16: Gene Expression Flashcards
Regulation of Gene Expression, Prokaryotic Gene Regulation, Eukaryotic Epigenetic Gene Regulation, Eukaryotic Transcription Gene Regulation, Eukaryotic Post-transcriptional Gene Regulation, Eukaryotic Translational and Post-translational Gene Regulation, Cancer and Gene Regulation
What does it mean to be epigenetic?
Heritable changes that do not involve changes in the DNA sequence.
What is gene expression?
Processes that control the turning on or turning off of a gene.
What is post-transcriptional gene expression?
Control of gene expression after the RNA molecule has been created by before it is translated into a protein.
What is post-translational gene expression?
Control of gene expression after a protein has been created.
Where is gene expression regulated in prokaryotes?
In prokaryotes, to synthesize a protein, the processes of transcription and translation occur almost simultaneously. When the resulting protein is no longer needed, transcription stops. As a result, the primary method to control what type of protein and how much of each protein is expressed in a prokaryotic cell is the regulation of DNA transcription. All of the subsequent steps occur automatically. When more protein is required, more transcription occurs. Therefore, in prokaryotic cells, the control of gene expression is mostly at the transcriptional level.
Where is gene expression regulated in eukaryotes?
Regulation may occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors (epigenetic level), when the RNA is transcribed (transcriptional level), when the RNA is processed and exported to the cytoplasm after it is transcribed (post-transcriptional level), when the RNA is translated into protein (translational level), or after the protein has been made (post-translational level).
How did gene regulation evolve?
Some cellular processes arose from the need of the organism to defend itself. Cellular processes such as gene silencing developed to protect the cell from viral or parasitic infections. If the cell could quickly shut off gene expression for a short period of time, it would be able to survive an infection when other organisms could not. Therefore, the organism evolved a new process that helped it survive, and it was able to pass this new development to offspring.
What is an activator?
A protein that binds to prokaryotic operators to increase transcription.
What is a catabolite activator protein (CAP)?
A protein that complexes with cAMP to bind to the promoter sequences of operons that control sugar processing when glucose is not available.
What is an inducer?
A small molecule that either activates or represses transcription depending on the needs of the cell and the availability of substrate.
What is an inducible operon?
An operon that can be activated or repressed depending on cellular needs and the surrounding environment.
What is a lac operon?
An operon in prokaryotic cells that encodes genes required for processing and intake of lactose.
What is a negative regulator?
A protein that prevents transcription.
What is an operator?
A region of DNA outside of the promoter region that binds activators or repressors that control gene expression in prokaryotic cells.
What is an operon?
Collection of genes involved in a pathway that are transcribed together as a single mRNA in prokaryotic cells.
What is a positive regulator?
A protein that increases transcription.
What is a repressor?
A protein that binds to the operator of prokaryotic genes to prevent transcription.
What is the transcriptional start site?
The site at which transcription begins.
What is a trp operon?
A series of genes necessary to synthesize tryptophan in prokaryotic cells.
What is tryptophan?
An amino acid that can be synthesized by prokaryotic cells when necessary.
What are the types of regulatory molecules in prokaryotic cells?
There are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers.
What are some examples of repressors, activators, and inducers?
The trp operon is a repressor, catabolite activator protein (CAP) is an activator, and the lac operon is an inducer.
What happens to the trp operator in the presence of tryptophan?
A DNA sequence called the operator sequence is encoded between the promoter region and the first trp coding gene. This operator contains the DNA code to which the repressor protein can bind. When tryptophan is present in the cell, two tryptophan molecules bind to the trp repressor, which changes shape to bind to the trp operator. Binding of the tryptophan–repressor complex at the operator physically prevents the RNA polymerase from binding, and transcribing the downstream genes.
Is the trp operon positively or negatively regulated?
When tryptophan is not present in the cell, the repressor by itself does not bind to the operator; therefore, the operon is active and tryptophan is synthesized. Because the repressor protein actively binds to the operator to keep the genes turned off, the trp operon is negatively regulated and the proteins that bind to the operator to silence trp expression are negative regulators.
What is an example of positive regulation in prokaryotes?
When glucose is scarce, E. coli bacteria can turn to other sugar sources for fuel. To do this, new genes to process these alternate genes must be transcribed. When glucose levels drop, cyclic AMP (cAMP) begins to accumulate in the cell. The cAMP molecule is a signaling molecule that is involved in glucose and energy metabolism in E. coli. When glucose levels decline in the cell, accumulating cAMP binds to the positive regulator catabolite activator protein (CAP), a protein that binds to the promoters of operons that control the processing of alternative sugars. When cAMP binds to CAP, the complex binds to the promoter region of the genes that are needed to use the alternate sugar sources. In these operons, a CAP binding site is located upstream of the RNA polymerase binding site in the promoter. This increases the binding ability of RNA polymerase to the promoter region and the transcription of the genes.
How does the lac operon work?
E. coli is able to use other sugars as energy sources when glucose concentrations are low. To do so, the cAMP–CAP protein complex serves as a positive regulator to induce transcription. One such sugar source is lactose. The lac operon encodes the genes necessary to acquire and process the lactose from the local environment. CAP binds to the operator sequence upstream of the promoter that initiates transcription of the lac operon. However, for the lac operon to be activated, two conditions must be met. First, the level of glucose must be very low or non-existent. Second, lactose must be present. Only when glucose is absent and lactose is present will the lac operon be transcribed. This makes sense for the cell, because it would be energetically wasteful to create the proteins to process lactose if glucose was plentiful or lactose was not available.
What is a transcription factor?
A protein that binds to the DNA at the promoter or enhancer region and that influences transcription of a gene.
What happens to nucleosomes when their DNA must be transcribed?
If DNA encoding a specific gene is to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate transcription. Nucleosomes can move to open the chromosome structure to expose a segment of DNA, but do so in a very controlled manner.
How can signals be used for epigenetic regulation in eukaryotes?
How the histone proteins move is dependent on signals found on both the histone proteins and on the DNA. These signals are tags added to histone proteins and DNA that tell the histones if a chromosomal region should be open or closed. These tags are not permanent, but may be added or removed as needed. They are chemical modifications (phosphate, methyl, or acetyl groups) that are attached to specific amino acids in the protein or to the nucleotides of the DNA. The tags do not alter the DNA base sequence, but they do alter how tightly wound the DNA is around the histone proteins. DNA is a negatively charged molecule; therefore, changes in the charge of the histone will change how tightly wound the DNA molecule will be. When unmodified, the histone proteins have a large positive charge; by adding chemical modifications like acetyl groups, the charge becomes less positive.
How can CpG islands be used for epigenetic regulation in eukaryotes?
The DNA molecule itself can also be modified. This occurs within very specific regions called CpG islands. These are stretches with a high frequency of cytosine and guanine dinucleotide DNA pairs (CG) found in the promoter regions of genes. When this configuration exists, the cytosine member of the pair can be methylated (a methyl group is added). This modification changes how the DNA interacts with proteins, including the histone proteins that control access to the region. Highly methylated (hypermethylated) DNA regions with deacetylated histones are tightly coiled and transcriptionally inactive.
What is a cis-acting element?
A transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it.
What is an enhancer?
A segment of DNA that is upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence the transcription of a specific gene.
What is a trans-acting element?
A transcription factor binding site found outside the promoter or on another chromosome that influences the transcription of a particular gene.
What is a transcription factor binding site?
A sequence of DNA to which a transcription factor binds.
