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The genetic code is universal and contains the instructions for all life on Earth. But the diversity of life relies on more than just the genetic code itself — it also relies on the variety of ways in which this code is used in different organisms. In much the same way that an orchestra depends upon a conductor to direct the individual musicians, all cells depend upon regulatory mechanisms to determine which of their genes are "turned on" and which are "turned off" at any given time. In other words, these regulatory mechanisms control gene expression.
But why is this control necessary? To better understand the answer to this question, consider the example of a skin cell and a brain cell located within the same organism. Both of these cells contain the same set of genetic information, but each has a unique function within the organism. Both cells, for instance, carry the gene associated with skin pigmentation, but only the skin cell actually expresses this particular gene and produces the pigment. In order for this gene to be expressed by the skin cell, it must be transcribed into mRNA and then translated into protein — and regulatory mechanisms are what trigger the transcription of this particular gene to occur (or not occur, in the case of the brain cell). In fact, regulatory mechanisms are the reason why some genes are expressed in every cell in an organism regardless of type, but other genes are expressed by only certain types of cells under specific sets of circumstances.
In order to understand how regulatory mechanisms work, it's first necessary to understand that not all nucleotide sequences in a strand of DNA code for the production of proteins. Rather, some of these noncoding sequences serve as binding sites for the various protein molecules required to start or regulate the transcription process. For example, a group of nucleotides known as a promoter sequence lies near the beginning of most genes and provides a binding site for RNA polymerase to begin transcription. Similarly, other noncoding sequences near the promoter sequence function as protein binding sites that can either induce or block transcription. This basic system affects gene expression in both prokaryotes and eukaryotes, albeit in different ways.
One especially well-known operon is the lac operon found in E. coli bacteria. This operon contains the three genes E. coli cells need to break down lactose. (Lactose is a sugar molecule that these cells often use as a source of energy.) When lactose is not present in a bacterium's environment, the protein products of these three genes aren't needed. As a result, a repressor protein binds to the operator of the lac operon and blocks transcription of the three genes. In contrast, when lactose is present, a molecule of this sugar binds to the repressor protein and changes its shape. The shape change prevents the repressor from binding to the operator, thereby permitting transcription of the three genes in the lac operon to occur. In this case, lactose itself "turns on" the genes of the lac operon, which means that it acts as an inducer.
In prokaryotes, a similar system can also be used to turn genes off. Consider, for example, the E. coli trp operon, which contains the genes required to make the amino acid tryptophan. This operon functions much like the lac operon except for one major difference — specifically, the repressor protein in this system only binds with the operator sequence when tryptophan is present. Here, tryptophan binds with the repressor, thereby changing the repressor's shape such that it fits with the operator. This means that tryptophan acts as a co-repressor, because it helps turn the genes of the trp operon off.
Gene expression is much more complicated in eukaryotic cells than it is in prokaryotic cells. This is due, in large part, to the fact that eukaryotic cells must differentiate into different cell types, and they also contain a greater number of genes than prokaryotic cells. Furthermore, the transcription and translation sites of eukaryotic DNA are separated from one another by the nuclear membrane. Given these complicating factors, eukaryotic cells employ a greater variety of control strategies than prokaryotic cells, and they do so at various steps in both transcription and translation. Nonetheless, each of these strategies begins at the level of DNA.
In eukaryotes, control at the level of transcription is specific and efficient. Eukaryotic cells do not have operator sequences like prokaryotic cells do; rather, different kinds of regulator sequences occur upstream of eukaryotic promoters and serve as sites for the binding of RNA polymerase. In some instances, enhancer sequences occur upstream of these regulator sequences and bind to activator proteins to further stimulate transcription. Silencer sequences that reduce transcription may also be present. These sequences bind to repressor proteins and turn transcription off by interfering with RNA polymerase binding.
Sometimes, the stability of the mRNA molecule itself affects levels of eukaryotic gene expression. Once created, mRNA does not last forever; stable mRNAs will last long enough to be translated many times (thereby producing many protein molecules), but unstable mRNAs may not last long enough to be translated at all. The stability of an mRNA molecule depends upon its nucleotide sequence and the length of its poly-A tail, or the long sequence of adenines added to one end of the mRNA after transcription. The longer an mRNA's poly-A tail is, the more stable the mRNA molecule will be.
After a gene has been transcribed, control mechanisms can still regulate its expression during the translation process. Within eukaryotes, special repressor proteins can bind to mRNA molecules and physically block their translation. In addition, after translation, unneeded proteins may be marked for degradation by certain molecules before they have the opportunity to do their job.
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