Genes can be constitutive, which means that they are always on, and sometimes you'll see this referred to as a housekeeping gene, or they can be facilitated, which means they assist and help processes when needed. Prokaryotes utilize many control mechanisms, which we will explore in this chapter. or some of which we'll explore in this chapter because they are too many, and they're doing so to efficiently use their carbon source and their energy source.
The first level of control is at the DNA level or the transcriptional level, and proteins can interact with the promoter to turn on or turn off transcription. However, if the gene has already been transcribed, other events such as shutting down translation, may need to occur. And even when a protein has been translated, these molecules can be degraded, modified, or inhibited to prevent them from functioning.
And again, the idea is to conserve and use in a manner that is going to be helpful for the cell, both the carbon source and the energy source. The first level of control is transcription, and to alter transcription, proteins must first bind to the DNA. These DNA binding proteins interact in a sequence specific manner. They are not, however, recognizing specific base sequences, so not the order or the number, but instead specific molecular contacts that are associated with those base sequences. And that's a little bit more biochemistry than we have time to get into, but you should know it's not the sequence, it's the molecular contacts.
Now, these contacts are interacting with specific what we call domains on these proteins. And these domains include, for example, the zinc finger, the leucine zipper, and the one I'm asking you to remember here, which is called a helix-turned-helix. Now, these DNA binding proteins are typically what we call homodimeric.
So homo meaning the same, dimeric meaning there's two. So there are two identical subunits here. And on each polypeptide chain within these proteins is a domain that's interacting with these sequences. These sequences are specialized in a particular way because they are inverted repeat sequences in the major groove.
And we've talked about binding to that major groove of the DNA previously. So an inverted repeat. means the sequences are reversed in the two locations. That's easier if we actually look at the sequence.
So here we have our 5'to 3'direction, 5'to 3'here. On this top strand, we have T, G, T, G, T, G. That's one of our inverted repeats. If we look on this strand, we have exactly the same sequence.
So that is considered to be an inverted repeat. And these are often referred to as being palindromic sequences. And a great palindromic sequence that you may have heard of or come across before is race car. And what that means is you can read race car from left and it says race car, but you can also read it from the right and it still says race car. Now this contact with these inverted repeats that we're seeing here.
means that each of the polypeptides in the dimer is combining with each of the DNA strands in this binding process. And that's going to be important for controlling transcription. So many of the proteins that we've talked about previously are also DNA binding proteins.