Transcription
They help RNA polymerase recognize the promoter and for them transcription initiation site
Why is the genetic code considered “degenerate” but not ambiguous?
Multiple codons can specify the same amino acid, but each codon specifies only one amino acid.
Why are introns advantageous for genomic evolution?
They allow exon shuffling and recombination, creating new gene combinations.
Explain how the lac repressor can both inhibit and permit transcription in the same operon depending on lactose presence.
It blocks RNA polymerase when bound to the operator but detaches when lactose binds allosterically, allowing transcription.
Why do identical twins sometimes have different gene expression profiles later in life?
Environmental factors cause epigenetic changes like methylation and histone modification.
How can mutations in the promoter region alter gene expression without changing the protein product?
They change transcription factor binding affinity, affecting transcription rate and mRNA levels.
What role do release factors play in translation termination, and how do they differ from tRNAs?
Release factors bind stop codons in the A site and trigger peptide release; they’re proteins, not RNAs.
Why is Taq polymerase ideal for PCR, and what would happen if a non-thermostable polymerase were used instead?
Taq is heat-stable and survives high-temperature denaturation; a non-thermostable polymerase would denature and stop functioning after the first cycle.
How does glucose concentration influence cAMP levels and CAP activity in the lac operon?
High glucose → low cAMP → CAP inactive → reduced transcription; low glucose → high cAMP → CAP binds promoter → enhanced transcription.
Why is gene expression more complex in eukaryotes than in prokaryotes?
Compartmentalization, chromatin structure, and multiple regulatory layers (transcriptional, post-transcriptional, etc.).
Differentiate between enhancer and promoter sequences in terms of position, function, and transcription factor interaction.
Promoters are close to the transcription start site and bind general factors; enhancers can be far away and bind activator proteins to increase transcription.
How does translation initiation work in eukaryotes?
Ribosome binds to 5' cap and scans for start codon
PCR can amplify a specific DNA segment exponentially. What are the three main temperature steps of PCR and their purposes?
Denaturation (≈95°C): DNA strands separate.
Annealing (≈55–65°C): Primers bind to target sequence.
Extension (≈72°C): Taq polymerase synthesizes new DNA strands.
Compare repression in the lac operon vs the trp operon in terms of corepressor/inducer mechanisms.
Lac = inducible; lactose inactivates the repressor. Trp = repressible; tryptophan activates the repressor.
Explain how post-translational modifications regulate protein activity and give one specific example.
Change protein shape and therefore function (phosphorylation, acetylation, methylation)
Explain how histone acetylation influences transcription at the molecular level.
Acetylation neutralizes histone positive charges, loosening DNA-histone interactions, allowing transcription machinery better access to DNA.
A sequence of DNA switches from GAA to TAA. What type of mutation occurs in the protein?
Nonsense
How does CRISPR naturally function in bacteria, and how is that mechanism exploited for genome editing in eukaryotes?
In bacteria, CRISPR-Cas recognizes and cuts viral DNA; in labs, Cas9 is guided by sgRNA to specific target sites for precise DNA editing.
Suppose the CAP-binding site in the lac operon is deleted. How does this affect transcription when lactose is present but glucose is absent?
Transcription occurs at a much lower rate because CAP-cAMP cannot bind to enhance RNA polymerase attachment, reducing promoter efficiency.
What effect does histone deacetylase (HDAC) activity have on gene expression?
It removes acetyl groups, tightening DNA-histone interactions, and silencing transcription.
How does the presence of multiple RNA polymerases (I, II, III) in eukaryotes contribute to regulation efficiency?
Each polymerase specializes in different RNA classes (rRNA, mRNA, tRNA), allowing independent regulation of synthesis rates for each type.
A single base insertion near the start of a coding sequence causes an early stop codon. How could a second mutation later in the sequence restore partial protein function?
A compensatory deletion or insertion (frameshift reversion) could restore the reading frame, producing a mostly functional protein.
PCR and gel electrophoresis are used to confirm the insertion of a target gene in a GMO plant. What specific result on a gel would confirm that the plant was successfully transformed?
A DNA band at the expected size for the inserted gene appears in transformed samples but not in wild-type controls.
How could an operon structure benefit prokaryotes compared to eukaryotes in terms of gene regulation efficiency?
It allows coordinated expression of functionally related genes under a single promoter. This allows for quick changed to environmental signals
A miRNA is overexpressed in a cell line. Describe how this would affect its target mRNAs and protein levels.
The miRNA binds complementary sequences in target mRNAs, causing either mRNA degradation or translational inhibition, resulting in reduced protein production.