SAPLING GENE TEST 5
Activator proteins increase gene expression, whereas repressor proteins inhibit gene expression. Which statement concerning activator and repressor proteins in eukaryotes is true?
-Activators are more common than repressors in eukaryotes. -Transcription factors are proteins that bind to specific DNA sequences and alter transcription levels. Transcription factors are composed of at least two domains, a DNA‑binding domain and at least one regulatory domain. The DNA‑binding domain provides specificity in binding to particular DNA sequences, and the regulatory domain allows the protein to alter gene expression. Transcription factors with a domain that increases transcription are known as activators, whereas transcription factors with a domain that decreases transcription are known as repressors. In eukaryotes, the majority of transcription factors are activators. The prevalence of activator proteins in eukaryotes is due to the inability of RNA polymerase II to bind DNA without the assistance of activators. Activators are required to recruit RNA polymerase II to the promoter in order for the gene to be transcribed. As a consequence, gene expression is regulated by the presence or absence of activator proteins on specific DNA sequences. In prokaryotes, RNA polymerase can bind without the assistance of activators. Both prokaryotes and eukaryotes possess transcription factors that can function as either activators or repressors.
How are proteins regulated after translation?
-Active proteins can be inactivated by feedback inhibition Inactive proteins can be activated by covalent modification Proteins can be tagged with small molecules and subsequently degraded -There are several mechanisms by which proteins are regulated after translation. During translation, ribosomes read a messenger RNA (mRNA) template and synthesize a protein. Thus, the regulation of proteins after translation involves modification of proteins, rather than the modulation of mRNA to produce fewer proteins. Rather than be transported out of the cell, a protein that is no longer needed is either degraded, to recycle the protein's amino acid subunits, or inactivated so that it can be used at a later time. Proteins, including damaged proteins, can be tagged with a small molecule called ubiquitin, which signals that the protein needs to be degraded. Proteins tagged with ubiquitin molecules are degraded by a large protein complex called the proteasome. Another way that a protein can be inactivated is by feedback inhibition, which is a type of allosteric regulation. Allosteric regulation is a process by which a ligand binds to a site on the protein other than the active site. Binding of the ligand then causes a conformational change in the protein, which leads to a change in the activity of the protein. Allosteric regulation can increase or decrease the activity of a protein. In feedback inhibition, molecules that are typically products of the pathway in which the protein is involved bind to and inactivate the protein. The protein's activity is restored when the molecules dissociate from the protein. Proteins can be both activated and inactivated through post‑translational modification. Post-translational modification, also known as covalent modification, involves the attachment of molecules to a protein's surface by an enzyme. Some proteins are synthesized in an inactive form and need to be modified before they are activated. For example, phosphorylation can activate an inactive protein. Post-translational modifications are reversible, and thus, removal of the molecules from the protein's surface allow the protein to resume its active or inactive state.
In Arabidopsis thaliana, the Flowering Locus C (FLC) gene codes for a regulatory protein that suppresses flowering. FLC is expressed in seedlings to prevent premature flowering. In mature plants, FLC expression decreases with cooler temperatures, and flowering occurs once sufficiently cool temperatures are reached. If small‑interfering RNA (siRNA) that is complementary to FLC mRNA is introduced, how would RNA interference (RNAi) affect flowering?
-RNAi would degrade FLC mRNA and stimulate flowering. -RNA interference (RNAi), also called RNA silencing or post‑transcriptional gene silencing, combats foreign genes, most frequently from viruses, and modulates overexpression of native genes. When double‑stranded RNA is present, Dicer protein activates and cleaves it into small‑interfering RNA (siRNA) or microRNA (miRNA). One class of siRNA combines with the RNA‑Induced Silencing Complex (RISC) and acts as a template for the RISC protein complex to identify and degrade other copies of the RNA. A second class of siRNA binds to complementary sequences in DNA and attracts enzymes that inhibit transcription via demethylation of DNA and histones. If Dicer cleaves the double‑stranded RNA into miRNA, the miRNA combines with the RISC protein complex, which imperfectly pairs with and remains attached to other copies of the RNA, thereby inhibiting translation. Because the siRNA in the question is complementary to FLC mRNA, it would combine with the RISC protein complex, which would cleave and degrade FLC mRNA. Without FLC mRNA, the regulatory protein that represses flowering is not translated and flowering will occur.
Enhancer I can stimulate the transcription of gene A, but the insulator blocks its effect on gene B. Enhancer II can stimulate the transcription of gene B, but the insulator blocks its effect on gene A. A--promoter--enhancer I--insulator--enhancer II--promoter--B
-The newly positioned insulator prevents enhancer II from stimulating the transcription of gene B. -An insulator is a region of DNA that binds proteins to block the effect of an enhancer when it is physically located between the enhancer and the promoter of a gene. The new positioning of the insulator separates both enhancer I and enhancer II from gene B. Thus, neither enhancer activates gene B expression. The original insulator position separated gene A from enhancer II, but the new position allows enhancer II to stimulate gene A expression.
U937D cells express high levels of creatine kinase (CK‑B) mRNA but do not translate the mRNA into protein. Ribosomes bind the 5' end of the CK‑B mRNA; however, translation into protein is repressed in these cells. U937D cells synthesize the CK‑B enzyme when researchers introduce numerous short segments of RNA containing 3' UTR consensus sequences into the cells. The total amount of CK‑B mRNA does not change after adding RNA containing 3' UTR sequences. Introducing short RNA segments without the 3' UTR consensus sequences does not stimulate CK‑B synthesis. -Which of the statements explains how the introduction of short RNA containing 3' UTR sequences allows CK‑B translation in U937D cells?
-Translational repressor proteins inhibit CK‑B translation by binding 3' UTR sequences in the CK‑B mRNA. These repressors bind the 3' UTR sequences in the introduced RNA instead of the CK‑B mRNA, allowing the ribosomes to freely translate CK‑B mRNA. -U937D cells express CK‑B mRNA but do not synthesize CK‑B protein. A possible mechanism for the inhibition of translation could be the binding of translational repressors to the 3' UTR region of the CK‑B mRNA. The response of the U937 cells to short RNA molecules containing the 3' UTR sequence suggests the action of soluble proteins that inhibit translation. The additional 3' UTR sequences could bind to translational repressor proteins that normally bind the 3' UTR of CK‑B, making these repressors unavailable to bind to the CK‑B mRNA. CK‑B protein can be translated when the repressor proteins bind to the added 3' UTR instead of the CK‑B mRNA 3' UTR. The finding that U937D cells continue to repress CK‑B mRNA translation after researchers add RNA molecules that do not contain the 3' UTR excludes the possibility that changes in translation efficiency occurred because of differences in intracellular RNA or nucleotide concentration. Recombination between the exogenous RNA and CK‑B mRNA is unlikely to occur. Furthermore, ribosomes do not translate longer mRNA molecules more efficiently.
In eukaryotes, transcription factors and enhancer sequences are used to regulate transcription. Classify the statements as true or false.
-True: Enhancer sequences can be located thousands of base pairs downstream from the transcription start site. Enhancer sequences are composed of DNA base pairs False: Enhancer sequences directly alter transcription levels Transcription factors always increase transcription levels. Transcription factors bind to the entire enhancer sequence. -Transcription factors are proteins that bind to specific DNA sequences and alter transcription levels. Transcription factors are composed of at least two domains, a DNA‑binding domain and at least one regulatory domain. The DNA‑binding domain recognizes specific DNA sequences, usually six to ten base pairs in length, and confers specificity to the transcription factor. The regulatory domain is used to alter gene expression. Depending on which regulatory domain is present, transcription factors may increase or decrease expression. Regions of DNA that contain multiple transcription factor binding sites and promote transcription are called enhancer sequences. Enhancer sequences can vary in length from 5050 to 15001500 base pairs. Transcription factors do not bind the entire enhancer sequence, but instead only bind the regions of the enhancer sequence that can be recognized by the transcription factor's DNA‑binding domain. A single enhancer sequence may require several different transcription factors to bind simultaneously to promote transcription. Enhancer sequences can function even when they are over 100,000100,000 base pairs upstream or downstream from a transcription start site. The ability of enhancers to work at such great distances is due to the three‑dimensional arrangement of DNA within a cell. DNA sequences that are separated by many base pairs may be adjacent when packaged as chromatin. This proximity allows a transcription factor to bind an enhancer sequence and recruit the transcription machinery to the transcription start site.
How can microRNAs (miRNAs) regulate gene expression?
-prevent translation by binding to mRNA and degrading the mRNA strand -There are many different mechanisms that function within a cell to control gene expression at the level of both transcription and translation. MicroRNAs (miRNAs) are functional RNA molecules that can bind to RNA. MicroRNAs can control gene expression by binding to messenger RNA (mRNA) and preventing translation. These miRNAs are typically 21-22 base pairs long. Some miRNA molecules base pair exactly with their target molecule and cause the target mRNA to degrade. Other miRNAs imperfectly bind their target mRNA and slow down translation. Plants and animals, as well as some viruses, have been shown to contain miRNAs. There are several mechanisms that miRNAs use to inhibit translation of mRNA. The binding of a miRNA to its target mRNA can result in cleavage of the mRNA into two pieces. Once cleaved, the mRNA cannot be translated and is degraded. The binding of a miRNA to an mRNA can also result in the shortening of the poly‑A tail of the mRNA. This results in destabilization and prevents translation of the mRNA. The binding of a miRNA to an mRNA reduces the number of mRNA molecules available to be translated and thus decreases the amount of a particular protein present in cell. Since miRNAs bind to mRNAs and inhibit the mRNAs translation, miRNAs control gene expression at the level of translation rather than transcription. Transcription factors are an example of a molecule that regulates gene expression at the level of transcription. Transcription factors bind to DNA and activate or repress transcription through a number of different mechanisms. Neither transcription factors nor RNA polymerase is affected by miRNAs.
The yeast Saccharomyces cerevisiae has several genes encoding enzymes that function in the importation and metabolism of galactose. The genes are located on several chromosomes, and are transcribed separately. The GAL genes have similar promoters, and gene transcription is under regulation by the proteins Gal3p, Gal4p, and Gal80p. Place the statements about GAL gene regulation in the correct order, starting from conditions with an absence of galactose through conditions with abundant galactose.
GAL gene transcription is inhibited when galactose is absent, preventing the wasteful synthesis of unneeded enzymes. When galactose is absent, the transactivator Gal4p is bound to DNA, and the inhibitor Gal80p is bound to Gal4p. This results in a Gal4p‑Gal80p‑DNA complex that prevents transcription. As galactose becomes available, it binds to Gal3p. The bound Gal3p then associates with Gal80p. The interaction results in the abatement of the Gal80p inhibition of Gal4p. Once the inhibition is relieved, Gal4p functions as an activator at GAL promoters, resulting in gene transcription.
Which description applies to post‑translational gene regulation?
Gene regulation is a tightly controlled process that can occur at several different stages within a cell. Operons and epigenetic changes control whether transcription occurs. Following transcription, RNA molecules can be altered through additions of molecules and alternative splicing of exons. Finally, proteins can also be altered after translation. Post‑translational modifications occur after a polypeptide chain is synthesized by the ribosome. These modifications can include the addition of functional groups and peptides, the alteration of the chemical nature of the amino acids, and structural changes such as protein folding. Gene regulation can occur much earlier than the post‑translational stage. For example, both operons and epigenetic modifications influence whether and how often genes are transcribed. An operon is a cluster of genes along a stretch of DNA that operate under the coordinated control of a single promoter. The genes in an operon turn on or off together and are controlled by environmental influences, such as the availability of certain nutrients. Epigenetic changes alter gene expression by means other than direct changes to the DNA sequence, and are also influenced by the environment. Following transcription, messenger RNA (mRNA) undergoes modifications such as the addition of a 5′5′ cap and 3′3′ poly‑A tail, the removal of introns, and the splicing of exons. Without such modifications, an mRNA molecule will not be transcribed properly. Furthermore, exons transcribed from a gene may not always get spliced together the same way. Alternative splicing of exons in mRNA is a regulated process that allows a single gene to code for multiple proteins.
