Tag Archives: regulation

A quick followup on that lac operon post

Last week I posted a quick link about operons for my micro class to check out before taking their quiz on bacterial gene regulation This post is intended to complement that one. To go back to that post, click here. If there’s one thing to remember about operons it is that bacteria, lacking a nuclear membrane, regulate their genes differently than Eukaryotes. Having a nuclear membrane separates transcription and translation into two distinct compartments allowing for more subtle tweaking of Eukaryotic mRNAs before they are exported for translation.


Click on this figure to go to a good description of how polycistronic genes work

One thing this does is it makes it very beneficial to package genes with related function closely on the genome and use a single regulatory region to control them all together. They wind up getting packed so closely together that they are actually expressed as a single messenger RNA – known as a polycistronic (meaning ‘many gene’) message.

Upstream of this polycistronic cassette are regulatory elements. One element common to all regulatory elements is the promoter. The promoter consists of several elements which ‘promote’ the binding of an RNA polymerase to the DNA. Additional regulatory elements exist to ensure that this polymerase only transcribes the genes if they are needed. In doing so, the cell conserves energy and components (e.g. Amino Acids) for only necessary processes.

In the case of the paradigm lac operon, lactose is a fuel source, but not as good as glucose. Therefore, enzymes to digest lactose are only needed when lactose is present, but glucose is not. In order to interrogate both conditions, two additional regulatory elements are present.

First, the operator sequence. This sequence binds a repressor protein that physically blocks the polymerase’s path in the absence of lactose. However, if lactose is present, the sugar binds to the repressor, causing a conformational (shape) change that causes the protein to release its grip on the operator sequence.

Second, a catabolite activator protein (CAP) will only bind to the DNA behind the RNA polymerase if cAMP is present. Let’s not get too distracted, other than to say that cAMP levels are high in the ABSENCE of glucose, and low when that sugar is present. When cAMP binds to the CAP protein it can now bind the DNA and do it’s other job: making a nice binding site for the RNA polymerase. Without CAP, the polymerase binds very inefficiently.

Together, the production of lactase enzymes (those that digest lactose) is exquisitely controlled in a way that conserves the most energy.

ImagePs – take a look at this graph and tell me why (not mechanistically, but rationally) the cell does not make lactase enzymes when both glucose and lactose are present.

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Posted by on March 15, 2014 in Uncategorized


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Allosteric Enzymes

I have found that many readers find my blog with the search terms ‘allosteric enzymes.’ But in looking back to the post that I wrote describing these enzymes I find it a bit wanting. So I’ve decided to write a new post on that topic here.


Consider first what an enzyme is: biological catalysts.

And, what is a catalyst? It’s something that is involved in a chemical reaction, but is not changed by the reaction.

-If a catalyst was a person it might be a matchmaker who, through their personal network, sets people up together to see if they are compatible. But like matchmakers, catalysts just bring molecules together, they don’t actually become part of the couple themselves. Catalysts remain unchanged at the end of the reaction ready to do the same job again.



Enzymes do their work by binding their substrates in a location called the active site. In the active site, the reaction takes place usually breaking one molecule into two or joining two molecules into one or some other such reaction.


Figure 1

Figure 1: Enzyme with active site for substrates


So, enzymes catalyze reactions in biological systems. They are typically proteins, but can also be RNA molecules that fold up to have the same properties.

In my class, I always emphasize that

Form Dictates Function.’

That is, in cells (or even outside of them) biomolecules work or don’t work because of their form. In this case, if an enzyme is folded into the proper conformation, it may bind molecules and facilitate a reaction to take place. If they are not in a conformation to bind the molecules, they won’t do it and the reaction does not take place.


Figure 2: An unregulated enzyme. This enzyme is always in the active conformation capable of processing substrates (A) into product (B)

Some enzymes might appear to be always in the proper conformation and always catalyze reactions amongst the molecules around them (like the one pictured above in Figure 2). However, some others are shapeshifters, that are sometimes in a conformation favorable to catalyzing the reaction (an active conformation)

Other times, these enzymes are in conformations unfavorable to catalyzing the reaction (an inactive conformation).


But what dictates what conformation an enzyme is in?

One thing might be whether there are other molecules that bind to the enzymes in the nearby (micro-)environment. These molecules are called effectors and reasonably enough, they bind a site on the enzyme called an effector site. An effector site is a binding site on the enzyme that exists anywhere outside of the active site.

Figure 3

Figure 3: Allosteric enzyme with active site and effector site. A) Effector unbound, Active site in active conformation – capable of processing substrate B) Effector bound, Active site in inactive conformation – incapable of processing substrate


When an effector molecule binds to the effector site, the shape of the whole enzyme changes to a new conformation. In the illustration above, the active form is shown when the effector is unbound (A), the inactive form is shown when the effector is bound (B). In this case, binding of the effector caused a change to the inactive form, so the effector is called an inhibitor. It is possible that another enzyme is in the inactive form when the effector is unbound, but changes into an active conformation when bound. In that case, the effector would be an activator.


Enzymes that change shape like this are called allosteric enzymes. ‘Allo-‘ translates as different and ‘–steric’ translates as shape, so these are enzymes that change their shape (from active to inactive forms).


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Posted by on December 8, 2012 in Uncategorized


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Enzyme regulation


Effector Actions may be Inhibitory (top) or Activating (bottom)

I’ve been looking for an animation (or something similar) that would illustrate how enzyme activity can be regulated by effectors. However, this seems to be lacking… I’m thinking about making one myself and will post it here if I do.

Recall that effectors are the molecules that bind to enzymes outside of the active site and have either a positive (activator) or negative (inhibitor) effect on the enzyme’s activity. Regardless of the positive or negative effect, both of these molecules are considered effectors and bind to an effector site. The effector site can be any location on the enzyme other than the active site. Inhibitory effectors are called non-competitive inhibitors because they do not compete with the binding of substrate directly at the active site. Activating effectors are called activators. Because these molecules bind away from the active site, they do not directly interact with the substrate, but instead influence the enzyme’s ability to bind (and/or modify) substrate by changing the shape of the enzyme. For this reason, enzymes that bind effectors are called allosteric enzymes, from the greek allo– ‘other’ and steric ‘shape/ conformation.’

Allosteric enzymes can be in one of two conformations: Active Conformation or Inactive Conformation. The conformation state that these enzymes exist in is dependent upon the presence or absence of their effector proteins.

Competitive Inhibition

The other major class of regulator is that of competitive inhibitors, these molecules bind directly to an enzyme’s active site and prevent substrate processing. This is a much more straightforward kind of inhibition and does not alter a enzyme’s shape into an inactive conformation.

I hope this helps to organize your thoughts about enzyme regulation. I plan on reviewing this in class this week using a couple example problems.

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Posted by on September 19, 2012 in Uncategorized


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Enzyme Regulation Animation

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Posted by on September 18, 2012 in Uncategorized


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