Chapter 11 Regulation of Cellular Processes BIOL 3340

Regulation of Gene Expression

Control of gene activity in cells.

Transcription Initiation

First step in gene expression process.

Transcription Elongation

Process of RNA strand lengthening.

Translation

Synthesis of proteins from mRNA.

Posttranslational Modification

Chemical changes to proteins after synthesis.

Constitutive Genes

Genes expressed continuously for basic functions.

Inducible Genes

Genes activated under specific environmental conditions.

β-Galactosidase

Enzyme that hydrolyzes lactose into glucose.

Inducible Enzymes

Enzymes present only when substrates are available.

Repressible Genes

Genes that are usually active unless inhibited.

Biosynthetic Pathways

Metabolic routes for synthesizing cellular components.

Transcriptional Regulatory Proteins

Proteins that control gene transcription by binding DNA.

DNA-Binding Domain

Region of protein that attaches to DNA.

Allosteric Site

Site on protein that interacts with effectors.

Negative Control

Regulatory mechanism that inhibits gene expression.

Repressor Proteins

Proteins that prevent transcription when bound to DNA.

Inducers

Molecules that activate repressor proteins.

Positive Control

Regulatory mechanism that promotes gene expression.

Operon

DNA sequence controlling gene expression with promoter.

Lactose Operon

Operon regulating lactose metabolism in bacteria.

lac Repressor

Protein that inhibits transcription in lactose operon.

Tetramers of Repressor

Four subunit complexes that bind operator sites.

Operator Sites

DNA regions where repressor proteins bind.

lac Operon

Regulated by lac repressor and CAP.

Allolactose

Binds repressor, allowing transcription.

CAP

Regulates operon based on glucose levels.

Tryptophan Operon

Contains genes for tryptophan synthesis.

trp Repressor

Inhibits transcription when tryptophan is present.

Attenuation

Regulation of transcription termination during elongation.

Riboswitches

mRNA structures that regulate transcription termination.

Arabinose Operon

Controlled by AraC protein, responds to arabinose.

AraC Protein

Acts positively or negatively based on arabinose.

Transcription Elongation Regulation

Controlled by termination mechanisms like attenuation.

Leader Region

Site for transcription termination in trp operon.

Stem-loop Structures

Form in mRNA, affecting transcription based on trp.

Gram-positive Riboswitches

Regulate transcriptional termination in bacteria.

Gram-negative Riboswitches

Regulate translation of mRNA in bacteria.

Effector Molecule

Binds riboswitch, altering mRNA folding.

Small RNA Molecules

Regulate translation by binding to mRNA.

Cis-acting sRNAs

Control a single gene, synthesized from sense strand.

Trans-acting sRNAs

Control multiple genes, synthesized from distinct templates.

Translation Initiation

Can be regulated by small RNA molecules.

Negative Transcriptional Control

Repression of gene expression by repressor proteins.

Global Regulatory Systems

Regulatory systems affecting multiple genes and pathways.

Regulon

Genes or operons controlled by a common regulator.

Two-Component Signal System

Links external events to gene expression regulation.

Sensor Kinase

Extracellular receptor for metabolites in signaling.

Response Regulator

Activated by sensor kinase to regulate transcription.

Phosphorelay System

Signal transduction involving phosphorylation events.

Env Z

Sensor kinase that autophosphorylates in high osmolarity.

OmpR

Response regulator that controls porin gene expression.

OmpF

Larger porin protein allowing high solute diffusion.

OmpC

Smaller porin protein with lower diffusion capacity.

Sigma Factor

Protein directing RNA polymerase to specific genes.

σ70

Transcribes genes needed during exponential growth.

σ54

Transcribes genes involved in nitrogen metabolism.

σ38

Transcribes genes for stationary phase and stress response.

σ32

Transcribes genes protecting against heat shock.

σ28

Transcribes genes for flagellum assembly.

σ24

Transcribes genes for membrane protein folding.

σ19

Transcribes genes responding to iron starvation.

Second Messengers

Small molecules responding to external signals.

cAMP

Cyclic adenosine monophosphate, a second messenger.

Diauxic Growth

Biphasic growth using preferred carbon source first.

Catabolite Repression

Inhibition of less preferred sugar metabolism.

Lag Phase

Growth pause after preferred substrate is exhausted.

CAP Binding Site

Site where CAP binds to regulate operons.

Catabolite Activator Protein (CAP)

Regulates catabolite operons based on cAMP levels.

cAMP Active Form

When bound to CAP, promoting transcription.

cAMP Inactive Form

Free of cAMP, CAP cannot activate transcription.

Adenyl Cyclase

Enzyme converting ATP to cAMP and PPi.

Glucose Presence

Inhibits adenyl cyclase activity, lowering cAMP.

Transcription Promotion

CAP binding allows RNA polymerase to initiate transcription.

Phosphotransferase System

Regulates cAMP levels via phosphate transfer.

Methyl-Accepting Chemotaxis Proteins (MCPs)

Chemoreceptors that bind environmental chemicals.

CheA Kinase

Sensor kinase that autophosphorylates upon activation.

CheY Response Regulator

Controls flagellar rotation based on phosphorylation.

Flagellar Rotation CCW

Occurs when attractant concentration is high.

Flagellar Rotation CW

Occurs when attractant concentration decreases.

MCP Methylation

Methylation by CheR affects MCP activity.

MCP Demethylation

Demethylation by CheB leads to CheA inactivity.

Quorum Sensing

Cell communication regulating gene expression based on density.

N-acyl-homoserine lactone (AHL)

Signaling molecule in quorum sensing.

LuxR Regulator

Transcriptional regulator activated by AHL in V. fischeri.

Sporulation in Bacillus subtilis

Global regulatory system responding to starvation signals.

Alternative Sigma Factors

Proteins that initiate transcription during sporulation.

pppGpp Production

Downregulates tRNA and rRNA synthesis during amino acid starvation.

Stringent Response

Cellular adaptation to amino acid starvation.

Restriction-modification

Microbes modify DNA bases to combat viruses.

Methylases

Enzymes that add methyl groups to DNA.

Restriction endonucleases

Enzymes that cut unmethylated DNA.

CRISPR/Cas system

Adaptive immune system in bacteria against viruses.

Adaptation stage

Viral genome pieces added to CRISPR array.

Expression stage

CRISPR region transcribed into large RNA.

Cas proteins

Proteins that process CRISPR RNA into crRNAs.

Interference stage

Cas-crRNAs destroy viral DNA or mRNA.

Chromatin remodeling

Rearranging chromatin structure to facilitate transcription.

Nucleosome-free core promoter

Region where transcription factors assemble.

Upstream activating sequences

Binding sites for transcriptional activators.

Enhancers

Regulatory sites that boost transcription rates.