Unit 10: Gene Regulation, Chromatin, and Epigenetics
How a cell decides which genes to read, from a bacterium's operon to a human genome folded around histones.
7 topics · 22 questions
Each topic is a path, not a menu: work down it in order and every question builds on the one above. Click any of them to watch the answer draw itself.
The Lac Operon and Inducible Gene Expression
- How it worksHow does the lac repressor block RNA polymerase from transcribing the lac operon when lactose is absent?
- How it worksWalk me through how lactose itself binds the repressor and knocks it off the DNA to switch the operon on.
- Common mistakeWhy isn't the lac operon simply always on whenever lactose is present, no matter how much glucose is around?
- Going furtherWhat happens to the lac operon's activity when both glucose and lactose are available to the cell at the same time?
Your turn1 of 2
A bacterium has plenty of lactose available, and a student assumes the lac operon should therefore be fully switched on, full stop, regardless of anything else in the cell's environment. Why isn't the lac operon simply always fully on whenever lactose is present, no matter how much glucose is around?The Trp Operon and Repressible Gene Expression
- How it worksHow does tryptophan itself bind the trp repressor and activate it to block its own operon's transcription?
- Going furtherWhat happens to the trp operon's activity once the cell's tryptophan levels drop back down?
- Ties togetherHow does the trp operon's repression by its own end product mirror the same feedback-inhibition logic an enzyme pathway uses?
Your turn1 of 2
Unlike the lac repressor, which is knocked off DNA by its inducer, the trp repressor is actually activated by binding tryptophan rather than released by it. A student assumes this must be a typo or an exception with no real mechanistic logic behind it. What is actually happening when tryptophan binds the trp repressor?Transcription Factors and How They Find Their DNA Targets
- How it worksHow does a transcription factor's shape read the pattern of hydrogen-bond donors and acceptors exposed in DNA's major groove?
- Common mistakeWhy isn't a transcription factor recognizing its target sequence by peeking at the bases from outside the helix without touching them?
- Going furtherWhat happens to a gene's expression when a mutation changes the DNA sequence a transcription factor is supposed to bind?
Your turn1 of 2
A transcription factor reliably finds and binds one specific short sequence among billions of bases in the genome. A student assumes it must scan the outside of the intact double helix, somehow sensing the sequence without ever touching the bases themselves. How does a transcription factor actually recognize its target?Chromatin Structure: DNA Wrapped Around Histones
- How it worksHow does DNA wrap around a core of eight histone proteins to form a single nucleosome?
- Worked exampleFind roughly how many nucleosomes are needed to package a 20,000 base pair stretch of DNA if each nucleosome wraps about 200 base pairs.
- Common mistakeWhy isn't chromatin just DNA sitting loosely tangled inside the nucleus?
Your turn1 of 2
Find roughly how many nucleosomes are needed to package a 44214 base pair stretch of DNA if each nucleosome wraps about 195 base pairs.Histone Modification and Chromatin Accessibility
- How it worksHow does acetylating a histone's tail loosen its grip on DNA and open that region up for transcription?
- Going furtherWhat happens to a gene's accessibility when its histones get modified in a way that condenses the chromatin instead?
- Common mistakeWhy isn't histone modification changing the DNA sequence of the genes that it regulates?
Your turn1 of 2
Adding a small acetyl group to a histone's tail can open up a whole stretch of chromatin for transcription. A student assumes such a tiny chemical addition should be too small to have any real structural effect on how tightly DNA is packaged. How does acetylation actually loosen a histone's grip on DNA?DNA Methylation and Epigenetic Inheritance
- How it worksHow does adding a methyl group to cytosine bases in a gene's promoter silence that gene without changing its sequence?
- Going furtherWhat happens to a cell's pattern of gene expression when it divides and passes its DNA methylation marks to daughter cells?
- Ties togetherHow does DNA methylation's chemistry connect back to the same acid-base chemistry that governs a molecule's protonation state?
Your turn1 of 2
A skin cell and a neuron carry an identical DNA sequence, yet express very different sets of genes and never switch identities. A student assumes such a permanent difference between genetically identical cells must come from some difference in their actual DNA sequence after all. How can DNA methylation explain a permanent difference without any sequence change?Why Eukaryotic Gene Regulation Needs More Machinery Than a Bacterium's
- How it worksHow do enhancers sitting far from a gene loop the DNA around to reach the promoter and help switch it on?
- Common mistakeWhy isn't an enhancer required to sit right next to the gene that it regulates?
- Ties togetherHow does an enhancer looping DNA to reach its promoter reuse the same three-dimensional folding logic a protein uses to fold?
Your turn1 of 2
An enhancer sitting tens of thousands of base pairs away from a gene still manages to help switch that gene on. A student assumes a regulatory sequence that far away could not possibly have any real functional connection to the gene, since it is nowhere near the promoter along the linear DNA sequence. How does a distant enhancer actually reach the gene it regulates?