regulation of gene expression
CHAPTER 16 KEY POINTS
16.1 Prokaryotic Gene Expression Is Regulated in Operons
Positive regulation occurs when binding of an activator to DNA increases transcription. Negative regulation occurs when binding of a repressor to DNA decreases transcription.
Expression of the lac operon requires high lactose (repressor not bound to the operator) and low glucose (cAMP-CRP bound to the promoter)
The lac operon repressor is bound to its operator when lactose is absent; the top operon repressor is bound to its operator when tryptophan is present
Sigma factors bind to RNA polymerase and direct it to specific classes of prokaryotic promoters
Questions
Suppose a mutation occurs in the lac operon repressor gene so that the repressor can no longer bind its inducer (allolactose) but it can still bind DNA. What effect will this have on regulation of the lac operon?
Suppose a mutation occurs in the trp operon repressor gene such that the repressor can no longer bind its co-repressor (tryptophan) but it can still bind DNA. What effect will this have on regulation of the trp operon?
What would the effect of a mutation in sigma-70 that rendered it non-functional be on an E. coli cell?
16.2 Eukaryotic Gene Expression Is Regulated by Transcription Factors
Protein transcription factors bind to silencer and enhancer sequences on DNA to regulate transcription in eukaryotes
General transcription factors are required for initiation of transcription at all eukaryotic protein-coding promoters
Specific transcription factors differ among genes and interact with the basal transcription apparatus through mediator
Transcription factors possess particular structural motifs that allow them to bind to particular DNA sequences.
Transcription factors are responsible for differences in gene expression in cells that contain the same genome, and thus underlie cell differentiation
Questions
What effects on gene expression and cell viability would occur if a general versus a specific transcription factor were knocked out (rendered nonfunctional)?
What effects on gene expression and cell viability would occur if a binding site for a general versus a specific transcription factor were knocked out (rendered unable to bind a transcription factor)?
What would be the effect of knocking out mediator in a cell?
How might a researcher prevent muscle precursor cells from differentiating into myoblasts?
16.3 Viruses Regulate Their Gene Expression during the Reproductive Cycle
Bacteriophages are viruses that infect bacteria and can have lytic or lysogenic life cycles
Eukaryotic viruses include DNA, RNA, and retroviruses
Retroviruses such as HIV make a DNA copy of their genome that integrates into the host genome, and then transcription leads to production of new virus
Questions
A bacterial strain that has been growing for many hours in a closed tube suddenly succumbs to bacteriophage infection. What do you think happened?
How might an early gene product turn off transcription of its bacterial host genes?
HIV may spend many years in the host genome before producing virions. Transcription initiation occurs during these years, but no viral proteins are made. Why not?
16.4 Epigenetic Changes Regulate Gene Expression
In many species, DNA methylation occurs at CpG islands, shutting down transcription
Histone deacetylation increases histone affinity for DNA, which reduces transcription
Epigenetic changes can be passed on through mitosis
X inactivation involves production of an Xist RNA, which coats the chromosome from which it was transcribed, causing it to become heterochromatic
Questions
Some cytosine bases are never methylated. Why?
Explain why CpG methylation sites facilitate inheritance of methylation across cell division.
What would be the effect of deleting the Xist gene in a typical (XY) male mammal? In a typical (XX) female mammal?
16.5 Eukaryotic Gene Expression Can Be Regulated after Transcription
Alternative splicing allows many different proteins to be produced from the same gene
mRNA levels can be uncorrelated with protein levels due to differences in stability and translational control of expression
The microRNA (miRNA) pathway inhibits translation; the similar small interfering RNA (siRNA) pathway degrades mRNAs
Protein stability is controlled by ubiquitination
Questions
A gene encodes f four-exon pre-mRNA. Assuming that the first and last exons remain in the mature mRNA, how many different proteins can be produced by alternative splicing of the pre-mRNA?
Why might the abundance of a protein in a cell be quite low compared with its mRNA level?
A protein-coding gene experiences a missense mutation that changes a lysine to an arginine, both of which have positively charged side groups. This change substantially increases the stability of the protein. Why might this be the case?
TERMS TO KNOW
activator: a transcription factor that stimulates transcription when it binds to a regulatory sequence for a gene
alternating splicing: a process for generating different mature mRNAs from a single gene by splicing together different sets of exons during RNA processing
bacteriophage: any of a group of viruses that infect bacteria. aka phage
basal transcription apparatus: the RNA polymerase II and general transcription factors bound to a promoter
CpG islands: DNA regions rich in C nucleotides adjacent to G nucleotides. especially abundant in promoters, these regions are where methylation of cytosine usually occurs
enhancer: regulatory DNA sequences that bind transcription factors that either activate or increase the rate of transcription
general transcription factor: in eukaryotes, transcription factors that bind to the promoters of most protein-coding genes are required for their expression. distinct from specific transcription factors, which have regulatory effects only at certain promoters of classes of promoters
lytic cycle: a viral reproductive cycle in which the virus takes over a host cell’s synthetic machinery to replicate itself, then bursts (lyses) the host cell, releasing the new viruses
mediator: a regulatory protein composed of multiple subunits that interacts with the general transcription factors and RNA polymerase II of the basal transcription apparatus and with specific transcription factors
methylation: the addition of a methyl group (—CH3) to a molecule
microRNA (miRNA): a small, noncoding RNA molecule, typically about 21 bases long, that binds to mRNA to inhibit its translation
negative regulation: a type of gene regulation in which the binding of a repressor protein to DNA prevents transcription
operator: the region of an operon that acts as the binding site for the repressor
operon: a genetic unit of transcription, consisting of two or more structural genes that are transcribed together; the operon contains at least two control regions; the promoter and the operator
positive regulation: a form of gene regulation in which the binding of an activator protein to DNA increases transcription; in its absence, transcription will not occur
repressor: a transcription factor that reduces or prevents transcription when it binds to a regulatory sequence for a gene
retrovirus: an RNA virus that contains reverse transcriptase. its RNA serves as a template for cDNA production, and the cDNA is integrated into a chromosome of the host cell
sigma factor: in prokaryotes, a protein that binds to RNA polymerase, allowing the complex to bind to and stimulate the transcription of a specific class of genes
silencer: a gene sequence binding transcription factors that repress transcription
small interfering RNA (siRNA): short, double-stranded RNA molecules used in RNA interference
specific transcription factor: in eukaryotes, transcription factors that have specific regulatory effects only at certain promoters or classes of promoters
transcription factors: proteins that assemble on a eukaryotic chromosome, allowing RNA polymerase II to perform transcription