SAU 19 Flashcards
Explain why cell types differ
The DNA in specialized cell types of multicellular organsims still contain the entire set of instructions needed to form a whole organism. The various cell types of an organism therefore differ not because they contain different genes, but because the express them differently.
Give an example of how a cell can change the expression of its genes in response to external signals
If a liver cell is exposed to the steroid hormone cortisol, the production of several proteins is dramatically increased. Released by the adrenal gland during periods of starvaion, intense exercise, or prolonged stress, cortisol signals liver cells to boost the production of glucose from amino acids and other small molecules. The set of proteins whose production is induced by cortisol includes enzymes such as tyrosine aminotransferase, which helps convert tyrosine to glucose. When the hormone is no longer present, the production of these proteins return to its resting level.
Other cell types respond to cortisol differently.
Explain how gene expression can be regulated at various steps from DNA to RNA to protein
A cell can control the proteins it contains by
1) controlling when and how often a given gene is transcribed
2) controlling how an RNA transcript is spliced or otherwise processed
3) selecting which mRNAs are exported from the nucleus to the cytosol
4) regulating how quickly certain mRNA molecules are degraded
5) selecting which mRNAs are translated into protein by ribosomes
or 6) regulating how rapidly specific proteins are destroyed after they have been made
In eukaryotic cells, gene expression can be regulated at each of these steps. However, for most genes, the control of transcription (step 1) is paramount. This makes sense because only transcriptional control can ensure that no unnecessary intermediates are synthesized.
Show how gene expression in eukaryotic cells can be controlled at various steps
Explain how transcription regulators bind to regulatory DNA sequences
The promoter region of a gene binds the enzyme RNA polymerase and correctly orients the enzyme to begin making an RNA copy of the gene. The promoters include a transcription initiation site, where RNA synthesis beginds, plus nearby sequences that contain recognition sites for proteins that associate with RNA polymerase: the general transcription factors.
The vast majority of genes include regulatory DNA sequences that are used to switch the gene on or off. Some regulatory DNA sequences act as molecular microprocessors, integrating information from a variety of signals into a command that determines how often transcription of the gene is initiated.
To have any effect, regulatory DNA sequences must be recognized by proteins called transcription regulators. It is the binding of a transcription regulator to a regulatory DNA sequence that acts as the switch to control transcription.
Show how many transcription regulators bind to DNA as dimers
Explain how switches allow cells to respond to changes in their environment
In E. coli, five genes code for enzymes that manufacture tryptophan when this amino acid is scarce. These genes are arranged in a cluster on the chromosome and are transcribed from a single promoter as one long mRNA molecule; such coordinately transcribed clusters are called operons. Operons are common in bacteria, but rare in eukaryotes, where genes are transcribed and regulated individually.
When tryptophan concentrations are low, the operon is transcried; the resulting mRNA is translated to produce a full set of biosynthetic enzymes, which work in tandem to synthesize the amino acid. When tryptophan is abundant fx, when the bacterium is in the gut of a mammal of a mammal that has just eatan a protein-rich meal - the amino acid is imported into the cell and shuts down production of the enzymes, which are no longer needed.
Within the operon’s promoter is a short DNA sequence called the operator, that is recognized by a transcription regulator. When this regulator binds to the operator; it blocks access of RNA polymerase to the promoter, thus preventing transcription of the operon and the production of the tryptophan-synthesizing enzymes. The transcription regulator is known as the tryptophan repressor. The repressor can bind to DNA only if it is also bound to tryptophan. The tryphtophan repressor is an allosteric protein: the binding of tryptophan causes a sublt change in its three-dimensional structure so that the protein can bind to the operator sequence. When the concentration of free tryptophan in the bacterium drops, the repressor no longer binds to DNA, and the tryptophan operon is transcribed. The repressor is thus a simple device that switches production of a set og biosynthetic enzymes on and off according to the availability of tryptophan - a form of feedback inhibition.
Show how a transcription regulator interacts with the DNA double helix
Show ho genes can be switced off by repressor proteins
Show how a cluster of bacterial genes can be transcribed from a single promoter
Explain how repressors turn genes off and activators turn them on
the tryptophan repressor, is a transcriptional repressor protein: in its active form, it switches genes off, or represses them. Some bacterial transcription regulators do the opposite: they switches genes on/activates. Transcriptional activator proteins work on promoters that are only marginally able to bind and position RNA polymerase on their own.
Activator proteins often have to interact with a second molecule to be able to bind DNA. For example, the bacterial activaotr CAP has to ind cAMP before it can bind to DNA. Genes activated by CAP are switched on in response to an increase in intracellular cAMP concentration, which occurs when glucose, is no longer availale; as a result, CAP drives the production of enzymes that allow the bacterium to digest other sugars.
Explain how the lac operon is controlled by an activator and a repressor
In many instances, the activity of a single promoter is controlled by two different transcription regulators.
E.coli: The control region of the Lac operon integrates two different signals, so that the operon is highly expressed only when two condiditions are met: glucose must be absent and lactose must be present. When lactose is present AND glucose is absent, the cell executes the appropriate program - transcription of the genes that permit the uptake and utilization of lactose.
In a eukaryotic cell, similar transcription regulatory devices are combined to generate increasingly complex circuits.
Explain how eukaryotic transcription regulators control gene expression from a distance
Eukaryotes use transcription regulators - oth activators and repressors - to regulate the expression of their genes. The DNA sites to which eukaryotic gene activators bind are called enhancers, becuase their presence enhances the rate of transcription. Eukaryotic activator proteins could enhance transcription even when they are bound thousands of nucleotide pairs upstream - or downstream - of the gene’s promoter. The DNA between the enhancer and the promoter loops out, brining the activator protein into close proximity with the promoter. The DNA acts as a tether, allowing a protein that is bound to an enhancer - even one that is thousands of nucleotide pairs away - to interact with the proteins in the vicinity of the promoter. Often, additional proteins serve as adaptors to close the loop; the most important of these is a large complex of proteins known as Mediator. Together, all of these proteins attract and position the general transcription factors and RNA polymerase at the promoter, forming a transcription initiation complex. Eukaryotic repressor proteins do the opposite: they decrease transcription by preventing the assembly of this complex.
Explain how eukaryotic transcription regulators help initiate transcription by recruiting chromatin-modifying proteins
Eukaryotic DNA is wound around clusters of histone proteins to form nucleosomes, which are folded into higher-order structures. In eukaryotic cells, activator and repressor proteins can exploit the mechanisms used to package DNA to help turn genes on and off. Chromatin strucutre can be altered by chromatin-remoddeling complexes and by enzymes that covalently modify the histone proteins that form the core of the nucleosome. Many gene activators take adventage of these mechanisms by attacting such chromatin-modifying proteins to promoters. The recruitment of histone acetyltransferases promotes the attachment of acetyl groups to selected lysines in the tail of histone proteins; these acetyl groups themselves attract proteins that promote transcription, including some of the general transcription factors. And the recruitment of chromatin-remodeling complexes makes nearby DNA more accessible. These actions enhance the efficiency of transcription initiation.
Gene repressor proteins can also modify chromatin in ways that reduce the efficiency of transcription initiation. Many repressors attract histone deacetylases - enzymes that remove the acetyl groups from histone tails, thereby reversing the effects that acetylation has on transcription initiation. Some eukaryotic repressor proteins work on a gene-by-gene basis, others can orchestrae the formation of large swathes of transcriptionally inactive chromatin. These transcription-resistant regions of DNA include the heterochromatin found in interphase chromosomes and the inactive X chromosome in the cells of female mammals.
Explain how the arrangement of chromosome into looped domains keeps enhancers in check
All genes have regulatory regions, which dictate at which times, under what conditions, and in what tissues the gene will be expressed. Eukaryotic transcription regulators can act across very long stretches of DNA, with the intervening DNA looped out.
To avoid unwanted cross-talk, the chromosomal DNA is arranged in a series of loops that hold individual genes and their regulatory regions in rough proximity. This localization restricts the eaction of enhancers, recenting them from wandering across to adjacent genes. the chromosomal loops are formed by specialized proteins that bind to sequences that are then drawn together to from the base of the loop.
The importance of these loops is highlighted by the effects of mutations that prevent the loops from properly forming. Such mutations, which lead to genes being expressed at the wrong time and place, are foun in numerous cancers and inherited diseases.
Explain how eukaryotic genes are controlled by combinations of transcription regulators
Most eukaryotic transcription regulators work as part of a large “committee” of regulatory proteins, all of which cooperate to express the gene in the right cell type, in response to the right conditions, at the right time, and in the required amount.
Combinatorial control refers to the process by which groups of transcription regulators work togehter to determine the expression of a single gene. A typical gene is controlled by dozens of transcription regulators that bind to regulatory sequences that may be spread over tens of thousands of nucleotide pairs. Togehter, these regulators direct the assembly of the mediator, chromatin-remodeling complexes, histone-modifying enzymes, general transcription factors, and RNA polymerase. In many cases, multiple repressors and activators are bound to the DNA that controls transcription of a given gene.
Explain how the expression of different genes can be coordinated by a single protein
Cells need to coordinate the expression of different genes. When a eukaryotic cell receives a signal to proliferate a number of hitherto unexpressed genes are turned on together to set in motion the events that lead eventually to cell division. Bacteria often coordinate the expression og a set of genes by having them clustered together in an operon under the control of a single promoter. Such clustering is rarely seen in eukaryotic cells, where each gene is transcribed and regulated individually.
Even though the control of gene expression is combinatorial, the effect of a single transcription regulator can still be decisive in switching any particular gene on or off, simply by completing the combination needed to activate or repress that gene. As long as different genes contain regulatory DNA sequences that are recognized by the same transcription regulator, they can be switched on or off together as a coordinated unit.
Explain how combinatorial control can also generate different cell types
One of the means by which eukaryotic cells diversify types of cells during embryonic development is the ability to switch many different genes on or off using a limited number of transcription regulators.
Some transcription regulators can maintain cells in an undifferentiated state, like the precursor cell. Some undifferentiated cells are so developmentally flexible they are capable of giving rise to all the specailized cell types in the body. The embryonic stem (ES) clls retain this quality, a property called pluripotency.
The differentiation of a particular cell type involves changes in the expression of thousands of genes: genes that encode products needed by the cell are expressed at high levels, while those that are not needed by the cell are expressed at high levels. A given transcription regulator, therefore, often controls the expression of many genes.
Explain how transcription regulators can be used to experimentally direct the formation of specific cell types in culture
Unusual outcome is made possible by the cooperaton of numerous transcription regulators in a varity of cell types - a situation that is common in a develiping embryo. Some transcription regulators can convert one specialized cell type to another in a culture dish.
Explain how differentiated cells maintain their identity
Once a cell has become differentiated into a particular cell type in the body, it will generally remain differentiated, and all its progeny cells will remain that same cell type. Skeletal and neurons never divide again once they have differentiated - terminally differentiated. Fibroblasts, smooth muscle cells, and liver cells - will divide many times in the life of an individual. These specialized cell types give rise only to cells like themselves.
For a proliferating cell to maintain its identity - a property called cell memory - that patterns of gene expression responsible for that identity must be “remembered” and passed on to its daughter cells through all subseqeunt cell divisions.
Positive feedback loops are the most prevalent way of ensuring that daughter cells remember what kind of cells they are meant to be, there are other ways of reinforcing cell identity. There are other ways of reinforcing cell identity. One involves the methylation of DNA. DNA methylation occurs on certain cytosine bases. This covalent modifiction generally turins off the affected genes by attracting proteins that bind to methylated cytosines and block gene transcription. DNA methylation patterns are passed on to progeny cells by the action of an enzyme that copies the methylation pattern on the parent DNA strand to the daughter DNA strand as it is synthesized.
Cell-memory mechanisms transmit patterns of gene expression from parent to daughter cell without altering the actual nucleotide sequence of the DNA, they are considered to be forms of epigenetic inheritance.
Explain DNA methylation
Show how DNA methylation patterns can be faithfully inherited when a cell divides.
Explain inherting gene expression patterns involving the modification of histones
Reporter genes allow specific proteins to be tracked in living cells
