Genetics: Chapter 16 HW

The trp operon contains five genes: trpE, trpD, trpC, trpB, and trpA. These five genes code for components that produce three enzymes that catalyze the biosynthesis of tryptophan. The trpL region is the leader region, which helps regulate transcription once RNA polymerase has initiated transcription. -The trp operon also undergoes negative regulation by a repressor. Tryptophan is the signal molecule (effector molecule) that binds to the repressor. Determine which events lead to an increase in transcription. -The trp operon is transcribed when:

-the trp repressor dissociates from DNA. -tryptophan is present at low concentrations inside the cell.

What is the function of the repressor in the E. coli lac operon?

The repressor is a protein that prevents the transcription of the lactose genes by binding to the beginning of the lac operon.

Which statement describes an operon?

a gene cluster controlled by a single promoter that transcribes to a single mRNA strand

The lac operon in E. coli controls the gene expression of the enzymes that digest lactose in the cell. In the presence of lactose, the lac operon will turn on and the genes will be expressed. Place the events of gene regulation by the lac operon in order of their occurrence, from the introduction of lactose to the environment to when the cell begins to digest lactose.

-Lactose is introduced to the environment. -the repressor is inactivated by allolactose -The repressor is removed from the operator as it changes shape and can no longer bind to operator -RNA Polymerase binds to the Promoter region -Lactose enzyme genes are expressed by operon -The cell begins to digest lactose.

Suppose an operon has the following characteristics: (1) The operon codes for structural proteins that convert compound Q to compound B. (2) The operon is controlled by a constitutively expressed regulatory gene called reg. (3) In wild‑type individuals, the operon is transcribed in the absence of compound B but not in the presence of compound B. (4) In reg− mutants, the operon is constitutively transcribed. -Is this operon inducible or repressible? Why?

Answer: (e) It is repressible because wild-type transcription is repressed in the presence of compound B. Explanation: Because the operon is transcriptionally inactive in the presence of compound B, the regulatory gene reg most likely codes for a repressor protein that requires compound B as a corepressor. The data suggest that the operon is repressible because it is inactive in the presence of compound B, but active when compound B is absent

An operon is a group of genes under the control of a single promoter. Match each type of operon with the descriptions.

Inducible: Transcription is turned on when a specific molecule is present. -Under default (normal) conditions, transcription is inhibited -Explanation: An operon is inducible when a metabolite formed early in the pathway activates, the operon by interacting with the repressor. In the lac operon, allolactose serves as an inducer that interacts with the repressor and induces the transcription of the downstream gene Repressible: -Transcription stops when the repressor gene product is activated. -Sufficient amounts of the gene product inhibit further transcription Explanation- An operon becomes repressible when an excess amount of gene product of the pathway leads to termination of transcription of the genes of the operon. Lac repressor is reported to inhibit lac operon. Constitutive: -The amount of gene product is constant Explanation- Constitutive genes are transcribed continuously, so the proteins coded by such genes are formed continuously and the rate of their formation is constant. This is the opposite of facultative genes, as they are transcribed only when it is needed.

Tryptophan is an amino acid necessary for E. coli survival and growth. E. coli contain genes coding for enzymes that synthesize tryptophan. These genes are grouped together on a segment of DNA called the tryptophan (trp) operon. Cells can use these enzymes to synthesize tryptophan when it is not present in the environment. However, when tryptophan is already present in the environment, cellular resources are shifted away from manufacturing the enzymes for tryptophan synthesis. Tryptophan binds with and activates the trp repressor, which then binds to the trp promoter and blocks RNA polymerase. Blocking RNA polymerase decreases the normal transcription rate of the operon. -What type of regulation does the trp operon exhibit?

Negative Regulation -Tryptophan is an amino acid, and if it is excessively synthesized by the organism, it control its transcription through "trp Operon." In this, the tryptophan (corepressor) binds to the repressor protein, and makes it get activated. This activated repressor now binds to the operator site, and prevents the binding of RNA polymerase enzyme, there by inhibiting the protein synthesis.

The trp operon is composed of the structural genes, the promoter (P), and the operator (O). The trp repressor binds to the operator and blocks transcription. -Select the image that correctly orders the three components of the trp operon and identifies, with an arrow, the component to which the trp repressor binds.

Promoter is the site where RNA polymerase bind and strats the transcription of structural genes.this promoter is regulated by Operator and repressor complex. repressor is the one which binds to operator there by inhibiting the RNA polymerase to start the transcription process of structural genes. in trp operon in the presence of trp , repressor go and bind to the operator and stops the transcription of strucutral genes.

The lac operon in E. coli controls the gene expression of the enzymes that digest lactose in the cell. In the absence of lactose, the lac operon will turn off and gene expression will be inactivated. Place the events of gene regulation by the lac operon in order of their occurrence, from the removal of lactose from the environment to when the cell no longer digests lactose.

-Lactose is scarce in the environment. -The repressor is activated in the absence of lactose -The Repressor binds to the operator -RNA polymerase is prevented from moving FROM the promoter -Lactose enzyme genes are NOT transcribed (ex: B-Gal) -The cell no longer digests lactose.

What would be the most likely effect on the transcription of the trp structural genes for the mutation scenarios provided?

Mutation that prevents ribosome binding to the mRNA 5' UTR -no Transcription occurs Mutation that changes region 1 tryptophan codons into alanine codons -transcription when Alanine is low Mutation that creates a stop codon in region 1 of mRNA 5' UTR -no Transcription occurs B/C If ribosome stops at region 1, it falls off from the transcript. This allows 1&2 and 3&4 hair-pin loop formation. So, transcription will not occur. Deletions in region 2 of the mRNA 5' UTR -no transcription occurs B/C If region 2 is deleted, anti-terminator loop can not be formed, Deletions in region 3 of the mRNA 5' UTR -transcription occurs B/C If region 3 is deleted, terminator loop (3 and 4) can not form. So, continuous transcription occurs. Deletions in region 4 of the mRNA 5' UTR -Transcription occurs B/C of same reason as above Deletion of the string of adenine after region 4 of the mRNA 5' UTR -transcription occurs B/C Terminator loop (3 and 4) requires a string of A downstream to it. If these nucleotides are deleted, transcription will proceed. ***Simple logic: if 1 & 2 and 3 & 4 loops form, transcription does not occur. If 2 & 3 loop forms, transcription occurs.

Arrange the steps of the regulation of the trp operon in order of occurrence.

The Steps of regulation of trp operon from the level of tryptophan is low I. RNA polymerase binds to promoter, allowing transcriptions of trp genes to proceed. II. Products of trp gene synthesize tryptophan. III. Levels of tryptophan rise and no more tryptophan is required. IV. Trytophan binds to the trp repressor and induces a conformational change. V. The trp repressor protein binds to repressor. VI. The trp repressor blocks RNA polymerase from binding to the promoter. Transcription of gene sto The Steps of regulation of trp operon from the level of tryptophan is low I. RNA polymerase binds to promoter, allowing transcriptions of trp genes to proceed. II. Products of trp gene synthesize tryptophan. III. Levels of tryptophan rise and no more tryptophan is required. IV. Trytophan binds to the trp repressor and induces a conformational change. V. The trp repressor protein binds to operator. VI. The trp repressor blocks RNA polymerase from binding to the promoter. Transcription of gene stop

What is the function of the promoter in the E. coli lac operon?

-the promoter is a region of DNA at the start of the lac operon, where RNA polymerase binds to begin transcription of the lactose gene. Just with the binding of the enzyme RNA polymerase, transcription of all the genes starts, which binds to the promoter which is a specific DNA binding site.cAMP-bound catabolite activator protein CAP also known as the cAMP receptor protein helps in binding of RNA polymerase to the promoter.

Classify the given examples of prokaryotic gene expression as positive or negative gene regulation.

Positive gene regulation: -In the presence of lactose and low glucose the lac operon is expressed 20-fold higher than in .the absence of lactose. -If the sugar arabinose is present, an activator protein binds the promoter of the genes responsible for PROCESSING arabinose and induces their transcription. Negative gene regulation: -In the presence of iron, the dtxR repressor protein binds DNA, and the gene that encodes for the diphtheria toxin is not expressed. -In the absence of lactose, the lacR repressor protein binds the lac operon (thus inhibiting genes that encode for breaking down of lactose). -When excess of tryptophan is present, a repressor protein binds the operator of the trp operon

A ribozyme is

an RNA catalyst. -a type of RNA that can act as an enzyme In the 1960s, scientists predicted that ribonucleic acid (RNA) molecules would one day be found that could act as catalysts. They made this prediction based on the observation that RNA molecules show a large diversity of structures and functions. Catalytic RNA molecules, now known as ribozymes, were first discovered in the 1980s. Ribozymes are therefore not proteins or carbohydrates. In recent decades, ribozymes have been found that catalyze the formation of phosphodiester bonds to form RNA molecules. Other ribozymes are known to catalyze peptide bonds to form polypeptides. RNA molecules have therefore been shown to play major roles in many aspects of transcription and translation. DNA is transcribed into messenger RNA (mRNA) molecules, which travel to the ribosome and are transcribed into protein. Transfer RNA (tRNA) molecules carry specific amino acids, the building blocks of proteins, to the ribosome. The ribosome itself is made of ribosomal RNA (rRNA) and protein. Ribozymes are found within the ribosome and give it its catalytic function. Before ribozymes had been observed, most enzymes were believed to be proteins. The discovery of RNA molecules that can catalyze both RNA synthesis and protein synthesis provides insights into how the earliest life on Earth may have formed and self‑replicated.

A mutation at the operator site of an operon prevents the repressor from binding. 1. What effect will this mutation have on transcription in a repressible operon? 2. What effect will this mutation have on transcription in an inducible operon?

1) The operon will always be transcriptionally active.. -In a repressible operon such as Trp operon, the repressor cannot bind to operator when the operon in active state. In the presence of Tryptophan, aporepressor binds to Trp molecule to form an active repressor that binds to operator, thereby preventing transcription of structural genes. If a mutation occurs in the operator site such that repressor cannot bind to it, then the active repressor will never bind to operator even in presence of Trp amino acid. Thus, the operon will always be transcriptionally active in this case. 2) The operon will always be transcriptionally active.. -In an inducible operon such as lac operon, an inducer such as allolactose or lactose binds to repressor so that it is unable to bind to operator sequence, thereby releasing the repression and switching on the operon, thus allowing the transcription of the structural genes. Therefore, a mutation in the operator sequence which prevents repressor from binding to it will result in the operon being always transcriptionally active.

A mutant strain of E. coli produces β‑galactosidase in the presence and in the absence of lactose. -Where in the operon might the mutation in this strain occur, and why?

Answers: d) in the operator region, where the mutation leads to the failure of the operator to normally bind the repressor e) in the lac/gene, which leads to an inactive lac repressor near the lacl gene. -Reason: Lac operon is negatively inducible and kept shut in the absence of lactose due to repressor binding on the operator region. therefore, a mutation in either the binding region of the operator or in the lacI gene (to make it inactive) will lead to the expression of the beta-galactosidase gene even in the absence of lactose. - galactosidase is the enzyme which is the product of lacZ gene. LacZ gene is one of the structural genes in the lac operon system.-galactosidase enzyme is responsible for hydrolyzing the lactose ( a disaccharide) into glucose and galactose. According to the question, a mutant strain of E.coli might have the mutation in the lacI gene that codes for the repressor molecule. Due to this mutation, repressor would not be formed. If that won't be formed then the promotor site will not be blocked by the repressor molecule even in the absence of lactose molecule. Then, adenylate cyclase enzyme is activated which will produce cAMP (cyclic AMP) which will bind to CAP (catabolite activator protein) site to form cAMP-CAP complex that will act as the sign where RNA polymerase enzyme can bind, where it will effectively initiate the transcription of the structural genes (lacZ is one of then that will code for -galactosidase)