- DNA and RNA structure
- Introduction to nucleic acids and nucleotides
- Molecular structure of RNA
- Antiparallel structure of DNA strands
- Semi conservative replication
- DNA structure and replication review
- The genetic code
- DNA and chromatin regulation
- Intro to gene expression (central dogma)
- Cellular specialization (differentiation)
- Eukaryotic gene transcription: Going from DNA to mRNA
- Regulation of transcription
- Transcription and RNA processing
- Non-coding RNA (ncRNA)
- Regulation of gene expression and cell specialization
- Post-transcriptional regulation
- Differences in translation between prokaryotes and eukaryotes
- Prokaryote structure
Regulation of transcription
Created by Tracy Kim Kovach.
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- This video confused me because it mixes prokaryote and eukaryote transcriptional regulation together in ONE diagram.
Things to note:
1) Operator region is found only in prokaryotes, not eukaryotes.
2) The repressor binds to the operator only in prokaryotes (not eukaryotes) since eukaryotes don't have operator regions.
3) Enhancer and silencer regions are found only in eukaryotes, not prokaryotes
4) Activator binds to enhancer to increase rate of transcription; repressor binds to silencer to decrease rate of transcription
Hope this helps clear up any confusion!(41 votes)
- #3 is wrong; though we originally thought enhancers were only found in eukaryotes, we more recently discovered enhancer-like elements are found in prokaryotes as well.
Source: https://pubmed.ncbi.nlm.nih.gov/11282468/(4 votes)
- I'm a little confused - is this video solely applicable to prokaryotic organisms? How much of this is common to eukaryotes?(26 votes)
- Eukaryotic organisms don't have operator sequences. Instead, they have regulatory sequences upstream of the promoter which recruit all the necessary machinery.(11 votes)
- Your 5
and 3are backwards. 5
is upstream...3is downstream.(1 vote)
- Nope, she has it down correctly....although a bit unusual. Usually, it is more common to see people note that the 5' end of DNA is upstream because they are referring to the coding (non-template) strand....as you indicated. Here, she is referring to the other strand, the template strand (the one that the RNA physically uses to match the bpairs) so 'upstream' in this case would be a the 3' end.(29 votes)
- Just to clarify, repressor and activator proteins are considered mediator multiple protein complexes? Correct?(6 votes)
- No, repressor and activator proteins are transcription factors. The mediator complex is different: http://en.wikipedia.org/wiki/Mediator_%28coactivator%29(5 votes)
- Hi all, this was a great video, however, I feel I could add a couple of things more for people that are a bit confused.
First, this video is more focused on gene regulation on eukaryotes, however, there are some similarities with prokaryotes
-Eukaryotic cells do not have a specific operator as bacteria do, remember that the operator is the binding site for the repressor and thus has a function equivalent to the silencer region in Eukaryotic DNA. When a repressor protein is bound to the operator, RNA polymerase cannot bind to the promoter to initiate the transcription of the operon.
-When she mentions that for prokaryotes there is the General Transcription Factor, that is true, however, as there is only one it is better known as Sigma Factor, meanwhile in Eukaryotes (as they are far more complex) there are many GTFs and all of them have binding DNA sites. Many of them interact with the RNA pol forming the Transcription preinitiation complex
Note: Some of them work along with activators binding enhancer regions or repressors binding silencer regions and can even bind promoters of the gene they regulate.
-Activators usually bind a specific region of the DNA so they can influence positively on the transcription of a Gene, the example she gives is of the CAP and cAMP that work together allowing transcription of mRNA for Lac Operon.
Most activators function by binding sequence-specifically to a DNA site located in or near a promoter and making protein–protein interactions with the general transcription machinery (RNA polymerase and general transcription factors), thereby facilitating the binding of the general transcription machinery to the promoter; however they also bind to enhancers and after this interaction, they bend the DNA allowing the interaction of the transcription machinery with the promotor site of the gene.
Finally, Silencers work similarly to enhancers, but in the opposite way so they avoid interaction with the transcription machinery.
Hope this works!(5 votes)
- Are activators and inducers different?(3 votes)
- An inducer can bind to an activator or repressor. It can cause the repressor to be disabled,. As far as activators, they generally bind poorly to activator DNA sequences unless an inducer is present. The activator binds to an inducer and the complex binds to the activation sequence and activates target gene.
Source: Slonczewski, Joan, and John Watkins. Foster. Microbiology: An Evolving Science. New York: W.W. Norton &, 2009. Print.(5 votes)
- So genes can require an activator OR repressor? Can the same DNA have both activators and repressors? Activators and repressors don't ever work simultaneously, correct?(3 votes)
- The activator is attached to the activator site, which is either directly in the promoter region or near the promoter region, and promotes the attachment of the RNA polymerase to the promoter, while the repressor binds to the operator region, which is downstream from the promoter, and prevents the RNA polymerase from moving along the template strand thus preventing transcription. One enables a bind and the other prevents advance, and while they seem close on the illustration, note that these regions are typically hundreds of base pairs long so there's unlikely to be physical blockage except in specific cases.
Many of these mechanisms are antagonistic or competitive, they all work to a certain degree and their combined effect determines a certain rate for transcription. Remember that these are fundamentally molecules randomly and spontaneously bumping into one another, and one certain bump that happens to cause an attachment makes more likely or less likely a bump of another kind to cause an attachment, they're not exact 1s and 0s, so the term "ever" is hardly "ever" going to apply to any one of these cases.(4 votes)
- Hello. I noticed many comments clarifying differences this process has between prokaryotes and eukaryotes (which have been very helpful!)
From my understanding, a repressor protein can inhibit transcription by binding to an operator gene in prokaryotes and a silencer gene in eukaryotes.
However, I would still like to ask about the function of inducers (4:30). Do they affect repressors on silencers like they affect repressors on operators?
- Hey, Ashley. Nice question!
Here's one example of how an inducer works in a bacterial cell:
An inducer (signal) molecule binds to a specific site on the Lac repressor, causing a conformational change that results in dissociation of the repressor from the operator. The inducer in the lac operon system is not lactose itself but allolactose, an isomer of lactose.
So, in a nutshell, inducers are small molecules that mediate dissociation of the repressor from the operator.
Inducers can also bind to activator proteins, allowing them to bind to the operator DNA where they promote RNA transcription.
Eukaryotic cells have much more complicated regulation of gene expression. Inducers and their mechanisms in these organisms can vary greatly.
There is an entire field of research called epigenetics, which deals with problems like these. If you are interested in it so much, getting some textbook on epigenetics will answer your question much better than I can.
David, L., Nelson, D. L., Cox (2017). Lehninger principles of biochemistry.
- 5:29She's saying that silencers can be distant from the promoter in the upstream or downstream direction. Then she said that when a repressor binds to the silencer region, RNA Pol is prevented from binding to the promoter region. Why? How? She said the "mechanism is very similar to that of the enhancer sequences I just talked about" (where she said that the enhancer loops the DNA, but gives no explanation as to why that actually enhances the transcription or how the looping occurs in the first place.).(2 votes)
- This subject is actually both complicated and incompletely understood. For example, there is evidence that some enhancers don't result in loops at all — instead their influence travels along the chromatin to a nearby promoter.
You can think of enhancers as being staging areas where protein complexes that promote transcription are assembled. In some cases enhancers are where the RNA polymerase complex is first bound.
When loops do form, this allows the proteins at an enhancer to interact directly with the transcriptional start site.
Silencers can also be very complex, but many appear to act on promoters in a similar manner — i.e. by recruiting proteins that then more-or-less directly affect transcription.
You may find this 2015 review helpful:
- So are activators on the promoter sequence required for DNA transcription to even occur for that set of gene sequences or does it only enhance the transcription factor and just sorta make it happen better?(2 votes)
Voiceover: So what makes a cell that's located inside of your nose responsible for smelling, say, a slice of pizza look and act differently from a cell that lines your gut and is responsible for absorbing the nutrients from that pizza? They have the exact same DNA so the differences can't be attributed to that fact alone. The answer actually lies in the expression of that DNA, which genes are actively transcribed and which ones aren't and there are several ways in which gene regulation occurs at the level of transcription and so we're going to be talking about the main ones here. Now let's draw out a hypothetical gene here and associated with this gene is a sequence upstream so towards the three prime region of the antisense strand, also called the template strand. And this sequence is called the promoter and there is another sequence in between the promoter and the gene called the operator. The operator is the sequence of DNA to which a transcription factor protein combined and the promoter is the sequence of DNA to which the RNA polymerase binds to start transcription. Now first off in prokaryotes we have what are called general transcription factors, which are a class of proteins that bind to specific sites on DNA to activate transcription. General transcription factors plus RNA polymerase and another protein complex called the mediator multiple protein complex constitute the basic transcriptional apparatus, which positions RNA polymerase right at the start of a protein coding sequence or a gene and then releases the polymerase to transcribe the messenger RNA from that DNA template. Now there's another type of DNA binding protein called activators and these enhance the interaction between RNA polymerase and a particular promoter, encouraging the expression of the gene and activators can do this by increasing the attraction of RNA polymerase for the promoter through interactions with sub units of the RNA polymerase or indirectly by changing the structure of the DNA. An example of an activator is the catabolite activator protein or CAP and this protein activates transcription of the lac operon in E. coli. In the case of the lac operaon and E. coli, cyclic adenosine monophosphate or cAMP is produced during glucose starvation and so this cAMP actually binds to the catabolite activator protein or CAP which causes a confirmational change that allows the CAP protein to bind to a DNA site located adjacent to the promoter and then this activator, the CAP, then makes a direct protein to protein interaction with RNA polymerase that recruits the RNA polymerase to the promoter. Now enhancers are sites on the DNA that are bound to by activators in order to loop the DNA in a certain way that brings a specific promoter to the initiation complex and as the name implies this enhances transcription of the genes in a particular gene cluster. And while enhancers are usually what are called cis-acting, cis meaning the same or acting on the same chromosome, an enhancer doesn't necessarily need to be particularly close to the gene that it acts on and sometimes it's not even located on the same chromosome. Enhancers don't act on the promoter region itself, but are actually bound by activator proteins and these activator proteins can interact with that mediator complex I mentioned earlier which recruits RNA polymerase and the general transcription factors which then can lead to transcription of the genes. So here I've drawn a little schematic of what it might look like to have the enhancer actually change the structure of the DNA so that the DNA is now looping around. Here you still have your promoter sequence, the operator sequence, the gene sequence, and the enhancer sequence, and having the DNA looped in such a way so that you could then recruit RNA polymerase, the transcription factors, the mediator protein complex, and then you have transcription begin of this gene here. Now let's talk about repressors. Repressors are proteins that bind to the operator, impending RNA polymerase progress on the strand and thus impeding the expression of the gene. Now if an inducer, which is a molecule that initiates gene expression, is present, then it can actually interact with the repressor protein in such a way that causes it to detach from the operator and then this frees up RNA polymerase to then transcribe the gene further down on the DNA strand. One example of a repressor protein is the repressor protein associated again with the lac operon operator, which prevents the transcription of genes used in lactose metabolism unless lactose, which is the inducer molecule, is present as an alternative energy source. Now silencers are regions of DNA that are bound by repressor proteins in order to silence gene expression and this mechanism is very similar to that of the enhancer sequences that I just talked about. And similarly, silencers can be located several bases upstream or downstream from the actual promoter of the gene and when a repressor protein binds to the silencer region of the DNA, RNA polymerase is prevented from binding to the promoter region. Now a few notes about the differences between prokaryotes and eukaryotes when it comes to transcriptional regulation. In prokaryotes, the regulation of transcription is really needed for the cell to be able to quickly adapt to the ever-changing outer environment that it is sitting in. The presence, the quantity, the type of nutrients actually determines which genes are expressed and in order to do that, genes must be regulated in some sort of fashion so a combination of activators, repressors, and rarely enhancers, at least in the case of prokaryotes, determines whether a gene is transcribed. In eukaryotes, transcriptional regulation tends to involve a combination of interactions between several transcription factors which allows for a more sophisticated response to multiple conditions in the environment. And another major difference between eukaryotes and prokaryotes is the fact that eukaryotes have a nuclear envelope which prevents the simultaneous transcription and translation of a particular gene and this adds an extra spacial and temporal control of gene expression.