Some questions on Enzymes

Kyriakos

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Not meaning for very technical answers, just correct ones to the general questions... :D

1) Can enzymes be concisely defined as catalysts with complex make-up that makes them highly specific (selective) in the reactions they cause?

2) Do most enzymes catalyse in a rate only limited by their ability to diffuse in that which they are reacting with?

3) I read that some enzymes at least appear to catalyse even faster than it takes them to diffuse in what they react with. On the surface this sounds like a paradox, cause in effect it would mean that parts of the enzyme or its reactive core sort of reach the entire field of the reaction before this happens for the entirety of the enzyme.

and last, but certainly not least:

4) If an enzyme diffuses very fast in a distinct volume it reacts with, how will this possibly be a predetermined factor for it to not extend its effects in nearby (but not in the immediate one) volumes? In other words: is this a safeguard for even more specialised use of the enzyme?

Thanks. As usual i just need the general info for the prospect that some of the new story's exosceleton will not be corroded by myself throwing wrong enzymes (info) on it :mischief:
 
I'm not an enzymologist in any way (and certainly not a clinical one), but hopefully these answers will make sense, and won't be (too) wrong.


1) Can enzymes be concisely defined as catalysts with complex make-up that makes them highly specific (selective) in the reactions they cause?

Yes, they're catalysts with a complex make-up (depending on what that means exactly, and depending on the specific enzyme too), but they're not necessarily highly specific. "Enzyme promiscuity" - the ability to react with diverse substrates (other molecules which constitute the targets of the enzyme) - is a big thing. Sometimes this happens because the conformational state of the enzyme has been (reversibly) changed, and therefore its specificity is biased towards one substrate and away from the other. In other cases, the same enzymatic state can bind to different substrates, although the affinities might be substantially different for each.


2) Do most enzymes catalyse in a rate only limited by their ability to diffuse in that which they are reacting with?

Staying with a simple model, let us define an enzymatic reaction the set of the following sub-reactions:
1 - The reaction where the enzyme meets and binds the target, which may be accompanied by the opposite reaction (dissociation from the target before completing the catalysis);
2- The actual catalytic reaction which transforms the substrate into a different molecule.

The (global) reaction rate depends therefore on the rates of association and dissociation of enzyme and substrate, on the rate of the catalytic reaction, on the concentrations of enzyme and substrate(s), and on the concentration of possible competing enzymes. These rates are population averages (i.e., averaged across many molecules. The timing of the reactions at the single molecule scale is random). At this level of detail, you can just imagine the the diffusion rate is lumped into the reaction rates.
Assuming all else is equal (that, in your words, the ability to diffuse is the same), the relative numbers of enzymes and substrates will change the global reaction rate though. Production will saturate for high amounts of substrate. Intuitively you can think of it this way: if all the enzymes are busy doing their good catalytic work, then they're blind to the addition of more work, because they're already operating at their maximum speed and have no free hand to spare.
The picture gets a bit more complicated if you put them in a crowded environment full of other proteins, and in very small volumes. The output of an enzymatic reaction can be substantially different in those conditions (both quantitatively and qualitatively), and this is an active area of research at present.


3) I read that some enzymes at least appear to catalyse even faster than it takes them to diffuse in what they react with. On the surface this sounds like a paradox, cause in effect it would mean that parts of the enzyme or its reactive core sort of reach the entire field of the reaction before this happens for the entirety of the enzyme.

Not sure what this means. Where did you read that and what is the exact quote? Enzymes are molecules (or form a part of larger molecular complexes) that move around in a random fashion or get transported by other types of molecules. They interact "physically" with their targets through a region of the enzyme's "surface" called the active site. This is where the catalytic reaction takes place. From this point, while the speed of the catalytic reaction(s) appears to be typically slower than the speed of the earlier binding reaction(s), that needn't be the case in some solutions. There is no part of the enzyme that reaches the "field of the reaction" before the rest of the enzyme: there is one bit of the enzyme that is active in the reaction, but is always attached to the rest of the molecule.
You also need to be careful when translating enzymology jargon into a mental picture: such jargon is usually a description of the output of an ensemble of molecules, not of an individual molecule.


and last, but certainly not least:

4) If an enzyme diffuses very fast in a distinct volume it reacts with, how will this possibly be a predetermined factor for it to not extend its effects in nearby (but not in the immediate one) volumes? In other words: is this a safeguard for even more specialised use of the enzyme?

If an enzyme diffuses very fast it will spread faster to nearby volumes, unless there is some sort of barrier (and often there is). There are mechanisms to maintain enzyme "specialisation" in a given moment or process though. For example, they can be sequestered by other molecules, or they can be activated and inactivated by other proteins or smaller chemicals (by either blocking the active site or changing the 3D structure of the enzyme (e.g., by changing its distribution of electrical charges), such that the enzyme can't recognise its target anymore).
 
Thank you for the great answers :D

I needed that info for a story which i completed earlier today, and i had some replies in the same questions in other forums.

As for question #3, i read (iirc not in wiki, but some biology site, however the history is erased now cause days passed) that some catalytic events seem to include a sort of tunnelling of the active site to the end of the substrate (before it has actually reached it through diffusion). But i won't be needing info on that anyway.. :)

(btw, i was interested in the specific enzyme Chinitase, for a plot involving catalysing some Chitine, as in the protective layers of the wings of Coleoptera).
 
As for question #3, i read (iirc not in wiki, but some biology site, however the history is erased now cause days passed) that some catalytic events seem to include a sort of tunnelling of the active site to the end of the substrate (before it has actually reached it through diffusion). But i won't be needing info on that anyway.. :)

What they probably meant is that the molecule gets there faster than it would if it moved just by diffusion.
 
Not meaning for very technical answers, just correct ones to the general questions... :D

1) Can enzymes be concisely defined as catalysts with complex make-up that makes them highly specific (selective) in the reactions they cause?

2) Do most enzymes catalyse in a rate only limited by their ability to diffuse in that which they are reacting with?

3) I read that some enzymes at least appear to catalyse even faster than it takes them to diffuse in what they react with. On the surface this sounds like a paradox, cause in effect it would mean that parts of the enzyme or its reactive core sort of reach the entire field of the reaction before this happens for the entirety of the enzyme.

and last, but certainly not least:

4) If an enzyme diffuses very fast in a distinct volume it reacts with, how will this possibly be a predetermined factor for it to not extend its effects in nearby (but not in the immediate one) volumes? In other words: is this a safeguard for even more specialised use of the enzyme?

Thanks. As usual i just need the general info for the prospect that some of the new story's exosceleton will not be corroded by myself throwing wrong enzymes (info) on it :mischief:

I think part three may relate to a synergistic effect; I'm not so sure about skipping distances during diffusion, but it would make sense to me that an enzyme could change the conformational shape of the substrate--which would, in turn, act as a new catalytic product on another player on the chemical pathway. Something to keep in mind is that chemical reactions aren't strictly linear in nature, but rather they can exist in a complex three dimensional soup where the dance partners can change.

Perhaps it's related to your first question, but I seem to recall that Enzymes can be defined as both proteins and catalysts. This is how you run into weird situations where Enzyme A chaperons Protein B and C into Product D. Product D might then act as an inhibitor to the B+C reaction, or conversely ramp up the reaction rate even further. This is all while Enzyme A might still be active, maybe not even fully saturating the chemical substrate available. It's a dynamic process.
 
It is true that enzymes meet the general definition of a chemical catalyst for general reaction kinetics. They are a place for substrates to meet to improve reaction rate. The specific difference is that enzymes are biological, based on protein structure, and have a broad variety of mechanism, form, size, etc... and occur within living things.


I think a short answer on the low importance of enzyme diffusion rate vs enzyme mechanism rate is twofold:

1. enzymes are usually compartmentalized to where they are needed in cells, so the substrates come to the enzyme. The arrangement makes is so that the substrates are more less funneled to the enzyme, in vivo. The compartmentalization means that the enzyme will be localized to bounded area in the cell (bounded by membrane that usually blocks uncontrolled flow of substrates). The enzyme may even be physically embedded in such membranes at choke points. Enzymes might even be linked close to each other in series so substrates are funneled towards the next enzymes in sequence. This makes the general diffusion of reaction kinetics kind of negligible. Maybe it even makes it zeroth order reaction kinetics?

2. Enzymes are usually much larger than their substrates, and the substrates are usually very common molecules, so the rate of the enzyme diffusal is less relevant than how long it takes the substrate to get to the enzyme, which might be negligible if due to the point in #1 (e.g. one enzyme may be funneling directly to another enzyme), and fairly negligible if the substrate is present in saturating concentrations in the same compartment as the enzyme.. I think that would again be approximated as zeroth order reaction kinetics, if at all.

So if the impact of diffusion is I guess zeroth order, it will at most be a constant that will be factored into the kinetics of the enzyme mechanism (e.g. the Michaelis-Menten or other kinetics model used to the study the enzyme).

Applications using enzymes ex vivo tend to mimic compartmentalization of enzymes someone. E.g. physically linking the enzyme to a surface for example, and blocking temporarily blocking enzyme with non-specific chemical reactions.


I think if I was writing fiction on enzymes, I'd start with the simplest concept, and then add in extra detail on the mechanism for plot twists, or to just to 'jump the shark'.

Enzyme reactions can get pretty crazy when redox reactions are involved. In those reactions electrons can jump distances between metal elements embedded in enzymes. Kind of like a spooky at a distance jump.

I take it you want your character's exoskeleton to be impervious to same enzymes that it uses to attack other creatures? Just think of a way to inactivate those enzymes, perhaps through surface excretions from local organs. Enzymes can be inactivated by inhibition by other molecules (e.g. competition for the active site of the enzyme), or just degraded like any old protein can be (e.g. by extreme pH). You could have secretions of semi extreme pH that don't harm the armor, but would protect the armor against enzyme attacks.
 
^Thanks :D

I just want to use the Chitinase enzyme to catalyse/destroy or weaken a surface made of Chitin, while not do anything to the border of that surface which is made by some un-named substance. I am just using the enzyme due to the specificity (i trust it would not react with the other substance) and also due to Scarabs being a part of the plot. It is not about coleoptera themselves attacking, but having chitinase thrown at a hardened chitine part of them (namely the inverted triangle just above the hardened wing-covers/'elytra').
 
A small bump, with a very specific question:

Would one need access to an actual laboratory (eg a uni chemistry one) to isolate some Chitinase? (i was told he would). And when isolated (in whatever manner, i guess largely artificial creation-- is it possible here?-- would be easier than extraction?) would it then be 'easy' to contain it so as to use on some Chitine to erode/catalyse the latter?

Thanks :) (as a safeguard i included the passing info that the character had access for a very limited period to the uni laboratory, and had an infered background in working with chemical reactions, although his actual work- and laboratory- is as a creator of amulets from semi-precious stones).
 
Also:

chtininolytic stuff said:
http://www.sciencedirect.com/science/article/pii/S1687157X13000061][/url]
2.2. Preparation of colloidal chitin

Colloidal chitin was prepared from the chitin (Hi Media) by the modified method of Hsu and Lockwood [20]. In brief, chitin powder (40 g) was slowly added with 600 ml of concentrated HCl and kept for 60 min at 30 °C with vigorous stirring. Chitin was precipitated as a colloidal suspension by adding it slowly to 2 l of water at 4–10 °C. The suspension was collected by filtration with suction on a coarse filter paper and washed by suspending it in about 5 l of DW. Washing was repeated 3 times until the pH of the suspension was 3.5. After the above treatment, the loose colloidal chitin was used as a substrate [50].
2.3. Screening of chitinase producing bacteria

Screening was performed with bacterial isolates on the colloidal chitin agar medium incubated at 37 °C. Bacterial isolates were selected on the basis of a larger hydrolysis zone after 96 h of incubation and further screened for maximum enzyme production in nutrient broth media. The cultures were centrifuged at 10000 rpm for 15 min at 4 °C and the crude was used for chitinase assay.
2.4. Assays of chitinase activity and protein estimation

The chitinase activity was assayed by measuring reducing sugar released from colloidal chitin as per the modified method of Toharisman et al. [46]. Briefly, crude enzyme (150 μl) was added to the mixture consisting of 300 μl of 0.1% colloidal chitin and 150 μl of 0.1 M phosphate buffer pH 7.0. After incubation at 55 °C for 10 min, the reaction mixture was subjected to a refrigerated centrifugation at 10,000 rpm for 5 min. The resulting supernatant (200 μl) was added with 500 ml of DW and 1000 ml of Schales reagent then boiled for 10 min. After cooling, the absorbance of the mixture was measured at 420 nm. One unit of the chitinase activity was defined as the amount of enzyme which yields 1 μmol of reducing sugar as N-acetyl-d-glucosamine (GlcNAc) equivalent per minute.
2.5. Characterization of bacterial isolates

2.5.1. Identification of chitinolytic bacterium

The identification of bacterial isolates HS4 and HS6 was carried out according to the methods described in Bergey’s Manual of Systematic Bacteriology [21].

and i think that (for the very limited scope of enzyme use in my short story) i just need to ask the following:

1) Do the above paragraphs mean that in a chemistry lab one would place bacteria in a chitine preparation, and those bacteria would (somehow? i just need to know if it does happen) function as creators of chitinase?
2) Would those bacteria be easy to place in such a chitine base? Also, what is a "bacterial isolate" (very very generally)?
3) is the afforementioned chitine base something generally easy to create in such a lab, with some uni knowledge of chemistry?

Thanks for any help.. Currently i am thinking that i would just add the sentence that the chitinase was prepared in that uni lab (he had access to and had used in his uni years) using those bacterial isolate(s) in prepared (for other lab works) chitine.
 
1) Do the above paragraphs mean that in a chemistry lab one would place bacteria in a chitine preparation, and those bacteria would (somehow? i just need to know if it does happen) function as creators of chitinase?
Yes. Bacteria often produce enzymes depending on what's available in the environment.

2) Would those bacteria be easy to place in such a chitine base? Also, what is a "bacterial isolate" (very very generally)?
Yeah, you can just mix the chitin into the agar plates bacteria are grown on. Isolates refer to colonies on the plate. If you dilute the bacterial mixture enough, these would be formed from only single cells and thus all the bacteria in the colony would have the same genetic background.

3) is the afforementioned chitine base something generally easy to create in such a lab, with some uni knowledge of chemistry?

Yes. The methods you quoted show that the researcher bought chitin powder from commercial suppliers, diluted it in acid and water, filtered it, and washed it while measuring pH with a meter.
 
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