chapter 8 Flashcards
In multicellular organisms, what is the primary reason two different cell types (e.g., neurons and liver cells) exhibit vastly different structures and functions despite having nearly identical genomes?
A. Certain genes are permanently removed from the genome in different cell types.
B. Different cell types rely on energy from different organelles.
C. Gene expression patterns differ, leading cells to produce distinct sets of proteins.
D. Some cells store DNA in the nucleus, while others do not.
Answer: C
Explanation: Both neurons and liver cells contain the same DNA, but they express different subsets of genes, producing cell type–specific proteins and resulting in distinct structures and functions.
Which of the following statements is most consistent with current understanding of how cell differentiation occurs in a multicellular organism?
A. All cells in an organism express every gene at all times, leading to uniform phenotypes.
B. Each cell type eliminates the unnecessary genes from its genome during development.
C. Cell differentiation arises because of precise regulation of which genes are turned on or off.
D. Gene expression is irrelevant to the development of specialized cells; signaling molecules alone determine cell fate.
Answer: C
Explanation: Extensive evidence shows that cells differentiate through selective gene expression rather than permanent deletion of specific genes or expression of all genes simultaneously.
Question 1:
Transcription regulators achieve highly specific interactions with DNA sequences primarily by:
A) Forming strong covalent bonds with the DNA backbone
B) Binding randomly to both the major and minor grooves of DNA
C) Interacting noncovalently with nucleotide bases, mostly within the major groove
D) Catalyzing enzymatic reactions to modify the DNA structure directly
Answer: C
(Transcription regulators rely on noncovalent interactions such as hydrogen bonds, ionic bonds, and hydrophobic interactions, mostly within the major groove.)
Which of the following best explains why transcription regulators often bind to DNA as dimers?
A) It increases the DNA’s flexibility, allowing easier transcription initiation.
B) It allows transcription regulators to form stronger and more specific interactions due to increased contact with DNA.
C) It promotes DNA denaturation and unwinding necessary for transcription initiation.
D) It ensures transcription regulators only bind to minor grooves, preserving the DNA structure.
Answer: B
(Dimerization increases the contact area, enhancing specificity and strength of protein-DNA interactions.)
Why do transcription factors typically recognize DNA sequences in the major groove rather than the minor groove?
A) The minor groove contains more methyl groups, preventing protein binding.
B) Only the major groove allows covalent bonds to form with transcription factors.
C) The major groove displays a more diverse and distinct pattern of hydrogen bond donors, acceptors, and hydrophobic groups.
D) The major groove has fewer available hydrogen-bonding features, simplifying recognition.
Answer: C
(The major groove provides more distinctive chemical patterns, enabling specific recognition by transcription factors.)
Why does dimerization of transcription regulators enhance their ability to bind DNA specifically and strongly?
A) It allows covalent bond formation between regulators and DNA bases.
B) It simplifies recognition by only binding to the minor groove.
C) It increases the total number of noncovalent contacts with the DNA, enhancing affinity and specificity.
D) It prevents the binding of RNA polymerase, thus increasing specificity.
Answer: C
(Dimerization doubles the potential contact points, greatly enhancing binding specificity and strength through additional noncovalent interactions.)
In a regulatory sequence “logo,” the height of each nucleotide symbol at each position represents:
A) The strength of covalent bonds formed with the transcription regulator.
B) The frequency at which that nucleotide is found at that specific position.
C) The total number of hydrogen bonds the nucleotide can form.
D) The affinity of the nucleotide to the DNA sugar-phosphate backbone.
Answer: B
(Logos visually represent the preferred nucleotide at each position based on its frequency in the transcription factor binding site.)
Why do certain bacterial promoters require activator proteins to initiate efficient transcription?
A) These promoters strongly bind repressors, blocking RNA polymerase binding sites. B) They contain mutated regulatory sequences that prevent RNA polymerase binding altogether. C) They inherently have low affinity for RNA polymerase, requiring activator proteins to enhance polymerase binding and positioning. D) Activator proteins prevent repressor proteins from interacting with DNA.
Answer: C
(Activator proteins compensate for weak promoters by interacting with RNA polymerase, positioning it efficiently for transcription initiation.)
Question 2:
In bacterial cells, how does the availability of alternative food sources (like sugars other than glucose) typically influence gene expression?
A) RNA polymerase becomes directly activated by alternative sugars.
B) Small metabolites bind transcription activator proteins, enabling them to activate the transcription of relevant metabolic genes.
C) DNA regulatory sequences spontaneously change their nucleotide sequences.
D) Transcription repressors bind to DNA and block transcription of operons that degrade alternative sugars.
Answer: B
(Activator proteins bind specific regulatory DNA sequences when glucose is unavailable, activating genes necessary to metabolize alternative sugars.)
How do histone acetyltransferases (HATs) influence transcription initiation in eukaryotic cells?
A) They tightly package nucleosomes, preventing transcription initiation. B) They add acetyl groups to histone tails, making chromatin more accessible for transcription. C) They directly recruit RNA polymerase to promoters without the need for other proteins. D) They remove acetyl groups from histones, causing chromatin compaction.
Answer: B
(Histone acetyltransferases modify histones by adding acetyl groups, leading to a more open chromatin structure that enhances transcription.)
What is the primary role of the Mediator complex in eukaryotic transcription?
A) To chemically modify nucleosomes by removing acetyl groups
B) To serve as a structural protein stabilizing DNA during replication
C) To bridge interactions between distant activator proteins and transcription machinery at promoters
D) To prevent RNA polymerase from binding prematurely to the promoter
C
(Mediator connects activators bound at distant enhancers with the transcription initiation complex at the promoter.)
How do eukaryotic repressor proteins typically reduce gene expression?
A) By permanently altering DNA sequences near promoters
B) By degrading RNA polymerase before it initiates transcription
C) By blocking assembly or function of the transcription initiation complex
D) By enhancing histone acetylation near promoters
Answer:
C
(Repressors decrease gene expression by interfering with or blocking assembly and function of the transcription initiation complex.)
Question 2:
Which statement best explains how eukaryotic repressors can affect transcription initiation from distant locations?
A) They chemically modify RNA polymerase to prevent transcription.
B) They recruit chromatin remodeling enzymes to open DNA structure.
C) They physically interact with transcription machinery through DNA looping, preventing its assembly or movement.
D) They degrade enhancer sequences upstream of the promoter.
C
(DNA looping allows repressors to physically interact with transcription machinery, interfering with its assembly or progression.)
What role does the “recognition helix” of a helix-turn-helix transcription factor play in DNA binding?
A) It stabilizes protein dimerization.
B) It directly contacts and binds specific DNA sequences.
C) It binds only nonspecifically to the DNA backbone.
D) It helps recruit histone acetyltransferases to DNA.
B
(The recognition helix specifically interacts with nucleotide sequences in DNA.)
A mutation in a gene encoding a homeodomain-containing protein results in an antenna developing instead of a leg in a fruit fly. Which of the following best explains why such a dramatic change occurs?
A) The mutation prevents DNA looping required for activator-enhancer interactions.
B) It alters the ability of histones to bind DNA, leading to widespread gene repression.
C) It changes the DNA-binding specificity of a transcription factor involved in controlling developmental genes.
D) It completely stops the synthesis of housekeeping proteins.
C
(Homeotic mutations alter transcription factors’ DNA-binding specificity, causing misexpression of developmental genes and incorrect body part formation.)
What structural feature of zinc finger proteins allows them to specifically recognize and bind DNA sequences?
A) A DNA-binding site formed exclusively by a β-sheet domain
B) The zinc ion coordinating two cysteines and two histidines, stabilizing the DNA-binding structure
C) An RNA intermediate facilitating contact between zinc fingers and DNA
D) An elongated α-helix without β-sheet involvement, binding DNA nonspecifically
B
(Zinc fingers use a coordinated zinc ion bound by cysteines and histidines to stabilize their structure, enabling specific DNA binding.)
Considering transcription factor diversity in humans, why might zinc finger proteins be so abundant and versatile?
A) They require fewer amino acids than other motifs, making their synthesis energetically favorable.
B) Zinc fingers can bind nonspecifically, reducing the need for precise DNA sequences.
C) The modular structure of zinc fingers allows diverse, specific interactions with numerous DNA sequences.
D) Zinc fingers permanently alter chromatin structure through covalent interactions with DNA.
C
(The modular and flexible nature of zinc finger motifs enables them to specifically recognize diverse DNA sequences, contributing to their widespread use in gene regulation.)
Question 1:
Why does the leucine zipper motif promote effective DNA binding by transcription regulators?
A) Because leucines directly bind DNA sequences, enhancing specificity
B) Because hydrophilic interactions between leucines tightly anchor the proteins to DNA
C) Because hydrophobic interactions between leucines promote stable dimerization of the transcription factors
D) Because leucines coordinate metal ions essential for DNA binding
C
(Leucine zippers form stable dimers through hydrophobic interactions between leucines, increasing DNA-binding specificity and strength.)
What advantage does the ability to form heterodimers give to leucine zipper transcription regulators?
A) It allows transcription factors to degrade DNA sequences, silencing genes permanently
B) It expands the range and specificity of DNA sequences that can be recognized by transcription regulators
C) It prevents transcription factors from binding DNA sequences nonspecifically
D) It facilitates the binding of activators directly to RNA polymerase, eliminating the need for Mediator
B
(Forming heterodimers allows transcription factors to recognize diverse DNA sequences, significantly expanding the range of possible regulatory interactions.)
How does the structural arrangement of the helix-loop-helix motif contribute to its function as a transcription factor?
A) It forms a rigid, linear structure enabling transcription factors to bind exclusively to minor grooves of DNA.
B) The flexible loop prevents any specific DNA interaction, ensuring only nonspecific DNA binding.
C) It allows dimerization, creating a stable 4-helix bundle that positions the DNA-binding domains to recognize specific DNA sequences.
D) The loop directly contacts and stabilizes the DNA backbone through covalent bonds.
C
(HLH proteins form dimers through hydrophobic interactions, creating a stable four-helix bundle critical for DNA binding specificity.)
How do histone acetyltransferases (HATs) promote transcription initiation?
A) By directly binding RNA polymerase to histones
B) By removing acetyl groups from histone tails, tightening DNA packaging
C) By catalyzing covalent modifications to histone tails that loosen chromatin structure
D) By cutting the DNA to expose promoter sequences
C
(Histone acetyltransferases add acetyl groups, loosening chromatin structure and facilitating transcription initiation.)
What role do chromatin-remodeling complexes play in transcription regulation?
A) They covalently modify transcription regulators to increase DNA binding strength
B) They reposition nucleosomes to make regulatory DNA regions accessible to transcription machinery
C) They methylate DNA bases to promote permanent gene silencing
D) They degrade histones to permanently expose DNA sequences
B
(Chromatin-remodeling complexes reposition nucleosomes to expose DNA, enabling transcription initiation.)
In eukaryotic cells, why can a single transcription regulator, such as the cortisol receptor, simultaneously activate multiple distinct genes?
A) Each gene shares identical promoter sequences that permanently bind RNA polymerase.
B) The transcription regulator chemically modifies RNA polymerase, enabling rapid transcription at multiple sites.
C) Each target gene has similar regulatory DNA sequences that can bind the same transcription regulator complex.
D) One transcription regulator binds directly to multiple RNA polymerases simultaneously, activating multiple genes at once.
C
(Multiple genes sharing similar regulatory sequences can be simultaneously controlled by a single transcription regulator.)
What advantage does combinatorial control of gene expression offer eukaryotic cells compared to simple, operon-based bacterial systems?
A) It permanently activates gene expression, making transcription irreversible.
B) It ensures rapid expression by permanently rearranging DNA into operons similar to bacteria.
C) It allows a single transcription regulator to decisively activate or repress groups of genes through shared DNA regulatory elements.
D) It requires fewer proteins overall, thus simplifying gene regulation.
C
(Combinatorial control allows single transcription regulators to coordinate the expression of multiple genes by recognizing common regulatory DNA elements.)
