-binding proteins, which may promote a closed chromatin conformation.
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
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.
When we say that DNA methylation is heritable, what do we mean? How is it passed from a mother to a daughter cell?
In many eukaryotic species, the attachment occurs on cytosine at a CG sequence. After de novo methylation has occurred, it is passed from mother to daughter cell. Because DNA replication is semiconservative, the newly made DNA contains one strand that is methylated and one that is not. DNA methyltransferase recognizes this hemimethylated DNA and methylates the cytosine in the unmethylated DNA strand; this event is called maintenance methylation.
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.
What is the difference between an miRNA and an siRNA. How do these ncRNAs affect mRNAs?
MicroRNAs (miRNAs) are ncRNAs that are transcribed from endogenous eukaryotic genes—genes that are normally found in the genome. They play key roles in regulating gene expression, particularly during embryonic development in animals and plants. Most commonly, a single type of miRNA inhibits the translation of several different mRNAs. By comparison, small-interfering RNAs (siRNAs) are ncRNAs that usually originate from sources that are exogenous, which means they are not normally made by cells. The sources of siRNAs can be viruses that infect a cell, or researchers can make siRNAs to study gene function experimentally. They usually promote mRNA degradation.
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. It could be in the DNA-binding domain, so that the receptor would not recognize GREs. 2. It could be in the HSP90 domain, so that HSP90 would not be released when the hormone binds. 3. It could be in the dimerization domain, so that the receptor would not dimerize. 4. It could be in the nuclear localization domain, so that the receptor would not travel into the nucleus. 5. It could be in the domain that activates RNA polymerase, so that the receptor would not activate transcription, even though it could bind to GREs.
What is a CpG island?
A CpG island is a stretch of 1,000 to 2,000 base pairs that contains a high number of CpG sites.
What is a histone variant?
A histone variant is a histone with an amino acid sequence that is slightly different from the sequence of a core histone. Histone variants play specialized roles with regard to chromatin structure and function.
What is a nucleosome-free region?
A nucleosome-free region (NFR) is a location in the genome where nucleosomes are missing.
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?
A. Eventually, the glucocorticoid hormone will be degraded by the cell. The glucocorticoid receptor binds the hormone with a certain affinity. The binding is a reversible process. Once the concentration of the hormone falls below the affinity of the hormone for the receptor, the receptor will no longer have the glucocorticoid hormone bound to it. When the hormone is released, the glucocorticoid receptor will change its conformation, and it will no longer bind to the DNA.
Describe two different ways that insulators may exert their effects.
An insulator may act as a barrier to changes in chromatin structure or block the effects of a neighboring enhancer.
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 is the correct one. Because we already know that the E protein and the Id protein form heterodimers with myogenic bHLH, we expect all three proteins to have a leucine zipper. Leucine zippers promote dimer formation. We also need to explain why the Id protein inhibits transcription, while the E protein enhances transcription. As seen in possibility 2, the Id protein does not have a DNA-binding domain. Therefore, if it forms a heterodimer with myogenic bHLH, the heterodimer probably will not bind to the DNA very well. In contrast, when the E protein forms a heterodimer with myogenic bHLH, there will be two DNA-binding domains, which would promote good binding to the DNA. (Note: A description of these proteins is found in Chapter 26.)
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.
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.
These results indicate that the fibroblasts perform maintenance methylation because they can replicate and methylate DNA if it has already been methylated. However, the fibroblasts do not perform de novo methylation, because if the donor DNA was unmethylated, the DNA in the daughter cells remains unmethylated.
Is each of the following statements true or false? A. An enhancer is a type of regulatory element.
True
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.
What is meant by the term transcription factor modulation?
how transcription factors are regulated.
Discuss the common points of control in eukaryotic gene regulation.
transcriptional regulation=energy-efficient
Briefly describe three ways that ATP-dependent chromatin-remodeling complexes may change chromatin structure.
ATP-dependent chromatin remodeling complexes may change the positions of nucleosomes, evict histones, and/or replace histones with histone variants.
How are nucleosome-free regions thought to be functionally important?
An NFR at the beginning of a gene is thought to be important so that genes can be activated. The NFR at the end of a gene may be important for the proper termination of transcription.
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.
Perhaps 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.
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?
The binding of IRP to the IRE inhibits the translation of ferritin mRNA and enhances the stability of the transferrin receptor mRNA. The increase in the stability of transferrin receptor mRNA increases the concentration of this mRNA and ultimately leads to more transferrin receptor protein. Conditions of low iron promote the binding of IRP to the IRE, leading to a decrease in ferritin protein and an increase in transferrin receptor protein. When the iron concentration is high, iron binds to IRP, causing it to be released from the IRE. This allows the ferritin mRNA to be translated and also causes a decrease in the stability of transferrin receptor mRNA. Under these conditions, more ferritin protein is translated, and less transferrin receptor is made.
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?
B. An enzyme known as a phosphatase will eventually cleave the phosphate groups from the CREB protein. When the phosphates are removed, the CREB protein will stop activating transcription.
Briefly describe the method of chromatin immunoprecipitation sequencing (ChIP-Seq). How is it used to determine nucleosome positions within a genome?
The method of ChIP-Seq is described in Figure 15.11. In the method described in this figure, only DNA fragments that are bound to nucleosomes are precipitated and sequenced. By comparing these sequences with the entire genome sequence, this information tells you which DNA sequences within a genome have nucleosomes bound to them.
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 If other genes were properly regulated by the CREB protein, you could conclude that the mutation is probably within the tyrosine hydroxylase gene itself. Perhaps a CRE has been mutated and no longer recognizes the CREB protein.
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′
The sequence found in A would work as an enhancer, but the ones in B and C would not. The sequence that is recognized by the transcriptional activator is 5'-GTAG-3' in one strand and 3'-CATC-5' in the opposite strand. This is the same arrangement found in A. In B and C, however, the arrangement is 5'-GATG-3' and 3'-CATC-5'. In the arrangement found in B and C, the two middle bases (i.e., A and T) are not in the correct order.
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? Actually, only a few dozen genes are activated by the CREB protein. Does the value of a few dozen agree with the number of random occurrences expected in the human genome? 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.
There are four types of bases (A, T, G, and C), and this CRE sequence contains 8 bp, so according to random chance, it should occur every 4^8 bp, which equals every 65,536 bp. If we divide 3 billion by 65,536, this sequence is expected to occur approximately 45,776 times. This is much greater than a few dozen. There are several reasons why the CREB protein does not activate over 45,000 genes. 1. To create a functional CRE, there needs to be two of these sequences close together, because the CREB protein functions as a homodimer. 2. CREs might not be near a gene. 3. The conformation of chromatin containing a CRE might not be accessible to binding by the CREB protein.
