Ch. 15 Reading Guide

Posttranscriptional control includes regulation of mRNA degradation. Explain how this affects translation.

The central idea is that the longer mRNA is in the cytoplasm, the more protein that can be formed by translation. In general, prokaryotes degrade their mRNA more quickly than eukaryotes

What percentage of the genes of a typical human cell is expressed at any given time?

20%

What is a promoter?

A promoter is a sequence of DNA nucleotides where RNA polymerase binds to in order to start transcription.

How does a repressor protein work?

A repressor protein binds to the operator and blocks the attachment of RNA polymerase tot the promoter, which prevents transcription of a gene.

What occurs in histone acetylation? How does it affect gene expression?

Acetyl groups are attached to lysines in histone tails. This promotes transcription initiation by giving proteins easier access to the genes.

What is DNA methylation? What role may it play in gene expression?

Addition of a methyl group on the DNA bases of eukaryotes makes cells heavier and turns off genes.

The inactive mammalian X chromosome is heavily methylated. What is the result of this methylation?

After an X chromosome is inactivated in a particular cell, all mitotic descendants of that cell have the same inactive X. Thus, if a female is heterozygous for a sex-linked trait, about half her cells will express one allele, while the others will express the alternative allele.

What is the operator? What does it do?

An operator is a sequence of nucleotides near the start of an operon where an active repressor can attach. It prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon.

What is an operon?

An operon is a unit of genetic function found in bacteria and phages. It includes a promoter, an operator, and the genes they control.

Compare and contrast the lac operon and the trp operon. (Remember that compare means "to tell how they are similar," and contrast means "to tell how they are different.")

Both operons code for an allosteric repressor protein that can switch on and off. The trp operon is inactive by itself and requires tryptophan as a compressor. The lac operon is active by itself.

Explain why CAP binding and stimulation of gene expression is positive regulation.

CAP binding increases the rate of transcription (gene expression), which is a positive regulation because it is perpetually increasing.

What is CAP? How does CAP work?

CAP is Catabolic Activator Protein. This is a regulatory protein that binds to DNA and stimulates transcription of a gene.

In prokaryotes, functionally related genes are usually clustered in a single operon. What has been found to be the case in eukaryotes?

Co-expressed eukaryotic genes, such as genes coding for the enzymes of a metabolic pathway, are typically scattered over different chromosomes. In these cases, coordinate gene expression depends on the association of a specific combination of control elements with every gene of a dispersed group

Operons have not been found in eukaryotic cells, and the genes coding for the enzymes of a particular metabolic pathway are often scattered over different chromosomes. What is a plausible mechanism for the coordination of gene expression?

Coordinate control of dispersed genes in a eukaryotic cell often occurs in response to chemical signals from outside the cell. A steroid hormone, for example, enters a cell and binds to a specific intracellular receptor protein, forming a hormone-receptor complex that serves as a transcription activator.

How can alternative RNA splicing result in different proteins derived from the same initial RNA transcript?

Different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns. Regulatory proteins specific to cell type control intron-exon choices by binding to regulatory sequences within the primary transcript.

All genes are not "on" all the time. Using the metabolic needs of E. coli, explain why not.

E. coli works by activating a metabolic pathway that makes tryptophan. This only happens when the human does not eat any meat. Once meat is eaten, E. coli stops to save its energy for when the meat is gone.

Gene expression can be regulated by modifications of the chromatin. Distinguish between heterochromatin and euchromatin as to their structure and activity.

Heterochromatin is highly condensed and rarely expressed. Euchromatin ("true chromatin") is lightly condensed and help regulate gene expression.

What is genomic imprinting, and how is it maintained? Give an example discussed earlier in human genetics.

Genomic imprinting is the phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent.

One of the noncoding RNAs that regulate gene expression is microRNA. On the sketch below, follow an RNA loop, called a "hairpin," from its creation. Explain the two modes of action of microRNAs

If mRNA and mRNA bases are complementary all along their length, the mRNA is degraded (left side of figure); if the match is less complete, translation is blocked (right side of figure

Explain what is meant by epigenetic inheritance, and give an example of epigenetic changes discussed in the text or in class.

Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome. Examples may vary.

Feedback inhibition is a recurring mechanism throughout biological systems. In the case of E. coli regulating tryptophan synthesis, is it positive or negative inhibition? Explain your choice.

It is negative inhibition because the accumulation of the product stops the enzyme from catalyzing it.

How do these "little chambers of horrors" function? Annotate the sketch below to describe their action. Then explain their role in regulation of gene expression.

Multiple ubiquitin molecules are attached to a protein by enzymes in the cytosol. The ubiquitin- tagged protein is recognized by a proteasome, which unfolds the protein and sequesters it within a central cavity. Enzymatic components of the proteasome cut the protein into small peptides, which can be further degraded by other enzymes in the cytosol.

It is now known that much of the RNA that is transcribed is not translated into protein. these RNAs are called noncoding RNAs. Read carefully to discern a crucial role played by these RNAs. What is this role?

Regulating gene expression

What are regulatory genes?

Regulatory genes code for a protein that controls the transcription of another gene or group of genes.

Even though all cells of an organism have the same genes, there is differential gene expression. What does this mean?

The expression of different genes by cells with the same genome are showing.

What happens when a repressor is bound to the operator?

The gene is not transcribed because the RNA polymerase cannot bind. (the operon is off)

How can proteins be activated, processed, and degraded? Give an example or describe each process.

The process of making proteins through activation can best be seen in the developing embryo. Many mRNA molecules are made ahead of fertilization, but they do not have a poly-A tail and are therefore not active. At the appropriate time, an enzyme in the cytoplasm adds the adenines, activating the mRNA and producing proteins. A second method of activation is the zygote wide release of translation initiation factors that triggers a burst of protein synthesis. Proteins are often processed by altering amino acids or changing the sequence of amino acids to form an active, functioning protein. Finally, the length of time each protein functions in the cell is strictly regulated by means of selective degradation utilizing proteasomes.

How can both repressible and inducible operons be negative regulators?

Their products inhibit the production of more products, making them negative regulators.

An article in Scientific American about proteasomes was entitled "Little Chamber of Horrors." Explain how proteins are targeted for degradation, and give a specific example of when this might occur.

To mark a particular protein for destruction, the cell commonly attaches molecules of a small protein ubiquitin to the protein. Proteasomes then recognize ubiquitin-tagged proteins and degrade them. The importance of proteasomes is underscored by the findings that mutations making specific cell cycle proteins impervious to proteasome degradation can lead to cancer.

What is the common control point of gene expression for all organisms?

Transcription

Describe the relationship between glucose supply, cAMP, and CAP.

cAMP is attached to the regulatory protein. When the amount of glucose in a cell increases, cAMP concentration lowers, CAP detaches from the operon because there isn't enough cAMP to hold it.

What are the two main ways of controlling metabolism in bacterial cells?

• Cells can adjust the activity of enzymes already present with chemical cues through feedback inhibition • Cells can adjust the production level of the genes encoding the enzymes

List the three components of an operon, and explain the role of each one.

• Promoter- starts transcription • Operator- On/Off switch- synthesizes enzymes at once • Genes they control- determines whether or not a certain amino acid will be coded for

Distinguish between inducible and repressible operons, and describe one example of each type.

• Repressible operons are usually on but can be inhibited when a specific small molecule binds allosterically to a regulatory protein. (ex: tryptophan operon) • An inducible operon is usually off but can be stimulated when a specific small molecule interacts with regulatory proteins. (ex: lactose operon)