The rest of chapter 2 (biochem)

I want to apologize for all the vulgarity before I start talking about water. Two glasses of wine (white wine...) and I'm smashed. So this is a decent time to talk about biochemistry.



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.

Biochem...Chapter 2...

This is mildly embarrassing because I feel like this makes me look like I just started chapter 2 yesterday...but I swear I didn't. I know chapter 2. And three! And FIVE! Four, less so...

We can start off by talking about the different types of bonds that we encounter in biochem. And chem. And everywhere. I like to think about covalent and non-covalent like...A covalent bond is like tying someone's shoe-laces together REALLY tight...you can still untie them, but it's going to require more energy to untie shoe-laces that were just interwoven without tying...which I compare to a non-covalent bond. 

In DNA and in Proteins, there's both covalent and non-covalent bonds. Nucleotides in the strands are held in covalent bonds while the 3-D STRUCTURE is stabilized by non-covalent interactions. In Proteins, amino acids are linked (we'll see this a bit later in glyglycine molecule) by covalent peptide bonds (we'll discuss that in chapter 5), while the folding of proteins is managed by non-covalent bonds.

Just some energy comparisons. Obviously non-covalent bonds are much weaker but they wouldn't be if they didn't HAVE to be. Lenny always says "nature doesn't waste energy" and in this case, I guess this would be more like... nature doesn't use less energy on purpose...or something. What I'm trying to say is that it's IMPORTANT for non-covalent bonds to be weaker because that's what lets them break and reform when they need to. This applies to shit like salt bridges and Van der Waal's forces (to be discussed later)... The textbook says that non-covalent bonds are electrostatic, meaning they rely on forces that electrical charges exert on each other

A bad summary of types of non-covalent bonds.

This is kind of all over the place, but this is a summary of non-covalent bonds and examples of those types of interactions. Charge-induced dipole and dipole-induced dipole interactions are shorter in range than permanent dipoles. VDW's are significant at short range. Hydrogen bond lengths are fixed.

We can start off by talking about charge-charge interactions. These are the "long-range" ones. They need less distance between each other to notice each other. These can be cell ions like Na+, K+, Cl-, HPO42-...etc

These interactions, when in a vacuum, depend on Coulomb's Law (above).

When the charges are like, the force between them will be +, indicating they're repelling, and when they're opposite, the force between them will be negative, indicating they're attracted to each other. 

However..in cells, there's no vacuum.

Charges are going to be separated by either water or other dielectric media...this basically means that interactions between charges are reduced, they "sense" each other less than they would if they had only air between them. 

E is the measure for dielectric constant...measures how much the electric field between charges is reduced..I guess you can compare this to walking to a cookie through water or through jello. It's easier to get there in water than in jello. I'm bad at these comparisons.

Anyway. A higher dielectric constant means a weaker interaction (less force) between charged particles. 

In water, E = 80, which is high, since the E of other organic liquids is 1-10. In water, particles interact weakly with each other unless they're really close to each other.

We can now define a newish value, the not E, but the E. Energy of interaction. That's different between E which is the dielectric constant. E is the energy that you need to separate two charged particles from a distance r to infinity. 

When the shit is attracted to each other, Q1, Q2 have opposite charges, energy is going to be negative.

As r becomes large (long, whatever), E --> 0

This basically means that in terms of charge-charge interactions, energy of interaction is inversely proportional to distance and interactions are strong over greater distances. 

This shit is important when you want to isolate proteins from a mix of other cellular crap.

We can now move onto permanent and induced dipoles. This shit depends on orientation..which end is pointed towards which end. Molecules that have no net charge (neutral crap) can become an induced dipole by getting asymmetrical internal charge distribution.

Here, μ is the magnitude of polarity...how polar the molecule is...how much separation of charge there is inside it. When you see δ it means "partial" so, not a full charge. Partial charge. Carbon monoxide has a permanent dipole of μ

Partial charges are separated by a distance x, and the dipole moment is indicated by a vectro pointing towards the partial positive end of the molecule. The magnitude of the dipole is the charge * distance

In water's case, the dipole moment is the vector sum of the two dipole moments that are along each bond between O & H...the polar bonds. Water has a dipole moment because the electrons get pulled FROM the hydrogens TOWARD the oxygen because of a difference in electronegativity. 

Here's a few dipole moments. 

Here's two things with significant dipole moments. The values of their dipole moments are large because they have real charge separation over a large distance (compared to the other molecules that don't have so much distance between separation of charges)

At neutral pH, glycine has both a positive and a negative charge on its ends. These are whole charges, separated by the length of the molecule, giving it a largeish dipole moment. 

In glycylglycine, there's a covalent link of two glycines (remember peptide bonds and shit?). The dipole moment will basically be twice as large because you doubled the charge separation (distance). 

Molecules with large dipole moments are very polar. 

This one's blurry. I'm sorry. It's late and I'm lazy.

The presence of an electric field can make molecules that can be polarized (induced to have a dipole moment) polar. You can either do it externally or it can come from a neighboring charge or dipole particle. Benzene has no net charge or dipole moment on its own but a nearby charge can force benzene's electrons to redistribute throughout the rig to produce an induced dipole moment. 

So...aromatic rings are polarizable because electrons can be displaced throughout the rings. 

In induced dipole interactions, an anion/cation can create a dipole moment in a polarizable molecule, and then become attracted to it. I KNOW this shit is sort of redundant but that's what I need. This interaction depends on how polarizable the molecule is. Permanent dipoles, not just charges, can induce dipoles.

In neutral-neutral interactions, we find the most sensitivity to changes in distance. They're strongest when the distance is small enough. Two molecules with no net charges or permanent dipoles can become attracted to each other if they're close enough, and within them, the distribution of charge will fluctuate.

VDW forces, also called dispersion forces, involve fluctuating charges synchronizing up. Two molecules can approach each other, sync up their charge fluctuations, and get a combined attractive force. You see this shit in proteins and nucleic acids. Individually, VDW forces are weak but collectively, they make really significant contributions to stability/structural integrity of shit. 

When we think about why benzenes have a tendency to stack, it's because of the fluctuation in their electron clouds, reacting with each other, producing dispersion forces. 

Now...lets consider the VDW Radius...when molecules with no covalent bonds between them approach each other, their outer electron orbitals will eventually overlap (when they come too close), causing mutual repulsion. At this rate, the repulsion will increase as the distance between the centers of the molecules decreases. That's kind of what this giant next thing is about:

This is a non-covalent energy summary of two particles that approach each other. The energy of repulsion is steep at short distances...who wants to be THAT close to someone else? It can act like a barrier until you get to rv...which is the distance of closest approach. That's the VDW distance, where you get the closest molecular packing.

ro is the distance of minimal energy. It's the most stable distance between the centers of the particles. If you let them do whatever they want, this is how close they will come to each other.

So, by this thing, the total interaction, the total ENERGY of interaction, at a distance of...whatever the distance, is going to be the sum total of Energy of attraction and energy of repulsion. 

As the distance between the particles decreases (going from the right side to the left), the attractive energy and repulsive energy increase, but at very different rates. In longer-range interactions, we have attraction controlling things, but the repulsive energy will go up so quickly that it is going to act as a prevention, which then defines the distance of closest approach and the VDW radii. 

Last thing I want to talk about is hydrogen bonds. They're technically non-covalent but they're also sort of covalent. This is confusing. They're important because they determine structure of ...pretty much fucking everything.

The hydrogen bond is defined as the interaction of a hydrogen that's covalently bonded to a "donor" atom to a pair of non-covalent electrons on an "acceptor" atom.

The ability of something to act like a donor depends on electronegativity. Something that's MORE electronegative is going to take away more negative charge from the H, making the H more and more positiveish, and attracting is strongerly (right, strongerly) to the electron pair on an acceptor atom. Only N & O are strongly electronegative enough to act as strong donors. Hydrogen bonds are going to be the strongest when there's a 180degree angle between the donor and acceptor atoms.

A hydrogen bond can be thought of/compared to a charge-charge interaction between a partially charged H (δ+) and a partially negatively charged pair of electrons (δ-). But there's electron sharing going on between the Hydrogen and the Acceptor atom...kind of covalentish. 

And the lengths of hydrogen bonds reflect this "double character". They're smaller than you would assume based on a table of VDW radii. The energy of hydrogen bonds is higher than that of other non-covalent bonds because it is slightly covalent in character. 

Tomorrow, I'll finish talking about shit in chapter three...so I'll discuss water, ionic equilibria, which I still fucking hate, then molecules that have several ionizing groups, and ionic strength. Then we'll start chapter 3, my least favorite chapter so far...deals with energy and free energy and other things that I don't believe in. Just kidding.

A thing of beauty is a joy....until it eventually gets hydrolized

Say what you will about whatever you will say things about, but I think that the integrity of the hydrogen bonding stabilizing paired bases is the most beautiful thing of all things that you can say anything about, or be too mind blown to say anything about coherently. 

I've been itching to write about what I've been learning in Biochem, but haven't had time to write about it yet. SOON.

These boys are handsome! Rem and Archie :)

...more microbiology

Let's pick up...sort of where we left off. Oh yikes, you can see my reflection.

Anyway...here's some cell shapes.

...and here are the groupings/arrangements of cocci and bacilli cells.

Take note on the Neisseria gonorrhoeae which is a diplococcus!

Here we have the UGLIEST bacterial cell ever drawn. I've labeled stuff, too. You've got the capsule on the outsides. Need to talk a bit about capsules at some point...

Then comes the cell wall, followed by the cytoplasmic membrane and the cytoplasm on the inside.

{I'll talk a very tiny bit about glycocalyx (capsules and slime layers) before we go onto lipid bilayers. Glycocalyx is the protective outer layer. Not all bacteria have it. It can either be a capsule or a slime layer. Capsules are thick while slime layers are thin and diffuse. The glycocalyx also helps bacteria stick to surfaces of things.}

Luckily since I took orgo, I'm quite familiar with lipid bilayers. Hydrophobic insides and hydrophilic (water-loving) on the outside and within. These make up cytoplasmic membranes in cells.

Here's a more (only sadly slightly more..) 3-D version of the plasma membrane. It has proteins in it that typically enable the passing of material that can't pass through the membrane itself.If you somehow destroy a bacterium's plasma membrane, you effectively kill the bacterium. Shit's important. Bacteria and archaea have the same structural features in the plasma membrane but the lipids differ (duh). 

Things that can and can't pass through the lipid bilayer.

A horrible rendition of transport proteins. They change shape apparently, when letting things pass through them.

I want to switch gears for a sec and talk about Cell Walls and the peptidoglycan that makes them up. I talked in the last post about N-acetylmuramic acid and N-acetylglucosamine and how they're the structural components of peptidoglycan...Here's how the structure is laid out. Ugh the photo is AWEFUL but bear (bare?) with me here. There's chains of ...NAM-NAG-NAM-NAG... and they're attached by layers of tetrapeptide (four peptides..) chains in between. In G+ cells, there's peptide interbridges that are not present in G- cells. There's an enzyme in our saliva and tears called Lysozyme, which has the capacity to break the bond in peptidoglycan between the NAM and NAG units..This messes with the structural integrity of the cell wall. Antibiotics like penicillin have acting mechanisms similar to this.

Here's a visual and slightly better idea of G- cells than what I had in the last post...Ehh...sort of. The lipopolysaccharide is on the outside, part of the outer membrane. The outer membrane is a protective lipid bilayer. It has porin proteins that let small molecules into the periplasmic space...then comes the periplasmic space where the thin layer of peptidoglycan is, and finally the plasma membrane (phospholipid bilayer) with integral proteins. When people first get to the end of orgo 2/beginning of biochem they're like: "ugh phospholipid bilayers like THAT matters"....well it does. Just sayin'. In G - cells, the plasma membrane regulates what goes in/out of the cell. It has transporters (those proteins) to regulate movement of shit that doesn't pass through the bilayer on its own. 

It might also be a good idea to talk about the growth curve in laboratory conditions. This is produced by batch cultures, which are closed systems - meaning you don't renew nutrients or remove waste from the plates/flasks. In open systems, you would need to add nutrients and remove waste to ensure continuous growth.

But this curve is for closed systems. Initially we have the lag phase, in which the cells are figuring out their environment, turning on whatever genes are needed, and feeling out their surroundings. Next is the log or exponential growth phase. Cells grow rapidly and there's almost no variability in their activities. Following that is the stationary phase. Cell death and cell replication are in equilibrium; there is variation/heterogeneous activity. The death phase soon follow as cells run out of nutrients, followed by the phase of prolonged decline.

Cells are most sensitive to antibiotics in the log phase when they're actively replicating. Endospores are formed in the stationary phase, when cells are kind of realizing that they are running low on nutrients. If you're testing enzyme activity, you want to do it in the log phase since there's little to no variation in what the cells are doing. To calculate growth rate, you have:

N(t) = No x 2^n

# cells at time (t) = initial number of cells x 2^number of cell divisions

Some things to leave myself off with before I try to fall asleep..

Prokaryotes naturally have no nuclear membrane. 

Only bacteria have peptidoglycan in their cell walls.

Protozoa is the only group in Eukaryotes that have only single-celled members...they're also bigger than Prokaryotic cells by about 50-100 times.

Antibiotics are intended to target the cell walls of gram positive cells, fucking with the peptidoglycan in there. Some shit may not be effective for gram negative cells since 

a) the peptidoglycan is UNDERNEATH the outer membrane and

b) the peptidoglycan is a significantly thinner layer

Gram positive cells have techoic acids and lipotechoic acids intermingling with the peptidoglycan layer.

Gram negative cells have an outer membrane, whose outside layer is lipopolysaccharide and their cell wall is in between the outer membrane and cytoplasmic membrane. The LPS is important when considering pathogens since our immune systems see the LPS of bacterial cells first. Some pathogens can fuck with our immune system and modify the LPS.

Only gram positive bacteria is sensitive to penicillin and lysozyme. 

Bacillus and Clostridium are infamous for forming endospores. Fuck that shit.

Mycoplasma refers to a genus of bacteria that lacks a cell wall.

Mycobacteria are acid-fast Gram positive bacteria that have a very thick, protective, waxy cell wall.

^That is thanks to : http://ntmnews.blogspot.com/2012/08/mycobacteria-and-mycoplasma-what-is.html

Lets learn some shit.

My first microbiology exam is TOMORROW and thus, I've decided to do a small thing.

The shit we're learning about in microbio is divided into two main categories...living shit and non-living (infectious agent) shit. 

Living shit falls into two subcategories: Prokarya and Eucarya

Non-Living shit's categories are: Viruses, Viroids, and Prions (the really fucking scary ones)

Eucarya gets people like: Algae, Protozoa, Fungi (yeasts and molds), and Helminths (rounds and shit like that)

Some relative sizes of shit. Viruses are obviously the smallest, maxing out at 100nm (usually less). Bacteria & Archaea are relatively the same size, different things have told me different sizes, but on average of 1-5 or 1-10 micrometers (10^-6). Eukaryotes are bigger at 10-100micrometer cell sizes.

As far as Eukaryotes go, they mostly come single and multicelled with exception of protozoa which are always going to be single-celled organisms. 

These terrifying motherfuckers.

Viruses have DNA, RNA and a protein coat while viroids (mostly infect plants) and have only RNA, no protein coat.

Prions are misfolded proteins and can cause neurodegenerative disease, mostly from eating prion-infected tissue. They're resistant to any possible form of killing, so they're scary as shit.

Some words on bacteria. Since they're prokaryotes (something dealing with pre-real nuclear membrane structure), they have no membrane bound nucleus or organelles. Their cell walls are made out of peptidoglycan (to be discussed later). 

This whole hypo-hyper tonic shit really confused me (and really still kind of does)

Bacteria live in hypotonic environments meaning their insides are hypertonic. Google defines this as "having increased pressure or tone", measuring osmotic pressure. So, they like not having pressure on their outsides, but their insides are pressurized? Things outside of them that can't come in cause pressure. Hypertonic environments will have a lot of crap in them (that's outside the cell), which makes water want to flow out of the cell to try to create equilibrium, which is unfortunate for the cell. The cell membrane ends up getting pulled away from the cell wall, resulting in plasmolysis. 

Just a few words about Archaea. What's crazy is that they're actually evolutionarily closer to us than they are to bacteria. Which I think is nuts. Most of them are extremeophiles, living in the arctic and deep sea vents. Their cells walls don't have the peptidoglycan crap that I'm going to talk about later.

Some staining methods we've done in the lab. Gram stains tell the difference between Gram positive cells and gram negative cells. This deals with how much peptidoglycan is in the cell walls, whether or not that cell wall will retain the dye. Crystal violet and iodine form a complex in the cell that when you decolorize with alcohol, doesn't wash out of gram positive cells. (These will be purple when you look at them under a microscope). Gram negative cells have a thin layer of peptidogylcan in their cell walls, and the decolorizer damages their outer membranes (not present in Gram+ cells). After you decolorize the G- cells, you counter-stain with safranin, making your G- cells look red/pink. 

The other stain we did in lab was the Acid Fast Stain which applies to microorganisms that don't take up dyes like G-/G+. A type of these are Mycobacteria...scary shit that causes TB and leprosy. The cell wall in these things have lots of waxy mycolic acids (which is why they don't take up dyes)

A HORRIBLE rendering of a G+ cell wall. The cell wall is on the outside, with techoic acids in it. They give the bacteria a negative exterior charge, sticking out above the peptidoglycan later (which, remember, is super thick in G+ cells). There's also lipotechoic acids somewhere in the cytoplasmic membrane (made of a lipid bilayer...my favorite thing).

If my "art" couldn't get any worse...it just did. Here's a G- cell wall structure. The cell wall has only a thin peptidoglycan layer but has a sick outer membrane (which is not present in G+ cells). The outer membrane has lipids and porin proteins inside of it and lipopolysaccharide (an endotoxin) on the outside of it. The LPS is what our immune system sees, and recognizes foreign crap. 

The LPS is made out of Lipid A and O Antigen. O Antigen is directed outside of the membrane, with Lipid A anchoring the LPS into the lipid bilayer... Lipid A is toxic. 

The outer membrane is why G- cells are less sensitive to antimicrobial things than G+ cells. 

I said I would talk about Peptidoglycan and now I will.

It's basically repeating units of N-acetylmuramic acids (NAM) and N-acetylglucosamine (NAG). Only bacterial cells have peptidoglycan in their cell walls. PEPGLY determines the strength of the cell wall...In G+ bacteria, there are peptide interbridges. 

Here's some interesting (and frightening) bacteria we have discussed thus far...

Yersinia pestis: I still remember this from a class called Marvelous Microbes I took at Rutgers. This shit is the black plague (from the 1300s).

Vibrio chloera: The cholera outbreak that happened in the 1850's in London, resulting from a contaminated water pump. Vibrio refers to a "curved bacillus" shape - basically a curvy rod bacterium. It's salt tolerant, which is scary as fuck, but luckily, not all Vibrio are human pathogens. 

Treponema pallidum: This shit is a pathogenic spirochete, basically an elongated curvy twisting rod like thing. Longer and twistier than a spirillum. This shit causes syphilis and can't be cultivated in the lab.

Neisseria gonorrhoeae: A G- diplococcus (another bacterial shape), which has the power to modify its lipopolysaccharide...this is really scary because that means it can keep "changing it's jacket" to confuse our immune systems. 

 Staphylococcus aureus and Staphylococcus epidermis: Two very different things. S. aureaus causes a whole HOST of terrifying shit from endocarditis to your SKIN FALLING OFF, depending on the site of infection and the strain it is. It affects about 25-30% of people...It's G+ cocci growing in grapelike clusters. Terrifyingly delicious. S. epidermis, on the other hand is part of your skin's normal microflora. Obviously, also a G+ coccus structure.

Streptococcus pyogenes: G+ bacteria causing anything from strep throat to, again, your skin falling off (impetigo?), and toxic shock syndrome...also necrotizing fasciitis. Do. Not. Want.

Bacillus and Clostridium: are two types of bacteria that make endospores, which can survive in high heat, high pressure, unfavorable conditions by slowing down or discontinuing their metabolic processes. B. anthracis is a G+ bacterium causing ANTHRAX while C. tetani's spores like to live in rust...giving me tetanus when I climb fences. 

Deinococcus radiodurans: is a really tough bacteria that doesn't form endospores but relies on a really good DNA repair mechanism. 

I have to go get ready for class now, so we'll continue this later tonight, after lab...