When we compare water to things that are similar in molecular weight to water, like methane, ammonia, etc, we see that at room temperature, the other crap is in a gas state while water is in a liquid state. Other crap of similar molecular weight to water, therefore, has lower boiling points (than water's boiling point, which is technically unusually high for a molecule of its molecular weight).
Water has a strong tendency to hydrogen bond with itself, and also has a significant net dipole moment.
The two clouds up there with the electrons can act as hydrogen acceptors while the two hydrogens that are covalently bonded to the O let the water act as a hydrogen donor. In it's outer shell, water has six electrons...two are in those covalent bonds to the H's and the other four are in those clouds, existing as non-bonded pairs.
Water has a high heat capacity, which is the energy needed to raise the temperature of a THING by a degree, because of all the Hydrogen bonding it participates in. In this next photo it's going to look like I drew water in its liquid state and made it look like it doesn't participate in hydrogen bonding, but it does, I promise. It's just simpler to show it like I did to talk about liquid vs. "solid" water...ice
Anyway.
When water freezes, the hydrogen bonds that it has even in the liquid state, even though it's not shown in my shitty drawing, become rigid, and form a tetrahedral lattice that I wasn't able to draw properly because I'm not good at it. Each molecule becomes bonded to four others. When we compare liquid to solid states, in the liquid states there's something like 15% fewer bonds. Because of the length of the hydrogen bonds, we have this low density thing that comes into play.
The molecules in the liquid are technically denser because when the lattice breaks up, the molecules can get closer together.
When we think of water acting as a solvent, we first need to consider that it is dipolar, and has a high dielectric constant. We've talked about that. Basically, there's an electric field generated between two ions in the solution, which causes the water particles between them to intervene, form dipoles, and induce polarization...that's a shitty explanation of what goes on but I can't do better in the moment.
All the oriented dipoles that are there are going to contribute to a "counterfield" and decrease any attraction that exists between the ions. The ions, in a sense, won't be able to "feel" each other's presence.
Now, comparing shit that is dissolved in water/in aqueous solution.
There's the hydrophilic shit which has groups in it that can participate in hydrogen bonding with water molecules...if they can, they will. You can find groups like this on the surfaces of things in which the surface is in contact with some sort of aqueous environment...so nucleic acids and proteins.
The fact that water is bipolar helps it to solvate ionic compounds, like NaCl. NaCl is a solid stable lattice of ions, but when you put that shit in water and stir it around, it gets hydrated and surrounded by hydration shells. These hydration shells are energetically favored. Water's high dielectric constant (it interferes with shit that wants to talk to each other in solution) results in a decreased electrostatic force between ions of opposite charge..water basically just gets in the way and interferes with the force that otherwise wants to pull these ions back together.
We can think of hydration shells as the opposite thing to clathrate structures. Hydrocarbons have no love for water. They're not really soluble because of their bond energies. They're not polar, they're not ionic, and they don't hydrogen bond. I would say that makes them useless except, I'd just be being mean, and the're not useless.
So, around hydrophobic shit, we have a formation of ice-like clathrate structures. They're kind of like cages that develop around shit that's non polar (since like-dissolves like, and water is polar). They cause water molecules to become highly ordered, which means that these highly ordered things will have low entropy. Low entropy means low solubility of this crap in water. Low entropy also happens to be thermodynamically unfavorable and so dissolving hydrophobic shit in water is entropically unfavorable.
So...all this really shitty entropy means there has to be SOMETHING that can help to make the situation less shitty. Which is how we get to the hydrophobic effect. All the hydrophobic crap that is in water will self-associate, basically cluster together, and instead of dissolving in the water (which, remember, it can't because of all the order you would put the water molecules in), the aggregation of molecules that are hydrophobic together will release some water molecules from the awful clathrate cages, thereby increasing entropy, and making the situation less shitty for at least SOME of the water molecules.
This shit is really important in the folding of proteins and in lipid bilayers.
I should probably talk a little about amphipathic molecules so I don't...forget that they exist.That's shit that has both hydrophobic and hydrophilic properties - fats, lipids, detergents.
When you saturate water with this crap, you first get a monolayer forming on the surface, all the crap trying to minimize how much its hydrophobic parts have to interact with the water. However, when you add more, or when you stir it up, you get formation of micelles or bilayer vesicles where the hydrocarbon tails of the molecules are going to form in parallel things, interacting through VDW forces. Crap like this builds up biological membranes that surround cells and compartments... I talked about this briefly a few posts ago when we talked about cell walls and shit.
Alright. Now we can talk about ionic equilibria. My least favorite thing, which means I need to learn it better, and make it my favorite thing. Ionization is basically eventually dissociating SOMETHING into ions. In our situation, we talk about it when pH changes in solution...so when there's like a giant protein molecule with a bunch of side groups on it (side chains of amino acids) and we start changing the pH, different groups will be deprotonated at different rates. Not sure if that relates to this EXACTLY but that's the best way I can relate to it right now.
Acids are things that want to donate protons to solution (or to other things) and strong acids are going to completely dissociate to a proton and their conjugate base in solution.
Bases are things that will accept protons, and strong bases are going to ionize in solution to release OH- ions.
Weak acids and bases will only partially dissociate in solution, and in a solution of weak acid, we have equilibrium between the acid and it's conjugate base, as pictured below:
Here you have formic, acetic, and lactic acids and their conjugate bases, and the pka's at which the hydrogen gets plucked off. More on pka's in a bit.
There are some things out there that have more than one hydrogen that they can lose to solution or to other crap, and these things will have multiple pka's for the removal of those several hydrogen. These are two examples.
Water acts like a weak acid/base and will autoionize, forming OH- and H+
The kw (ion product) is basically the way to express the equilibrium that is occurring. Concentration of products divided by concentration of the reactants, which is water, which gets a value of 1. Then, math.
This sort of brings us to pH, which is the negative log of the concentration of H+ ions in solution. When you have a lot of H+ ions in solution, you have a low pH, which means it's acidic.
There is a thing called the physiological pH range, which is what we function at, which is what we focus on.
This is kind of what I started talking about at the beginning of the discussion. Pretend that's a protein. It's made up of many, many amino acids, which have acidic or basic side chains, which will lose their protons at different points in a titration. The way that the protein functions is going to be affected by how the groups that are on it's surface respond to changes in pH. The activity/function of enzymes also depends on the ionization states of the groups that are on the enzymes...enzymes are only going to be successfully active/effective in very well-defined pH ranges. The overall charge on proteins and other things that can lose H+'s is going to depend on the pH that they're in.
There's some stuff that I talked about a little while ago.
When we talk about weak acids dissociating, and we want their pka figured out we do this.
The pka is the inverse log of ka, which is the equilibrium constant for the dissociation of a weak acid.
When you have a larger ka, you have a greater tendency for an acid to dissociate, which means you have a stronger acid. When you have a smaller pka, you've got a strong acid. A larger pka is a weaker acid.
When you titrate weak acids - cause them to lose their protons, the structure and function of what you create as a result is going to depend on the pH. Changing the pH means that you change what on a molecule is protonated.
The Henderson Hasselbalch equation lets you track how charges on a molecule at a pH are determined by the concentration of the conjugate base divided by the concentration of the acid (ratio of A-/HA).
You can use the A-/HA ratio to get the pH of a buffered solution that is made UP of HA & A-:
This is just a cute little example of figuring things out.
Why are buffers important? We use weak acid/base mixtures for making buffers to minimize any changes in pH after you add either OH-/H+ in to the solution. When you're in a buffered solution that you're adding H+/OH- to, you want to make sure there is enough HA and/or A- in there to combine with the shit you add and neutralize.
In reactions, you're constantly making or using up H+'s and buffers help to keep the pH of a solution stable. When the pH of a solution is equal tot he pka, the A- and HA are in equilibrium/equimolar concentrations.
When I do more buffer problems and have time to write about them, maybe we'll get further into detail.
Now I want to talk about those molecules that have multiple ionizing groups on them.
We have these three things; Ampholytes, polyampholytes, and polyelectrolytes.
We'll start off with ampholytes, which are groups that have acidic and basic pkas on the molecule. An example is the amino acid glycine. Titration of this thing occurs in two steps, since there are two protons that you can remove - one from the COOH group and one from the NH3+ group. The pka is smaller for the COOH group, so you would remove that one first, at a pka of 2.3. An H+ would be removed from the NH3 side at a pka of 9.6.
Since the COOH loses it's H+ very early on, at a relatively low pka, when the pH of the solution is low, before the COOH loses it's H+, the molecule has a positive charge on it, from the NH3 group.
As you increase the pH, getting to the 2.3 pka value, the H will get deprotonated, and when you pass the pka of NH3+ (9.6), that thing will lose it's proton eventually as well, giving the molecule an overall negative charge.
A Zwitterion is an ampholyte that has an equal amount of positive/negative charges, making it neutral. We usually think of it as having just one positive and one negative charge. The isoelectric point is the point at which the net charge on the molecule is zero. A the isoelectric point, most molecules are in the zwitterion form.
Polyampholytes are big molecules (like proteins) that have a bunch of acidic and basic side chains on them. For example, in people, hemoglobin, which is kind of a big deal, has 148 ionizable groups, with an isoelectric point at 6.85, in the physiological pH range.
When you're looking at a polyampholyte molecule, if it has a bunch of acidic groups on it, it's going to have a low isoelectric point. This is because you don't need to get to a high pH to deprotonate those things, meaning that it will reach it's neutral point when the pH of the solution is still relatively low.
On the other hand, if you have a bunch of basic crap on it, you're going to have a lot of groups with high pkas. Because you need to raise the pka of the thing further up before you can deprotonate those groups, you're going to get your molecule to the neutral form at a higher pka, which means it'll have a higher pI.
When the pH of the solution is HIGHER than the isoelectric point, you're in a place where almost everything will have been deprotonated, meaning you'll have a net negative charge.
When your pH is LOWER than the isoelectric point, you're still going to have a bunch of positively charged shit that you didn't deprotonate yet, meaning your net charge is going to be positive.
You can figure out the isolectric point using electrophoresis, applying an electric field to charged molecules. Positive and negative charges will travel to opposite poles (cations to cathode, anions to anode) and anything at the pI won't move because the net charge is zero.
We can now talk about polyelectrolytes, which have multiples of either positive or negative charge.
Nucleic acids are negatively charged strong polyelectrolytes that are ionized over large pH ranges.
When you have weak polyelectrolytes, you're going to have a whole bunch of weakly ionizing groups. The pka of each group is going to be affected by the ionization states of the groups around it.
So lets say you have a whole bunch of positively charged groups on a molecule. The first H's are going to be nice and easy to remove, because you're doing a nice favorable thing...reducing like-charge-
repulsion. The last hydrogens are going to be a lot harder to remove because you're now creating negative charges, and removing the nice positive things will create a different type of charge-charge repulsion. That's why successive pkas will rise for further and further deprotonation.
This finally brings us to macroions. Nucleic acids are large polyelectrolytes while proteins are large polyampholytes. Depending on the pH of the solution, macroions may have a net charge.
Macroions that have like charges will repel each other in solution and those with opposite charges will attract each other. The electrostatic interactions is what is going to let those macroions associate with each other, like protein interacting with DNA. Chromatin is a complex of negatively charged DNA that's associated with positively charged histone proteins.
Another example is b-lactoglobulin, a milk protein with a pI of 5.3. When you're not at the pI, the molecules of it will have like charges and repel each other.
This can bring us into the topic of ionic strength, which modifies macroion behavior.
A macroion with a charge will get surrounded by a bunch of counterions (counterion atmosphere), which encloses the molecule. The more little counterions that surround the macroion, the more you get electrostatic screening of the macroions away from each other. They basically can't feel each other because of the interactions they're having with the small counterions.
Some formula crap here.
The counterion atmosphere is going to have an effective radius, at which point the two macroions are going to be able to sense each other through the small clouds of ions around them.
This, finally, brings us to ionic strength.
Low ionic strength means that the counterion atmosphere is expanded and diffuse.
It's not really getting in the way of the macroions sensing each other, and has low screening. Macroions will attract and repel strongly with low ionic strength.
High ionic strength means that there is a small counterion atmosphere in high concentrations around the macroion. There's a lot of screening going on and the macroions can't really interact with each other.
As you increase the ionic strength of something....let's say you have a protein that you want to dissolve in some shit. When you increase the strength of the ions dissolving it, thereby decreasing the protein's interaction with itself, you're going to increase the solubility but only up to a certain point.
This brings us, finally, to salting and and out.
Salting in applies to having proteins get put into a solution by increasing the concentration of salt, thereby increasing the concentration of ions. But when you put in too much, and you have too high of a concentration of salt, you actually start to introduce the opposite effect. In very highly concentrated salt solutions, water is going to be bound up in hydration shells dealing with the salt and won't be free to solvate the proteins. This type of thing comes up a lot in chemistry, I've found...questions of why is something happening. In this case, the water has two things that it can solvate...the proteins and the salt particles. When the amount of salt is greater than the amount of proteins, water is just going to be busy dealing with the salt and won't be free to deal with the protein.
Salting out refers to the highly concentrated states where salt is in high concentrations, and the solubility of proteins in solution will decrease.
Different proteins are going to have different behaviors and respond differently to salting in and out, which is why you can use salting in/out to separate proteins.
Hopefully I'll be able to make another post tonight and start talking about free energy. You know. The stuff I don't believe in.
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