Chromatin and DNA packaging
A gene is actively transcribed but suddenly becomes inaccessible after histone deacetylation. What chromatin state did it shift into?
Heterochromatin
What paradox describes the lack of correlation between genome size and organism complexity?
C-value paradox
In what direction does DNA polymerase synthesize DNA?
5’ to 3’
What modification protects mRNA from degradation at the 5’ end?
5’ cap
What codon starts translation?
AUG
A mutation reduces lysine content in histone tails. Predict the effect on DNA-histone interaction.
Why are microsatellites useful in forensic analysis?
They are highly polymorphic and vary between individuals
Why is a primer required for DNA replication?
DNA polymerase cannot initiate synthesis, it can't recognize single stranded DNA, and needs a free 3'-OH group for DNAp to start adding nucleotides.
What sequence signals polyadenylation?
AAUAAA
What happens at the A site?
What happens at the A site?
Why are nucleosomes considered regulatory hotspots for transcription rather than just structural units?
Their positioning and modification directly control DNA accessibility to transcription machinery
hy can organisms with similar gene numbers have vastly different complexity?
Alternative splicing and transcriptional regulation increase functional diversity
What would happen if ligase were nonfunctional?
Okazaki fragments would not be joined
What happens if U1 cannot bind to the 5’ splice site?
Splicing would fail. The intron would stay in the RNA.
What is the role of elongation factors?
Ensure correct codon-anticodon pairing
A drug inhibits topoisomerase II. Predict the effect on higher-order chromatin structure.
Disruption of chromatin loop formation, leading to impaired organization and compaction
How can moderately repetitive DNA influence gene expression despite being non-coding?
Affects transcription factor binding, splicing, methylation, and mRNA processing
A mutation disables DNA pol III proofreading. Predict the consequence.
Increased mutation rate due to loss of error correction
Why can multiple RNA polymerases transcribe the same gene simultaneously?
If it's a protein we really need in our bodies, this increases transcription efficiency and mRNA output
What are disulfide bonds, and how do they form? What phase of protein folding would you find them?
A mutation prevents histone acetyltransferase (HAT) activity in a specific genomic region. Predict downstream effects on transcription, chromatin structure, and protein production.
Without HAT, histones remain positively charged, and there's tighter DNA binding. This means chromatin remains condensed (heterochromatin-like), transcription factors cannot access DNA, and there's a decrease in transcription, reducing mRNA, and decreasing protein production
Explain how the G-value paradox challenges the concept of “one gene = one function.”
Gene number does not equal functional output because one gene can produce multiple proteins via alternative splicing, RNA editing, and regulatory mechanisms.
A mutation prevents primase from functioning. Explain the full replication consequence mechanistically.
No RNA primers, so DNA polymerase cannot initiate synthesis. Replication halts entirely, and cell cannot divide
Explain mechanistically how CTD phosphorylation regulates transcription.
Unphosphorylated RNA Pol II binds promoter but is inactive (off) phosphorylation (on) activates elongation and allows transition from initiation to RNA synthesis. It is phosphorylated by the PIC.
Explain energetically why protein synthesis is costly and how this relates to regulation.
Each peptide bond requires 4 high-energy phosphates. 2ATP are used to charge the tRNA, 1GTP is used for the binding of tRNA to the ribosome, and 1GTP is used for translocation of the tRNA.