Brock Chapter 6 (Part 1)

B) Catabolite repression

Explanation: Catabolite repression is the mechanism that allows E. coli to preferentially use glucose over other sugars when both are present, ensuring efficient energy use.

B) It acts as a corepressor

Explanation: In the arginine operon, arginine serves as a corepressor that binds to the arginine repressor, activating it to block transcription when arginine is plentiful.

C) Binds a zinc ion

Explanation: The helix-turn-helix structure does not bind a zinc ion; that characteristic is associated with the zinc finger domain, which is a different type of protein structure.

B) It is repressed

Explanation: The presence of glucose represses the synthesis of enzymes needed for the breakdown of other sugars, such as lactose or maltose, to optimize energy use.

C) Cyclic AMP levels must be high and an inducer must be present

Explanation: For the lac operon to be transcribed, two conditions must be met: high levels of cyclic AMP for CRP binding and the presence of an inducer to inactivate the LacI repressor.

C) It is not made

Explanation: In the absence of lactose, the synthesis of β-galactosidase does not occur, demonstrating the regulation of enzyme production based on substrate availability.

B) It blocks transcription by binding to the operator

Explanation: The LacI protein acts as a repressor that blocks transcription of the lac operon by binding to the operator, but it does not do so when glucose is absent and lactose is present, allowing transcription to begin.

B) Chemotaxis

Explanation: Chemotaxis is the process by which motile bacteria can sense and respond to their environment, moving toward attractants like nutrients and away from repellents like toxins.

A) Diauxic growth

Explanation: Diauxic growth occurs when E. coli first consumes the preferred carbon source (glucose) and then, after a lag, resumes growth on the second source (lactose) once the first is depleted.

B) Positive control

Explanation: The maltose-degrading enzymes are under positive control, meaning that transcription requires the binding of an activator protein to the DNA, specifically after binding to maltose, the inducer.

C) It recruits RNA polymerase to the promoter

Explanation: CRP, when bound to cyclic AMP, acts as an activator that recruits RNA polymerase to the promoter region of the lac operon, facilitating transcription.

B) It cleaves lactose into glucose and galactose

Explanation: β-galactosidase is essential for E. coli to utilize lactose as a carbon and energy source by breaking it down into glucose and galactose.

B) It interacts specifically with DNA

Explanation: The recognition helix is the part of the helix-turn-helix structure that specifically interacts with DNA, allowing the protein to bind to its target sequence.

B) Helix-turn-helix

Explanation: The helix-turn-helix structure is a common motif in many DNA-binding proteins, consisting of two segments of polypeptide chain with an alpha-helix connected by a short turn, crucial for DNA interaction.

B) Effectors

Explanation: The substances that influence enzyme activity, including inducers and corepressors, are collectively referred to as effectors.

C) It lowers cyclic AMP levels

Explanation: The presence of glucose inhibits the synthesis of cyclic AMP and stimulates its transport out of the cell, resulting in lower levels of cyclic AMP, which affects the regulation of the lac operon.

C) It allows CRP to bind to DNA

Explanation: Cyclic AMP (cAMP) is crucial for the binding of the cyclic AMP receptor protein (CRP) to DNA, which is necessary for the transcription of the lac operon. High levels of cAMP enable CRP to bind to the CRP-binding site, facilitating RNA polymerase's binding to the promoter.

C) IPTG

Explanation: Isopropylthiogalactoside (IPTG) is an inducer of β-galactosidase, even though it cannot be hydrolyzed by the enzyme, demonstrating the role of structural analogs in enzyme regulation.

C) Pseudomonas aeruginosa

Explanation: Pseudomonas aeruginosa is an opportunistic pathogen that utilizes chemotaxis to respond to signals from damaged tissues, particularly in cystic fibrosis patients.

C) They sense environmental signals

Explanation: Chemoreceptors extend from the bacterial cell and allow the bacteria to sense a variety of signals, which helps direct their movement toward or away from certain substances.

D) It allows RNA polymerase to begin transcription

Explanation: The maltose activator protein binds to the DNA after binding maltose, which facilitates the binding of RNA polymerase and initiates transcription.

B) A substance that induces enzyme synthesis

Explanation: An inducer is defined as a substance that triggers the synthesis of specific enzymes, such as lactose inducing the production of β-galactosidase.

A) Lac repressor

Explanation: The lac repressor is a well-known DNA-binding protein in E. coli that utilizes the helix-turn-helix structure to regulate transcription by binding to the operator region of the lactose operon.

C) Negative control

Explanation: Regulation by repressors is termed negative control because the repressor's role is to prevent transcription, thereby inhibiting mRNA synthesis.

C) Hydrogen bonds and van der Waals contacts

Explanation: DNA-binding proteins recognize specific sequences through noncovalent interactions, including hydrogen bonds and van der Waals contacts, which are essential for binding specificity.

B) By binding to the operator

Explanation: A repressor inhibits mRNA synthesis by binding to the operator region of the DNA, preventing RNA polymerase from binding and initiating transcription.

B) The prevention of enzyme synthesis when products are abundant

Explanation: Enzyme repression occurs when the presence of a product, such as arginine, inhibits the synthesis of enzymes needed for its production, conserving resources.

C) Within minutes

Explanation: The response of Pseudomonas aeruginosa to damaged epithelial cells can occur remarkably quickly, within minutes, showcasing the efficiency of bacterial regulatory mechanisms.

B) Amino acids

Explanation: Pseudomonas aeruginosa senses amino acids released from injured cells to scavenge nutrients, demonstrating its ability to respond to specific environmental cues.

C) It is important mostly in eukaryotes

Explanation: Cyclic GMP (cyclic guanosine monophosphate) is highlighted as a regulatory nucleotide that plays a significant role primarily in eukaryotic cells, distinguishing it from other regulatory nucleotides.

C) They die and release nutrients

Explanation: Following lung damage, epithelial cells can die, releasing nutrients that Pseudomonas aeruginosa scavenges, which is critical for its survival and pathogenicity.

C) It activates RNA polymerase binding

Explanation: In positive control, the regulatory protein acts as an activator that facilitates the binding of RNA polymerase to DNA, promoting transcription.

C) Enzymes required for using lactose

Explanation: Enzymes that are needed for utilizing lactose are only useful when lactose is available, making them condition-dependent rather than constitutive.

B) Degradative (catabolic) enzymes

Explanation: Enzyme induction usually pertains to the production of degradative enzymes, which are synthesized only when their substrates are present, contrasting with enzyme repression affecting biosynthetic enzymes.

B) A group of operons controlled by a single regulatory protein

Explanation: A regulon consists of multiple operons that are regulated by the same regulatory protein, allowing coordinated control of related functions.

C) Activator-binding site

Explanation: The region on the DNA where the activator protein binds is referred to as the activator-binding site, distinguishing it from the operator site found in negative control systems.

C) It represses its expression

Explanation: When glucose is present, catabolite repression prevents the expression of the lac operon, meaning that lactose cannot be utilized until glucose is depleted.

C) Both positively and negatively controlled

Explanation: The lac operon is regulated through both positive control (activation by cAMP and CAP) and negative control (repression by the LacI protein), allowing for a complex response to the presence of glucose and lactose.

D) They regulate the binding of other proteins to DNA

Explanation: Regulatory proteins influence gene expression by affecting the binding of other proteins to specific sites on the DNA, thereby turning transcription on or off.

B) They are homodimeric

Explanation: Many DNA-binding proteins are homodimeric, meaning they consist of two identical polypeptide subunits that interact with specific regions of DNA.

C) They bind RNA polymerase weakly

Explanation: The promoters of positively controlled operons have nucleotide sequences that bind RNA polymerase weakly, making it difficult for RNA polymerase to initiate transcription without the help of an activator protein.

B) They can function as both repressors and activators

Explanation: The TrmB family of transcriptional regulators can exhibit dual functionality, acting as both repressors and activators depending on the cellular conditions and the presence of specific inducer molecules.

C) By recruiting the transcription initiation complex

Explanation: TrmBL1 activates gene expression for glucose synthesis by binding to a DNA sequence upstream of the BRE/TATA binding sites, which helps recruit the archaeal transcription initiation complex, allowing for transcription to occur.

C) It can act as both an activator and a repressor

Explanation: TrmBL1 functions as both an activator for glucose synthesis by binding upstream of the promoter region and as a repressor for sugar uptake by blocking RNA polymerase binding, demonstrating its dual functionality in transcriptional regulation.

C) Constitutive

Explanation: Constitutive expression refers to proteins and RNA molecules that are consistently needed at similar levels regardless of growth conditions, ensuring essential functions are maintained.

C) It regulates both hydrogenase and sulfur metabolism

Explanation: SurR functions as both an activator for hydrogenase production when sulfur is absent and as a repressor for genes involved in sulfur metabolism, showcasing its dual regulatory role depending on environmental conditions.

B) To maximize the use of available resources

Explanation: Cells regulate the types, amounts, and activities of proteins to efficiently orchestrate reactions and maximize the use of available resources, which is crucial for their survival and reproduction.

C) At both transcription and translation levels

Explanation: The amount of protein synthesized can be regulated at both the transcription level (by varying mRNA production) and the translation level (by controlling mRNA translation).

B) Accumulation of a-ketoglutarate

Explanation: When nitrogen becomes limiting, the accumulation of a-ketoglutarate binds to NrpR, causing it to release from the DNA and allowing transcription of nitrogen assimilation genes to proceed.

C) It is released from DNA

Explanation: The presence of maltose causes TrmBL1 to release from the DNA, which prevents it from activating glucose synthesis genes and allows RNA polymerase to bind for transcription of sugar uptake genes.

C) It serves as a signal that glucose is absent

Explanation: Cyclic AMP (cAMP) acts as a signaling molecule indicating that glucose is absent, which is crucial for the activation of the lac operon when lactose is present.

B) DNA looping is required

Explanation: When the activator-binding site is several hundred base pairs away from the promoter, DNA looping is necessary to allow the activator protein to interact with RNA polymerase and facilitate transcription.

B) Major groove

Explanation: The major groove of DNA is the primary site for protein binding, allowing for specific interactions between proteins and the DNA sequence.

B) It represses genes encoding nitrogen assimilation functions

Explanation: The NrpR protein acts as a repressor for genes involved in nitrogen assimilation, blocking their transcription when organic nitrogen is plentiful.

B) Oxidation of cysteine residues

Explanation: The release of SurR from DNA when sulfur is present is due to the oxidation of cysteine residues within its DNA-binding motif, which prevents it from binding to regulatory regions and alters gene expression.