AP Biology: Chapter 18: Regulation of Gene Expression

What is a promoter?

A promoter is a specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place

What are the two main ways of controlling metabolism in bacterial cells?

1. Cells can adjust the activity of enzymes already present. This is a fairly fast response, which relies on the sensitivity of many enzymes to chemical cues that increase or decrease their catalytic activity. 2. Second, cells can adjust the production level of certain enzymes; that is, they can regulate the expression of the genes encoding the enzymes.

List the three components of an operon, and explain the role of each one.

1. Operator: The segment of DNA that operates as the "switch." 2. Promoter: The site where RNA polymerase can bind with DNA to begin transcription. 3. Genes: Nucleotide sequences that specifically encode subunits of the enzyme.

oncogene

A gene found in viral or cellular genomes that is involved in triggering molecular events that can lead to cancer.

ras gene

A gene that codes for Ras, a G protein that relays a growth signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases, ultimately resulting in stimulation of the cell cycle.

egg-polarity gene

A gene that helps control the orientation (polarity) of the egg; also called a maternal effect gene.

inducer

A specific small molecule that binds to a bacterial repressor protein and changes the repressor's shape so that it cannot bind to an operator, thus switching an operon on.

morphogen

A substance, such as Bicoid protein in Drosophila, that provides positional information in the form of a concentration gradient along an embryonic axis.

p53 gene

A tumor-suppressor gene that codes for a specific transcription factor that promotes the synthesis of cell cycle-inhibiting proteins.

Explain the multistep model of cancer development by using the specific example of colorectal cancer.

Affecting the colon and/or rectum, this type of cancer is one of the best understood. Changes in a tumor parallel a series of genetic changes, including mutations affecting several tumor suppressor genes (such as p53) the ras proto-oncogene. Mutations of tumor-suppressor genes often entail loss (deletion) of the gene. Other mutation sequences can also lead to colorectal cancer.

The inactive mammalian X chromosome is heavily methylated. What is the result of this methylation?

After an X chromosome is inactivated in a particular cell, all mitotic descendants of that cell have the same inactive X. Thus, if a female is heterozygous for a sex-linked trait, about half her cells will express one allele, while the others will express the alternative allele.

homeotic gene

Any of the master regulatory genes that control placement and spatial organization of body parts in animals, plants, and fungi by controlling the developmental fate of groups of cells.

Use the sketch below to explain how enhancers and activators interact with transcription factors to affect gene expression. 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 called activators bind to the enhancer DNA sequences and then to a group of mediator proteins, which in turn bind to general transcription factors, assembling the transcription initiation complex. These protein-protein interactions facilitate the correct positioning of the complex on the promoter and the initiation of RNA synthesis. A gene may have several enhancers that act at different times or in different cell types.

What three processes lead to the transformation of a zygote into the organism?

Development of a zygote into a fully fledged organism results from cell division, cell differentiation, and morphogenesis.

Explain how proteins are targeted for degradation, and give a specific example of when this might occur.

Many proteins, such as the cyclins involved in regulating the cell cycle, must be relatively short lived if the cell is to function appropriately. To mark a particular protein for destruction, the cell commonly attaches molecules of a small protein called ubiquitin to the protein. Giant protein complexes called proteasomes then recognize the ubiquitin-tagged proteins and degrade them. Mutations making specific cell cycle proteins impervious to proteasome degradation can lead to cancer.

What mechanism is involved in the beginning of tumor growth? Discuss oncogenes and proto-oncogenes.

Mutations in the genes that normally regulate cell growth and division in somatic cells can lead to cancer. An oncogene is a gene found in viral or cellular genomes that is involved in triggering molecular events that can lead to cancer. A proto-oncogene is a normal cellular gene that has the potential to become an oncogene.

Much of the RNA that is transcribed is not translated into protein. These are called noncoding RNAs. What is their role?

Regulation by both small and large ncRNAs is known to occur at several points in the pathway of gene expression, including mRNA translation and chromatin modification. A class of small ncRNAs called piwi associated RNAs also induces formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons.

One of the noncoding RNAs that regulate gene expression is microRNA. On the sketch below, follow an RNA loop, called a "hairpin," from its creation. Be sure to label the location of hydrogen bonds and Dicer. Explain the two modes of action of microRNAs.

Small single-stranded RNA molecules, called microRNAs, are capable of binding to complementary sequences in mRNA molecules. An miRNA-protein complex then either degrades the target mRNA or blocks its translation.

pattern formation

The development of a multicellular organism's spatial organization, the arrangement of organs and tissues in their characteristic places in three-dimensional space.

morphogenesis

The development of body shape and organization.

induction

The process in which one group of embryonic cells influences the development of another, usually by causing changes in gene expression.

determination

The progressive restriction of developmental potential in which the possible fate of each cell becomes more limited as an embryo develops. At the end of determination, a cell is committed to its fate.

cell differentiation

The structural and functional divergence of cells as they become specialized during a multicellular organism's development. Cell differentiation depends on the control of gene expression.

Feedback inhibition is a recurring mechanism throughout biological systems. In the case of E. coli regulating tryptophan synthesis, is it positive or negative inhibition?

This is an example of negative inhibition, which is a form of regulation in which accumulation of an end product of a process slows the process. In this case, the accumulation of tryptophan in the cell shuts down the synthesis of more tryptophan.

What happens when a repressor is bound to the operator?

When a repressor is bound to the operator, it blocks attachments of RNA polymerase to the promoter, preventing transcription of the genes.

regulatory gene

A gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes.

maternal effect gene

A gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offspring's genotype. Maternal effect genes were first identified in Drosophila.

tumor-suppressor gene

A gene whose protein products inhibits cell division, thereby preventing the uncontrolled cell growth that contributes to cancer.

proteasome

A giant protein complex that recognizes and destroys proteins tagged for elimination by the small protein ubiquitin.

bicoid

A maternal effect gene that codes for a protein responsible for specifying the anterior end in Drosophila.

cytoplasmic determinant

A maternal substance, such as a protein or RNA, placed into an egg that influences the course of early development by regulating the expression of genes that affect the developmental fate of cells.

embryonic lethal

A mutation with a phenotype leading to death of an embryo or larva.

proto-oncogene

A normal cellular gene that has the potential to become an oncogene.

genomic imprinting

A phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent.

activator

A protein that binds to DNA and stimulates gene transcription. In prokaryotes, activators bind in or near the promoter; in eukaryotes, activators bind to control elements in enhancers.

repressor

A protein that inhibits gene transcription. In prokaryotes, repressors bind to the DNA in or near the promoter. In eukaryotes, repressors may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to DNA.

Distinguish between inducible and repressible operons, and describe one example of each type.

A repressible operon is usually on, but can be inhibited (repressed) when a specific small molecule binds allosterically to a regulatory protein. One example of a repressible operon is the trp operon (trp for tryptophan). An inducible operon is usually off but can be stimulated (induced) when a specific small molecule interacts with a regulatory protein. One example of an inducible operon is the lac operon (for lactose).

enhancer

A segment of eukaryotic DNA containing multiple control elements, usually located far from the gene whose transcription it regulates.

control element

A segment of noncoding DNA that helps regulate transcription of a gene by binding a transcription factor. Multiple control elements are present in a eukaryotic gene's enhancer.

corepressor

A small molecule that binds to a bacterial repressor protein and changes its shape, allowing it to switch an operon off.

small interfering RNA (siRNA)

A small, single-stranded RNA molecule generated by cellular machinery from a long, double-stranded RNA molecule. The siRNA associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence. In some cases, siRNA can also block transcription by promoting chromatin modification.

microRNA (miRNA)

A small, single-stranded RNA molecule, generated from a hairpin structure on a precursor RNA transcribed from a particular gene. The miRNA associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence.

RNA interference (RNAi)

A technique used to silence the expression of selected genes. RNAi uses synthetic double-stranded RNA molecules that match the sequence of a particular gene to trigger the breakdown of the gene's messenger RNA.

alternative RNA splicing

A type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are tested as exons and which as introns.

operon

A unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway.

How can both repressible and inducible operons be negative regulators?

Both repressible and inducible operons can be negative regulators as long as the operons are switched off by the active form of the repressor protein. In the case of the lac operon, allolactose induces enzyme synthesis not by acting directly on the genome, but by freeing the lac operon from the negative effect of the repressor. Remember that gene regulation is said to be positive only when a regulatory protein interacts directly with the genome to switch transcription on.

Explain why CAP binding and stimulation of gene expression is positive regulation.

By facilitating the binding of RNA polymerase to the promoter and thereby increasing the rate of transcription, the attachment of CAP to the promoter directly stimulates gene expression, qualifying CAP as positive regulation.

What is CAP? How does CAP work?

CAP refers to catabolite activator protein, and is a regulatory protein that binds to DNA and stimulates transcription of a gene.

In prokaryotes, functionally related genes are usually clustered in a single operon. What has been found to be the case in eukaryotes?

Co-expressed eukaryotic genes, such as genes coding for the enzymes of a metabolic pathway, are typically scattered over different chromosomes. In these cases, coordinate gene expression depends on the association of a specific combination of control elements with every gene of a dispersed group.

Operons have not been found in eukaryotic cells, and the genes coding for the enzymes of a particular metabolic pathway are often scattered over different chromosomes. What is a plausible mechanism for the coordination of gene expression?

Coordinate control of dispersed genes in a eukaryotic cell often occurs in response to chemical signals from outside the cell. Many signaling molecules, such as growth factors, bind to receptors on a cell's surface and never actually enter the cell. Such molecules can control gene expression indirectly by triggering signal transduction pathways that lead to activation of particular transcription activators or repressors.

cyclic AMP (cAMP)

Cyclic adenosine monophosphate, a ring-shaped molecule made from ATP that is a common intracellular signaling molecule (second messenger) in eukaryotic cells. It is also a regulator of some bacterial operons.

What is DNA methylation? What role may it play in gene expression?

DNA methylation is the process of adding methyl groups to DNA bases. At least in some species, DNA methylation seems to be essential for the long-term inactivation of genes that occurs during normal cell differentiation in the embryo.

How can alternative RNA splicing result in different proteins derived from the same initial RNA transcript?

Different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns. Regulatory proteins specific to cell type control intron-exon choices by binding to regulatory sequences within the primary transcript.

Explain what occurs in cell differentiation and morphogenesis.

During embryonic development, cells not only increase in number, but also undergo cell differentiation, the process by which cells become specialized in structure and function. Moreover, different kinds of cells are not randomly distributed but are organized into tissues and organs in a particular three-dimensional arrangement. The physical processes that give an organism its shape constitute morphogenesis, meaning "creation of form."

How do these "little chambers of horrors" (proteasomes) function? Explain their role in regulation of gene expression.

First, multiple ubiquitin molecules are attached to a protein by enzymes in the cytosol. Next, the ubiquitin-tagged protein is recognized by a proteasome, which unfolds the protein and sequesters it within a central cavity. Finally, enzymatic components of the proteasome cut the protein into small peptides, which can be further degraded by other enzymes in the cytosol.

Distinguish between heterochromatin and euchromatin.

Genes within heterochromatin, which is highly condensed, are usually not expressed. In contrast, euchromatin's looser structure allows RNA polymerase to bind to the DNA strands and proceed with transcription. Certain chemical modifications to the histone proteins and to the DNA of chromatin can influence both chromatin structure and gene expression.

Describe the relationship between glucose supply, cAMP, and CAP.

If the amount of glucose in the cell increases, the cAMP concentration falls, and without camp, CAP detaches from the operon. Because CAP is inactive, RNA polymerase binds less efficiently to the promoter, and transcription proceeds only at a low level.

All genes are not "on" all the time. Using the metabolic needs of E. coli, explain why not.

If the environment is lacking in the amino acid tryptophan, which the E. coli bacterium needs to survive, the cell responds by activating a metabolic pathway that makes tryptophan from another compound. Later, if the human host eats a tryptophan-rich meal, the bacterial cell stops producing tryptophan, thus saving itself from squandering its resources to produce a substance that is available from the surrounding solution in prefabricated form. Thus, bacteria tune their metabolism to changing environments.

operator

In bacterial DNA, a sequence of nucleotides near the start of an operon to which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon.

Compare and contrast the lac operon and the trp operon.

In both lac and trp operons, the entire transcription unit is under the command of one main operator and promoter. The lac operon is an inducible operon, while the trp operon is repressible. In both operons, regulation involves negative control of genes, because operons are switched off by the active form of the repressor protein.

What are three mechanisms for converting a proto-oncogene to an oncogene?

In general, an oncogene arises from a genetic change that leads to an increase either in the amount of the proto-oncogene's protein product or in the intrinsic activity of each protein molecule. The genetic changes that convert proto-oncogenes to oncogenes are movement of DNA within the genome, amplification of a proto-oncogene, and point mutations in a control element or in the proto-oncogene itself.

What occurs in histone acetylation? How does it affect gene expression?

In histone acetylation, acetyl groups (-COCH3) are attached to lysines in histone tails; deacetylation is the removal of acetyl groups. When the lysines are acetylated, their positive charges are neutralized and the histone tails no longer bind to neighboring nucleosomes. Such binding promotes the folding of chromatin into a more compact structure; when this binding does not occur, chromatin has a looser structure. As a result, transcription proteins have easier access to genes in an acetylated region. Some enzymes that acetylate or deacetylate histones are closely associated with or even components of the transcription factors that bind to promoters, suggesting that histone acetylation enzymes may promote the initiation of transcription not only by remodeling chromatin structure, but also by binding to and thus "recruiting" components of the transcription machinery.

epigenetic inheritance

Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome.

positional information

Molecular cues that control pattern formation in an animal or plant embryonic structure by indicating a cell's location relative to the organism's body axes. These cues elicit a response by genes that regulate development.

Posttranscriptional control includes regulation of mRNA degradation. Explain how this affects translation.

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. Translation cannot occur when an mRNA molecule lacks a poly-A tail of sufficient length to allow initiation.

How can proteins be activated, processed, and degraded?

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. Many proteins also undergo chemical modifications that make them functional. Regulatory proteins are commonly activated or inactivated by the reversible addition of phosphate groups, and cell-surface proteins must be transported to target destinations in the cell in order to function. The length of time each protein functions in the cell is strictly regulated by means of selective degradation.

histone acetylation

The attachment of acetyl group sto certain amino acids of histone proteins.

differential gene expression

The expression of different sets of genes by cells with the same genome.

There seem to be two categories of genes involved in cancer: oncogenes, which code for proteins to regulate cell growth, and should not be stuck "on," much like the accelerator in a car; and tumor-suppressor genes, which work like the brakes on a car and must function! Let's begin with a look at the ras gene, which codes for a G protein and is an oncogene. Label the sketch below to explain how a ras mutation leads to cancer.

This pathway is triggered by a (1) a growth factor that binds to (2) its receptor in the plasma membrane. The signal is relayed to (3) a G protein called Ras. Like all G proteins, Ras is active when GTP is bound to it. Ras passes the signal to (4) a series of protein kinases. The last kinase activities (5) a transcription activator that turns on one or more genes for proteins that stimulate the cell cycle. If a mutation makes Ras or any other pathway component abnormally active, excessive cell division and cancer may result.

What is the common point of gene expression for all organisms?

Transcription

Differential gene expression results from different activators in different cells. How do different sets of activators come to be present in two cells? Explain how each of these occurs:

a. distribution of cytoplasmic determinants After fertilization, early mitotic divisions distribute the zygote's cytoplasm into separate cells. The nuclei of these cells may thus be exposed to different cytoplasmic determinants, depending on which portions of the zygotic cytoplasm a cell received. The combination of cytoplasmic determinants in a cell helps determine its developmental fate by regulating expression of the cell's genes during the course of cell differentiation. b. different inductive signals The molecules conveying these signals within the target cell are cell-surface receptors and other proteins expressed by the embryo's own genes. In general, the signaling molecules send a cell down a specific developmental path by causing changes in its gene expression that eventually result in observable cellular changes.

Tumor-suppressor genes help prevent uncontrolled cell growth. One that is found mutated (and therefore nonfunctional) in more than 50% of human cancer is p53. So important is the p53 gene that it is sometimes called the "guardian angel of the genome." Describe the double whammy that results from mutation of p53.

p53 acts in several ways to prevent a cell from passing on mutations due to DNA damage. If mutations do accumulate and the cell survives through many divisions—as is more likely if the p53 tumor-suppressor gene is defective or missing cancer may ensue.