Transcriptional Control of Eukaryotic Gene Expression

A comprehensive set of flashcards covering key vocabulary, definitions, and concepts from Chapter 8 on transcriptional control of eukaryotic gene expression.

Transcription

The process of copying a segment of DNA into RNA.

Eukaryotic Gene Expression

The process by which information from a gene is used to synthesize functional gene products, particularly proteins.

Chromatin Structure

The complex of DNA and protein found in eukaryotic cells that help regulate gene expression.

Transcription Rates

The speed at which RNA polymerase synthesizes RNA from a DNA template.

Histone Proteins

Proteins that package and order DNA into structural units called nucleosomes.

Nucleosomes

The fundamental unit of DNA packaging in eukaryotes, consisting of a segment of DNA wrapped around a core of histone proteins.

Run-on Experiment

A method used to measure transcription rates by assessing the quantity of newly synthesized RNA.

Cis-regulatory Elements

Non-coding DNA sequences that regulate the transcription of nearby genes.

Promoter

A DNA sequence that initiates transcription of a particular gene.

Transcription Initiation Complex

A complex of proteins that forms at the promoter to initiate transcription.

Pol II

RNA polymerase II, the enzyme responsible for synthesizing mRNA in eukaryotes.

TFIID

A complex of proteins that binds to the TATA box in eukaryotic promoters.

General Transcription Factors (GTFs)

Proteins that help initiate transcription by RNA polymerase.

Pre-Initiation Complex

A complex formed by the assembly of GTFs and RNA polymerase at the promoter.

Mediator Complex

A multi-protein complex that serves as a liaison between transcription factors and RNA polymerase II.

Enhancers

Regulatory DNA sequences that increase the likelihood of transcription of a particular gene.

Silencer

A DNA sequence that can repress transcription from a promoter.

Epigenetics

The study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself.

Histone Acetylation

The addition of acetyl groups to histones, which typically enhances transcription.

DNA Methylation

The addition of methyl groups to DNA, which usually suppresses gene expression.

Transcription Elongation

The stage of transcription where RNA polymerase moves along the DNA template to elongate the RNA strand.

Cis-acting Elements

Regulatory elements located on the same DNA molecule as the genes they regulate.

Trans-acting Factors

Proteins that bind to cis-acting elements to regulate gene expression.

Transgenic Mice

Mice that have had a foreign gene inserted into their genome.

RNA Polymerase III

An enzyme that transcribes genes encoding small RNAs such as tRNA and 5S rRNA.

RNA Polymerase I

An enzyme that synthesizes rRNA, excluding 5S rRNA.

Nuclear Receptors

A class of proteins that regulate gene expression in response to steroid hormones.

Zinc Finger Proteins

Transcription factors that have zinc finger motifs that allow them to bind to DNA.

Leucine Zipper Proteins

Transcription factors that contain a leucine-rich region involved in dimerization.

Basic Helix-Loop-Helix Proteins

Transcription factors characterized by a helix-loop-helix structure.

Activators

Proteins that increase the likelihood of transcription of a gene by binding to an enhancer.

Repressors

Proteins that inhibit transcription of a gene by binding to a silencer or interfering with activators.

HLH

Basic helix-loop-helix, a structural motif in some transcription factors.

Competitor Binding

The process by which repressor proteins may block activators from binding to their targets.

Cooperativity

The interaction of multiple proteins at the level of gene regulation, allowing for fine-tuning of transcriptional responses.

Footprinting Assays

Techniques used to determine the specific binding sites of proteins on DNA.

Gel Shift Assays

Techniques that allow researchers to observe the binding of proteins to specific DNA sequences.

SWI/SNF Complex

A chromatin remodeling complex that alters the structure of chromatin to allow for transcription.

HAT

Histone Acetyltransferases; enzymes that add acetyl groups to histones.

HDAC

Histone Deacetylases; enzymes that remove acetyl groups from histones.

Insulator Sequences

DNA elements that block the interactions between enhancers and promoters.

Nuclear Pore Complex

Structure that regulates the transport of proteins and RNA in and out of the nucleus.

Developmental Gene Regulation

The controlled expression of genes during development.

TATA Box

A DNA sequence that indicates where a genetic sequence can be read and decoded.

RNA Sequencing

A method used to determine the quantity and sequences of RNA in a sample.

Active Chromatin

Regions of chromatin that are associated with active gene transcription.

Heterochromatin

A tightly packed form of DNA that is associated with gene silencing.

Chromatin Remodeling

The dynamic modification of the chromatin architecture to allow access to regulatory elements.

Mediator Complex Role

Acts as a bridge between transcription factors and RNA Polymerase II.

Transcription Factors

Proteins that influence the transcription of specific genes by binding to nearby DNA.

MicroRNA (miRNA)

Small non-coding RNA molecules that regulate gene expression.

Small Interfering RNA (siRNA)

Short double-stranded RNA molecules that interfere with mRNA translation.

Distant Enhancers

Enhancers located far away from the promoters they regulate.

Single Cell Yeast vs Multi-cellular Organisms

Contrast between gene regulation mechanisms, where yeast rely more on environment, and multi-cellular organisms on developmental programs.

CTD of RPB1

C-terminal domain of the largest subunit of RNA polymerase II, important for transcription regulation.

Carboxy-terminal Domain phosphorylation

Modification that can activate or regulate RNA polymerase II.

Bidirectional Transcription

Transcription that occurs in both directions on the same DNA strand.

RNA Pol Polymerase Sensitivity

The varying sensitivities of different RNA polymerases to inhibitors like α-amanitin.

RNA Processing Proteins

Proteins that are involved in the modification of RNA transcripts after synthesis.

Splicing Factors

Proteins involved in the removal of introns from pre-mRNA.

Pre-mRNA

The precursor to mRNA that contains introns and exons before processing.

Exon-Intron Structure

The arrangement of coding sequences (exons) and non-coding sequences (introns) in mRNA.

Constitutive Expression

Genes that are expressed at a constant rate in cells regardless of the cell's condition.

Gene Regulation Mechanisms

Processes that control the timing and degree of gene expression.

Tissue Specific Gene Regulation

Control of gene expression that is specific to particular tissues in multicellular organisms.