DNA and RNA Structure
Describe the structural differences between DNA and RNA. Include the sugar, nitrogenous bases, and strand structure.
DNA contains deoxyribose, uses thymine, and is double-stranded. RNA contains ribose, uses uracil instead of thymine, and is typically single-stranded.
What is the role of RNA polymerase during transcription?
RNA polymerase binds to the promoter region of DNA, unwinds the DNA strands, and synthesizes a complementary mRNA strand in the 5' to 3' direction.
What is the function of a promoter in gene expression?
A promoter is a DNA sequence upstream of a gene where RNA polymerase and transcription factors bind to initiate transcription.
What causes different cell types to express different proteins if they all have the same DNA?
Differential gene expression, regulated by transcription factors, signaling pathways, and epigenetic modifications, determines which genes are transcribed in each cell type.
What is the purpose of PCR (polymerase chain reaction)?
PCR amplifies a specific DNA segment exponentially using primers, DNA polymerase, and thermal cycling, allowing analysis of small DNA samples.
Explain how the antiparallel structure of DNA affects replication.
The antiparallel structure means that DNA strands run in opposite 5' to 3' directions. This affects replication by causing the leading strand to be synthesized continuously and the lagging strand discontinuously in Okazaki fragments.
Differentiate between the roles of mRNA, tRNA, and rRNA in protein synthesis.
mRNA carries the genetic code from DNA to the ribosome; tRNA brings specific amino acids to the ribosome based on codon-anticodon matching; rRNA forms the core of ribosome structure and catalyzes peptide bond formation.
How do repressors regulate gene expression in prokaryotes?
Repressors bind to the operator region of an operon, blocking RNA polymerase and preventing transcription of downstream genes.
How does a point mutation differ from a frameshift mutation in terms of impact on the resulting protein?
A point mutation alters one nucleotide, possibly changing one amino acid (missense), or causing no change (silent), or a stop codon (nonsense). A frameshift mutation (insertion/deletion) changes the reading frame, usually resulting in a completely nonfunctional protein.
How does gel electrophoresis separate DNA fragments?
DNA fragments are loaded into a gel and subjected to an electric field; smaller fragments migrate faster toward the positive end due to size differences.
How does base pairing specificity support the semiconservative model of replication?
Base pairing (A-T, C-G) ensures that each new DNA strand is complementary to the original strand. This allows one original strand to be conserved in each new double helix, supporting the semiconservative replication model.
Explain the significance of the 5’ cap and poly-A tail added to eukaryotic pre-mRNA.
The 5’ cap protects mRNA from degradation and aids in ribosome binding; the poly-A tail stabilizes the transcript and regulates nuclear export and translation efficiency.
Describe how an inducer molecule can activate gene expression in the lac operon.
In the presence of lactose, allolactose (an inducer) binds to the lac repressor, causing it to release from the operator, allowing RNA polymerase to transcribe the genes for lactose metabolism.
What is the role of master regulatory genes in cell differentiation?
Master regulatory genes encode transcription factors that activate a cascade of gene expression patterns, initiating a developmental program for a specific cell type.
Explain how restriction enzymes and plasmids are used in recombinant DNA technology.
Restriction enzymes cut DNA at specific sequences. Plasmids (circular DNA vectors) can be opened with the same enzyme and recombined with the target gene. The recombinant plasmid is introduced into bacteria for gene expression or cloning.
How do hydrogen bonds and covalent bonds function differently in the DNA double helix?
Hydrogen bonds hold complementary nitrogenous bases together across strands (A-T, C-G), allowing for strand separation during replication and transcription. Covalent phosphodiester bonds form the backbone between the sugar and phosphate groups, maintaining strand integrity.
How does alternative splicing contribute to protein diversity?
Alternative splicing allows a single gene to produce multiple mRNA variants by including or excluding specific exons, leading to different proteins with potentially distinct functions from the same gene.
Explain how enhancers and transcription factors regulate eukaryotic gene expression.
Enhancers are distal DNA elements where activator proteins bind. These activators interact with transcription factors at the promoter through DNA looping, increasing RNA polymerase binding and transcription rate.
How can mutations in non-coding regulatory regions affect gene expression and phenotype?
Mutations in promoters, enhancers, or silencers can alter transcription factor binding, affecting when, where, and how much a gene is expressed, potentially changing phenotype without altering coding sequences.
What is the function of CRISPR-Cas9 in genome editing?
CRISPR-Cas9 uses a guide RNA to target a specific DNA sequence. The Cas9 enzyme makes a double-strand break at this site, allowing genes to be inserted, deleted, or altered during the repair process.
Predict how replacing a purine with another purine versus a pyrimidine would affect DNA structure. Use molecular reasoning.
Replacing a purine with another purine (e.g., A → G) keeps the DNA width relatively unchanged, but may affect hydrogen bonding. Replacing a purine with a pyrimidine (e.g., A → C) changes the helix diameter and may distort the DNA, potentially interfering with replication or repair.
Compare and contrast DNA replication and transcription in terms of enzymes involved, directionality, and final products.
DNA replication uses DNA polymerase to produce two identical DNA molecules in a semi-conservative manner. Transcription uses RNA polymerase to produce a single-stranded mRNA copy of one gene. Both proceed 5' to 3', but replication involves more enzymes (e.g., helicase, primase) and generates DNA, while transcription creates RNA.
How can epigenetic modifications such as DNA methylation and histone acetylation affect gene expression without altering the DNA sequence.
DNA methylation typically silences genes by compacting chromatin or blocking transcription factor binding. Histone acetylation loosens chromatin structure, allowing greater access to DNA for transcription machinery, thereby enhancing gene expression.
Describe how gene expression is altered in cancer cells and relate this to mutations in proto-oncogenes and tumor suppressor genes.
Mutations that activate proto-oncogenes (e.g., Ras) can cause unchecked cell growth. Loss-of-function mutations in tumor suppressor genes (e.g., p53) impair cell cycle checkpoints or apoptosis, allowing damaged cells to proliferate, leading to cancer.
Evaluate the ethical considerations and potential risks of using gene editing technologies in human embryos.
Ethical concerns include unintended off-target effects, long-term consequences, consent issues, and the potential for eugenics. While gene editing holds promise for disease prevention, its use in germline cells raises significant societal and moral questions.