How many atoms does alpha-Amylase consist of?

[Kageyaiba]

I know that's not that relevant to anyone actually studying or working with enzymes, which is probably why this is so hard to find out as a layman.

I'm working on very simplified school materials, designed to help young adults preparing for a rudimentary school degree. (German system)

They need a very basic introduction to chemistry in order to even be able to work with the recommended materials. When I explain what a Molecule is, I try to make them understand that they can be as simple as Water or incredibly complex. For the latter I chose alpha-Amylase as an example, because the students already know the enzyme from biology and it would certainly help to illustrate the scale of atoms, if they understood, that such 'huge' molecules exist in their saliva. Now of course I could just write "...thousands of atoms...", but in my experience that wouldn't have the same impact as providing more concrete figures. From what I gathered so far, not every alpha-Amylase is built exactly the same way (there seem to be genetic variations, which exact amino acid chains are used by the body to produce the enzyme), but I would be surprised if the differences were anything but negligible. 

The best I could come up with so far is to assume it's mostly made of Hydrogen and Carbon in a 2:1 ratio and then use its molecular mass (55,4 kDa) to calculate the number of Atoms (55400/14*3=11871). Now considering that other atoms in the molecule are certain to be heavier, I'd say roughly 11000 would be a fair guess.

Am I close or way off. Or is there a better solution?

[scooke]

Dear Max,

In today's world, even numbers don't pack a lot of punch.  I would suggest that "A picture is worth 1000 words."!  If you can get any version of a picture of your enzyme at a level where you could identify a carbon atom, for example (even just a dot), a corresponding to scale picture or diagram of a water or carbon dioxide molecule might be more impressive and memorable.

Best regards,

Steven

[Kageyaiba]

Hey Steven,

Thanks for your response. You are right of course and a rough visual comparison between a water molecule and Amylase will be part of the work sheet, but if I've learned anything as a teacher, it's that different people learn in different ways and whilst some will certainly benefit from a visual aid, others will be more impressed by the big number.

On a related note: You don't happen to know the diameter of alpha-Amylase, do you?

[scooke]

Dear Max,

Well, yes, I try to teach in a "multi-modal" fashion as well.  In that case, it REALLY does not matter about accuracy, as you are going for orders of magnitude!  You initial conversion of Daltons to atoms is sufficient for that purpose (that's why we invented Daltons).  An "atomic ratio" of 11000:3 for amylase to water looks as good as it gets.

Similarly, diameters of molecules are tricky things, especially as they get to huge proportions (atomically).  Biological molecules are notoriously convoluted and often very flexible.

Best regards,

Steven

[Kageyaiba]

Dear Steven,

Thanks again for taking the time.

I'll just take that number and run with it then. I know that I'm probably being way too pedantic about this since what I'm trying to teach essentially boils down to "enzyme biiiig molecule", but I teach my students to be as accurate as possible and try to hold myself to the same standard.

Cheers

[scooke]

Dear Max,

It all depends on what you want the real learning to be.  If "order of magnitude" is the goal, then a precise value is not needed, as long as it is a reasonable one.  You COULD make a project out of it and have the students look up that enzyme or similar ones and find out for themselves what "ranges" of atoms they contain - just so they know that you are not making this stuff up.

In chemistry we always seem to have that 'disconnect' between talking about atoms and molecules and really knowing how they work in the macroscopic observations.  It gets even worse sometimes dealing with material interactions in space!  Why IS a biological molecule so large, and how does that make it different from other molecules?  Yet, compared to a cell, an enzyme is still small.  And cell walls are made of what?  In general science at an early level it is often difficult to know whether you should address an observation from a biological, chemical, or physics perspective!

Cheers,

Steven

[brupalf]

Hi Max

One of the structures of the enzyme, determined by X-ray crystallography (1SMD.pdb), has 3946 C, N, O, and S atoms, a.k.a. "heavy-atoms". In most crystal structures H-atoms are invisible because they don't have enough electron density to diffract strongly. The protein backbone will generally have two H-atoms (only one for proline, but they're not highly abundant), while each side-chain might have as few as 1 (glycine) to - oh, I don't feel like getting an exact count - maybe close to ~10 for the larger side-chains like tryptophan, methionine, etc. The enzyme has 496 amino acid residues. So, maybe ~7 H-atoms on average per residue? That adds maybe ~3500 H-atoms to the 3946 heavy atoms, so call it ~7500 total atoms?

You can learn a bit about the structure here:  RCSB PDB - 1SMD: HUMAN SALIVARY AMYLASE  and get the so-called pdb file, a rather crude text-file that contains the cartesian coordinates of the heavy atoms, here: https://files.rcsb.org/view/1SMD.pdb  From either of these sources, you could get the amino acid sequence and actually calculate the exact number of atoms from the standard structures of amino acid residues. A bit laborious, but straight-forward, I think.

The enzyme is sort of egg-shaped. It's ~74 Å across on its long axis, and ~40 Å cross its "equator".

Good luck.

ciao,

Bruce

[karenwiz]

Dear Max

Steve and Bruce have given you some great information. I wanted to chime in to ask if you're interested in making another contrast. 

I understand you wanting to use the amylase as an example of a large molecule, both because it's personal (it exists in saliva) and that they've heard of it from another class. Amylase has the property of being very big but as this conversation thread also demonstrates, it is also very complex in both its sequence of atoms and its physical shape.  I don't think you want the students to think that this type of complexity is an inherent property of all large molecules - that large molecules are required to be complicated. 

Might you also want to give the intermediate example of a linear polymer?  A compound of that type would be a huge number of atoms in the molecule but its structure makes it much easier to calculate the number of atoms, and a polymer of commercial importance would also be well characterized as to its physical size with such information published.  A long polymer chain can also assume both extended and coiled up structures in solution which explains the viscosity of a solution of the polymer - extended chains make a solution thicker than coiled up ones.  That also makes it possible to make a demonstration of the effect of this physical change - adding salt to a water solution of polymer should transform from thick to thin as the polymer chains go from extended to coiled.

Don't know if you have considered something like this.  Just a suggestion.

Best regards,

Karen

[saustin]

Hello Max

I think Karen's idea is great - and since you are interested in alpha-amylase, why not pick starch ?  Starch is very polydisperse, but can reach a molecular weight of around 1 million daltons.  At that mass is would be composed of around 6200 glucose monomers giving you 6200 x 6 carbon atoms  6200 x 5 oxygen atoms and 6200 x 10 hydrogen atoms (then you have to add one molecule of water to complete the polymer)  so in total you would have 130203 atoms. 

[major]

As you probably know, there are many different amylase enzymes, with somewhat different sequences.  However, as an example, one of the human enzymes (1A) has the formula of C(2589)H(3857)N(715)O(752)S(23), so a total of 7936 atoms.  

Douglas W. Rea