I suppose this would be a good time to admit it: I read and re-read my posts after I put them up. It’s not unusual for me to read a post (for the fourth or fifth time) and edit it. My brain works faster than my fingers and I’ve been known to forget words, miss a letter, or sometimes I get angry that the color scheme I have going on is not exactly the way I want it. (If you haven’t noticed yet, all figures are colored green, all post names are colored purple, defined-at-the-end words are blue, and all parenthetical thoughts are gray). I also read them for content. I spend a tremendous amount of time pretending to know nothing about chemistry and reading my posts as an outsider. I try to decide if everything makes sense. Let me know how I’m doing, dear readers!
This brings me to today’s topic. I don’t think I did a good job explaining the difference between the left and right panels of this figure (Figure 7.4, Protein Folding). To more thoroughly explain, I’m going to first talk about an atom. Information in this post will be helpful towards Protein Folding, Spanish Influenza, Part 3, and Fun with Radioactivity.
Around 400 B.C., some Greeks were supporting the idea that matter was made up of small, indivisible particles, which Democritus called atomos. Other Greeks felt that matter was continuous. Unfortunately, this controversy was as far as they got because scientists then busied themselves with alchemy for about 2000 years. But, the Greeks did leave us with our present name for particles: atoms.
So what does an atom look like?
It’s made up of three smaller particles: protons, neutrons, and electrons. Yeah, yeah – you’re thinking that you knew that. Okay, but I’m going to tell you more, anyway.
Protons and neutrons hang out in the nucleus. They are of similar size and mass, however protons have a charge of +1 and a neutron, which is aptly named, is neutral. Nuclei are pretty fascinating. Think about what happens when you have two magnets. Each has a positive pole and a negative pole. A positive pole attracts a negative pole. But, if you try to put two positive poles together, you feel a very strong repulsion. How does an atomic nucleus handle all those positive charges together without completely exploding? Ah, a topic for another day.
Electrons, which have a charge of -1, balance out the positive charge in the nucleus to make a neutral atom. The number of protons in the nucleus is called the atomic number and defines the atom. 6 protons in your nucleus? You are carbon. I don’t care how many electrons or neutrons you have; 6 protons always always always means you are a carbon atom.
The number of neutrons can vary, giving rise to isotopes. For example, some carbon atoms have 6 proton and 6 neutrons (called 12C or carbon twelve); others have 6 protons and 8 neutrons (called 14C). Carbon twelve and carbon fourteen are isotopes of carbon. 32P is a particular isotope of phosphorous, which also happens to be radioactive (aha!). Figure 13.1 shows you how chemists thoroughly describe different atoms so others know exactly what they are talking about.
The electrons are “floating” around the outside of the nucleus. Some people think that “floating” means they are just statically there, like stars. Others think that electrons orbit the nucleus like planets around the sun. Neither option is correct. Electrons are zipping around the nucleus – yes – but we don’t know exactly where. All scientists really know is probably where the electrons are. Isn’t that interesting? In reality, an electron could be anywhere*. It could be 75 feet away from the nucleus. Of course that is not probable, but according to the math, it is possible. Weird. (I’ll explain the math another day. It’s really complicated and involves a crazy theory called “particle in a box.” Really, just say “particle in a box” to introductory chemistry students and watch them dissolve into tears. It’s a kinda funny.)
The majority of atomic size is due to its electrons. If we are thinking in terms of a stadium, the nucleus takes up about as much room as a dime placed at midfield and the remaining space is due to electrons flying about.
When pictures like those in Figure 7.4 are shown, they depict an atom like a sphere. If we only know probably where an electron is, how can we definitely say how big an atom is?
Let’s think of a hydrogen atom, which is the simplest case. Hydrogen has one proton in its nucleus and one electron spinning about it. According to the math, the probability of the electron lying close to the nucleus is high and gets progressively weaker as you move away (Figure 13.2). Imagine drawing a sphere around the nucleus and saying “There is a 90% chance that the electron falls within this sphere and a 10% chance that it does not.” The 90% sphere that you just drew becomes the boundary of the atom. This same 90% line was drawn around all atoms allowing us to define atomic radii for each and every one. Each element’s atom has a slightly different size and atoms will follow certain trends. But, as I keep saying: another post, another post.
So let’s get back to Figure 7.4. What the hell is going on here?
LEFT panel: Back in the Protein Folding post, I talked about how all amino acids looked exactly the same except for the R group. I also said that all amino acids hook together in the exact same way. When you have a tertiary protein structure, you can see exactly how all those amino acids fold up on each other. Imagine you could draw a line from the very first NH3 group, through the first carbon, to the next carbon, to the next nitrogen, and onwards. (Ignore the R groups for this panel.) This is called the protein backbone (Figure 13.3). In three dimensions, your line would twist and travel all over the molecule. This is exactly what is being shown in the left panel. PyMOL (a quite lovely program created by Warren DeLano, who died last year. Following his death, PyMOL went corporate. Boo.) will trace this line for you. When you reach alpha helices, the program will put in nice loopy-loops and when you hit beta strand, it will draw thick arrows. If it is just random coil, then the line will follow the N-C-C-N bonds all over in their random ways.
In essence, the left panel is just showing the outline of the protein. Where, in general, the protein backbone is going and highlighting the secondary structure so it is easily seen.
RIGHT panel: This is the exact same protein structure, exact same everything, except that each atom in the molecule (backbone atoms and R group atoms included!) is now represented as a 90% probability sphere (as defined above). It’s called space-filling because it is showing you how all the atoms sit together. It’s also showing you what the surface of a protein would look like. Structural biologists can now see filled space from empty holes in the protein. (Some proteins have tunnels in them!) I’m sure you can also appreciate that it is difficult to decipher secondary structure from the right panel. For these reasons, structural biologists flip back and forth between these two representations of the molecule depending on what they are trying to show.
In the Protein Folding post, I said to think of the left panel as a tree without its leaves (it is easy to see how the branches twist and turn) but the right panel is showing how the tree looks when covered with leaves (giving the tree a “surface” and giving the tree a “fullness”).
Atoms: smallest form of an element that still retains the chemical properties of that element
Proton: elementary particle, positively charged, found in the nucleus of atoms
Neutrons: elementary particle, neutral in charge, found in the nucleus of atoms
Electrons: elementary particle, much smaller than protons or neutrons, negatively charged, found circling atomic nuclei
Isotopes: Atoms of the same element, but that have differing numbers of neutrons in their nuclei
Protein Backbone: N-C-C-N-C-C-N-etc bonds within a protein molecule
* - According to the math, there are nodes of probability - places where there is no chance of an electron being. But since this isn't a post about Schrodinger, I'm going to skip right over that complexity for now.
References
Zumdahl, Steven S. “Chemical Principles, 4th Edition” (2002) Houghton Mifflin Company, Boston, MA.
Alberts et al. “Molecular Biology of the Cell, 4th Edition.” Garland Science, New York, New York. (2002).
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