QCE Biology: Gene Expression and Regulation Flashcards

Comprehensive vocabulary flashcards covering chromatin structure, epigenetic chemical tags, transcription factors, cell differentiation pathways, and epigenetic cancer therapies as outlined in the QCE Biology revision booklet.

Genome Paradox

The phenomenon where every cell in an organism contains an identical DNA sequence (e.g., $3\text{ billion}$ base pairs and $20{,}000$ genes), yet cells differ completely in appearance, function, and protein production because they read different sections of that DNA.

Gene Expression

The process by which a gene's sequence is actively used to produce a protein through mRNA transcription and subsequent translation.

Nucleosome

The fundamental repeating unit of chromatin, composed of approximately $147$ base pairs of DNA wound $1.65$ times around a core of $8$ histone proteins.

Euchromatin

A loosely wound, spread-apart state of chromatin where DNA is physically accessible to RNA polymerase, allowing active gene transcription (gene ON).

Heterochromatin

A tightly packed, condensed state of chromatin where DNA is physically blocked from RNA polymerase, leaving genes silent and unread (gene OFF).

Histone Acetylation

An epigenetic modification where HAT enzymes add acetyl groups to positively charged lysine residues on histone tails, neutralising their charge, loosening DNA, and relaxing chromatin into euchromatin.

Histone Acetyltransferases (HATs)

Enzymes that attach acetyl groups to lysine residues on histone tails, weakening their electrostatic attraction to negatively charged DNA and opening chromatin.

Histone Deacetylases (HDACs)

Enzymes that remove acetyl groups from histone tails, restoring positive charge on lysine residues and compacting chromatin back into heterochromatin.

CpG Site

A DNA region where a cytosine (C) base sits directly adjacent to a guanine (G) base on the same strand, connected by a phosphate bond ('p').

CpG Islands

Clusters of CpG sites located near a gene's promoter region that function as target sites for DNA methylation.

DNA Methylation

An epigenetic mechanism where DNA methyltransferases add a methyl group ($-\text{CH}_3$) onto carbon-5 of cytosine bases at CpG islands, obstructing transcription factor binding and recruiting MBDs to silence the gene.

DNA Methyltransferases

Enzymes responsible for transferring a methyl group ($-\text{CH}_3$) directly onto carbon-5 of cytosine bases at CpG islands.

Methyl-CpG-binding Proteins (MBDs)

Proteins attracted to methylated CpG sites on DNA that induce further compaction of chromatin into dense heterochromatin.

Transcription Factor

A protein that binds to the promoter region of a specific gene to regulate whether RNA polymerase can initiate transcription.

Activators

Transcription factors that land on promoter regions and assist RNA polymerase in initiating transcription, switching the gene ON.

Repressors

Transcription factors that block promoter regions or recruit HDACs to condense chromatin, keeping the gene OFF.

Signal Transduction

The four-step intracellular pathway through which an extracellular signal binds a receptor, produces secondary messengers, activates a transcription factor, and triggers gene expression in the nucleus.

HSF1

A transcription factor that trimerises in response to heat/thermal shock and activates chaperone protein genes to refold denatured proteins.

HIF-1

A transcription factor activated during low oxygen (hypoxia) that avoids degradation and switches on the erythropoietin (EPO) gene to produce more red blood cells.

p53

A transcription factor phosphorylated in response to UV irradiation that activates cell cycle arrest or apoptosis genes to repair DNA or destroy the cell.

mTORC1

A transcription factor pathway component activated by nutrient availability that switches on ribosomal protein genes to boost cellular protein synthesis capacity.

Cell Differentiation

The developmental process by which dividing stem cells permanently commit to specific lineage identities through selective gene regulation.

Totipotent

The state of maximum cellular potency (such as a zygote) capable of developing into any body cell type as well as extraembryonic structures like the placenta.

Pluripotent

A developmental potency level (found in the inner cell mass of an embryo) that allows differentiation into any body cell type except the placenta.

Multipotent

A potency level restricted to tissue stem cells (e.g., blood stem cells) that can differentiate into any cell type within a single specific lineage.

Terminally Specialised

A fully committed cell state (e.g., muscle cell, liver cell, neuron) with zero developmental flexibility and a permanently fixed identity.

Master Regulators (Pioneer Factors)

Transcription factors powerful enough to bind promoter regions within condensed heterochromatin and recruit remodeling factors to permanently rewrite cell identity.

MyoD

The master regulator transcription factor for muscle identity that forces entry into heterochromatin at muscle gene promoters, recruits HATs, and transforms non-muscle cells into functional skeletal muscle.

Epigenetics

Modifications that alter gene expression patterns without making any changes to the underlying DNA base sequence.

Epigenome

The full set of chemical tags (including DNA methyl tags and histone acetyl groups) across a cell's entire genome that determines gene accessibility.

Hemi-methylated DNA

A DNA double helix immediately following replication where the parent strand retains original methyl marks but the newly synthesized daughter strand is unmethylated.

DNMT1

The maintenance methylase enzyme that recognizes hemi-methylated CpG sites during DNA replication and copies methyl marks to the newly synthesized strand, preserving cell identity across divisions.

DNMT Inhibitors

Epigenetic drugs that block DNA methyltransferase activity, causing methyl marks to progressively dilute out across cell divisions and reactivating silenced tumour suppressor genes.

HDAC Inhibitors

Epigenetic drugs that block histone deacetylase enzymes, allowing acetyl groups to accumulate so that chromatin surrounding tumour suppressor genes remains open as euchromatin.