Tag Archives: biochem

The Lehrer Method

Start with Acetyl CoA.



Posted by on February 23, 2014 in Uncategorized


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eteRNA RNA folding game


Proper Folding Achieves Lowest Energy Conformation

My general biology students were asked yesterday to check out eteRNA, an interesting online game designed around problems of RNA folding. RNA is a fascinating molecule for a number of reasons.

  • What we might think of immediately, mRNA as an information carrying molecule, is just one of its many jobs.
  • In addition to this, RNA serves as a delivery molecule in the form of tRNA. These molecules are capable of both ‘reading’ the mRNA message, through codon:anti-codon interactions, and they also recruit and deliver Amino Acids that correspond to the codon in question. 
  • RNA also functions as ribozymes, enzymes comprised entirely, or in part, of RNA. An example of this is the ribosome that is mostly rRNA with only a small protein contribution.

EteRNA explores the plasticity of RNA function by demonstrating the capacity of this molecule to fold into a variety of shapes. As I frequently remind my class, FORM DICTATES FUNCTION. This is true of all things in biology (and perhaps beyond). When a molecule is formed correctly, it carries out its function appropriately. When that form is altered due to mutation, misfiling or other denaturing processes, the function is also altered. This may be for better or worse, but mostly for worse.  Depending on this function, the ‘fitness’ of the cell for survival / reproduction may be affected leading to selection for or against this cell.



I set up a group titled: FortScott_Treml that I invite my students (or anyone else) to join. For my students, anyone who completes the the tutorials will receive 5 extra credit points. Anyone who earns a puzzle master badge will earn another 5.

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Posted by on November 13, 2013 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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