Chapter 11: Regulation of Gene Expression

Merged flashcards from Chapter 11 of Principles of Life, 3rd Edition.

Regulatory networks

Collections of interacting regulators that determine the expression level of a gene

• Allows for multi-faceted gene expression

Transcription regulation

The most common type of regulation due to the need for energy conservation

Inducers

Compounds that stimulate the transcription of specific inducible genes

• Includes genes required in particular conditions, such as those for triglyceride synthesis given high glucose levels

• Generally control catabolic pathways

Repressors

Compounds that reduce the transcription of specific repressible genes

• Includes genes that are normally expressed with reduced functionality when the product is present, such as synthesizers of nonessential amino acids

• Generally control anabolic pathways

Constitutive genes

Genes that are expressed most of the time at a constant rate in all cells

• Includes genes required for protein synthesis, such as tRNAs and ribosomal proteins

Transcription factors

Regulatory proteins that control whether a gene is active; includes repressors and activators

• Type of activation does not imply repressibility or inducibility, as both kinds may apply

Negative regulation

A type of regulation where a transcription factor binds to a specific site to reduce or prevent transcription

• Transcription factor serves as a repressor

Positive regulation

A type of regulation where a transcription factor binds to a specific site to increase transcription

• Transcription factor serves as an activator

DNA binding domain

The region in a protein that is able to bind to a particular sequence of DNA

• Enables recognition of specific sequences by transcription factors

Sigma factors

Transcription factors present in prokaryotes, with expression changing with the environment

• Enables multiple genes to be expressed simultaneously

Beta-galactoside

A disaccharide containing galactose linked to glucose

• Includes the compound lactose

• Induces beta-galactosidase and permease levels to increase following mRNA transcription

Permease

A carrier protein in the bacterial cell membrane that moves lactose into the cell

Beta-galactosidase

An enzyme that hydrolyzes lactose to glucose and galactose

Operon

A cluster of genes with a single promoter

• Seen in prokaryotic responses to lactose producing three mRNA strands via one promoter, termed lac

Lac operon

The operon that encodes the three lactose-metabolizing proteins in prokaryotes

• Has variable rates of efficiency depending on environment as an inducible operon

• Contains an operator that controls transcription of the genes following promotion, with a repressor negatively regulating production

  • Activation occurs in the presence of allolactose, a lactose byproduct, which allosterically binds to the repressor

  • Also requires the absence of glucose

Operator

A transcription factor binding site that reduces transcription rates when bound to a repressor

• Typically examples of negative regulation when the repressor is bound, only allowing activation following a change of conditions (such as the addition of allolactose in prokaryotes)

Regulatory gene

A gene that encodes a regulatory protein

• One for the regulatory protein of the lac operon is located upstream of it

Structural gene

Any gene that encodes a protein that is not directly involved in gene regulation

• Seen with the three lactose-metabolizing enzymes due to their lack of regulatory power

Trp operon

The operon that encodes five enzymes that catalyzes the synthesis of tryptophan from a precursor, as a repressible operon

• Repression requires the presence of a co-repressor, which binds to the operon’s repressor to change shape and enable binding as a form of allosteric regulation

  • Here, tryptophan serves as the co-repressor, due to it always being needed until sufficient levels are reached

Lytic cycle

This is triggered following the injection of viral genetic material into a cell, where viral particles are immediately produced and the cell lyses

Lysogeny

A method of viral reproduction where the viral genome is incorporated into the host and replicated with the host genome, remaining dormant until an environmental signal triggers the lytic cycle

Inducibility

For a gene, the ability to be expressed only when needed; this is important in multicellular eukaryotes for cell specialization

TATA box

One of the core promoters of protein-coding genes in eukaryotes

• Contains several A-T base pairs

RNA polymerase II

The form of RNA polymerase present in eukaryotes, it requires several general transcription factors to bind to the promoter first

General transcription factors

Transcription factors that bind to a promoter before RNA polymerase; these can bind to several promoter classes

Basal transcription apparatus

The combination of RNA polymerase II and general transcription factors on a strand of DNA

• Requires the binding of specific transcription factors on other sequences for higher rates

Mediator

A protein complex that facilitates interactions between specific transcription factors and the basal transcription apparatus

• Joins the two as the DNA helix bends for proximity

• Help determine how genes are regulated and produced

Enhancers

DNA binding sites that increase transcription and are not in the basal promoter

Silencers

DNA binding sites that decrease transcription and are not in the core promoter

Differentiation

The development of cells from a fertilized egg to adult, triggered by the varying activations of transcription factors

Human immunodeficiency virus (HIV)

The virus that causes AIDS in humans; it uses mechanisms mimicking receptor-mediated endocytosis via its enclosure in a membrane derived from its pervious host cell

• Contains the enzyme reverse transcriptase, creating a DNA strand from its RNA genome which is later incorporated into the host and released in new viral particles

Epigenetic changes

Reversible changes in DNA that involve varying levels of chromatin packaging, resulting from histone chemical modification or DNA methylation

• Seen through identical twins growing differently as a result of the environment

Nucleosome

A core of eight positively charged histones around which DNA is wound, forming closed chromatin

Acetylation

Performed by histone acetyltransferases, this neutralizes the charges of the amino acid tails on histones and loosens the compact nucleosome for regulatory protein binding

• Can be recruited by transcription factors

• May be reversed by histone deacetylases

Methylation

Performed by DNA methyltransferase, this typically occurs to cytosine bases adjacent to guanines, giving rise to the name CpG sites

• Results in the binding of repressing transcription factors in stable, long-term bonds

• Can be maintained by maintenance methyltransferase or reversed by demethylase for replication needs

CpG islands

Regions of DNA that are rich in CpG sites, typically found in promoters that are not expressed

Euchromatin

DNA that is transcribed into mRNA with lower DNA methylation rates; this stains lightly under a microscope

Heterochromatin

DNA that is more condensed with little transcription and heavy methylation rates; this stains darkly under a microscope

• Seen with female mammals’ X inactivation, resulting in differently expressed traits as one X chromosome is methylated to prevent aneuploidy

Genomic imprinting

The passing down of specific methylated genes from each parent resulting in some transcriptionally active and inactive genes

Alternative splicing

The inclusion or exclusion of particular genomic exons through the selective splicing of specific introns, resulting in differently-functioning or defective proteins

• Seen in Drosophila’s Sxl gene including two or four exons per protein, dependent on being female or male

• Enables more mRNAs to be produced from a smaller number of genes

mRNA stability

How long mRNA remains in the cell before it is degraded

• Can be regulated through the attachment of proteins that inhibit RNA nuclease activity or the activity of functional RNAs that regulate gene expression, like miRNAs

microRNAs (miRNAs)

Functional RNA molecules that reduce gene expression in eukaryotes through the alteration of mRNA stability, binding directly to its structure

Small interfering RNAs (siRNAs)

Functional RNA molecules like miRNAs that are 22 nucleotides long

• Degrades only mRNA molecules that are completely complementary

• Interferes in mRNA translation for mismatched molecules

RNA interference

The silencing of genes through the degradation or inhibition of mRNA molecules by miRNAs or siRNAs, found in many eukaryotes

5’ cap modification

mRNA transcription regulation through the modification of guanine triphosphate (GTP) at the 5’ end of the mRNA molecule, remaining dormant until activated through this process

Translational repressor proteins

Proteins that bind to mRNA and prevent attachment to the ribosome, regulating translation

• Seen with the mRNA that codes for ferritin (an iron-storing protein), with a protein bound when iron levels are low but unbound when iron levels are high

Ubiquitin

A protein that marks other proteins (specifically their lysine residues) for destruction through the formation of a chain that attaches to a proteasome for unfolding and digestion

• Aids in the breaking down of cyclins for gene expression regulation