Biology Chapter 8

Which of the following is considered a housekeeping protein? Choose one: A. hemoglobin B. an antibody C. cortisol D. RNA polymerase E. insulin

D. Proteins common to all the cells of a multicellular organism are called housekeeping proteins. For example, all cells must carry out gene expression, which requires RNA polymerase. Thus, RNA polymerase is considered a housekeeping protein. Proteins that are produced only in certain cell types and give those cells their specialized function are not housekeeping proteins. Examples of these specialized gene products include hormones like insulin and cortisol or the antibodies produced by B lymphocytes of the immune system.

lthough all of the steps involved in expressing a gene can in principle be regulated, what is the most important stage of control for most genes? Choose one: mRNA degradation transcription initiation RNA processing RNA transport and localization mRNA translation

Transcription initiation Regulation of gene expression can occur at multiple stages as shown in the figure. However, the most important stage for control of gene expression is at the earliest point, transcriptional control (step 1 in the figure). This should make sense intuitively because without the synthesis of an RNA transcript, there can be no production of the protein coded for by that gene. It's reasonable to think of step 1 as an "on/off switch" while the other stages are fine-tuning the level of expression.

Name the seven steps at which gene expression can be regulated in eukaryotes

1. Transcriptional control (most important) 2. RNA processing control 3. mRNA transport and localization control 4. mRNA degradation control 5. Translation control 6. Protein degradation control 7. Protein activity control

Clinicians and the public are excited about the prospects of replacing damaged and diseased tissues with patient-derived (autologous) cells. Using autologous cells, as opposed to cells from a donor, avoids complications such as immune rejection. What series of steps could lead to the production of smooth muscle cells from the fibroblasts of a patient? 1 Grow iPS cells in culture 2 Obtain fibroblasts 3 Use transcription factors to convert iPS cells to smooth muscle cells 4 Use transcription factors to convert fibroblasts to iPS cells

2, 4, 1, 3 The transcription factors Oct4, Sox2, and Klf4 can cause fibroblasts to de-differentiate into induced pluripotent stem (iPS) cells. These iPS cells can be further reprogrammed to take on different cell fates via activation of tissue-specific transcription factors. The conversion of fibroblasts to iPS cells and finally to different tissue types is seen as a viable strategy for creating patient-specific cells for disease treatment, as reviewed in a 2014 article by Fox and colleagues

How do transcription regulators, general transcription factors, and RNA polymerase gain access to DNA wrapped up in a nucleosome?

Activators and repressors can recruit chromatin-modifying proteins such as chromatin-remodeling complexes or histone-modifying enzymes (histone acetyltransferases and histone deacetylases)

How many transcription regulators control the 24,000 genes for a human?

Approximately 1000

What are transcription regulators

Bind to regulatory DNA sequences to have an effect on transcription.

What prevents a transcription regulator-bound to the control region of one gene-from looping in the wrong direction and inappropriately influencing the transcription of a neighboring gene?

Chromosomal DNA of plants and animals is organized into loops by chromosome loop-forming clamp proteins (topological associated domains or TADs). This holds individual genes and their regulatory genes in close proximity.

What are operons? Are they found usually in bacteria or eukaryotes?

Coordinately regulated gene clusters (regulated by one promoter). They are usually found in bacteria

How does DNA methylation work for vertebrate cells and how does it generate cell memory?

Cytosine nucleotides that fall next to a guanine (5'-CG-3') are methylated, turning off the affected genes by attracting certain proteins. This methylation is passed on to daughter cells by the action of an enzyme that copies the methylation patterns on the parent DNA strand to the daughter strand as it is synthesized.

What are the sites that eukaryotic gene activators bind to called? How do these sites differ from the sites for prokaryotic activators in terms of location?

Enhancers. They can be thousands of nucleotides upstream or downstream of the gene's promoter.

How does the modification of histones generate cell memory?

Enzymes responsible for histone modifications can bind to the parental histones and confer the same modifications to the new histones nearby (each daughter double helix receives half of its parent's histone proteins).

What are iPS cells

Induced pluripotent stem cells. The combination of specific transcription regulators can be used to coax differentiated cells to de-differentiate into iPS cells, which can then be differentiated again.

Where do most transcription regulators insert themselves in the DNA?

Into the major groove

What is the transcription initiation site, and where is it located?

It is where RNA synthesis begins. It is located in the promoter along with nearby sequences that contain recognition sites for proteins that associate with RNA polymerase (sigma factor in bacteria and general transcription factors in eukaryotes)

What does it mean for a cell to be terminally differentiated?

It will never divide again once it has been differentiated (skeletal muscle cells and neurons)

How do eukaryotic repressor proteins decrease transcription rates?

Prevent assembly of the transcription initiation complex

What is the difference between a transcriptional repressor protein and a transcriptional activator protein. What kind of promoters (weak or strong/inefficient or efficient) do activators usually work on? What about repressors?

Repressors switch off genes in their active form while activators turn on genes in their active form. Activators work on inefficient promoters while repressors work on efficient promoters.

How can enhancer sequences impact transcription if they are so far away? How does the activator protein enhance the rate of transcription?

The DNA between the enhancer and the promoter loops out, bringing the activator protein into close proximity with the promoter. The activator protein attracts RNA polymerase and the general transcription factors to the promoter, with the large protein complex named Mediator serving as an adaptor to close the loop.

Describe reprogramming of cells

The addition of certain transcription regulator(s) can cause a differentiated cell, such as a fibroblast, to form a different cell type, such as a musclelike cell. Introduction of the transcription regulator MyoD into fibroblasts can cause this exact change.

Describe the lac operon

The lac operon is controlled by a Lac repressor and a CAP activator. It controls genes that encode proteins required to import and digest lactose. Thus, for the operon to be on, lactose must be present, but glucose must be absent as well. This corresponds to the Lac repressor being inactivated as a result of binding to allolactose and the CAP activator being activated by binding to cAMP.

What is cell memory?

The patterns of gene expression responsible for a particular cell type are "remembered" and passed on to daughter cells.

What is combinatorial control?

The process by which groups of transcription regulators work together to determine the expression of a single gene.

Describe the RITS complex

The siRNAs produced by Dicer are packaged into a RITS complex (RNA-induced transcriptional silencing). The single-stranded siRNA is used to attach to complementary RNA sequences as they emerge from an actively transcribing RNA polymerase. The RITS complex then attracts proteins that covalently modify nearby histones in a way that promotes heterochromatin formation, thus blocking further transcription initiation.

How do small interfering RNAs (siRNAs) usually regulate gene expression?

They are involved in RNA interference (RNAi), in which long, double-stranded RNA typical of viruses and transposable genetic elements is targeted. A protein called Dicer, which also generates the double-stranded intermediate in miRNA production, cuts the RNA into short fragments named small interfering RNAs. These pieces are taken up by RISC proteins (which can carry miRNA), and one strand is discarded. The remaining single strand is used to seek and destroy complementary RNA sequences.

How do long noncoding RNAs serve as scaffolds? Give an example of this

They form specific three-dimensional structures via complementary base pairing. The RNA molecule in telomerase holds different protein subunits together.

Determine whether the following statement is true or false: Master regulators such as Ey in Drosophila are so powerful that they can even activate their regulatory networks outside the normal location.

True Master regulator genes, such as Ey in Drosophila, are able to induce the expression of a cascade of additional regulatory genes and even result in the formation of complex organs, such as the eye. During normal development, the expression of these master regulators is confined to the precise anatomical location and cell type to result in the proper formation of the organ. However, the power of regulator genes like Ey can be demonstrated experimentally by inducing their expression in atypical locations. As shown in the image in this question, expression of Ey alone in cells that will give rise to the leg will result in the formation of an eye structure on the leg.

Describe the trytophan operator

When concentration of tryptophan is low, the trp. repressor is not bound to tryptophan and is thus inactive. The genes are expressed. When concentrations of tryptophan are high, the repressor is bound to tryptophan and is thus active. It binds to the operator within the promoter, blocking access of RNA polymerase to the promoter. As it changes shape due to the binding of tryptophan, the repressor is an allosteric protein

What is epigenetic inheritance?

When patterns of gene expression are transmitted from parent to daughter cell without altering the actual nucleotide sequence of the DNA. The cell-memory mechanisms are forms of epigenetic inheritance.

Which of the following statements is/are true of long noncoding RNAs? Choose one or more: A. They can trigger the activity of histone acetyltransferases. B. They are involved in X chromosome inactivation. C. They can regulate the translation and stability of mRNAs. D. They can silence genes by promoting the formation of euchromatin.

B,C Long noncoding RNAs are involved in X chromosome inactivation and can regulate the translation and stability of mRNAs. For example, Xist is a long noncoding RNA that remains nearby the X chromosome after transcription and recruits chromatin-remodeling enzymes that condenses one of the X chromosomes in females. Alternatively, long noncoding RNAs can act as scaffolds by virtue of their ability fold upon themselves and assume unique conformations. Indeed, the RNA in telomerase is believed to function as a scaffold for protein subunits.

Researchers assayed the activity of enzyme F in three different types of tissue from the same mouse by determining the amount of enzyme product produced per milligram of tissue per unit time. As shown in the graph below, results indicate more product generation in the liver compared to the kidney and muscle samples. Which of the following factors might explain the different results among the three tissues? Choose one or more: A. differences in the DNA content among the tissue types B. differences in the post-translational modifications of the enzyme among the tissue types C. differences in the transcription of the gene encoding the enzyme among the tissue types D. differences in the translation of the mRNA encoding the protein among the tissue types

B,C,D As seen in the figure below, there are many steps from DNA to active protein and gene expression can be controlled at any of these. Step 1, transcriptional control, is quite common and is the most energy efficient, but it takes the longest amount of time to produce an active protein. In contrast, control at step 7 can quickly lead to active protein but is more energy intensive.

Using powerful new sequencing technologies, investigators can now catalog every RNA molecule made by a cell and determine at what quantities these RNAs are present. In an experiment, researchers measured the relative quantities of two different mRNAs—one transcribed from gene A, the other from gene B—in two different cell types. Gene B is expressed in both the liver and the brain whereas gene A is expressed in the brain but not in the liver. Which most likely encodes a housekeeping protein? Choose one: A. gene A only B. gene B only C. neither gene D. both genes

B. Because gene B is expressed in both the liver and the brain, it could encode a housekeeping protein, which is the description of a gene product/protein that is found in all cells of a multicellular organism. Gene A, on the other hand, is expressed in the brain but not in the liver, which is consistent with a pattern of differential expression. However, an examination of additional cell types would be necessary to more conclusively support the prediction that gene B codes for a housekeeping protein. RNA polymerase, which is necessary to synthesize RNA from a DNA template, is an example of a housekeeping protein, as all cells utilize transcription to express genes.

Which would be the best method for determining which genes are being transcribed in a particular cell type? Choose one: A. DNA sequencing B. RNA sequencing (RNA seq) C. X-ray crystallography D. NMR spectroscopy E. electron microscopy

B. RNA sequencing, or "RNA seq," is a new, powerful technique that allows researchers to catalog the genes being transcribed by a particular cell type. From these types of studies, researchers have determined that a differentiated human cell expresses between 5000 and 15,000 out of a total of approximately 19,000 genes. It may seem like the range of genes expressed is quite large, but it is important to remember that even differentiated cells are sensitive to environmental stimuli, and therefore the mRNAs present in the cell are constantly changing in response to these signals. Furthermore, different cell types have different protein production needs. Together, these factors account for the wide range of expressed genes.

To reinforce cell identity, vertebrate cells can methylate which nucleotide? Choose one: A. any guanine B. guanine that falls next to cytosine in the sequence CG C. cytosine that falls next to guanine in the sequence CG D. any cytosine E. any cytosine or guanine

C. DNA methylation occurs in vertebrates on particular cytosine nucleotides located next to a guanine nucleotide in the sequence 5'-CG-3.' This modification is one of the ways that differentiated cells maintain their differentiated identity through rounds of cell division, because heavily methylated genes will not be transcribed. Additionally, methylation patterns are preserved through rounds of DNA replication because the enzyme that carries out methylation uses the pattern found on the parental strand of a newly replicated DNA molecule to add methyl groups to the appropriate cytosine nucleotides on the daughter DNA strand. Maintaining cell memory through DNA methylation is an example of a epigenetic inheritance.

Which of the following cell types, when fully differentiated, does not divide to form new cells? Choose one: A. fibroblasts B. liver cells C. smooth muscle cells D. skeletal muscle cells

D. All of the cell types listed in this question are examples of differentiated cells. However, only skeletal muscles are terminally differentiated, meaning that they no longer undergo cell division. The other cell types exhibit cell memory, meaning that when they divide, their daughter cells will have the same differentiated phenotype of the original parental cell.

How can untranslated regions control whether and how often the mRNA is translated for prokaryotes and for eukaryotes?

For prokaryotes, the ribosome binding sequence (Shine-Dalgarno sequence) forms base pairs with the rRNA in the small subunit, positioning the initiating AUG codon within the ribosome. This sequence can be blocked or exposed to control translation. In eukaryotes, if repressor proteins bind to certain sequences in the 5' UTR region, the ribosome is prevented from finding the first AUG. These repressors can be inactivated to initiate translation.

What is the impact of transcription regulators binding as dimers?

It doubles the area of contact with the DNA, thereby increasing the potential strength and specificity of the DNA interaction.

Describe Xist

It is a long noncoding RNA which is produced by only one of the X chromosomes in the female nucleus. The transcript sticks around, coating the chromosome and attracting enzymes and chromatin-remodeling complexes that promote the formation of heterochromatin.

Describe Ey

It is a master transcription regulator, meaning that some of the genes controlled by Ey encode additional transcription regulators which control the expression of other genes. It triggers the differentiation of all the specialized cell types that come together to form the eye.

How does miRNA regulate gene expression?

It is packaged with specialized proteins to form a RNA-induced silencing complex (RISC) which can bind to mRNAs complementary to the miRNA and either degrade it with a nuclease or block its translation and deliver it to a region of the cytosol where other nucleases degrade it.

Define and name some regulatory RNAs

They help regulate gene expression. MicroRNAs (miRNAs), small interefering RNAs, and long noncoding RNAs

How do positive feedback loops generate cell memory? Name some regulators that participate in positive feedback loops

A master transcription regulator will activate transcription of its own gene, in addition to that of other cell-type specific genes. When a cell divides, the regulator is distributed to both daughter cells, where the regulator stimulates the feedback loop. The Ey protein and the regulators involved in the generation of ES (embryonic stem) and iPS cells.

The maltose operon contains genes that code for proteins that catabolize the disaccharide maltose. Similar to the Lac operon, which is only efficiently transcribed in the presence of lactose, the maltose operon is only efficiently transcribed in the presence of maltose. How might induction of the maltose operon in response to maltose be achieved? Choose one or more: A. Maltose causes an activator to bind an operon with an inefficient promoter. B. Maltose removes a repressor from an operon with an efficient promoter. C. Maltose removes an activator from an operon with an inefficient promoter. D. Maltose causes an activator to bind an operon with an efficient promoter. E. Maltose causes a repressor to bind an operon with an efficient promoter.

A,B There are different ways to accomplish operon induction: (1) the sugar inducer can remove a repressor from an operon with an efficient promoter (releasing the brakes, in a sense), or (2) the inducer can cause an activator to bind to an operon with an inefficient promoter (stepping on the gas pedal). Cells use both of these mechanisms; for example, lactose removes a repressor. While in theory the maltose operon could be regulated by either method, in reality maltose causes an activator to bind, which increases the affinity for RNA polymerase at the otherwise inefficient promoter.

Which of the following statements about eukaryotic activator proteins is false? Choose one: A. They stimulate transcriptional initiation by opening up the double helix. B. They stimulate transcription initiation by recruiting proteins that modify chromatin structure. C. They stimulate transcription initiation by promoting the assembly of a transcription initiation complex at the promoter. D. They stimulate transcription initiation by aiding in the assembly of general transcription factors and RNA polymerase at the promoter.

A. Eukaryotic activator proteins do not help open up the double helix. However, they can help initiate gene transcription through other mechanisms, as shown in the figure. For example, activator proteins can recruit enzymes that will modify histones, thereby enabling them to bind other proteins necessary for transcription initiation. Also, chromatin-remodeling complexes can reconfigure chromatin to make it more accessible to transcription machinery. They do this by making the TATA box more accessible, for example.

What would happen to the helix-3 interaction with DNA if a mutation occurred that altered this adenine (as shown) to guanine? Choose one: A. The integrity of the interaction would decrease because one of the two hydrogen bonds would not be able to form. B. The integrity of the interaction would remain the same because the same two hydrogen bonds would still be able to form. C. The integrity of the interaction would increase because the hydrogen bonds would still be able to form and would be stronger.

A. If guanine replaced adenine, the integrity of the protein-DNA interaction would decrease because one of the two hydrogen bonds would not be able to form. This is because adenine contains an amino group hydrogen atom that interacts with an asparagine carbonyl oxygen atom; however, this interaction would not form if guanine were present in place of adenine. If guanine were present, there would actually be a repulsion between the partially negatively charged carbonyl group oxygen of the asparagine residue and the partially negatively charged carbonyl group oxygen of the guanine nitrogenous base. Hydrogen bonds form when there is a favorable interaction between a partial negative charge (from electronegative atoms such as O or N) and a partial positive charge, such as a hydrogen atom covalently bonded to a more electronegative atom.

Which of the following statements is not true about the differences between liver cells and kidney cells in the same organism? Choose one: A. They contain different genes. B. They contain different proteins. C. They contain the entire set of instructions needed to form the whole organism. D. They express different genes.

A. Specialized cells, such as liver and kidney cells, do contain the same genes, but they just express them differently. This is referred to as differential gene expression. We know that all cells in a human are the descendants of an initial cell that was created at fertilization, and so they must be genetically identical to one another. Because most specialized cell types in a multicellular organism contain all the same genes that were present in the fertilized egg that gave rise to them, they retain the instructions necessary to form the whole organism. Thus, cell differentiation is instead achieved by changes in gene expression.

Which of the following describes the Lac operon in E. coli when lactose, but not glucose, is present in the culture medium? Choose one: A. CAP, but not the Lac repressor, is bound to the Lac operon's regulatory DNA, and the Lac operon is expressed. B. CAP and the Lac repressor are both bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. C. The Lac repressor, but not CAP, is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. D. Neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the Lac operon is expressed. E. Neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed.

A. The expression of the Lac operon is tightly regulated by the type of carbohydrate present in the environment. Glucose is the preferred carbohydrate source and only in its absence will the necessary small molecule, cAMP, be found. cAMP binding to the CAP activator is necessary but not sufficient for the expression of the Lac operon. In addition to low glucose levels, there must also be lactose present in the environment. If this is the case, allolactose, a derivative of lactose, can bind to the Lac repressor and cause it to release from the promoter. Therefore, as outlined in the figure below, the Lac operon is only expressed when glucose is absent and lactose is present because the CAP activator is bound to the promoter, but the Lac repressor is not. This ensures that the genes in the Lac operon are expressed only in the conditions where lactose is the only carbohydrate source available.

Which is not an example of epigenetic inheritance? Choose one: A. the inheritance of a single point mutation in a gene B. the inheritance of patterns of chromosome condensation C. the inheritance of methylation patterns in DNA D. the inheritance of a regulatory protein that activates its own transcription

A. The inheritance of a single nucleotide point mutation in a gene is not an example of epigenetic inheritance. Epigenetic inheritance involves transmission of gene expression patterns that do not involve a change in nucleotide sequence, for example, DNA methylation. These types of modification allow cell memory to be established from even a short-lived environmental signal.

How or where do most transcription regulators bind? Choose one: to a DNA sequence called a leucine zipper to a DNA sequence called the homeodomain as dimers to the major groove of RNA to the minor groove of DNA

As dimers Most transcriptional regulator proteins bind DNA as dimers. Dimerization roughly doubles the area of contact with the DNA, making the interaction tighter and more specific. When the transcriptional regulating dimer associates with DNA, it associates with DNA at the major groove.

Researchers have created plasmids that only allow expression of inserted genes in response to a metabolite. Researchers can add these plasmids to E. coli cells and increase the expression of the inserted gene by adding the appropriate metabolite to the culture media. Plasmids containing which combination of operator and promoter allow activation of gene expression in response to an added metabolite? Choose one or more: A. weak promoter B. operator recognized by Lac repressor protein C. operator recognized by Trp repressor protein D. strong promoter

B,D Effective transcription relies on strong binding of RNA polymerase to promoters. This can occur if the promoter itself is strong because it is a good match for the consensus DNA sequences recognized by RNA polymerase or if RNA polymerase is recruited to a weak promoter by an activator binding to a regulatory site. Normally, robust transcription from the Lac operon requires both the presence of lactose (to remove the repressor protein) and the binding of the CAP activator protein (see image below). The requirement for the CAP activator can be overridden with a strong promoter.

Which of the following statements concerning leucine zipper protein dimerization and DNA binding is correct? Choose one: A. Leucine zipper protein dimerization is facilitated by polar amino acids in the dimerization domains. B. Leucine zipper proteins function as a dimer with both subunits making contact with the sequence-specific DNA site. C. Leucine zipper proteins contain many leucine amino acids in the DNA-binding region that facilitate sequence-specific DNA binding. D. Leucine zipper proteins use ionic bonds to bind with the sequence-specific DNA site.

B. Leucine zipper proteins dimerize through interactions between the leucine zipper domain α helices on two subunits. The helices contain hydrophobic side chains, including many leucine side chains, which pack tightly together. The α helices extend around both sides of the DNA molecule. The polar side chains in these regions of the α helices make hydrogen bonds with specific bases in the DNA major groove, leading to sequence-specific binding.

Which of the following describes the Lac operon in E. coli when both lactose and glucose are present in the culture medium? Choose one: A. CAP binds to the Lac repressor, preventing it from binding to the Lac operon's regulatory DNA, and the Lac operon is expressed. B. Neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. C. The Lac repressor, but not CAP, is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. D. CAP and the Lac repressor are both bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. E. CAP, but not the Lac repressor, is bound to the Lac operon's regulatory DNA, and the Lac operon is expressed.

B. The expression of the Lac operon is tightly regulated by the type of carbohydrate present in the environment. Glucose is the preferred carbohydrate source and only in its absence will the necessary small molecule, cAMP, be found. cAMP binding to the CAP activator is necessary but not sufficient for the expression of the Lac operon. In addition to low glucose levels, there must also be lactose present in the environment. If this is the case, allolactose, a derivative of lactose, can bind to the Lac repressor and cause it to release from the promoter. Therefore, as outlined in the figure, if both glucose and lactose are present, neither CAP nor the Lac repressor will bind to the promoter and the operon will remain turned off. This ensures that glucose remains the preferred carbohydrate source, even when lactose is also present.

c-Met is an oncogene that contributes to the development of certain cancers by triggering cell division and tumor growth. In a 2009 article, Yan and colleagues found regions in the 3' untranslated region of c-Met mRNA complementary to microRNA-1/206. In addition, higher levels of microRNA-1/206 were associated with slower cell proliferation. What is a likely explanation for the inverse correlation between microRNA-1/206 and cell proliferation? Choose one: A. MicroRNA-1/206 stabilizes c-Met mRNA, leading to enhanced translation. B. MicroRNA-1/206 targets c-Met mRNA for destruction via RISC. C. MicroRNA-1/206 codes for a protein that directly binds to and inhibits c-Met protein. D. MicroRNA-1/206 codes for a tumor suppressor protein that directly inhibits cell proliferation.

B. n their 2009 article (MicroRNA-1/206 Targets c-Met and Inhibits Rhabdomyosarcoma Development), Yan and colleagues found an inverse correlation between microRNA-1/206 and c-Met protein levels. MicroRNAs are noncoding regulatory RNAs that down-regulate gene expression by binding complementary mRNAs and destroying them via the RNA-induced silencing complex (RISC). Researchers use double-stranded RNAs to prevent the expression of selected genes, a technique known as RNA interference.

The image shows cells from the same organism. Which of the following statements is correct regarding these two human cells? Choose one: A. One human cannot contain both of these diverse cell types. B. The neuron contains more genes as compared to the liver cell. C. Both cells contain the same genes, but they are expressed differently. D. The neuron contains fewer genes as compared to the liver cell.

C. Both cells contain the same genes, but they are expressed differently. If both cells come from the same human organism, then they are necessarily descendants of the initial cell that was created at fertilization. This means that almost all of the cells in a multicellular organism, humans included, have the same genome in all of their cells. It is clear just from looking at the image of a neuron and a liver cell that they perform different functions. The ability of an organism to derive different specialized cells from the same genome is called gene expression. Thus, even though these two cell types contain the same collection of genes, they each express a different subset of them, which gives rise to their distinct functions.

The transcription initiation site of a eukaryotic gene is found at which location? Choose one: A. where transcription regulators bind B. where RNA polymerase first binds C. where RNA synthesis begins D. where general transcription factors bind

C. In eukaryotes, transcription regulators bind DNA sites that can be thousands of nucleotides away from a gene's promoter. However, it is this event that will prepare the chromatin for a potential transcription event. Once this is established, RNA polymerase assembles, along with these general transcription factors, at the TATA box, typically located 25 nucleotides upstream of the transcription initiation site. The transcription initiation site of a eukaryotic promoter is where RNA synthesis first begins, and this location is "downstream" of the core promoter region. In summary, the promoters of both bacterial and eukaryotic genes include a transcription initiation site, where RNA synthesis begins, plus nearby sequences that contain recognition sites for proteins that associate with RNA polymerase: σ factors in bacteria or transcription factors in eukaryotes.

The Drosophila regulatory segment that defines the location of Eve stripe 2 contains binding sites for four different transcription regulators: two repressors (Giant and Krüppel) and two activators (Bicoid and Hunchback). For Eve to be efficiently expressed in stripe 2, both repressors must be absent and both activators present. What would you expect to see in flies that lack the gene that encodes Bicoid? (Assume that Bicoid does not influence the expression of Hunchback, Giant, or Krüppel.) Choose one: A. Stripe 2 would expand toward the head of the embryo. B. Stripe 2 would expand toward the tail of the embryo. C. Stripe 2 would become fainter. D. All 7 stripes would disappear. E. Stripe 2 would become narrower.

C. In flies that lack the gene that encodes Bicoid, and assuming that Bicoid does not influence the expression of Hunchback, Giant, or Krüppel, we would expect that stripe 2 would become fainter due to lower level of expression. The stripe would not expand toward the embryo's head, as the repressor Giant is still expressed at the anterior border of stripe 2, and the stripe would not expand toward the embryo's tail, as the repressor Krüppel is expressed at the posterior border of stripe 2. The localization patterns of the repressors were not altered. If Giant and Krüppel were impacted (and for stripe 2 to become narrower), the distribution patterns of its repressor proteins would have to encroach on the area normally "reserved" for stripe 2. Alternatively, in flies deficient in either of the two repressors, Giant or Krüppel, stripe 2 would expand and cover an abnormally broad region of the embryo. Experimental approaches using a reporter gene have revealed the modular construction of the Eve gene regulatory region, and have been instrumental for developmental biologists studying Drosophila development.

Which of the following mutations would be least likely to disrupt the function of the leucine zipper protein in the animation? The structures of relevant amino acids are provided below. Choose one: A. mutation of the DNA-binding arginine to alanine in the DNA-binding domain of the protein B. mutation of the guanine nucleotide to a thymine nucleotide in the binding site on the DNA C. mutation of a leucine to aspartic acid in the dimerization domain of the protein D. mutation of a leucine to valine in the dimerization domain of the protein

D. Dimerization between the two subunits requires hydrophobic amino acids like leucine to pack tightly. Mutation of the hydrophobic leucine to another hydrophobic amino acid would be less disruptive than the other listed mutations. Changing the hydrophobic leucine to a charged amino acid in the dimerization domain will very likely disrupt dimerization, which is required for protein function. Changing the polar, charged arginine to a hydrophobic alanine will likely disrupt the ability of the protein to form hydrogen bonds and bind to the DNA, again disrupting protein function. Finally, altering the sequence of the binding site in the DNA will alter the bonds that can be formed and disrupt the sequence-specific interaction between the protein and DNA, disrupting function.

Which form of control directly influences which mRNAs are selected by ribosomes for the synthesis of proteins? Choose one: A. mRNA degradation control B. transcriptional control C. protein activity control D. translational control E. mRNA processing and localization control

D. The figure below shows the various steps from the information stored in a gene all the way through to the synthesis of a protein and highlights the places where gene expression can be controlled. The first and most important step is transcriptional control because without the production of mRNA, gene expression cannot occur. However, as you can see, there are multiple control steps that occur after transcriptional control, including the step addressed in this question: translation control. If an mRNA transcript does not interact with a ribosome, a protein cannot be produced. Also note that even once a protein is synthesized, there are additional steps of control still possible.

In bacterial cells, the tryptophan operon encodes the genes needed to synthesize tryptophan. What happens when the concentration of tryptophan inside a cell is high? Choose one: A. It activates the tryptophan repressor, which breaks down excess tryptophan. B. It inactivates the tryptophan repressor, which shuts down the tryptophan operon. C. It activates the tryptophan repressor, allowing transcription of the tryptophan operon. D. It activates the tryptophan repressor, which shuts down expression of the tryptophan operon. E. It inactivates the tryptophan repressor, allowing transcription of the tryptophan operon.

D. The tryptophan repressor is always present in the bacterial cell and its conformation depends on the presence or absence of the amino acid tryptophan. If tryptophan is present, it will bind to the repressor and this conformation is able to bind to the operator sequence of the Trp operon to turn off transcription. If tryptophan is absent, the repressor protein is no longer able to bind to the operator, which allows transcription to proceed. In this way, the concentration of tryptophan provides feedback inhibition of the Trp operon, using the tryptophan repressor as the on/off switch. The figure provides an overview of this regulation.

Where do transcription regulators usually bind on a DNA double helix? Choose one: A. 3' end B. minor groove C. single-stranded regions D. major groove E. 5' end

D. Transcription regulators make contact with nucleotide pairs within the major groove, as shown in part A of the figure. Many transcriptional regulators have a shared structural motif that comes into contact with the DNA, termed a homeodomain. The homeodomain consists of three α helices and one of them (labeled #3 in the figure) forms extensive hydrogen bonds with the bases in DNA, particularly adenine. This allows for specific and tight binding of the transcriptional regulator to DNA, enabling it to accomplish its function as a molecular switch that controls transcription.

What is an operon? Choose one: A. a set of genes that is constitutively active B. a short sequence of DNA to which a transcription regulator binds C. a sequence of DNA that produces a variety of mRNAs D. a set of genes controlled by the binding of two or more transcription regulators E. a set of genes transcribed as a single mRNA from a single promoter

E. Operons, a common feature of the prokaryotic genome, are defined by the coordinated expression of their resident genes under the control of a single promoter. Each operon produces a single mRNA that encodes multiple proteins, termed a polycistronic mRNA. This arrangement allows genes whose products function together in the cell, as in a metabolic pathway, to be regulated together. For example, the figure shows the Trp operon, which codes for the enzymes needed to synthesize the amino acid tryptophan.

Which of the following statements most accurately describes the expression of the repressor protein of the tryptophan operon? Choose one: A. The gene for the tryptophan repressor is turned on in response to high levels of tryptophan in the cell. B. The gene for the tryptophan repressor is turned off in response to high levels of tryptophan in the cell. C. The gene for the tryptophan repressor is turned on in response to low levels of tryptophan in the cell. D. The gene for the tryptophan repressor is turned off in response to low levels of tryptophan in the cell. E. The gene for the tryptophan repressor is expressed constitutively.

E. The Trp operon contains the genes that code for the necessary enzymes to synthesize the amino acid tryptophan from precursors. If tryptophan is low in a cell, the operon is expressed so that the cell can synthesize the tryptophan it needs. If tryptophan in the cell is high, then the operon is turned off. The Trp repressor is a molecular "switch" that controls gene expression at the Trp operon. If tryptophan binds to the Trp repressor, then the repressor adopts a conformation that allows it to bind to the promoter region of the Trp operon and prevent transcription. In the absence of tryptophan, the Trp repressor is inactivated and it can no longer bind to the promoter, allowing transcription to take place. This mechanism of regulation is depicted in the figure below. For the Trp repressor to be able to function as the molecular switch, it must always be present in the cell so that it can quickly respond to changes in the concentration of tryptophan in the cell.

Describe regulatory DNA sequences

Used to switch the gene on or off. Can be as short as 10 nucleotides and act as a simple switch (in prokaryotes) or as long as 100,000 nucleotides and act as molecular microprocessors, integrating info from a variety of signals into a command that determines how often transcription of the gene is initiated (eukaryotes)