POB Chapter 16

In negative regulation, binding of a repressor protein prevents transcription. In positive regulation, an activator protein binds DNA to stimulate transcription.

The "decision" regarding which genes to activate involves two types of regulatory proteins that bind to DNA: repressor proteins and activator proteins. In both cases, these proteins bind to the promoter to regulate the gene.

The workhorse protein in the transcription process is, of course, RNA polymerase—specifically, RNA polymerase II for protein-coding genes. RNA polymerase II creates a complementary RNA strand from the code in a DNA template strand. However, RNA polymerase II is unable to bind to DNA and begin transcription on its own. It requires other proteins, called transcription factors, to come into play.

Each general transcription factor has a role in gene expression: TFIIB binds both RNA polymerase and TFIID, and helps identify the transcription initiation site. TFIIF prevents nonspecific binding of the complex to DNA and helps recruit RNA polymerase to the complex; it is similar in function to a bacterial sigma factor. TFIIE binds to the promoter and stabilizes the denaturation of the DNA. TFIIH opens up the DNA for transcription.

Whichever mechanism is used, it must be both responsive to environmental signals and efficient. The earlier the cell intervenes in the process of protein synthesis, the less energy it wastes. Selective blocking of transcription is far more efficient than transcribing the gene, translating the message, and then degrading or inhibiting the protein. While all five mechanisms for regulating protein levels are found in nature, prokaryotes generally use the most efficient one: transcriptional regulation.

Prokaryotes conserve energy and resources by making certain proteins only when they are needed. The protein content of a bacterium can change rapidly when conditions warrant. Based on what you learned about gene expression in Chapter 14, you might suggest several ways in which a prokaryotic cell could shut off the supply of an unneeded protein. The cell could: decrease the rate of transcription of mRNA for that protein; hydrolyze the mRNA after it is made, preventing translation; prevent translation of the mRNA at the ribosome; hydrolyze the protein after it is made; or inhibit the function of the protein.

Epigenetics describes stable changes in gene expression that do not involve changes in DNA sequences. These changes involve modifications of DNA (cytosine methylation) or of histone proteins bound to DNA. Epigenetic changes can be affected by the environment. Large stretches of DNA can be epigenetically modified, leading to inactivtion of many genes.

RNA interference (RNAi): A mechanism for reducing mRNA translation whereby a double-stranded RNA, made by the cell or synthetically, is processed into a small, single-stranded RNA, whose binding to a target mRNA results in the latter's breakdown.

Structural gene: A gene that encodes the primary structure of a protein not involved in the regulation of gene expression. A cluster of genes with a single promoter is called an operon, and the operon that encodes the three lactose-metabolizing enzymes in E. coli is called the lac operon.

Structural genes specify the primary structures (the amino acid sequences) of protein molecules that act as enzymes or cytoskeletal proteins. The three genes are adjacent to one another on the E. coli chromosome. This arrangement is no coincidence: the genes share a single promoter, and their DNA is transcribed into a single, continuous molecule of mRNA. Because this particular mRNA governs the synthesis of all three lactose-metabolizing enzymes, either all or none of these enzymes are made, depending on whether their common message—their mRNA—is present in the cell.

The rate of transcription of this particular gene will be reduced. A mutation in a silencer for a specific gene makes it easier for proteins to bind to it. Which scenario is most likely to occur?

Suppose lactose is in high concentration and glucose is in low concentration in the surrounding media, yet the cell is not taking in much lactose. The lactose that is taken in is quickly metabolized. The most likely explanation for this is a mutation in Correct: the gene coding for β-galactoside permease.

transcription factors. In a vertebrate, the amount of production of β-globin varies tremendously among different cell types, largely because they have different?

A gene that encodes for a protein that is produced in response to oxidative stress Which gene would most likely be under inducible expression control?.

How does a protein recognize a sequence in DNA? As you learned in Key Concept 3.2, the complementary bases in DNA not only form hydrogen bonds with each other, but also can form additional hydrogen bonds with proteins, particularly at points exposed in the major and minor grooves. In this way, an intact DNA double helix can be recognized by a protein motif whose structure: 1. fits into the major or minor groove; 2. has amino acids that can project into the interior of the double helix; and 3. has amino acids that can form hydrogen bonds with the interior bases.

As we have seen, transcription factors with specific DNA-binding domains are involved in the activation and inactivation of specific genes. There are several common structural themes in the *protein domains that bind to DNA. These themes, or structural motifs, consist of different combinations of structural elements (protein conformations) and may include special components such as zinc. One of the common structural motifs is the helix-turn-helix, in which two α helices are connected via a non-helical turn. The interior-facing "recognition" helix interacts with the bases inside the DNA. The exterior-facing helix sits on the sugar-phosphate backbone, ensuring that the interior helix is presented to the bases in the correct configuration.

Proteins that are produced all the time at a constant rate are _______ proteins. Constitutive

Pharmaceutical companies are interested in developing miRNA drugs. How might they work in cancer? (Hint: See Figure 11.23, about oncogene and tumor suppressor proteins.) miRNAs targeted to activated oncogenes will block the translation of target mRNAs that would make proteins that otherwise stimulate cell division.

infect a cell, transcribe and translate their RNA to replicate their genomes, and then package those genomes into viral capsids just before they lyse the cell. Lytic bacterial viruses?

The rate of transcription of this particular gene will be reduced, even when it is needed most. A mutation in an enhancer for a specific gene causes it to be much less able to be bound by proteins. Which scenario is most likely to occur?

The outer shell of a virus is called a? Capsid

Transcription factors are? Proteins that bind to DNA

Some regulatory DNA sequences are positive elements termed enhancers: they bind transcription factors that either activate transcription or increase the rate of transcription. Other regulatory elements are silencers: they bind factors that repress transcription. The combination of transcription factors binding to a gene determines the rate of transcription.

A student claims that transcription factors, regulators, and activators only allow eukaryotic cells to turn on genes when they are needed, but do not help to shut down genes when the genes are not needed. Evaluate the accuracy of the student's statement. B. The statement is incorrect because transcription factors, regulators, and activators help shut down gene expression by their absence.

Like the prokaryotic RNA polymerase, eukaryotic RNA polymerase II cannot simply bind to the promoter and initiate transcription. Rather, it does so only after various general transcription factors have assembled on the chromosome (Figure 16.8). General transcription factors bind to most promoters and are distinct from transcription factors that act only at certain promoters or classes of promoters. First, the protein complex called TFIID ("TF" stands for transcription factor) binds to the TATA box. Binding of TFIID changes both its own shape and that of the DNA, presenting a new surface that attracts the binding of other general transcription factors to form a transcription initiation complex. RNA polymerase II binds only after several other proteins have bound to this complex.

As in prokaryotes, a promoter in a eukaryotic gene is a sequence of DNA near the 5′ end of the coding region, where RNA polymerase binds and initiates transcription. Although eukaryotic promoters are more diverse than those of prokaryotes, many contain a nucleotide sequence similar to the -10 element in prokaryotic promoters. This element is usually located close to the transcription start site and is called the TATA box because it is rich in AT base pairs. The TATA box is the site where DNA begins to denature so that the template strand can be exposed. In addition to the TATA box, eukaryotic promoters typically include multiple regulatory sequences that are recognized and bound by transcription factors: regulatory proteins that help control transcription.

microRNA (miRNA): A small, noncoding RNA molecule, typically about 21 bases long, that binds to mRNA to inhibit its translation.

As you'll see in Chapter 17, less than 5 percent of the genome in most plants and animals codes for proteins. Some of the genome encodes ribosomal RNA and transfer RNAs, but until recently biologists thought that the rest of the genome was not transcribed; some even called it "junk." Recent investigations, however, have shown that some of these noncoding regions are transcribed. The RNAs produced from these regions are often very small and therefore difficult to detect. In both prokaryotes and eukaryotes, these tiny RNA molecules are called microRNA (miRNA).

alternative splicing: A process for generating different mature mRNAs from a single gene by splicing together different sets of exons during RNA processing.

Before the RNA is exported from the nucleus, a splicing mechanism recognizes the boundaries between exons and introns and converts pre-mRNA, which has the introns, into mature mRNA, which does not:

Regulation of protein synthesis—that is, regulation of the concentration of enzymes—is slower but results in greater savings of energy and resources. Protein synthesis is a highly endergonic process, since assembling mRNA, charging tRNA, and moving the ribosomes along mRNA all require the hydrolysis of nucleoside triphosphates such as ATP.

Compounds such as lactose that stimulate the synthesis of a protein are called inducers. The proteins that are produced are called inducible proteins, whereas proteins that are made all the time at a constant rate are called constitutive proteins.

This covalent change in DNA is heritable: when DNA is replicated, a maintenance methylase catalyzes the formation of 5-methylcytosine in the new DNA strand. However, the pattern of cytosine methylation can also be altered, because methylation is reversible: a third enzyme, appropriately called demethylase, catalyzes the removal of the methyl group from cytosine.

Depending on the organism, from 1 to 5 percent of cytosine residues in the organism's DNA are chemically modified by the addition of a methyl group (—CH3) to the 5-carbon, to form 5-methylcytosine (Figure 16.14). This covalent addition is catalyzed by the enzyme DNA methyltransferase and, in mammals, usually occurs in C residues that are adjacent to G residues. DNA regions rich in these doublets are called CpG islands, and are especially abundant in promoters.

Today epigenetics is defined more specifically, referring to the study of changes in gene expression that are prompted without changes in the DNA sequence. Methylation of cytosine bases in DNA can enhance the binding of repressor proteins to promoter regions, resulting in silencing of gene expression. Acetylation and deacetylation of histone proteins alter the affinity of the histones for DNA, changing the accessibility of regions of the DNA to RNA polymerase. Environmental factors can cause epigenetic changes. Some heterochromatin such as the inactive X chromosome in female mammals results from extensive DNA methylation.

Describe positive and negative regulation of gene expression in the bacteriophage λ and HIV life cycles. In the bacteriophage: Phage DNA is injected into the host cell. Early phase genes are transcribed at phage promoters by using DNA sequences similar to those of the host cell (positive regulation). This leads to early protein that binds to host promoters to shut them down (negative regulation). Other early proteins lead host RNA polymerase to transcribe middle and late phage genes (positive regulation). In HIV: HIV RNA is injected into the host cell. HIV reverse transcriptase is activated to make cDNA and integrase to splice cDNA into the host chromosome (positive regulation). Later, host RNA polymerase binds to HIV promoters to make HIV mRNAs (positive regulation). HIV tat protein acts as an anti-terminator for the transcription of HIV genes integrated into the host genome.

HIV is an enveloped virus; it is enclosed within a phospholipid membrane derived from its host cells (a specific type of immune system cell) (Figure 16.13). During infection, proteins in this membrane interact with proteins on the host cell surface, and the viral envelope fuses with the host cell membrane. After the virus enters the cell, its capsid is broken down. The viral reverse transcriptase then uses the virus's RNA template to produce a complementary DNA (cDNA) strand, while at the same time degrading the viral RNA. The enzyme then makes a complementary copy of the cDNA, and the resulting double-stranded DNA is inserted into the host's chromosome by an enzyme appropriately named integrase. The integrated DNA is referred to as the provirus. Both the reverse transcriptase and the integrase are carried inside the HIV virion, along with other proteins needed at the very early stages of infection. Almost every step in the reproductive cycle of HIV is, in principle, a potential target for drugs to treat AIDS. The classes of anti-HIV drugs currently in use include: reverse transcriptase inhibitors that block viral DNA synthesis from RNA (at step 2 in Figure 16.13); integrase inhibitors that block the incorporation of viral DNA into the host chromosome (at step 3); and protease inhibitors that block the posttranslational processing of viral proteins (at step 5).

Eukaryotes are susceptible to infection by various kinds of viruses whose genomes may consist of RNA or DNA. A subgroup of RNA viruses are called retroviruses. DNA viruses. Many viral particles contain double-stranded DNA. However, some contain single-stranded DNA, and a complementary strand is made after the viral genome enters the host cell. Like some bacteriophages, DNA viruses that infect eukaryotes are capable of undergoing both lytic and lysogenic life cycles. Examples include the herpes viruses and papillomaviruses (which cause warts). RNA viruses. Some viral genomes are made up of RNA that is usually, but not always, single-stranded. The RNA is translated by the host's machinery to produce viral proteins, some of which are involved in replication of the RNA genome. The influenza virus has an RNA genome. Retroviruses. As we described in Key Concept 14.2, a retrovirus is an RNA virus that carries a gene for reverse transcriptase, a protein that synthesizes DNA from an RNA template. The *retrovirus uses this protein to make a DNA copy of its genome, which then becomes integrated into the host genome. The integrated DNA acts as a template for both mRNA and new viral genomes. HIV is a retrovirus that infects cells of the immune system and causes acquired immune deficiency syndrome (AIDS).

What are the ways whereby transcription factors regulate the rate of gene transcription? General transcription factors bind to the promoter and to RNA polymerase in a complex to direct RNA polymerase to the promoter to initiate transcription and locally denature DNA so that the template strand is available for base pairing during RNA synthesis. Specific transcription factors bind to specific promoters or promoters with recognition sequences. Other transcription factors bind to enhancer sequences that can be far from the actual promoter and induce DNA to bend to attract the rest of the initiation complex for transcription.

Eukaryotes can increase or decrease transcription in various ways to help regulate gene expression. A number of general transcription factors must bind to a eukaryotic promoter before RNA polymerase will bind to it and begin transcription. Other, specific transcription factors bind to regulatory DNA sequences and interact with the RNA polymerase complex to control differential gene expression.

Shared regulatory sequences enable organisms to respond to stress—plants, for example, use shared regulatory sequences to respond to drought. Under conditions of drought stress, a plant must simultaneously synthesize several proteins whose genes are scattered throughout the genome. To coordinate expression of the stress response, each of the associated genes has a specific regulatory sequence near its promoter called the stress response element (SRE). A transcription factor binds to this element and stimulates mRNA synthesis (Figure 16.10). The stress response proteins not only help the plant conserve water, but also protect the plant against excess salt in the soil and freezing. This finding has considerable importance for agriculture because crops are often grown under less than optimal conditions or are affected by weather.

How do eukaryotic cells coordinate the regulation of several genes whose transcription must be turned on at the same time? Prokaryotes solve this problem by arranging multiple genes in an operon that is controlled by a single promoter, and by using sigma factors to recognize particular classes of promoters. Most eukaryotic genes have their own separate promoters, and genes that are coordinately regulated may be far apart. In these cases, the expression of genes can be coordinated if they share regulatory sequences that bind the same transcription factors.

How does X chromosome inactivation occur, and why is it believed to occur? X chromosome inactivation is shown in Figure 16.16. The Xist gene on the X chromosome is transcribed to make a short RNA that binds to the rest of the X chromosome, inhibiting transcription of the other genes. Chromosome proteins bind to the inactive X chromosome, causing heterochromatin to form and inhibiting gene expression. X chromosome inactivation is believed to occur in order to balance the expression of X-linked genes between males (XY) and females (XX) since the Y chromosome does not usually contain X-linked genes.

How do histone modifications affect transcription? Histone proteins are positively charged and bind to DNA, generally blocking transcription. Acetylation of histones neutralizes the positive charge and thus the histones do not bind to DNA as tightly, which opens up the chromatin structure for transcription. By contrast, histone deacetylation removes acetyl groups, restoring positive charges on histones so transcription is repressed.

Viruses are small infectious agents that infect cellular organisms and that cannot reproduce outside their host cells. Most virus particles, called virions, consist of only two or three components: the genetic material made up of DNA or RNA, a protein coat that protects the genetic material, and in some cases, an envelope of lipids that surrounds the protein coat. As we will see in this section, viral genomes include sequences that encode regulatory proteins. These proteins "hijack" the host cells' transcriptional machinery, allowing the viruses to complete their reproductive cycles.

How do transcription factors recognize specific DNA sequences? Proteins such as transcription factors fit into the DNA double helix by structural motifs, and their amino acids may form hydrogen bonds with bases on the interior of the double helix. The sequences of amino acids (proteins) and of bases (DNA) are specific so that only certain proteins bind to certain DNA sequences.

What is the role of the proteasome? The proteasome binds to proteins that are targeted with ubiquitin for breakdown. Within the proteasome are proteases that hydrolyze targeted proteins.

How does the three-dimensional structure of mRNA contribute to the regulation of its expression? mRNA can fold back on itself by hydrogen bonding of complementary bases, forming looped structures. These structures can bind to proteins that then inhibit translation at the ribosome.

There are numerous mechanisms to control the transcription of operons; we will describe three examples: An inducible operon regulated by a repressor protein A repressible operon regulated by a repressor protein An operon regulated by an activator protein

In addition to the promoter, an operon has other regulatory sequences that are not transcribed. A typical operon consists of a promoter, an operator, and two or more structural genes. The operator is a short stretch of DNA that lies between the promoter and the structural genes. It can bind very tightly with regulatory proteins that either activate or repress transcription.

Enhancer regions are yet other transcriptionally important regions on the DNA, and they are frequently located some distance from the promoter, often tens of thousands of base pairs away. Activator proteins bind to enhancers, and then attach to the transcription-initiation complex, stimulating it strongly. If a cell has all of the appropriate DNA sequences, and if all the necessary regulator proteins and transcription factors are present and in place, transcription begins and the gene is expressed. Otherwise, no transcription or very little transcription takes place, and the gene is silent. RNA polymerase II requires other transcription factors in order to bind to a promoter site.

In eukaryotes, a number of proteins, called transcription factors, must bind to a promoter before RNA polymerase II can bind and initiate transcription. The first transcription factor to bind has been named TFIID. TFIID binds to a region of the promoter called the TATA box, which contains the sequence TATAT. Following TFIID binding, a succession of other transcription factors and RNA polymerase II bind, forming an initiation complex. Although this complex is often capable of initiating transcription, for many genes, other proteins are required for a high rate of transcription. In the promoter, there may be a region of DNA that can bind to regulator proteins. A regulator protein binds to the regulator region and to the transcription initiation complex, thereby activating it.

Which AIDS treatment works by preventing the synthesis of viral DNA? Correct: Reverse transcriptase inhibitors

In eukaryotic cells, a positive regulator or enhancer Correct: binds to transcription factors to increase transcription rates.

activator: A transcription factor that stimulates transcription when it binds to a gene's promoter. (Contrast with repressor.)

In negative control, transcription is decreased in the presence of a repressor protein. E. coli can also use positive control to increase transcription through the presence of an activator protein.

lysogeny: A form of viral replication in which the virus becomes incorporated into the host chromosome and remains inactive. Also called a lysogenic cycle. (Contrast with lytic cycle.) Prophage: (pro´ fayj) The noninfectious units that are linked with the chromosomes of the host bacteria and multiply with them but do not cause dissolution of the cell. Prophage can later enter into the lytic phase to complete the virus life cycle.

LYSOGENIC CYCLE Like all nucleic acid genomes, those of viruses can mutate and evolve by natural selection. Some viruses have evolved an advantageous process called lysogeny that postpones the lytic cycle. In lysogeny, the viral DNA becomes integrated into the host DNA and becomes a prophage (Figure 16.12). As the host cell divides, the viral DNA gets replicated along with that of the host. The prophage can remain inactive within the bacterial genome for thousands of generations, producing many copies of the original viral DNA.

LYTIC CYCLE... The viral genome contains a promoter that binds host RNA polymerase. In the early stage (1-2 min after phage DNA entry), viral genes that lie adjacent to this promoter are transcribed (positive regulation). These early genes often encode proteins that shut down host transcription (negative regulation) and stimulate viral genome replication and transcription of viral late genes (positive regulation). Three minutes after DNA entry, viral nuclease enzymes digest the host's chromosome, providing nucleotides for the synthesis of viral genomes. In the late stage, viral late genes are transcribed (positive regulation); they encode the proteins that make up the capsid (the outer shell of the virus) and other protein components of the virus and enzymes that lyse the host cell to release the new virions. This begins 9 min after DNA entry and 6 min before the first new phage particles appear.

LYTIC CYCLE The Hershey-Chase experiment (see Figure 13.4) involved a typical lytic viral reproductive cycle, so named because soon after infection, the host cell bursts (lyses), releasing progeny viruses. In this cycle, the viral genetic material takes over the host's synthetic machinery for its own reproduction immediately after infection. In the case of some bacteriophages, the process is extremely rapid—within 15 minutes, new phage particles appear in the bacterial cell. Ten minutes later, the "game is over," and these particles are released from the lysed cell. What happened? At the molecular level, the reproductive cycle of a typical lytic virus has two stages: early and late...

Condensation of the inactive X chromosome makes its DNA sequences physically unavailable to the transcriptional machinery. Most of the genes of the inactive X are heavily methylated. However, one gene, Xist (for X inactivation-specific transcript), is only lightly methylated and is transcriptionally active. On the active X chromosome, Xist is heavily methylated and not transcribed. The RNA transcribed from Xist binds to the X chromosome from which it is transcribed, and this binding leads to a spreading of inactivation along the chromosome. The Xist RNA transcript is an example of interference RNA (Figure 16.16B).

Like single genes, large regions of chromosomes or even entire chromosomes can have distinct patterns of DNA methylation. Under a microscope, two kinds of chromatin can be distinguished in the stained interphase nucleus: euchromatin and heterochromatin. The euchromatin appears diffuse and stains lightly; it contains the DNA that is transcribed into mRNA. Heterochromatin is condensed and stains darkly; any genes it contains are generally not transcribed.

How do miRNAs and siRNAs regulate gene expression? miRNAs and siRNAs can bind by base pairing to target mRNAs and prevent their translation because tRNA cannot bind; or the inhibitor RNAs can bind to pre-mRNA in the nucleus and lead to its hydrolysis by RNase; or the inhibitor RNAs can bind to DNA at the transcription site and block RNA polymerase from working for transcription.

One of the most important means of posttranscriptional regulation is alternative RNA splicing, which allows more than one protein to be made from a single gene. The stability of mRNA in the cytoplasm can also be regulated. MicroRNAs, siRNAs, mRNA modifications, and translational repressors can prevent mRNA translation. Proteins in the cell can be targeted for breakdown by ubiquitin and then hydrolyzed in proteasomes.

Gene expression in prokaryotes is most commonly regulated through control of transcription. An operon consists of a set of closely linked structural genes and a set of DNA sequences (promoter and operator) that control their transcription. Operons can be regulated by both negative and positive controls. Sigma factors control the expression of specific classes of prokaryotic genes that share recognition sequences in their promoters.

Sigma factors are the proteins in prokaryotic cells that bind to RNA polymerase and direct it to specific classes of promoters. The RNA polymerase must be bound to a sigma factor before it can recognize a promoter and begin transcription.

all the enzymes of the lactose operon are present in very small quantities? When E. coli is grown in a medium with low levels of lactose

Suppose a region of a chromosome is gene dense and stains lightly. What is it? Euchromatid

REGULATION OF TRANSLATION There are a variety of ways in which the translation of mRNA can be regulated. One way, as we saw in the previous section, is to inhibit translation with siRNAs and miRNAs. A second way involves modification of the guanosine triphosphate cap on the 5′ end of the mRNA (see Key Concept 14.4). An mRNA that is capped with an unmodified GTP molecule is not translated. For example, stored mRNAs in the egg cells of the tobacco hornworm moth are capped with unmodified GTP molecules and are not translated. After the egg is fertilized, however, the caps are modified, allowing the mRNA to be translated to produce the proteins needed for early embryonic development. In another system, repressor proteins directly block translation. For example, in mammalian cells the protein ferritin binds free iron ions (Fe2+). When iron is present in excess, ferritin synthesis rises dramatically, but the amount of ferritin mRNA remains constant, indicating that the increase in ferritin synthesis is due to an increased rate of mRNA translation. Indeed, when the iron level in the cell is low, a translational repressor protein binds to the 5′ noncoding region of ferritin mRNA and prevents its translation by blocking its attachment to a ribosome. When the iron level rises, some of the excess Fe2+ ions bind to the repressor and alter its three-dimensional structure, causing the repressor to detach from the mRNA and allowing translation to proceed (Figure 16.19). The binding site for the translational repressor on mRNA is a stem-and-loop region with sufficient three-dimensional structure for recognition by a protein or small molecule.

The concentrations of these proteins must therefore have been determined by factors acting after the mRNA was made. Cells have two major ways to control the amount of a protein after transcription: Page 355 They can regulate translation of the protein's mRNA. They can regulate how long a newly synthesized protein persists in the cell (protein longevity). REGULATION OF PROTEIN LONGEVITY The protein content of a cell at any given time is a function of both protein synthesis and protein degradation. Certain proteins can be targeted for destruction in a chain of events that begins when an enzyme attaches a 76-amino acid protein called ubiquitin (so named because it is ubiquitous, or widespread) to a lysine residue of the protein to be destroyed. Other ubiquitins then attach to the primary one, forming a polyubiquitin chain. The protein-polyubiquitin complex then binds to a huge protein complex called a proteasome (from protease + soma, "body") (Figure 16.20). Upon entering the proteasome, the polyubiquitin is removed and ATP energy is used to unfold the target protein. Three different proteases then digest the protein into small peptides and amino acids.

Prokaryotic promoters generally have two sites for these recognition sequences, which begin 10 and 35 base pairs upstream of the transcription start site (the -10 element and the -35 element). Different classes of promoters have different recognition sequences at these two sites. The largest class consists of promoters for "housekeeping genes," which are all the genes that are normally expressed in actively growing cells. In these genes, the -10 element is 5′-TATAAT-3′, and the -35 element is 5′-TTGACAT-3′ (N stands for any nucleotide)

The promoter binds RNA polymerase so that the enzyme can then catalyze the synthesis of RNA from a gene-encoding region of DNA. The promoter also orients the polymerase so that it transcribes the correct one of the two DNA strands. Not all promoters are identical, but they all have similar sequences by which they are recognized by the RNA polymerase and other proteins.

n prokaryotes, transcription and translation are often coupled in time and space. But in eukaryotes they are separated. What are the advantages of the nucleus as a compartment? An advantage of the nucleus is compartmentation—the separation of transcription/processing and translation. This allows for finer regulation of gene expression. Also, the nucleus is protected from nucleases in the cytoplasm, which might hydrolyze mRNA and reduce its lifetime as it is made.

The rate of transcription of a eukaryotic gene depends on the combination of transcription factors and other proteins binding to regulatory sequences associated with the gene. DNA binding proteins have certain structural motifs in common that are important in their binding function. Eukaryotic genes whose expression is coordinated share the same transcription factors.

(A) When lactose is absent, the synthesis of enzymes for its metabolism is inhibited. (B) Lactose (the inducer) leads to synthesis of the enzymes in the lactose-metabolizing pathway by binding to the repressor protein and preventing its binding to the operator. co-repressor: In the regulation of bacterial operons, a molecule that binds to the repressor, causing it to change shape and bind to the operator, thereby inhibiting transcription.

The repressor protein has two binding sites: one for the operator and the other for the inducer. The environmental signal that induces the lac operon (for example, in the human digestive tract) is lactose, but the actual inducer is allolactose, a molecule that forms from lactose once it enters the cell. In the absence of the inducer, the repressor protein fits into the major groove of the operator DNA and recognizes and binds to a specific nucleotide base sequence. This prevents the binding of RNA polymerase to the promoter, and the operon is not transcribed (Figure 16.5A). When the inducer is present, it binds to the repressor and changes the shape of the repressor. This change in three-dimensional structure (conformation) prevents the repressor from binding to the operator. As a result, RNA polymerase can bind to the promoter and start transcribing the structural genes of the lac operon

What is the function of the operator region of the trp operon? B. Provides a site for the repressor to bind

The trp operon is an example of a repressible system, meaning that the operon is automatically turned on unless a repressor becomes active and turns it off. The lac operon is an example of an inducible system. This operon is always turned off unless an inducer—lactose—is available from the environment; lactose triggers the expression of genes in this operon.

catabolite repression: In the presence of abundant glucose, the diminished synthesis of catabolic enzymes for other energy sources.

This is an example of catabolite repression, a system of gene regulation in which the presence of the preferred energy source represses other catabolic pathways.

2 TYPES OF OPERONS... In inducible systems, the substrate of a metabolic pathway (the inducer) interacts with a regulatory protein (the repressor), rendering the repressor incapable of binding to the operator and thus allowing transcription. In repressible systems, the product of a metabolic pathway (the co-repressor) binds to a regulatory protein, which is then able to bind to the operator and block transcription.

Usually, inducible systems control *catabolic pathways (which are turned on only when the substrate is available) Repressible systems control anabolic pathways (which are turned on until the concentration of the product becomes excessive). In both systems, the regulatory protein is a repressor that functions by binding to the operator.

Which HIV gene product is involved in regulation at the transcription elongation stage? TAT

Viruses are composed of? Nucleic acids and proteins

Another mechanism for epigenetic gene regulation is the alteration of chromatin structure, or chromatin remodeling. As we saw in Chapter 11, DNA is packaged with histone proteins into nucleosomes (see Figure 11.8), which can make DNA physically inaccessible to RNA polymerase and the rest of the transcription apparatus. Each histone protein has a "tail" of approximately 20 amino acids at its N terminus that sticks out of the compact structure and contains certain positively charged amino acids (notably lysine). Ordinarily there is strong ionic attraction between the positively charged histone proteins and DNA, which is negatively charged because of its phosphate groups. However, enzymes called histone acetyltransferases can add acetyl groups to these positively charged amino acids, thus changing their charges. Reducing the positive charges of the histone tails reduces the affinity of the histones for DNA, opening up the compact nucleosome (Figure 16.15). Additional chromatin remodeling proteins can bind to the loosened nucleosome-DNA complex, opening up the DNA for gene expression. Histone acetyltransferases can thus activate transcription.

What is the effect of DNA methylation? During replication and transcription, 5-methylcytosine behaves just like plain cytosine: it base-pairs with guanine. But extra methyl groups in a promoter attract proteins that bind methylated DNA. These proteins are generally involved in the repression of gene transcription; thus heavily methylated genes tend to be inactive. This form of genetic regulation is epigenetic because it affects gene expression patterns without altering the DNA sequence. DNA methylation is important in development from egg to embryo.

Alternative splicing in humans is generally regulated by binding between Correct: RNA and proteins..

Xist and X inactivation Which process(es) involve(s) interference RNA?