Tag Archives: biochemistry



Glucose – 6 Phosphate

For my Ecology class, consider the question below as you think over Why Evolution is True chapter 2. I will post this and several more questions later today on blackboard…

There a lot of talk about biochemical pathways in this chapter. Mostly, Coyne sticks to the one used to synthesize ascorbic acid (vitamin C), however this reaction involves the use of a compound called Glucose-6-Phosphate. This molecule is common to a number of important metabolic pathways. In addition to making vitamin C, see if you can find one anabolic and one catabolic pathway downstream of this molecule. 

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Posted by on January 26, 2014 in Uncategorized


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Cellular robotics? A cute video summarizing cellular functions from TedEd

Check out this video. I think I like it, but I’m not positive yet. It’s so well done that I’m kind of taken by the aesthetics, however, I’m not sure that this makes cell biology easier to understand. What’s your opinion?


Posted by on November 25, 2013 in Uncategorized


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Getting Oxygen Where It’s Needed

Getting Oxygen Where It’s Needed.

This is an older post of mine that I thought I should point back to because my general biology class is now covering cellular respiration.

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Posted by on October 3, 2013 in Education


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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 Animation

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Posted by on September 18, 2012 in Uncategorized


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