Bio 131 Regulation of Gene Expression Weeks 10/11 Lecture 2
- mRNA in the cytoplasm can be translated by several ribosomes blank--> ribosomes keep jumping on until blank is degraded - Long-lived mRNA will be able to support multiple rounds of blank synthesis. - Some transcripts have "blank" codons: some amino acids and the tRNAs which are more abundant. For example; if you have a mRNA that has a codon for lots of tRNA that always will be available, you'll have lots of them (blanks) being made as opposed to having rare tRNAs. With rare tRNAs, you'll have blank-optimal codons, meaning it will be abundant/short-lived.
- mRNA in the cytoplasm can be translated by several ribosomes simultaneously --> continues until mRNA is degraded - Long-lived mRNA will be able to support multiple rounds of polypeptide synthesis. - Transcripts have "optimal" codons: some amino acids and the tRNAs which are more abundant. For example; if you have a mRNA that has a codon for lots of tRNA that always will be available, you'll have lots of them (tRNAs) being made as opposed to having rare tRNAs. With rare tRNAs, you'll have non-optimal codons, meaning it will be short-lived.
A dozen or so short nucleotide sequences appear again and again in the control elements for different genes. On average, each enhancer is composed of about blank control elements, each binding only blank or blank specific transcription factors. It is the particular combination of control elements in an enhancer associated with a gene, rather than a unique control blank, that is important in varying/regulating transcription of the gene
A dozen or so short nucleotide sequences appear again and again in the control elements for different genes. On average, each enhancer is composed of about ten control elements, each binding only one or two specific transcription factors. It is the particular combination of control elements in an enhancer associated with a gene, rather than a unique control element, that is important in regulating transcription of the gene
Blank proteins bind to the control elements, promoting nonsimultaneous/simultaneous transcription of the genes, no matter where they are in the genome.
Activator proteins bind to the control elements, promoting nonsimulatenous/simultaneous transcription of the genes, no matter where they are in the genome.
An blank is a protein that binds to an enhancer and stimulates transcription of a gene.
An activator is a protein that binds to an enhancer and stimulates transcription of a gene.
As you can see in Figure 15.8, some control elements, named blank control elements, are located close to the blank.
As you can see in Figure 15.8, some control elements, named proximal control elements, are located close to the promoter.
For instance, the mRNAs for the hemoglobin polypeptides (X-globin and X-globin) in developing red blood cells are unusually stable, and these mRNAs are translated repeatedly in these cells. Nucleotide sequences that affect how long an blank remains intact are often found in the blank region (BLANK) at the 3′ end of the molecule
For instance, the mRNAs for the hemoglobin polypeptides (α-globin and β-globin) in developing red blood cells are unusually stable, and these mRNAs are translated repeatedly in these cells. Nucleotide sequences that affect how long an mRNA remains intact are often found in the untranslated region (UTR) at the 3′ end of the molecule
Generally, histone acetylation—the addition of an acetyl group to an blank acid in a blank tail—appears to promote/discourage transcription by opening/closing up the chromatin structure (Figure 15.7), while the addition of methyl groups to histones can lead to the condensation of chromatin and reduced transcription. Often, the addition of a particular chemical group may create a new binding site for enzymes that further modify chromatin structure.
Generally, histone acetylation—the addition of an acetyl group to an amino acid in a histone tail—appears to promote transcription by opening up the chromatin structure (Figure 15.7), while the addition of methyl groups to histones can lead to the condensation of chromatin and reduced transcription. Often, the addition of a particular chemical group may create a new binding site for enzymes that further modify chromatin structure.
In contrast, some mRNAs in multicellular blanks typically survive for hours, days, or even weeks.
In contrast, some mRNAs in multicellular eukaryotes typically survive for hours, days, or even weeks.
What do histone Deacetylases do (HDACS) ?
Proteins that remove acetyl groups from histones that make chromatin less accessible. DNA/Histone interactions increased DNA inaccessible Transcription repressed (on --> off)
Regulatory proteins specific to a cell type, control intron-exon choices by binding to DNA/RNA sequences within the primary blank.
Regulatory proteins specific to a cell type, control intron-exon choices by binding to RNA sequences within the primary transcript.
What are control elements? Segments of noncoding DNA having particular nucleotide sequences that serve as binding sites for the proteins called blank factors, which bind to the control elements and help regulate blank .
Segments of noncoding DNA having particular nucleotide sequences that serve as binding sites for the proteins called transcription factors, which bind to the control elements and help regulate transcription.
Some 3' UTR's drive shorter/longer tail formation. They can be 'blanked' experimentally to change xRNA life. Longer tails mean.... Long blank lives AND the longer the mRNA survives. The life of mRNA is greatly blanked in lactation by Prolactin hormone.
Some 3' UTR's drive longer tail formation. They can be 'traded' experimentally to change mRNA life. Longer tails mean.... Long blank lives AND the longer the mRNA survives. The life of mRNA is greatly prolonged in lactation by Prolactin hormone.
Concept Check 15.2 1. In general, what are the effects of histone acetylation and DNA methylation on gene expression? 2. Compare the roles of general and specific transcription factors in regulating gene expression. **3. WHAT IF? Suppose you compared the nucleotide sequences of the distal control elements in the enhancers of three genes that are expressed only in muscle cells. What would you expect to find? Why?
1. Histone acetylation is generally associated with gene expression, while DNA methylation is associated with lack of expression. 2. General transcription factors function in assembling the transcription initiation complex at the promoters for all genes. Specific transcription factors bind to control elements associated with a particular gene and, once bound, either increase (activators) or decrease (repressors) transcription of that gene. 3. The three genes should have some similar or identical sequences in the control elements of their enhancers. Because of this similarity, the same specific transcription factors in muscle cells could bind to the enhancers of all three genes and stimulate their expression coordinately.
A few general transcription factors bind to a DNA sequence such as the TATA box found within most promoters, but many bind to blanks, including other transcription factors as well as RNA polymerase II.
A few general transcription factors bind to a DNA sequence such as the TATA box found within most promoters, but many bind to proteins, including other transcription factors as well as RNA polymerase II.
Informational portion of text: A simple example of alternative RNA splicing is shown in Figure 15.12 for the troponin T gene, which encodes multiple distantly/closely related proteins with slightly similar/different effects on muscle contraction. Other genes code for many more products. For instance, researchers have found a gene in Drosophila with enough alternatively spliced exons to generate about 19,000 membrane proteins with different extracellular domains. At least 17,500 (94%) of the alternative mRNAs are actually synthesized. Each developing nerve cell appears to synthesize a different form of the protein, which acts as a unique identifier on the cell surface and helps prevent excessive overlap of nerve cells during nervous system development.
A simple example of alternative RNA splicing is shown in Figure 15.12 for the troponin T gene, which encodes multiple closely related proteins with slightly different effects on muscle contraction. Other genes code for many more products. For instance, researchers have found a gene in Drosophila with enough alternatively spliced exons to generate about 19,000 membrane proteins with different extracellular domains. At least 17,500 (94%) of the alternative mRNAs are actually synthesized. Each developing nerve cell appears to synthesize a different form of the protein, which acts as a unique identifier on the cell surface and helps prevent excessive overlap of nerve cells during nervous system development.
Activation domains bind other blank proteins or components of the transcription machinery, facilitating a series of blank -blank interactions that result in enhanced blank of a given gene.
Activation domains bind other regulatory proteins or components of the transcription machinery, facilitating a series of protein-protein interactions that result in enhanced translation/transcription of a given gene.
Activators can/can't work together, so the binding of one may be more easier/difficult for the next one to bind to help with blank expression.
Activators can work together, so the binding of one may be more easier for the next one to bind to help with gene expression.
All organisms, whether prokaryotes or eukaryotes, must blank (this is important) which genes are expressed at any given time. Do both unicellular organisms and the cells of multicellular organisms continually turn genes on and off in response to signals from their external and internal environments? Regulation of gene expression is also essential for cell blank in multicellular organisms, which are made up of different types of cells.
All organisms, whether prokaryotes or eukaryotes, must regulate which genes are expressed at any given time. And, yes, for both unicellular and multicellular organisms. Regulation of gene expression is also essential for cell specialization in multicellular organisms, which are made up of different types of cells.
Alternative RNA splicing can significantly expand the repertoire of a eukaryotic blank. In fact, alternative splicing was proposed as one explanation for the surprisingly high/low number of human genes counted when the human genome was sequenced. The number of human genes was found to be similar to that of a soil worm (nematode), mustard plant, or sea anemone. Scientists wondered what, if not the total number of genes, accounts for the more complex morphology (external form) of humans. It turns out that more than 90% of human protein-coding genes probably undergo alternative splicing. Thus, the extent of alternative splicing greatly multiplies the number of possible human proteins, which may be better correlated with complexity of form than the number of genes.
Alternative RNA splicing can significantly expand the repertoire of a eukaryotic genome. In fact, alternative splicing was proposed as one explanation for the surprisingly low number of human genes counted when the human genome was sequenced. The number of human genes was found to be similar to that of a soil worm (nematode), mustard plant, or sea anemone. Scientists wondered what, if not the total number of genes, accounts for the more complex morphology (external form) of humans. It turns out that more than 90% of human protein-coding genes probably undergo alternative splicing. Thus, the extent of alternative splicing greatly multiplies the number of possible human proteins, which may be better correlated with complexity of form than the number of genes.
Alternatively, translation of all the mRNAs in a cell may be regulated variously/simultaneously. In a eukaryotic cell, such "global" control usually involves activation or inactivation of one or more protein factors required to initiate translation. This mechanism plays a role in starting blank of mRNAs stored in eggs. Just after fertilization, translation is triggered by sudden activation of blank initiation factors. The response is a burst of synthesis of proteins encoded by the stored blank . Some plants and algae store blank during periods of darkness; light triggers reactivation of the translational apparatus.
Alternatively, translation of all the mRNAs in a cell may be regulated simultaneously. In a eukaryotic cell, such "global" control usually involves activation or inactivation of one or more protein factors required to initiate translation. This mechanism plays a role in starting translation of mRNAs stored in eggs. Just after fertilization, translation is triggered by sudden activation of translation initiation factors. The response is a burst of synthesis of proteins encoded by the stored mRNAs. Some plants and algae store mRNAs during periods of darkness; light triggers reactivation of the translational apparatus.
Figure 15.10 A model for the action of enhancers and transcription activators
Bending of the DNA by a protein enables enhancers to influence a promoter hundreds or even thousands of nucleotides away. Specific transcription factors (activators) bind to the enhancer DNA sequences and then to a group of mediator proteins, which in turn bind to general transcription factors and then RNA polymerase II, thus assembling the transcription initiation complex. These protein-protein interactions lead to correct positioning of the complex on the promoter and the initiation of RNA synthesis. Only one enhancer (with three gold control elements) is shown here, but a gene may have several enhancers that act at different times or in different cell types.
Figure 15.11 Cell type-specific transcription.
Both liver cells and lens cells have the genes for making the proteins albumin and crystallin, but only liver cells make albumin (a blood protein) and only lens cells make crystallin (the main protein of the lens of the eye). The specific transcription factors made in a cell determine which genes are expressed. In this example, the genes for albumin and crystallin are shown at the top, each with an enhancer made up of three different control elements. Although the enhancers for the two genes both have a gray control element, each enhancer has a unique combination of elements. All the activator proteins required for high-level expression of the albumin gene are present in liver cells only (left), whereas the activators needed for expression of the crystallin gene are present in lens cells only (right). For simplicity, we consider only the role of activators here, although the presence or absence of repressors may also influence transcription in certain cell types.
Recall that transcription factors, some of which are activators, turn genes on by binding to what? To add on, the addition of nucleotides to the ends of the RNA, with the 5' cap and 3' tail are important for blank binding and translation.
By binding to specific regions of DNA and stimulating gene transcription. To add on, the addition of nucleotides to the ends of the RNA, with the 5' cap and 3' tail are important for Ribosome binding and translation.
Blanks provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery. Once the chromatin of a gene is optimally modified for expression, the initiation of translation/transcription is the next major step at which gene expression is regulated. As in bacteria, the regulation of transcription initiation in eukaryotes involves proteins that bind to DNA and either blank or blank binding of RNA polymerase.
Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery. Once the chromatin of a gene is optimally modified for expression, the initiation of transcription is the next major step at which gene expression is regulated. As in bacteria, the regulation of transcription initiation in eukaryotes involves proteins that bind to DNA and either facilitate or inhibit binding of RNA polymerase.
Coordinate control of dispersed genes in a eukaryotic cell often occurs in response to blank signals from outside the cell. A steroid hormone, for example, enters a cell and binds to a receptor protein, forming a hormone-receptor complex that acts as a transcription repressor/activator (see Figure 5.25). Every gene whose transcription is stimulated by a given steroid hormone, on any chromosome, has a control element recognized by that hormone-receptor complex. This is how estrogen activates a group of genes that stimulate cell division in uterine cells, preparing the uterus for pregnancy.
Coordinate control of dispersed genes in a eukaryotic cell often occurs in response to chemical signals from outside the cell. A steroid hormone, for example, enters a cell and binds to a receptor protein, forming a hormone-receptor complex that acts as a transcription activator (see Figure 5.25). Every gene whose transcription is stimulated by a given steroid hormone, on any chromosome, has a control element recognized by that hormone-receptor complex. This is how estrogen activates a group of genes that stimulate cell division in uterine cells, preparing the uterus for pregnancy.
The expression of different genes by cells with the same genome is called? A typical human cell might express about 20-40% of its protein-coding genes at any given time. Highly differentiated cells, such as muscle or nerve cells, express an even smaller fraction of their genes. So, do most of the cells in a multicellular organism contain many genomes or an identical genome? Also, which cells are the exceptions (consider their location)?
Differential Gene Expression Also, almost all the cells in a multicellular organism contain an identical genome, with cells of the immune system as an exception.
Figure 15.8 A Eukaryotic Gene and Its Transcript
Each eukaryotic gene has a promoter, a DNA sequence where RNA polymerase binds and starts transcription, proceeding "downstream." A number of control elements (gold) are involved in regulating the initiation of transcription; these are DNA sequences located near (proximal to) or far from (distal to) the promoter. Distal control elements can be grouped together as enhancers, one of which is shown for this gene. At the other end of the gene, a polyadenylation (poly-A) signal sequence in the last exon of the gene is transcribed into an RNA sequence that signals where the transcript is cleaved and the poly-A tail added. Transcription may continue for hundreds of nucleotides beyond the poly-A signal before terminating. RNA processing of the primary transcript into a functional mRNA involves three steps: addition of the 5′ cap, addition of the poly-A tail, and splicing. In the cell, the 5′ cap is added soon after transcription is initiated, and splicing occurs while transcription is still under way (see Figure 14.12).
Essentially, post-transcriptional is the control of gene expression at the DNA/RNA level.
Essentially, post-transcriptional is the control of gene expression at the DNA/RNA level.
Eukaryotic RNA Polymerases (II) cannot bind DNA alone! While blank transcription factors are REQUIRED at initiation, distant blank sequences can also affect transcription.
Eukaryotic RNA Polymerases (II) cannot bind DNA alone! While Basal (General) transcription factors are REQUIRED at initiation, distant enhancer (specific transcription factors) sequences can also affect transcription.
Eukaryotic genes that are co-expressed are typically scattered over different chromosomes. Thus, coordinate gene expression depends on every gene of a dispersed group having a varied/specific combination of control elements.
Eukaryotic genes that are co-expressed are typically scattered over different chromosomes. Thus, coordinate gene expression depends on every gene of a dispersed group having a varied/specific combination of control elements.
Who survives longer? Eukaryotic mRNA or prokaryotic mRNA?
Eukaryotic mRNA typically survives longer than prokaryotic mRNA.
Finally, the length of time each protein functions in the cell is strictly regulated by selective blank. Many proteins, such as the cyclins involved in regulating the cell cycle, must be short-lived if the cell is to function appropriately. To mark a protein for destruction, the cell commonly attaches molecules of a small protein called blank (think of quit, but you ain't be quitten!) to the protein, which triggers its destruction by blank complexes.
Finally, the length of time each protein functions in the cell is strictly regulated by selective degradation. Many proteins, such as the cyclins involved in regulating the cell cycle, must be short-lived if the cell is to function appropriately. To mark a protein for destruction, the cell commonly attaches molecules of a small protein called ubiquitin to the protein, which triggers its destruction by protein complexes.
For these genes, the interaction of general transcription factors and RNA polymerase II with a promoter usually leads to only a high/low rate of initiation and many/few RNA transcripts. In eukaryotes, high levels of transcription of these particular genes at the appropriate time and place depend on the interaction of control elements with another set of proteins, which can be thought of as blank transcription factors. Blank transcription factors with enhancers in the DNA.
For these genes, the interaction of general transcription factors and RNA polymerase II with a promoter usually leads to only a high/low rate of initiation and many/few RNA transcripts. In eukaryotes, high levels of transcription of these particular genes at the appropriate time and place depend on the interaction of control elements with another set of proteins, which can be thought of as specific transcription factors. Specific transcription factors with enhancers in the DNA.
Blank proteins for the nucleosome are highly conserved and specialized while Blank proteins will help us form metaphase for the x chromosome until it is highly condensed.
Histone proteins for the nucleosome are highly conserved and specialized while nonhistone proteins will help us form metaphase for the x chromosome until it is highly condensed.
In addition to influencing transcription directly, some activators and repressors blank (ly) affect chromatin structure. Studies using yeast and mammalian cells show that some activators recruit blank that acetylate histones near promoters of specific genes, promoting blank (see Figure 15.7). Some repressors recruit proteins that remove blank groups from histones, leading to reduced transcription, a phenomenon called blank. The recruitment of proteins that modify blank seems to be the most common mechanism of repression in eukaryotic cells.
In addition to influencing transcription directly, some activators and repressors indirectly affect chromatin structure. Studies using yeast and mammalian cells show that some activators recruit proteins that acetylate histones near promoters of specific genes, promoting transcription (see Figure 15.7). Some repressors recruit proteins that remove acetyl groups from histones, leading to reduced transcription, a phenomenon called silencing. The recruitment of proteins that modify chromatin seems to be the most common mechanism of repression in eukaryotic cells.
In all organisms, gene expression is commonly controlled at blank; regulation at this stage often occurs in response to signals coming from outside the cell, such as hormones or other signaling molecules. For this reason, the term gene expression is often equated with blank, for (both/only eukaryotes) bacteria and eukaryotes.
In all organisms, gene expression is commonly controlled at transcription; regulation at this stage often occurs in response to signals coming from outside the cell, such as hormones or other signaling molecules. For this reason, the term gene expression is often equated with transcription, for both bacteria and eukaryotes.
In eukaryotes, the precise control of transcription depends largely on the binding of blanks to DNA control elements. Considering that many genes must be regulated in a typical animal or plant cell, the number of different nucleotide sequences in control elements is surprisingly small/large.
In eukaryotes, the precise control of transcription depends largely on the binding of activators to DNA control elements. Considering that many genes must be regulated in a typical animal or plant cell, the number of different nucleotide sequences in control elements is surprisingly small.
Figure 15.6 Stages in gene expression that can be regulated in Eukaryotic cells.
In this diagram, the colored boxes indicate the processes most often regulated; each color indicates the type of molecule that is affected (blue=DNA, red/orange=RNA, purple=protein). The nuclear envelope separating transcription from translation in eukaryotic cells allows post-transcriptional control (RNA processing) not possible in prokaryotes. Eukaryotes also have a greater variety of control mechanisms before transcription and after translation. Some genes are regulated at multiple stages. A miniature version of this figure accompanies several figures later in the chapter as an orientation diagram.
Epigenetic Inheritance is the inheritance of traits transmitted by mechanisms which are/are not directly involving (involved with) the nucleotide sequence. Whereas mutations in DNA are permanent, modifications to the chromatin can/can't be irreversible/reversed. For example, DNA methylation patterns are largely erased and reestablished during gamete formation.
Inheritance of traits transmitted by mechanisms are not directly involving the nucleotide sequence. Whereas mutations in DNA are permanent, modifications to the chromatin can be reversed. For example, DNA methylation patterns are largely erased and reestablished during gamete formation.
Long stretches of active/inactive DNA, such as that of activated/inactivated mammalian X chromosomes (see Figure 12.8), are usually more blanked than the regions of actively blanked (think of either transcription or translated) DNA.
Long stretches of inactive DNA, such as that of inactivated mammalian X chromosomes (see Figure 12.8), are usually more methylated than the regions of actively transcribed DNA.
Many regulatory mechanisms operate at similar/various stages after transcription (see Figure 15.6). These mechanisms allow a cell to rapidly fine-tune blank expression in response to environmental changes without altering its blank patterns.
Many regulatory mechanisms operate at similar/various stages after transcription (see Figure 15.6). These mechanisms allow a cell to rapidly fine-tune gene expression in response to environmental changes without altering its transcription patterns.
Many signaling molecules, such as nonsteroid hormones and growth factors, bind to receptors on a cell's surface and are located in the cell OR never enter the cell?
Many signaling molecules, such as nonsteroid hormones and growth factors, bind to receptors on a cell's surface and never enter the cell.
Molecules of mRNA do not remain intact forever, as they are broken down by blank enzymes in the cytoplasm, with the timing of the event an important factor in regulating the amounts of various proteins that are produced in the cell. After translation is complete, some polypeptides require alterations before they become functional. Protein-phosphorylating enzymes play an important in the blank, chemical blank and blank of proteins following translation.
Molecules of mRNA do not remain intact forever, as they are broken down by RNA-degrading enzymes in the cytoplasm, with the timing of the event an important factor in regulating the amounts of various proteins that are produced in the cell. After translation is complete, some polypeptides require alterations before they become functional. Protein-phosphorylating enzymes play an important in the cleavage, chemical modification and transport of proteins following translation.
On a smaller scale, the DNA of individual genes is usually less/more heavily methylated in cells in which those genes are/are not expressed. Once methylated, genes usually stay/alter that way through successive cell divisions in a given individual. At DNA sites where one/two strand(s) is already methylated, enzymes methylate the correct daughter strand after each round of DNA replication. In this way, methylation blanks can be inherited.
On a smaller scale, the DNA of individual genes is usually more heavily methylated in cells in which those genes are not expressed. Once methylated, genes usually stay that way through successive cell divisions in a given individual. At DNA sites where one strand(s) is already methylated, enzymes methylate the correct daughter strand after each round of DNA replication. In this way, methylation patterns can be inherited.
One example of blank at the RNA-processing level is blank, in which different mRNA molecules are produced from the same/various primary transcript(s), depending on which RNA segments are treated as exons and which as introns.
One example of regulation at the RNA-processing level is alternative RNA splicing, in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.
Only when the complete blank complex has assembled can the polymerase begin to move along the DNA template strand, producing a complementary strand of blank.
Only when the complete initiation complex has assembled can the polymerase begin to move along the DNA template strand, producing a complementary strand of RNA.
Protein-mediated bending of the DNA brings the bound blank into contact with a group of blank proteins, which in turn interact with general transcription factors at the promoter. These interactions help assemble and position the blank complex on the promoter.
Protein-mediated bending of the DNA brings the bound activators into contact with a group of mediator proteins, which in turn interact with general transcription factors at the promoter. These interactions help assemble and position the initiation complex on the promoter.
Recall that a cluster of proteins called a blank initiation complex assembles on the promoter sequence at the "blank" end of the gene (see Figure 14.9). One of these proteins, blank (think of RNA), then proceeds to transcribe the gene, synthesizing a primary blank transcript (blank). RNA processing includes enzymatic addition of a #′ cap and a blank-A tail, as well as splicing out of introns/exons, to yield a mature mRNA.
Recall that a cluster of proteins called a transcription initiation complex assembles on the promoter sequence at the "upstream" end of the gene (see Figure 14.9). One of these proteins, RNA polymerase II, then proceeds to transcribe the gene, synthesizing a primary RNA transcript (pre-mRNA). RNA processing includes enzymatic addition of a 5′ cap and a poly-A tail, as well as splicing out of introns, to yield a mature mRNA.
Recall that the DNA of eukaryotic cells is packaged with proteins in an elaborate complex known as blank, the basic unit of which is the nucleosome. A nucleosome consists of a cluster of blank amount histone proteins around which the DNA double helix is unwrapped/wrapped (see Figure 13.23). The structural organization of blank not only packs a cell's DNA into a compact form that fits inside the nucleus, but also helps regulate blank expression in several ways. Whether or not a gene is transcribed is affected by the location of nucleosomes along a gene's blank and also the sites where the blank DNA attaches to the protein scaffolding of the chromosome (see Figure 13.23). **Think about what attaches to the protein scaffolding of the chromosome. In addition, genes within highly condensed chromatin (heterochromatin) are usually is/is not expressed. Lastly, chromatin structure and gene expression can be influenced by chemical modifications to the blank proteins and DNA blank. (think of chromatin organization)
Recall that the DNA of eukaryotic cells is packaged with proteins in an elaborate complex known as chromatin, the basic unit of which is the nucleosome. A nucleosome consists of a cluster of eight histone proteins around which the DNA double helix is unwrapped/wrapped (see Figure 13.23). The structural organization of chromatin not only packs a cell's DNA into a compact form that fits inside the nucleus, but also helps regulate gene expression in several ways. Whether or not a gene is transcribed is affected by the location of nucleosomes along a gene's promoter and also the sites where the promoter DNA attaches to the protein scaffolding of the chromosome (see Figure 13.23). In addition, genes within highly condensed chromatin (heterochromatin) are usually is not expressed. Lastly, chromatin structure and gene expression can be influenced by chemical modifications to the histone proteins and DNA nucleotides.
Regulatory proteins are commonly activated or inactivated by the reversible addition of phosphate groups, and proteins destined for the surface of animal cells acquire sugars. Cell-surface proteins and many others must also be transported to target destinations in the cell in order to function. Regulation might occur at any of the steps involved in modifying or transporting a protein.
Regulatory proteins are commonly activated or inactivated by the reversible addition of phosphate groups, and proteins destined for the surface of animal cells acquire sugars. Cell-surface proteins and many others must also be transported to target destinations in the cell in order to function. Regulation might occur at any of the steps involved in modifying or transporting a protein.
Researchers are amassing evidence for the importance of epigenetic information in regulating gene expression. (Epigenetic variations might help explain why one identical twin acquires a genetically based disease, such as schizophrenia, but the other does not, despite their nonidentical/identical genomes). Alterations in normal patterns of DNA methylation are seen in some cancers, where they are associated with inappropriate blank expression. Evidently, enzymes that modify chromatin structure are integral parts of the machinery for regulating translation/transcription.
Researchers are amassing evidence for the importance of epigenetic information in regulating blank expression. (Epigenetic variations might help explain why one identical twin acquires a genetically based disease, such as schizophrenia, but the other does not, despite their identical genomes). Alterations in normal patterns of DNA methylation are seen in some cancers, where they are associated with inappropriate gene expression. Evidently, enzymes that modify chromatin structure are integral parts of the machinery for regulating transcription.
Researchers have identified two types of structural domains that are commonly found in a large number of transcription activators: a DNA-binding domain—a part of the protein's three-dimensional structure that binds to DNA—and one or more activation domains.
Researchers have identified two types of structural domains that are commonly found in a large number of transcription activators: a DNA-binding domain—a part of the protein's three-dimensional structure that binds to DNA—and one or more activation domains.
Specific transcription factors that function as repressors can inhibit gene expression in several different ways. Some repressors bind blank (bind how?) to control element DNA, blocking blank binding. Other repressors interfere with the blank itself so it can't bind the DNA.
Specific transcription factors that function as repressors can inhibit gene expression in several different ways. Some repressors bind directly to control element DNA, blocking activator binding. Other repressors interfere with the activator itself so it can't bind the DNA.
Such molecules can control gene expression indirectly by triggering blank blank pathways that activate particular blank factors (see Figure 5.28). Coordinate regulation in such pathways is the same as for steroid hormones: Genes with the various/same sets of control elements are activated by the varied/same chemical signals. Because this system for coordinating gene regulation is so widespread, biologists think that it probably arose early in blank history.
Such molecules can control gene expression indirectly by triggering signal transduction pathways that activate particular transcription factors (see Figure 5.28). Coordinate regulation in such pathways is the same as for steroid hormones: Genes with the same sets of control elements are activated by the same chemical signals. Because this system for coordinating gene regulation is so widespread, biologists think that it probably arose early in evolutionary history.
Control of gene expression in eukaryotes What is the most important stage in regulating gene expression? Additional: blank processing in the nucleus also provides opportunities for regulating gene expression?
The Initiation of Transcription (is the most important stage) RNA processing in the nucleus also provides opportunities for regulating gene expression.
Figure 15.9 MyoD, a transcription activator
The MyoD protein is made up of two polypeptide subunits (purple and salmon) with extensive regions of αα helix. Each subunit has one DNA-binding domain (lower half) and one activation domain (upper half). The latter includes binding sites for the other subunit and for other proteins. MyoD is involved in muscle development in vertebrate embryos (see Concept 16.1).
The expression of a protein-coding gene is measured by the amount of blank protein a cell makes, and much happens between synthesis of the RNA transcript and the activity of the protein in the cell.
The expression of a protein-coding gene is measured by the amount of functional protein a cell makes, and much happens between synthesis of the RNA transcript and the activity of the protein in the cell.
The final opportunities for controlling gene expression occur after blank. Often, eukaryotic polypeptides must be processed to yield functional protein molecules. For instance, cleavage of the initial insulin polypeptide (pro-insulin) forms the active hormone. In addition, many proteins undergo blank modifications that make them blank.
The final opportunities for controlling gene expression occur after translation. Often, eukaryotic polypeptides must be processed to yield functional protein molecules. For instance, cleavage of the initial insulin polypeptide (pro-insulin) forms the active hormone. Ex of active hormone: (insulin & other growth hormones) In addition, many proteins undergo chemical modifications that make them functional.
The life span of mRNA molecules in the cytoplasm is important in determining the pattern of blank synthesis in a cell. Bacterial mRNA molecules typically are degraded by enzymes within a few minutes. This short life span of mRNAs is one reason bacteria can keep/change their patterns of blank synthesis so quickly in response to blank changes.
The life span of mRNA molecules in the cytoplasm is important in determining the pattern of protein synthesis in a cell. Bacterial mRNA molecules typically are degraded by enzymes within a few minutes. This short life span of mRNAs is one reason bacteria can change their patterns of protein synthesis so quickly in response to environmental changes.
Remember: The location of a gene promoter helps to control the accessibility of blank to transcription factors and RNA blank.
The location of a gene promoter helps the control the accessibility of DNA to transcription factors and RNA Polymerase.
The more distant distal control elements, groupings of which are called blanks, may be thousands of nucleotides upstream or downstream of a gene or even within an intron. Probably should note. *A given gene may have multiple enhancers, each active at a different time or in a different cell type or location in the organism. Each enhancer, however, is generally associated with only that gene and no other.
The more distant distal control elements, groupings of which are called enhancers, may be thousands of nucleotides upstream or downstream of a gene or even within an intron. *A given gene may have multiple enhancers, each active at a different time or in a different cell type or location in the organism. Each enhancer, however, is generally associated with only that gene and no other.
DNA methylation is what? (think of methyl groups and DNA bases)
The presence of methyl groups on the DNA bases (usually cytosine) of plants, animals, and fungi. (The term also refers to the process of adding methyl groups to DNA bases.)
Figure 15.12 Alternative RNA splicing of the troponin T gene
The primary transcript of this gene can be spliced in more than one way, generating different mRNA molecules. Notice that one mRNA molecule has ended up with exon 3 (green) and the other with exon 4 (purple). These two mRNAs are translated into different but related muscle proteins.
There are two types of transcription factors: Blank transcription factors act at the promoter of all genes, while some genes require Blank transcription factors that bind to control elements close to or further away from the promoter.
There are two types of transcription factors: General transcription factors act at the promoter of all genes, while some genes require specific transcription factors that bind to control elements close to or further away from the promoter.
Control of Gene expression in Eukaryotes What is one way Nucleosomes control gene expression?
Through the unpacking and packing of the DNA, which causes a region of DNA to become more or less accessible to the transcription machinery.
To initiate transcription, eukaryotic RNA polymerase requires the assistance of transcription factors. Some transcription factors (such as those illustrated in Figure 14.9) are essential for the transcription of all protein-coding genes; therefore, they are often called blank factors.
To initiate transcription, eukaryotic RNA polymerase requires the assistance of transcription factors. Some transcription factors (such as those illustrated in Figure 14.9) are essential for the transcription of all protein-coding genes; therefore, they are often called general transcription factors.
Quick Question. T/F Transcription alone constitutes gene expression.
Transcription does not alone constitute gene expression.
Translation is another step where gene expression is regulated, most commonly at the blank stage (see Figure 14.18). For some mRNAs, the initiation of translation can be blocked by regulatory proteins that bind to blank sequences or structures within the translated/untranslated region (BLANK) at the 5′ or 3′ end, preventing the attachment of blank. (Recall from Concept 14.3 that both the 5′ cap and the poly-A tail of an mRNA molecule are important for ribosome binding.)
Translation is another step where gene expression is regulated, most commonly at the initiation stage (see Figure 14.18). For some mRNAs, the initiation of translation can be blocked by regulatory proteins that bind to specific sequences or structures within the untranslated region (UTR) at the 5′ or 3′ end, preventing the attachment of ribosomes. (Recall from Concept 14.3 that both the 5′ cap and the poly-A tail of an mRNA molecule are important for ribosome binding.)
You have learned that in bacteria such coordinately controlled genes are often clustered into an operon regulated (initiated) by a blank and further transcribed into an blank molecule. Thus, the genes are expressed together, and the encoded proteins are produced concurrently or separately. With few exceptions, operons that work in this way have been/not been found in eukaryotic cells.
You have learned that in bacteria such coordinately controlled genes are often clustered into an operon regulated by a promoter and transcribed into an mRNA molecule. Thus, the genes are expressed together, and the encoded proteins are produced concurrently. With few exceptions, operons that work in this way have been/not been found in eukaryotic cells.