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Operons in bacteria (mostly; but also sometimes in higher organisms) Cell differentiation in higher animals and plants Bacteria have mechanisms to make certain proteins only when they need them. They do this by repressing transcription of the gene for those proteins when they are not needed.
In the best-studied example, several sugar-digesting enzymes are made only when their sugar is available.
The control mechanism is one example of an "operon". This was the first operon to be discovered; but many others were later found. Many of the other operons control synthesis of enzymes used to make certain chemicals, instead of digest them. A good example is the "tryptophan operon" which controls transcription of the genes for a series of enzymes needed to make the amino acid tryptophan. When a bacterial cell already has plenty of tryptophan (like, maybe, there is plenty of in their culture medium!) then it would be a waste of energy and materials to make the enzymes for making more tryptophan; so they want to TURN OFF transcription of these genes when there is tryptophan around. As was true with the lactose operon, the tryptophan operon works by means of a special cytoplasmic protein that binds to the DNA just upstream of the genes for these enzymes, and that also binds to tryptophan. (if there is enough of it around) In this case, when this inhibitor ("repressor") protein binds to tryptophan, then that allows it to bind to the DNA, and to inhibit transcription of the genes for these enzymes.
An analogy would be if you had a device that could measure the amount of light in a room, and turn off the electric lights if there was enough sunlight coming through the window; but then at night, the mechanism would no longer "repress" the turning on of the electric lights.
So operons are mechanisms for "turning genes on and off" Embryonic development also depends on turning genes on and off (permanently!), so as to produce cell differentiation.
For example, red blood cells are a differentiated cell type. So cell differentiation results from "turning on" different combinations of genes, with a special set for each cell type. This "turning on" is mostly "at the transcriptional level" meaning that differentiated cells only make the messenger RNA for those proteins that they are going to make.
In contrast to the close linkage of genes controlled by an operon, the different genes that are co-expressed in a given differentiated cell type are usually in different (unrelated) locations. On the other hand, a few interesting cases are known in which the relative location of genes is related to their function. (and I will tell you if somebody asks) And now for a short digression about the kind of protein called histones. Histones bind strongly to DNA, and occur in eucaryotes (and also archaea) but procaryotes DON'T have them. Although it is probably best to think about histones as providing protection and mechanical support to DNA, they also have the effect of blocking RNA polymerase from touching the DNA, and therefore they inhibit transcription For this reason, stimulation of transcription of a certain gene (= making its m-RNA) is more of a DE-inhibition than in procaryotes (because it requires getting the histones out of the way) And now; back to embryonic development In the late 1800s, one hypothesis about embryonic development was that differentiation might be caused by giving different genetic material to the different cells (a reasonable guess!), with only the future sperm or egg cells getting to keep all the genes!
But this turned out not to be how it works (not ever!!?). One kind of experiment that proved this was nuclear transplantation.
Nuclei were sucked into tiny glass needles, and then injected into fertilized egg cells
If the transplanted nucleus had been taken from a differentiated cell, but the egg cell injected with it was then able to develop into an animal with all different cell types, then that proves In the 1950s and 60s, successful nuclear transplantations were done with frogs; and the method was then used for mammals in the late 1990s. (Dolly, the sheep; and all that; including all the wild claims about cloning humans)
For unknown reasons, only 1% or so of such embryos develop normally, but NOT for lack of enough DNA to make all cell types.
Each cell type turns on its special sub-set of genes by means of DNA binding proteins called "transcription factors" which are analogous to the inhibitor proteins in bacterial operons
An aspect of embryonic cell differentiation that is almost never discussed (and for which the mechanisms is NOT known) is mutual exclusiveness of expression of different sets of genes.
Questions that you should now be able to answer:1) What does it mean "to control gene expression" at the level of transcription?2) The lactose operon mechanism is a means for controlling transcription of the genes for what proteins? 3) In this operon, the inhibitor protein will either bind to what? or alternatively to what? ? 4) Adding lactose to a culture of bacteria with this operon will cause them to synthesize what? , which will then be translated to synthesize what? ? 5) What will then happen when all the lactose is used up? 6) A mutation in the gene for this inhibitor protein might either cause bacteria never to make the lactose-digesting enzymes, or possibly would produce what alternative abnormality? 7*) Suppose some bacteria were abnormal, and had two different genes for this inhibitor protein, one normal and one mutant; would you expect these bacteria to make the lactose-digesting enzymes? Always make it? Make it sometimes? Never make it? Or what? How would this be related to the phenotype of the mutant in bacteria that have only one copy of the gene for this inhibitor? 8*) Suppose that a mutation in the gene for this inhibitor protein caused it to bind to the control region of DNA only when this inhibitor protein is also bound to lactose sugar: then when would these bacteria make, and when would they NOT make, the lactose-digesting enzymes?
9*) In actual fact, in the lactose operon, and nearly all other operons, the different enzymes whose synthesis is being controlled are all located right next to each other, 1,2,3 in a row. 10) In the tryptophan operon, under what circumstances is it desirable to transcribe the genes for the enzymes that make tryptophan? 11) When is better to turn those genes off, and inhibit their transcription? Hint: when are these enzymes not needed? 12) How does this situation differ from the control of the genes for lactose digestion? (somewhat the opposite; but also the same) 13) In the case of the tryptophan operon, when should the inhibitor ("repressor") protein inhibit transcription of the enzymes for synthesizing tryptophan? 14) What should be the effect of adding tryptophan to a culture that had been living entirely off of, say, lactose? 15) What will happen when all this tryptophan gets all used up, synthesizing proteins? 16*) Suppose that didn't happen until after the very last tryptophan molecule had been used up! Why wouldn't those cells be able to make any more tryptophan? 17*) Suppose that you searched for mutant bacteria that constantly made enzymes for synthesizing more tryptophan, all the time, whether there was already enough tryptophan around, at what two locations would you expect to find these mutations might occur? 18*) Where might mutations occur that prevented cells from ever transcribing the genes for the enzymes needed to make tryptophan? 19*) Can you figure out which of these mutations would behave as if dominant, and which as if recessive, if a cell somehow had two complete sets of genes? (crazy "diploid" bacteria!) 20*) What change in the DNA of a bacterium might cause it to STOP make lactose-digesting enzymes whenever the concentration of tryptophan gets too high? (Think about changing a certain DNA base sequence, so as to make it the same as a certain other sequence) 21) What are histones? (And where are they located?) 22) What kinds of organisms have histones; and which don't?
23) In what sense do genes in eucaryotes have to be "de-inhibited"
in order for them to be transcribed?
24) What is meant by differentiated cell types, in multicellular animals and plants? 25)** Can you guess some further examples? What about in plants? 26) In the body of a human, or other higher animal, about what is the number of different kinds of differentiated cell types? 27) In embryonic development, do different cell types contain different genes, or what? 28) How did nuclear transplantation experiments (including those that produced Dolly the sheep) prove the answer to the preceding question? 29) About how many different differentiated cell types are there in humans? 30) Is cell differentiation due to translational or transcriptional control of gene expression and protein synthesis? 31) In the early development of eggs, which of these kinds of control allows a quick increase in the rate of protein synthesis after fertilization? 32*) Why would it be a tremendous waste of RNA to use any form of post-transcriptional control to cause cell differentiation? 33*) If a chemical poison blocks RNA synthesis, but is found NOT to block a particular process of embryonic development, then what does that imply about the mechanism of that process? 34**) But what if a developing egg becomes non-permeable to this poison, then what dumb mistake might somebody make? 35*) What sort of mutation might cause hemoglobin to be made in skin cells, instead of in blood cells? What region of DNA would need to be mutated? Would it be the part that codes for the amino acid sequence of the protein itself? (hint: NO)
36) Compare the control of gene expression in cell differentiation, as compared with in operons? 37*) A protein is known that, when injected into tissue culture cells, can cause them to switch differentiated cell types and redifferentiate as muscle cells! How would you guess it acts? 38*) Suppose that you have isolated DNA that codes for a protein that glows green when you shine UV light on it; and suppose that you can insert lengths of DNA with this sequence into the chromosomes of plants or animals; then what would it mean if only one differentiated cell type of the resulting organism glowed green when illuminated with UV?
39*) If it makes cells cancerous to make too much of a certain hormone receptor protein, then mutations in what location could cause cancer?
40) Why would it make sense to have very similar base sequences in the promoter regions of the different genes expressed in a given differentiated cell type?
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