The BE&HM Series ~ Part II: Atoms & The Periodic Table

As I outlined in the introductory post, Biophysical Electrochemistry and Human Metabolism, many of the reactions involved in human metabolism might well be better understood by understanding electrochemistry which deals with redox chemistry and the physical chemistry of ionic gradients and diffusion.  But in order to get to that, I think it is important to lay the groundwork of the chemical nature of all matter.  And while I could send you to any number of tutorials about the net, I thought it worth my while to put the content here.  

Atomic Structure

The basic unit of all matter is the atom.  While there have been all manner of subatomic particles and such in the news, we really don't need to "go there" and the most simplistic model of the atom holds up fairly well for discussions of both biochemistry and electrochemistry.  Atoms are comprised of three particles:
  • Protons:  mass 1 amu, +1 charge
  • Neutrons:  mass 1 amu, 0 charge
  • Electrons:  massless* , -1 charge
The number of protons tells you what you have, and is called the atomic number.  For example the simplest atom is hydrogen, H, atomic number 1 meaning it has one proton.  The next atom is helium, He, with two protons, atomic number 2.  We can't add a proton to an H atom to make it a He atom or remove one from He to make H (we're not going into fission/fusion land here). 
* mass e <<< mass P or N, so negligible in the context of the atomic mass. 

Now no simplified depiction of an atom quite does justice to what is really going on, and is woefully inadequate to describe bonding and reactivity, but the one I've chosen above is still helpful.  The protons and neutrons are in the center, like the sun of our solar system, that we call the nucleus.  Orbiting about the nucleus are the electrons.  This depiction demonstrates several concepts.  First, notice that the nucleus is a small and concentrated "glob" of protons and neutrons -- and this is highly exaggerated at that.  In proper scale, the nucleus would be a pin dot in the center.  Protons and neutrons are where the mass is, so the atom has a highly dense pinpoint of mass in the center.  The atomic mass and the number of neutrons is not necessarily related to the atomic number.  The mass will be the #P + #N and atoms can have more or fewer neutrons than the majority (most stable) form -- these are called isotopes and will not be part of the discussion here -- though these provide valuable tools in biochemistry as radioactive tracers.

The electrons orbit about the nucleus carving out the "space" occupied by the atom.  We can loosely envision a series of larger concentric spherical paths or shells, and for many applications a hard sphere model for the atom (and small molecules)  is used.  Note, however, that the atom is anything but a hard dense sphere (the nucleus is).  One can imagine a clear sphere with pinpoint LED's that were rotating every which way, very fast along the surface.  You would only see an illuminated sphere, whereas a snapshot would reveal several points of light.  Now if we took two of the atoms depicted above, we see that the interaction of these two atoms would only involve contact between the electrons in the outermost shell.  We call this the valence shell.   The two electrons in the gray orbits closer to the nucleus will not "see" other atoms.  Chemistry, aside from radioactive phenomena, is ALL about the electrons in general, and the interactions of these outermost electrons more specifically.  There are other phenomena associated with electrons transitioning between shells, etc., but those too are not relevant to this discussion.  

All neutral atoms contain the same number of electrons as protons, that are equally and oppositely charged.  The opposite charges are attracted to each other and the electrons are kept from slamming into the nucleus by virtue of orbiting rapidly, much like the rotational forces on a Hot Wheels car are sufficient to keep it from dropping off the loop-d-loop and crashing to the ground so long as the car is going fast enough.

The Periodic Table

Before moving on further with the behavior of the valence shell electrons, let's look at the periodic table of elements.  Took a while to find a version containing just what I was looking for and not too much more.  I think the one below fits the bill.

direct image link

The first thing you'll notice is that this table is not square or rectangular, it's quite oddly shaped and even has that "inset" that must be taken out of the 6th and 7th rows that we will not be discussing.  This arrangement is rather deliberate, however.  The atoms, aka elements, are arranged in the order of atomic number, that is the number of protons they contain, left-to-right and top-to-bottom.  
  • Periods:  The rows (horizontal, across) are called the periods.  Another name for the row number is the principal quantum number.  
  • Groups:  The columns (vertical) are called groups.  This table depicts both two different types of groups denoted by roman numerals, and 18 groups from left to right.  I prefer the former as it is far more instructive and useful for predicting chemical behavior.
Electrons, Shells and Periods:  Both periods and groups are determined by the way electrons are oriented about the nucleus -- this is usually referred to as the electron configuration.  Because the (-) electrons are attracted to the (+) nucleus, they will want to get as close as possible.  But there is only room for so many electrons in each shell, additional electrons must go to the nest level.  If you dump a bunch of ping pong balls in a pail and shake the pail a bit, eventually as many balls as can fit will settle to the bottom layer but you cannot put one more ball there.  If the bottom layer can hold 10 balls, the 11th will forever be rolling around on top in the next layer.  Now if the pail is conical, perhaps this next layer holds more balls, but gravity and a little jostling will result in this layer being filled before the next ball exceeding the capacity of two layers settle higher up in the pail.  This is what occurs with electrons about atoms.  We label the shells or levels from inside to out, and often these are designated with letters beginning with K (don't ask me why) ... so 1,2,3 ... are the K, L, M ... shells.  The periods (rows) indicate the outer most shell occupied by at least one electron.  The lowest shell can only fit 2 e's which is why H and He are in that row, but a new row is started for Li which has 3 electrons.  The L shell can fit 8 e's.  The sample atom I used earlier appears to be carbon, C, atomic number 6 which means 6 electrons.  The two in the gray orbits filled the K shell, leaving 4 for the L shell which is half filled.  Sodium, Na, a pretty common element in nutritional circles, is atomic number 11 -- that means it has filled K and L shells, and one electron in the M shell.

Electrons, Orbitals, Valence Shells & Groups:  Within each shell, there are different sub-levels commonly referred to as orbitals.  These orbitals are generally filled in the order as presented, but there are exceptions.  These are as follows:
  • s orbital:   Spherical, can hold 2 electrons
  • p-orbitals:  These are shaped like elongated infinity symbols oriented on each axis in 3 dimensions (x,y,z), and each can hold 2 electrons.  Thus the p-orbitals can hold a combined 3x2 = 6 total electrons
  • d and f orbitals:  These are present in larger molecules beginning with the N shell and have varying geometries.  Each orbital can hold 2 e's, there are 5 d's and 7 f's, therefore the d-orbitals can hold 5x2 = 10 e's while the f-orbitals can hold 7x2 = 14 e's.  These orbitals are not involved in the behavior of the organic molecules we're going to be discussing, so this is the last you'll here of them here.
Here are the breakdowns of each shell, the possible orbitals and total number of e's they can hold:
  • K:  one s-orbital = 2 e's
  • L:   one s-orbital + 3 p-orbitals = 2 + 6 = 8 e's
  • M:  one s-orbital + 3 p-orbitals = 2 + 6 = 8 e's
  • N:  one s-orbital + 3 p-orbitals + 5 d-orbitals = 2 + 6 + 10 = 18 e's
We can see that the "towers" on left and right are due to the 10 atoms in the 4th row/N shell where the d-orbitals first come into play.  You will also notice that the left two and right six columns or groups are designated "A".   The A group elements, and with few exceptions for the smallest atoms, only involve s and p orbitals in their outermost valence shell.  The A group elements are often called the Main Group elements.  Furthermore, while each row shares in common the quantum number or letter of the valence shell, each atom in a column or group shares the same electron configuration in terms of the number of electrons and the orbitals occupied in the valence shell.  

This is the beauty of the periodic table -- you need not memorize a dang thing I just told you, and a pox on all chemistry teachers who waste time having students memorize the periodic table rather than teaching how to read and interpret it.  From an atom's position on the table alone, numerous predictions can be made regarding the reactivity and types of compounds each element is likely to form and with what other elements.  It cannot predict every possibility, but it is an invaluable tool.  Helium, atomic #2 is in Groups VIIIA has a filled K shell ... this makes it non-reactive.  Carbon, atomic #6 in Group IVA has a half filled valence L shell which makes it highly suited to be a central or backbone atom in molecules.  Sodium, atomic #11, has a single electron occupying the M shell which is vulnerable to be knocked off, pure sodium metal is extremely reactive.  I will discuss this in greater detail in the next post.

Metals, Non-Metals & Metalloids:  The electron configurations of different atoms determine how they interact and bond with one another.  We further sub-classify atoms according to their behavior as metals, non-metals and metalloids.  The vast majority of atoms are metals, on the left of the periodic table and shown in blue.  Hydrogen behaves differently, so while it is in Group IA by virtue of its single valence electron, it is classed as a non-metal and shown in red.  In the upper right corner of the table we see the relatively small group of non-metals in red.  You'll notice that this is where on the periodic table we live when talking biochemistry.  Proteins, carbohydrates and fats are all molecules comprised of non-metal constituents ... organic molecules, which by definition contain carbon, and a few other non-carbon containing molecules like oxygen and water.  The elements on either side of the "staircase" exhibit some properties of metals and some of non-metals and are called metalloids (shown in purple).  This is probably the last thing you'll here about them on this blog.  (Well unless some guru starts claiming we can become silicon based lifeforms if we alter our diets ...)

Next up:  The Main Group Elements, The Octet Rule, Compounds & Bonding


garymar said…
Ach, reminds me of all that undergraduate chemistry I took. In my class we called the p-ortibals "balloons", 'cause that's what they looked like.

And at the right end of the table stand all the "noble gases". Anybody guess what makes them 'noble'? Do they do a lot of charity work?
CarbSane said…
The d-orbitals are my faves ;-) I took a 1 or 2 credit advanced class my senior year in college and it was on HOMO-LUMO interactions. I imagine it would have been easier to grasp, or just a little more interesting to learn, with animations like that YouTube video!

Chuckle. Yep that term noble is paleo alright - double grin!

I'm going quite a few places in this series, but we cannot talk about electron phenomena w/o going to basics. I expect to bore or turn off quite a few folks. That's OK!
bentleyj74 said…
Not bored! Timely :)
Hornet0123 said…
Are you going to go into Quantum Physics? Maybe a parallel universe where Jimmy Moore didn't go low carb?
Hornet0123 said…
This comment has been removed by the author.
markgillespie said…
Are you going to cover the Krebs Cycle or Electron transport chain? Gave up on those a few years ago as was lacking some fundamentals so hoping you can do a good job explaining!
CarbSane said…
When I learned biochem (two times, once in the chem dept and once in the bio department ... yeah I'm a sucker for self-torture!) the treatment of Krebs focused on the actual reactions and mechanisms. I will be addressing Krebs, but from a re-dox couple standpoint -- as in how those "reducing equivalents" via the NAD/NADH translate to ATP production. I will probably spend more time on the ETC. Lots and lots of woo woo flying around about the ETC.
CarbSane said…
LOL on the parallel universe! On a serious note, I hope to dispel the notion that what goes on in the mitochondria is related to what we normally associate with the term "quantum". I'm too lazy to dig it up, but if you search here on Quantum Bullshit, I discussed this vis a vis Kruse.
CarbSane said…
I'm counting on you Bentley ... to slog through the background until I tackle the timely stuff :p