Gene Expression and Regulation

Flashcards based on lecture notes about gene regulation in prokaryotes and eukaryotes, covering topics like operons, transcription factors, chromatin structure, and post-transcriptional control.

What is the action of the trp Repressor?

A regulatory protein that binds to DNA and prevents transcription when active; it requires tryptophan as a co-repressor to become active and bind to the operator.

What is a Co-repressor?

A molecule that binds to a repressor protein, allowing the repressor to bind to the operator and inhibit transcription of the operon (e.g., tryptophan in the trp operon).

What is the Operator?

A DNA sequence near a gene to which a repressor protein can bind, preventing RNA polymerase from transcribing the gene.

How does the trp Operon typically function?

An operon that is normally active, producing enzymes for making tryptophan, but can be repressed when tryptophan is present in the environment.

What is an Inducible Operon?

An operon that is normally off due to an active repressor, but can be turned on by an inducer that inactivates the repressor, like the lac operon.

What is an Inducer?

A molecule that binds to a repressor protein, causing it to detach from the operator and allowing transcription of the operon (e.g., allolactose in the lac operon).

What does the Lactose Operon regulate?

Regulates the metabolism of lactose; it is available to E. coli cells if the host consumes milk or milk products.

What is b-Galactosidase (b-Gal)?

An enzyme that cleaves the β-glycosidic bond in lactose, breaking it down into glucose and galactose.

What is the role of the lac Regulatory gene, lacI?

A regulatory gene (lacI) located upstream from the lac operon that encodes an allosteric repressor protein.

What is Allolactose?

An isomer of lactose that binds to and inactivates the lac repressor, acting as an inducer.

How is the lac Operon regulated by lactose?

In the absence of lactose, the lac repressor binds to the operator, keeping the operon inactive; when lactose is available, it is converted to allolactose, which binds to the repressor, causing it to detach and allowing transcription.

What is the key difference between the lac and trp Operons?

The lac operon is inducible (repressor normally bound and then unbinds), while the trp operon is repressible (repressor normally unbound and then binds).

How do inducible and repressible operons relate to metabolic pathways?

Inducible operons function in catabolic pathways (breaking things down if present), while repressible operons function in anabolic pathways (building things up when not available).

What is the difference between negative and positive control in operon regulation?

Operon transcription is switched off in the presence of an active form of a repressor, while in positive regulation, operon transcription is switched on in the presence of an active form of an activator.

How does glucose affect the regulation of the lac Operon?

E. coli prefers to use glucose as its energy source, and will activate genes for lactose metabolism only when lactose is present and glucose is absent (or low).

What is CAP?

A regulatory protein (Catabolite Activator Protein) that interacts with cAMP to regulate the lac operon; it is allosterically regulated.

How is [cAMP] related to [Glucose]?

Inversely related to glucose concentration; high glucose outside the cell correlates with low cAMP inside the cell.

How does CAP affect RNA Polymerase binding?

When CAP is active (bound to cAMP), RNA polymerase binding is increased, and transcription activity is high; when CAP is inactive, RNA polymerase binding is weak, and transcription activity is low.

How does the lac Operon respond to the presence/absence of Lactose and Glucose?

When lactose is present and glucose is also present, the operon is weakly active; when lactose is present and glucose is absent, the operon is highly active.

What are the primary means of Eukaryotic Gene Regulation?

Transcription factors, chromatin accessibility, mRNA splicing, translation, and protein modification/degradation; eukaryotic genes are regulated in more ways than prokaryotic genes.

How much of the genome is dedicated to coding proteins?

Less than 2% of the genome codes for proteins; specific transcription factors must locate the correct genes to express them.

What are the levels of control of Gene Expression in Eukaryotes?

DNA accessibility, transcription, RNA processing, mRNA export, mRNA stability, translation, posttranslational modification, and protein degradation.

What is Chromatin?

Eukaryotic DNA is packaged with protein in an elaborate complex; the fundamental unit of this structure is the Nucleosome.

What are Histones?

Most abundant chromatin protein; contains substantial basic (positively charged) amino acids like Arginine and Lysine.

What is Heterochromatin?

The most-condensed chromatin, where genes are inaccessible and transcriptionally silent.

What is Euchromatin?

Less-condensed chromatin, where genes are accessible and transcriptionally active.

How does Histone Acetylation affect Gene Activity?

Modification of histones affects gene activity; acetylation of lysines reduces the + charges on histones, increasing gene expression activity.

What is DNA Methylation?

Typically seen on Cytosine residues; DNA methylation is associated with reduced transcriptional activity, and removing methyl groups can reactivate genes.

What is X Chromosome Inactivation?

Early in development, one X chromosome in females is inactivated due to hypermethylation of DNA, leading to complete heterochromatinization.

What is the Organization of Eukaryotic Genes?

Includes the TATA box for transcription factor binding, transcription unit (exons and introns), poly-A addition signal, transcription termination signal, and proximal and distal control sequences.

What assistance is required for RNA Polymerase to bind to the Promoter?

Binding of RNA polymerase to the promoter requires assistance by other proteins; these can be either basal or specific/regulatory transcription factors.

What are Enhancers?

Distal gene control elements that may be thousands of bases upstream or downstream from the promoter and can function in either orientation.

What is Combinatorial control of Gene Activity?

Precise control of gene activity depends on the binding of transcription factors; gene activity depends on the combination of different factors rather than the binding of one specific factor.

Why are Coordinately Controlled Genes important?

Most functionally related genes are not closely linked and are often scattered on different chromosomes; coordinated expression depends on activation of a specific combination of control elements.

Why is RNA Processing important?

Removing introns and splicing exons together is an important part of eukaryotic mRNA processing; Alternative splicing helps explain how complex organisms can be generated with relatively few genes.

Why is mRNA Degradation important?

RNA stability is important in determining the amount of protein produced; eukaryotic RNAs can survive for hours, days, or months.

How is Translation Initiation controlled?

Initiation of specific mRNAs can be blocked by proteins preventing the mRNA and ribosomal subunits from binding together; translation can be arrested globally by modifying one or more translation factors.

How is Translational Control achieved?

Small RNAs can bind to mRNA and silence translation (microRNA and Silencer RNA); proteins can bind to mRNA and prevent translation.

What are the different steps of Posttranslational Control???

Folding, phosphorylation, glycosylation, protein targeting, and proteolytic cleavage; certain proteins are marked for destruction by tagging with Ubiquitin.