Exam 4: Gene Expression and Cell Signaling Concepts

Gene expression

Regulated, leading to different transcriptomes and proteomes.

Transcription factors (TFs)

Bind to cis-regulatory sequences, typically 5-12 bp in the major groove.

Transcription factor dimerization

Increases DNA-binding specificity and affinity.

DNA-binding motifs

Helix-Turn-Helix, Homeodomain, Zinc Finger, Leucine Zipper (bZIP), Basic Helix-Loop-Helix (bHLH).

Promoter

A DNA region where RNA polymerase and general TFs bind to initiate transcription.

Enhancers

Bind TFs, loop DNA to contact promoters, and increase transcription.

Mediator complex

Links enhancer-bound TFs to RNA polymerase II.

Histone modifications

Used to remodel chromatin structure and expose promoters.

Super-enhancers

Large clusters of enhancers driving high expression of key identity genes.

Repressors

Inhibit transcription by blocking activator binding, recruiting chromatin modifiers, or compacting chromatin.

Insulators

DNA sequences that block enhancers from activating the wrong genes.

Biomolecular condensates

Membraneless organelles that concentrate transcription machinery.

ATAC-seq

Used to identify open chromatin regions accessible to TFs.

Luciferase assay

A reporter gene assay measuring promoter activity by light output.

Tryptophan operon regulation

Tryptophan activates a repressor that blocks transcription when levels are high.

Lac operon regulation

Activated only when lactose is present and glucose is absent.

DNA looping in prokaryotic regulation

Brings distal regulatory sequences into contact with RNA polymerase.

Signaling molecules

Hydrophilic (cannot cross membranes) and hydrophobic (can diffuse across membranes).

Second messengers

Small intracellular molecules like cAMP, IP3, DAG, and Ca^2 that amplify signals.

Kinase and GTPase switches

Activate/inactivate proteins via phosphorylation or GTP binding.

GPCRs

Activate G-proteins that trigger downstream effects via second messengers.

Receptor tyrosine kinases (RTKs)

Activate intracellular cascades like Ras -> Raf -> MEK -> MAPK.

Notch/Delta signaling

A juxtacrine pathway where membrane-bound Delta activates Notch on adjacent cells.

Main phases of the cell cycle

Interphase (G1, S, G) and M phase (mitosis + cytokinesis).

Cell cycle progression control

Controlled by cyclins and cyclin-dependent kinases (CDKs).

Role of p53 in the cell cycle

Halts the cycle upon DNA damage, allowing for repair or apoptosis.

Cancer and the cell cycle

Loss of checkpoint control and mutations in genes like p53 lead to uncontrolled division.

Types of cell death

Apoptosis (programmed) and necrosis (accidental or regulated like necroptosis).

Key features of apoptosis

Cell shrinkage, DNA fragmentation, membrane blebbing, and non-inflammatory cleanup.

Caspases in apoptosis

Proteases that execute the death program.

Necrosis

Unregulated cell death causing inflammation, while apoptosis is regulated and non-inflammatory.