Most textbooks seem to describe enzymes as a “puzzle piece” with a site that only attaches to a compatible substrate. However, I am not clear on the details. Is there something that attracts the enzyme to the compatible substrate? Is it just a matter of probability and chance that the two join up? What mechinism does the enzyme use to break down the substrate?
Any help would be helpful.
Enzymes and their substrates rely on “chance” as you call it to combine. Keep in mind, though, a cell is very small, and concentrations of enzyme or substrate don’t have to be very high for one to encounter the other.
More evolved (eukaryotic) cells have internal divisions that contain specific enzymes and their substrates, such as the enzymes geared toward energy production in mitochondria. The enclosed areas within the cell make it even more likely enzymes and substrates will encounter each other.
As far as method of operation, a new theory known as “induced fit” better describes enzyme action. Simply put, the substrates don’t fit in the enzyme perfectly. This causes stress in the substrate’s chemical bonds, making it more likely the substrates will react with each other.
The three dimensional puzzle that is a created in any complex organic interaction is a matter of the precise relationship in space of the more positively, and more negatively charged regions of any molecule, compared to another molecule.
An enzyme is a molecule that “fits” into one spot, on a certain other molecule, and when it does, it twists that molecule into a shape which much more readily fits with a specific other molecule. When the two “catalyst” target molecules are both brought together, that same reaction causes the original enzyme molecule to be released by both target molecules. It is random for the target molecules to touch. But at the speed of molecular collisions even a minor increase in probability is very effective. Since the enzyme itself is not altered, it affects a very large number of target molecules.
Tris
“It should be possible to explain the laws of physics to a barmaid.” ~ Albert Einstein ~
“You should see the place where Einstein used to drink!” ~ Triskadecamus ~
Induced fit only applies to some enzymes, and it only refers to how an enzyme binds its substrate. Sometimes the substrate approaches the enzyme (which is, by the way, a protein, full of amino acids), causing the amino acid residues to be attracted/repelled, therefore leading to a shift in shape which allows the already-semi-bound substrate to bind even better. This allows for the enzyme to, for example, “flex” the substrate into a shape that is more like the transition state needed to make the product, therefore accelerating the reaction towards the product. The product doesn’t bind as well, and is released, allowing the enzyme to return to its original shape, and be used again. Enzymes are catalysts - they are not used up in reactions.
This description is simplified, though, and can only completely be applied to single-substrate enzymes. MANY enzymes are multi-substrate. In many cases, the binding of the two or more substrates simply allows for better proximity of the substrates, so that they can react with each other much like they would otherwise - just more frequently. Sometimes the transition-state mimic is also involved. Many processes (eg. gylcolysis - the breakdown of glucose to yeild energy) involve many enzymes, and essentially form a chain or reaction sites.
There are many things that we still don’t know about how enzymes work, and there is an entire field of study about them (Enzymology). I actually have an enzymology course this semester.
Anyways, beyond the structural ways in which they “work”, the traditional classification system of ensymes also describes the relatively simple chemistry that takes place in each enzyme. Currently there are 6 recognized enzyme classes (though there are efforts to revamp the system - I’ll just tell you what I was taught). The six classifications are (forgive me if I number them wrong):
- oxidoreductase/dehydrogenase (oxidation-reduction reactions)
- transferase (transfer a group off of one substrate onto another: A-B + C -> A +B-C)
- hydrolase (reactions involving water): AB + H2O -> AH + BOH
- liase (reactions that make/fill a double bond)
- isomerase/racemase (reactions that convert one isomer of something to another, such as D-glucose converted to L-gulcose)
- ligase (reactions that use ATP energy, phosphorylate)
Now I hope I got that right - my midterm was just yesterday!
There are a lot of books on this. A basic Biochemistry book should have more than enough to satisfy your curiosity, as well as likely references to learn more, if you’re interested.
New ? Koshland came up with induced fit in 1958, and it’s still going strong.
Simple
A bit more detail
Thanks, everyone.
I can’t wait to dazzle friends with my new knowledge of catalyzation
I did not know that. When the theory was described to me, I was under the impression it was recent.