Gene Expression in a Prokaryotic System – RNA Basics

by Kevin Ahern, PhD

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    00:00 Now we know, of course, that RNA is produced by the transcription of DNA, the copying of DNA-RNA polymerase.

    00:08 And if that is done to make the coding for a gene then, of course, we are thinking about gene expression In prokaryotic systems we have an interesting situation with respect to the layout of genes.

    00:21 Now in prokaryotic system, genes are very closely spaced to each other within the genome.

    00:27 Meaning that if we have a gene at one place and then the end of the gene the beginning of the next gene is not very far away. So they are very close to each other.

    00:38 And that's different in the arrangement that we see in eukaryotic systems; because, of this close spacing bacteria actually use this somewhat to their advantage and in an interesting way that eukaryotes do not do.

    00:51 So in prokaryotic systems genes are commonly organized in what are called operons.

    00:57 So an operon is a sequence that has multiple genes that are under the control of a single promoter.

    01:06 And when that single promoter is activated, as it is in the figure you see on the right here, the RNA polymerase copies all of those genes onto a single messenger RNA.

    01:18 Now that's different from the eukaryotic system where the widely spaced eukaryotic genes when transcription occurs, only one gene makes it onto the final transcript. So the operon arrangement in bacteria is unique to bacteria.

    01:34 Operons are transcribed and translated when they are needed and this organization means that it's important on a given operon that the genes that are there have related functions. And we will see in an example of that at the end of this lecture.

    01:50 The RNAs that are made in bacteria comes from transcription and the transcription that is controlled in bacteria uses very simple promoter elements.

    01:59 When we talk about elements and we are actually talking about the sequence of DNA that comprise the promoter.

    02:06 So the simple needs of bacteria actually work out fairly well; because, these simple controls means that there aren't too many different variations that bacteria use or need in fact during their life style.

    02:19 So in prokaryotes I would like to go through and show you an example of a system involving a fairly simple control and it involves an operon called the lac operon.

    02:28 Now the lac operon is a segment of the E-Coli genome that contains coding for three genes necessary for the metabolism of lactose.

    02:39 Lactose as we have seen in other discussions here is a disaccharide that is an energy source; because, it provides sugar.

    02:48 In order for the bacterium to use the lactose they have to be able to break it down; because, lactose contains two sugars.

    02:55 So one of the genes that's contained in the lac operon contains a gene called beta galactosidase that breaks lactose into glucose and galactose, its constituent sugars.

    03:08 So glucose and galactose can be metabolized in the metabolic pathways that we have discussed before.

    03:16 The operon contains the 3 genes for lactose metabolism, as I said.

    03:20 These include the lacZ gene, the lacY gene and the lacA gene, Now for our purposes here the only gene that really matters is the lacZ gene, because, that's the beta galactosidase that breaks down lactose.

    03:33 Nonetheless all three genes are made in the organism and all these genes are needed for the proper metabolism and proper functioning of the overall lactose operon.

    03:42 Now lacZ, as I said, cleaves lactose into glucose and galactose.

    03:47 And the cell really has this need to do this. But it's important that the cell be making this operon only when it needs it; because, cells don't have a lot of energy to throw into things that they don't need.

    04:01 And the synthesis of proteins, the synthesis of RNAs is a very energy intensive process.

    04:09 So ideally the cell is only making genes when it needs the genes and in the case of a lac operon the cell is ideally only making this operon when lactose is present and when the cell is needing it.

    04:24 So the transcription of the lac operon is controlled by several proteins.

    04:29 It's not very complicated but it's not simply just an RNA polymerase.

    04:35 The first protein that performs a function here is called the lac repressor.

    04:39 Now this is a protein that can bind to the site on the lac operon called the O site and it is highlighted on the DNA before.

    04:49 The O site is the part of the overall promoter or control sequence for the operon.

    04:55 We will see that the control sequence for the operon has several components and these are managed by the individual proteins.

    05:02 The function of the lac repressor is to bind to the O site.

    05:07 And when it binds to the O site it stops transcription from occurring.

    05:12 Now we will see there are times when it can bind and other times when it cannot bind.

    05:19 The second protein that plays a role in this overall transcription is called the CAP.

    05:24 So the CAP is a protein that binds to the CAP site and the CAP site, you can see, is located near the O site.

    05:33 The function of the CAP is to bind to the CAP site and in doing so facilitate the binding of the RNA polymerase to the P site which you can see is adjacent to the CAP site.

    05:46 So lac repressor and CAP have opposite functions.

    05:50 Lac repressor to block transcription and CAP to activate transcription.

    05:57 The RNA polymerase of course binds to the P site which we can describe here as the promoter. Although this entire region is technically a promoter.

    06:05 Now the factors that influence whether binding of these proteins occur to the control sites on the DNA or not are mediated by small molecules.

    06:17 Now one of the small molecules that plays a role here is cyclic AMP.

    06:22 Cyclic AMP is bound by CAP.

    06:26 And when cyclic AMP binds to CAP, CAP can bind to the CAP site.

    06:32 And if cyclic AMP is not present then CAP cannot bind to the CAP site.

    06:39 Allolactose is related to lactose and for our purposes we can think of it like lactose.

    06:44 But the important thing about allolactose is it binds to the lac repressor.

    06:50 Allolactose is present when lactose is present.

    06:55 So that means that when lactose is present, allolactose will bind to the lac repressor.

    07:00 The importance of that is that when allolactose is bound to the lac repressor, the lac repressor cannot bind to the O site.

    07:09 However, when allolactose is absent as it is when lactose is not present then lac repressor will bind to the O site and stop transcription.

    07:21 So we have really two scenarios here.

    07:22 One scenario where we are activating transcription, this is when cyclic AMP is present.

    07:28 And one scenario where we are stopping transcription and that's when lactose is absent.

    About the Lecture

    The lecture Gene Expression in a Prokaryotic System – RNA Basics by Kevin Ahern, PhD is from the course RNA and the Genetic Code.

    Included Quiz Questions

    1. It contains multiple genes under the control of a single promoter
    2. It is the way eukaryotes organize genes in their genome
    3. It is not found in prokaryotes
    4. It is a name for a set of spliced genes
    1. β-galactosidase, β-galactoside permease and β-galactoside transacetylase enzymes respectively.
    2. β-galactoside permease, β-galactosidase, and β-galactoside transacetylase enzymes, respectively
    3. β-galactosidase, β-galactoside transacetylase and β-galactoside permease enzymes, respectively
    4. β-galactoside permease, β-galactoside transacetylase, and β-galactosidase enzymes, respectively
    5. β-galactoside transacetylase, β-galactosidase, and β-galactoside permease and enzymes, respectively
    1. cAMP
    2. Allolactose
    3. cGMP
    4. CAP
    5. Repressor protein
    1. Both cAMP and allolactose prevent the expressions of lac operon by binding with the CAP protein
    2. The binding of the CAP on the CAP site near the operator region of lac operon starts the transcription of lactose metabolism enzymes by facilitating the binding of RNA polymerase to the promoter
    3. The allolactose resembles the lactose molecule, and it helps in lac operon expression by preventing the binding of the repressor protein to the operator site
    4. The repressor protein binding to the operator site prevents the transcription of lac genes
    5. The CAP protein binding to the CAP site is facilitated by the binding of the cAMP molecule to it under energy deficiency conditions

    Author of lecture Gene Expression in a Prokaryotic System – RNA Basics

     Kevin Ahern, PhD

    Kevin Ahern, PhD

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