Gene Regulation, Logic & Epigenetics – Vocabulary Flashcards

A set of vocabulary flashcards covering fundamental terms and concepts from the lecture on how cells regulate gene expression, including prokaryotic lac operon logic, eukaryotic transcription control, DNA-binding protein mechanisms, and epigenetic regulation.

Promoter

DNA sequence where RNA polymerase and associated factors bind to initiate transcription.

Terminator

DNA sequence that signals RNA polymerase to stop transcription.

Gene Regulation

Control of the timing and amount of gene transcription in response to cellular conditions.

Activator

DNA-binding regulatory protein that increases transcription when bound near a promoter.

Repressor

DNA-binding regulatory protein that decreases or blocks transcription when bound near a promoter.

Operator

Regulatory DNA site where a repressor (e.g., LacI) binds to block RNA polymerase.

Lac Operon

E. coli gene cluster whose transcription is regulated by lactose and glucose availability.

LacI

Repressor protein encoded by lacI that binds the Lac operator to inhibit lactose-gene transcription.

Allolactose

Lactose metabolite that binds LacI, preventing its DNA binding and inducing lac gene expression.

CAP (Catabolite Activator Protein)

cAMP-binding activator that stimulates lac transcription when glucose is low.

cAMP

Cyclic AMP; small molecule whose levels rise as glucose falls and which activates CAP.

Catabolite Repression

Regulatory effect where glucose inhibits alternative sugar metabolism via low cAMP/CAP activity.

Inducer (lac context)

Small molecule (e.g., allolactose or IPTG) that disables LacI and induces lac operon transcription.

RNA Polymerase

Enzyme that synthesizes RNA from a DNA template during transcription.

Basal Transcription Machinery

Core set of proteins (including Pol II and general factors) required to initiate transcription in eukaryotes.

Enhancer

Distal DNA element where activators bind to boost transcription of a target promoter.

Coactivator

Protein complex recruited by activators that helps assemble the transcription machinery.

Combinatorial Control

Regulatory strategy where multiple activators and repressors integrate signals to govern gene expression.

DNA-Binding Domain (DBD)

Protein region that confers sequence-specific binding to DNA.

Regulatory Domain

Portion of a transcription factor that activates or represses transcription once DNA is bound.

Modular Protein Architecture

Organization where separate domains mediate DNA binding and regulatory functions independently.

Helix-Turn-Helix Motif

Common structural motif in prokaryotic regulators (e.g., LacI) that fits into the DNA major groove.

Major Groove

Wide groove of B-form DNA where most sequence-specific protein contacts occur.

Sequence-Specific DNA Interaction

Hydrogen bonding of amino-acid side chains with base pairs without melting the DNA helix.

Gene Circuit

Interconnected set of regulatory interactions producing defined expression behavior.

Nucleosome

Core particle of ~147 bp DNA wrapped around a histone octamer.

Chromatin

DNA-protein complex forming chromosomes; exists as accessible euchromatin or compact heterochromatin.

Euchromatin

Open, transcriptionally active chromatin enriched in histone acetylation.

Heterochromatin

Condensed, transcriptionally silent chromatin enriched in histone methylation.

Histone Acetylation

Addition of acetyl groups to lysines by HATs, reducing histone-DNA affinity and promoting transcription.

Histone Methylation

Addition of methyl groups to lysines by histone methyltransferases, fostering compact, repressive chromatin.

Histone Acetyltransferase (HAT)

Enzyme that acetylates histone lysines, promoting euchromatin formation.

Histone Deacetylase (HDAC)

Enzyme that removes acetyl groups, restoring positive charge and encouraging chromatin compaction.

Histone Methyltransferase

Enzyme that adds methyl groups to histone lysines, initiating heterochromatin formation.

Histone Demethylase

Enzyme that removes methyl groups from histones, potentially re-activating genes.

Epigenetics

Heritable changes in gene expression not caused by alterations in DNA sequence.

5-Methyl Cytosine

DNA base modification that signals gene silencing without altering base-pairing.

DNA Methylation

Covalent addition of methyl groups to cytosines, often repressing transcription.

Maintenance DNA Methyltransferase

Enzyme that copies existing methylation patterns onto daughter strands after DNA replication.

De Novo DNA Methyltransferase

Enzyme that adds new methylation marks to previously unmethylated DNA, often during stress or development.

Ligand-Regulated Transcription Factor

Regulator whose DNA-binding affinity or activity changes upon binding a small molecule ligand.

Yeast Two-Hybrid Assay

Biotech method using modular activators to detect protein-protein interactions via reporter gene activation.

Inducible Expression System

Engineered construct (e.g., LacO-controlled plasmid) that produces a desired protein only after inducer addition.

Phase Separation (Chromatin)

Model proposing that heterochromatin and euchromatin form distinct liquid-like phases within the nucleus.

Operator Site (LacO)

Specific DNA sequence near the lac promoter where LacI binds to repress transcription.