chapter 16 regulation of gene expression

operator

a regulatory DNA sequence in an operon where a repressor protein binds to control whether the operon’s genes are transcribed

structural gene

a gene that encodes the primary structure of a protein not involved in the regulation of gene expression

lacZ

the structural gene of the lac operon the encodes B-galactosidase, the enzyme responsible for breaking down lactose into glucose and galactose; it also participates in the trans glycosylation of lactose into allolactose

regulatory sequence

a noncoding DNA sequence that controls when, where , and how much a gene is expressed by serving as a binding site for regulatory proteins

operon

a genetic unit of transcription in prokaryotes, typically consisting of several structural genes that are transcribed together; the operon contains at least two control regions: the promoter and the operator

specific transcription factors

regulatory proteins that bind to enhancers or regulatory DNA elements to increase or decrease transcription of particular genes, often in response to signals or environmental cues

inducer

a small regulatory molecule that turns on gene expression, usually by inactivating a repressors protein so transcription can occur

proteasome

a large protein complex that recognizes ubiquitin-tagged proteins and degrades them into peptides, helping regulate protein quality and turnover in the cell

general transcription factors

a sets of essential transcription factors that must bind to a core promoter to recruit RNA polymerase and initiate transcription, especially in eukaryotes (TFIIA, TFIIB, TFIID)

structural motif

a recurring three-dimensional pattern in a protein or nucleic acid that contributes to structure function, such as enabling DNA binding or protein-protein interactions

TATA box

a DNA sequence in many eukaryotic promoters, rich in T and A bases, that binds TBP ( part of TFIID) and helps position RNA polymerase II to start transcription

ubiquitin

a small regulatory protein that is covalently attached to other proteins to mark them for degradation by the proteasome

demethylase

an enzyme that removes methyl groups from methylate cytosines, helping reverse epigenetic marks and regulate gene expression

adenylyl cyclase

an enzyme that converts ATP into cyclic AMP (cAMP), linking cellular conditions ( like low glucose) to changes in gene regulation

lacY

the structural gene of the lac operon that encodes B- galactoside permease, a membrane protein that transports lactose into the cell

inducible operon

an operon that is normally off but can be turned on in the presence of a specific inducer molecule often involved is catabolic pathways ( breaking down sugars )

transcription factor

a regulatory protein that binds to specific DNA sequences to increase or decrease transcription by controlling RNA polymerase activity

CAP site

A DNA sequence near the promoter where the CAP ( catabolite activator protein) binds to enhance transcription, especially when glucose levels are low

chromatin

the complex of eukaryotic DNA and associated proteins ( mainly histones) that packages DNA in the nucleus and helps regulate gene expression and DNA accessibility

constitutive proteins

proteins that are produced continuously at a constant level, regardless of environmental conditions or regulatory signals

repressor protein

a regulatory protein that binds to an operator or regulatory DNA sequences to block transcription of a gene or operon

maintenance methylase

a DNA methyltransferase that copies existing methylation patterns onto newly synthesized DNA after replication, helping preserve epigenetic information after cell division

alternative splicing of exons

a process in eukaryotes in which different combinations of exons are joined from the same pre-mRNA, allowing one gene to produce multiple proteins variants

b-galactoside permease

a membrane transport protein that imports lactose into the cell, encoded by the lacY gene in the lac operon

DNA methyltransferase

an enzyme that adds a methyl group to DNA - usually to cytosine in CpG sites- playing a key role in epigenetic regulation of gene expression

sigma factor

a protein subunit of bacterial RNA polymerase that directs the enzyme to specific promoters,allowing different sets of genes to be transcribed under different conditions

lacl

the regulatory gene of the lac operon that encodes the lac repressor protein, which binds the operator to block transcription when lactose is absent

epigenetics

the study of heritable changes in gene expression that do not involve changes to the DNA sequence, often caused by chemical modifications to DNA or histone proteins

CpG islands

regions of DNA with a high frequency of CpG dinucleotides, often found near gene promoters, where DNA methylation status helps regulate gene expression

B- galactoside transacetylase

an enzyme encoded by the lac A gene that transfers acetyl groups to B-galactosidase, thought to help detoxify non-metabolizable lactose analogs

B-galactosidase

an enzyme that breaks down lactose into glucose and galactose encoded by the lacZ gene in the lac operon; it also participates in the trans glycosylation of lactose into allolactose

histone deacetylase

an enzyme that removes acetyl groups from histone proteins, tightening chromatins structure and generally reducing gene transcription

lacA

the gene in the lac operon that encodes B-galactoside transacetylase, an enzyme thought to help detoxify lactose-related compounds

promoter

a DNA sequence upstream of a gene where RNA polymerase binds to initiate transcription

repressible operon

an operon that is normally on but can be turned off when a specific corepressor is present, often involved in anabolic pathways ( synthesizing amino acids)

enhancers

regulatory DNA sequences that bind specific transcription factors to increase transcription, often functioning far from the gene they regulate and in either orientation

co-repressor

a small regulatory molecule that binds to a repressor protein and enables it to block transcription, turning gene expression off

activator protein

a regulatory protein that binds to DNA and increases transcription by helping RNA polymerase bind more effectively to the promoter

small interfering RNA (siRNA)

short, double-stranded RNAs, that trigger RNA interference ( RNAi) to degrade target mRNAs, playing a key role in defense against viruses and transposable elements

mediator

a large eukaryotic protein complex that intergrates signals from specific transcpriton factors bound to enhancers or silencers and relays them to the general transcription machinery and RNA polymerase Ii at the promoter, there by increasing or decreasing transcription

silencers

silencers are regulatory DNA elements that bind specific repressor transcription factors to decrease gene expression

microRNA(miRNA)

a small noncoding RNA molecule that regulates gene expression after transcription by binding to mRNA and blocking translation

histone acetyltransferase

an enzyme that adds acetyl groups to histone proteins, loosening chromatin structure and generally increasing gene transcription