Molecular Biology & Gene Regulation: Central Dogma, Operons, and Epigenetics

What is the central dogma of molecular biology?

The flow of genetic information: DNA is copied into mRNA (transcription), and then the mRNA code is used to build a protein (translation). DNA → RNA → Protein.

What is transcription?

The process where the DNA code is copied into messenger RNA (mRNA).

What is translation?

The process where the mRNA code is used to dictate the order of amino acids to build a protein.

How does prokaryotic gene regulation primarily work?

Prokaryotic gene regulation is primarily controlled at the transcriptional level (DNA → RNA) using operons that turn transcription on or off.

How does eukaryotic gene regulation differ from prokaryotic?

Eukaryotic gene regulation is multi-level — it occurs at many stages: during DNA replication/storage, during transcription, after transcription/before translation, and after translation.

What are housekeeping genes?

Genes expressed in almost every cell type to perform basic, essential cellular functions. They are constitutively expressed.

What are regulated genes?

Genes expressed only when needed, in response to a specific signal. They code for proteins not always required in every cell.

What are the three levels of gene expression control, ordered from slowest/most energy-efficient to fastest/most energy-costly?

1) Transcriptional control (slowest, saves the most energy — best). 2) Pre-translational control (moderate). 3) Post-translational control (fastest, uses the most energy).

What is a transcriptional unit?

The segment of DNA from the initial point to the final point of transcription for a gene or group of genes. These genes are typically involved in the same function.

What is an operon?

A prokaryote-only gene regulation system consisting of a promoter, operator, and a group of co-regulated structural genes that are transcribed together as a unit.

What is a promoter?

A regulatory DNA sequence where RNA polymerase binds to initiate transcription. It controls gene expression by starting a transcription event. Found in both prokaryotes and eukaryotes.

How does the promoter differ between prokaryotes and eukaryotes?

Prokaryotic promoters are usually coupled with an operator. Eukaryotic promoters are usually coupled with a TATA box and transcription factors.

What is an operator?

A regulatory DNA sequence (prokaryotes only) where a repressor can bind to block transcription, or an activator can bind to initiate transcription.

What is a repressor?

A regulatory protein that binds to the operator to block RNA polymerase and decrease (or stop) gene expression — this is negative regulation.

What is an activator (transcription factor)?

A regulatory protein that binds to a regulatory sequence to promote and increase transcription — this is positive regulation.

What is a coactivator?

A transcription factor that enhances transcription by bringing activators and the transcriptional machinery closer together.

What is an inducer?

A molecule that interacts with activators or repressors to influence gene expression, often by changing the shape/activity of those regulatory proteins.

What are the components of the lac operon and their functions?

Lac I: lac repressor protein. Lac Z: β-galactosidase — breaks down lactose into glucose, galactose, and allolactose. Lac Y: permease — protein channel that transports lactose into the cell. Lac A: transacetylase — exports excess sugar from the cell.

Under normal conditions (no lactose), is the lac operon on or off? Why?

Off. The lac repressor (Lac I) binds the operator and blocks transcription. There is no need to produce lactose-digesting enzymes if lactose is not present.

How does lactose turn on the lac operon?

Lactose is converted to allolactose. Allolactose (the inducer) binds to the lac repressor, inactivating it. The repressor can no longer block the operator, so RNA polymerase can transcribe the lac genes.

How does glucose level regulate the lac operon?

High glucose inhibits the lac operon (no need to digest lactose). Low glucose enhances the lac operon (need an alternative energy source). This is mediated through the CAP system.

What is CAP (Catabolite Activator Protein)?

The lac operon activator. It is synthesized in an inactive form and must be activated by cAMP to bind the CAP site in the promoter, enabling RNA polymerase to bind efficiently.

How is cAMP produced, and how does glucose affect it?

ATP is converted to cAMP by the enzyme adenylate cyclase. High glucose concentrations inhibit adenylate cyclase → no cAMP is made → CAP stays inactive → no enhanced transcription.

Summarize the domino effect of CAP regulation:

Low glucose → adenylate cyclase active → ATP → cAMP → cAMP activates CAP → active CAP binds promoter → RNA polymerase binds efficiently → transcription of lac operon increases.

What are the four combinations of glucose/lactose conditions and their effect on lac operon transcription?

1) High lactose + low glucose: high cAMP activates CAP + repressor off → maximum transcription. 2) Low lactose + high glucose: no CAP activation + repressor on → no transcription. 3) High lactose + high glucose: repressor off but no CAP → low/no transcription. 4) Low lactose + low glucose: CAP active but repressor on → no transcription.

What is negative control in the lac operon?

The repressor system — the lac repressor blocks transcription when lactose is absent. The repressor must be turned off (by allolactose) for transcription to occur.

What is positive control in the lac operon?

The CAP system — active CAP (activated by cAMP when glucose is low) binds the promoter and enhances transcription. CAP must be turned on for full transcription.

What is the TRP operon and how is it regulated?

The TRP operon controls tryptophan synthesis. It is regulated by negative feedback inhibition: when enough tryptophan is present, tryptophan binds to the inactive repressor, activating it. The active repressor then shuts off transcription of the TRP genes.

How does the TRP operon differ from the lac operon in terms of regulation logic?

Lac operon: the end product (lactose/allolactose) turns transcription ON (inducible system). TRP operon: the end product (tryptophan) turns transcription OFF (repressible system via negative feedback).

What is the TATA box in eukaryotic gene regulation?

A regulatory sequence in the eukaryotic promoter region where transcription factors bind to recruit RNA polymerase II to initiate transcription.

What is an enhancer in eukaryotic gene regulation?

A regulatory DNA sequence upstream of the transcriptional unit that binds activator proteins. The upstream region bends to allow activators to interact with transcription factors at the promoter, stabilizing the transcription machinery and promoting transcription.

What is a silencer in eukaryotic gene regulation?

A regulatory DNA sequence that binds repressor proteins, inhibiting transcription of the associated gene.

What are promoter proximal elements (PPEs)?

Regulatory sequences near the promoter that help enhance or inhibit transcription by binding regulatory proteins.

How do coactivators function in eukaryotic transcription?

Coactivators form a bridge between activator proteins bound at the enhancer and activator proteins bound at the promoter proximal region, helping to stabilize the transcription machinery and allow transcription to proceed.

What is chromatin remodeling (epigenetics)?

A pre-transcriptional regulation mechanism where DNA is either made more or less accessible for transcription by modifying its association with histone proteins.

What is euchromatin, and what modification is associated with it?

Euchromatin is "open" chromatin — DNA is accessible for transcription. It is associated with acetylation of histones, which loosens the DNA-histone interaction.

What is heterochromatin, and what modification is associated with it?

Heterochromatin is "closed" chromatin — DNA is tightly packed and inaccessible for transcription. It is associated with methylation of histones or DNA, which makes DNA less accessible.

What is alternative splicing, and why is it significant?

After transcription, introns are removed (exit) and exons are kept (stay) in the mRNA. Alternative splicing allows different combinations of exons to be included, producing different proteins from the same gene.

What are introns and exons?

Introns: non-coding sequences that are removed from pre-mRNA and NOT translated. Exons: coding sequences that remain in mRNA and ARE translated into protein.

What is miRNA (micro-RNA) and what is its role?

miRNA is a small RNA molecule that is part of RNA interference. It regulates gene expression post-transcriptionally by associating with the RISC protein complex, which binds to the 3' UTR of target mRNA. If the match is perfect, the complex cleaves the mRNA, silencing gene expression.

What is RNA interference (RNAi)?

A post-transcriptional gene regulation mechanism in which small RNA molecules (like miRNA) guide protein complexes to degrade or block translation of target mRNA sequences.

What is a proto-oncogene?

An unmutated gene in normal cells that stimulates cell division. They are expressed in balance with tumor suppressor genes to regulate normal cell growth.

What is an oncogene?

A mutated proto-oncogene that causes overactivity in cell division, potentially leading to cancer. Proto-oncogene → oncogene via mutation.

What is a tumor suppressor gene?

An unmutated gene that inhibits cell division. It acts as a brake on cell growth. Both alleles must be mutated/inactivated for the gene to lose its inhibitory function (two-hit hypothesis).

Why must both alleles of a tumor suppressor gene be mutated to cause cancer?

Because one functional copy is sufficient to inhibit cell division. Both copies must be lost for the tumor-suppressive function to be eliminated.

How do oncogenes and tumor suppressor genes both lead to cancer, and how do they differ?

Oncogenes cause cancer by being overactive (too much stimulation of division). Mutated tumor suppressor genes cause cancer by losing inhibition (not enough braking of division). Both result in uncontrolled cell growth, but through opposite mechanisms.

What is the difference between hereditary and sporadic cancer?

Hereditary cancers run in families and are due to inherited mutations in tumor suppressor genes or proto-oncogenes. Sporadic cancers are not inherited and result from new (somatic) mutations in those same genes.

What are driver mutations in cancer?

Mutations that directly drive tumor formation and progression — they provide a growth advantage to cancer cells.

What are passenger mutations in cancer?

Mutations present in tumor cells that have no effect on cancer progression — they are "along for the ride" but do not contribute to tumor growth.