Signaling intro

This is the simplest slide of cell signaling that has enough information to be useful. Start by looking at the types of signals that get to the cell (growth factors...survival factors...death signals” look at the type of receptors available and the way the messages leave the membrane area. Look up “Receptor-tyrosine kinase” either in the book or online just to pick an example of how a signal cascade starts off.


Signal Overview
  1. Here is a link to the signal talk I gave a while back, which includes some discussion on G proteins.

Overview

:
Cell communication takes many forms, but there are commonalities in most of them. Cells may communicate by direct contacts between proteins on their surface, but do not need to be in physical contact for most events. There are lots of examples of "distinctions without a difference." What I mean by that is that you will hear reference to endocrine or hormone signaling (signal molecule made in a gland and secreted into blood), autocrine signaling (signal molecule made by same cell receiving it), paracrine signaling (signal molecule made by cells nearby the receiver), neurotransmitters, cytokines, chemokines…there really is no difference in how any of these work. It's like asking "Did you drive in your car to get milk or walk to the store?" Sure…there are differences…but the milk is the same.
In general, there are three steps:
  1. A signal molecule, or “ligand,” usually soluble (but can be bound on another cell or on the extracellular matrix), floats up to the target cell. The signal molecule may be a small protein (such as insulin), or a much smaller molecule (such as epinephrine). It binds to the extracellular face of a receptor, a protein that spans the membrane of the target cell
  2. The receptor changes shape (conformation) when the ligand binds. This is no different in concept to the idea of allosteric changes to proteins we discussed when we talked about inhibitors of enzymes. The tertiary structure of the protein changes. These changes affect not only the outside face of the receptor, but the internal side as well. This is the transduction event. That’s how the information gets through the membrane.
  3. The change in shape on the inside of the receptor leads to some change in the biochemistry of the cell. It may make available a new binding site, or a new active site. But some change inside the cell happens and ultimately, there are changes to how the cell behaves. There is a nearly limitless set of possibilities. Frequently, some enzyme gets activated and makes something called a “second messenger.” In this way the signal is amplified and may have many effects in the cell.
  4. (so much for "three steps") Eventually, the cell has to stop responding. The pathway has to have a way to shut down. The ligand may release from the receptor, but that only stops new signal events. Enzymes that were activated need to be deactivated. Second messengers made need to be destroyed.

More specific


We have looked at a small subset of G-protein-coupled receptors. These are among the oldest and most diverse types of signal molecules. We won’t look at all the possibilities, just one or two.
There is a decent animation of G-protein signaling
here. The structural representation is not so good. But, it’s not too bad.
Here is a link to David's "molecule of the month"
blog on the beta adrenergic receptor.


The key points are that:
  • G proteins are inactive when GDP is bound, active when GTP is bound.
  • Turning them “on” requires exchanging the GDP (kicking it out) for a GTP (allowing it to enter). This exchange is facilitated by the receptor, once ligand is bound.
  • G proteins are molecular timers. Once turned on, they will turn themselves off by hydrolyzing the GTP to GDP.
  • While they are in the “on state,” they activate other target proteins, usually enzymes, which then generate second messengers.

In addition, if you have time, there is a wonderful lecture by Bob Lefkowitz, the discoverer of the beta andrenergic receptor (and the first GPCR other than rhodopsin) that can be found
here. It’s long (50 minutes, but may be worth class time to see and discuss). He does a great job of discussing out the experiments to show how it works were done.

You may notice that there are many other animations for G-protein coupled signaling at You Tube. Some of them open ion channels (as in nerve cells), some of them connect to adenyl cyclase, as we have discussed. Others connect to other pathways, such as the phospholipase pathway.
The cAMP is the “second” messenger that goes off and activates many other proteins in the cell. Because each cell will have its own cAMP-responsive proteins, each cell may respond differently to the same signal molecule. As we discussed, there also will be, potentially, more than one receptor for a given ligand, resulting in different pathways being induced.

How is the signal turned off? Well, ligand may leave the receptor..but that doesn’t stop everything that is happening away from the receptor. The G-protein is still active, as is the adenyl cyclase and there is a lot of the second messenger, cAMP still floating around. The G-protein turns itself off by hydrolyzing the GTP back to GDP and lets go of its target protein (in this case, the adenyl cyclase) That turns off the target protein. Well…you still have all that cAMP around.
There is another enzyme that destroys that, converting it to AMP (not cyclic anymore). That enzyme is phosphodiesterase, often abbreviated PDE.

Below is a list of common first and
"second messengers." You may run into some of them.
Screen Shot 2016-09-29 at 10.05.45 AM

Enolase: an example mechanism

I Thought I would take a minute to talk about a reaction mechanism. This is not something on which I would test you. However, I thought getting into the mechanism…even just the idea of a mechanism…would be useful.

What is a “mechanism” anyway?


Briefly, a mechanism is a detailed (as detailed as possible) description of the steps of a reaction. You got a little into it last year with the idea of an elemental step in kinetics. However, with the advent of crystal structures of enzymes, more details can emerge.
To review, we have talked about protein structure and the fact that the overall structure results in positioning particular reactive groups of the side chains in a position to carry out chemistry. I’ll add here that metal ions are important factors in the function of many enzymes. Many proteins coordinate metal ions in their active sites and the metal plays an important role in the chemistry (for now, think of “coordinate” as “bind”).
First, some images to get oriented. This is the protein molecule shown in familiar “ribbon” representation.
Enolase1

I’ve shown a dimer of two identical proteins. You should see a blue dot, which is the magnesium ion. On the right, you can see a couple of the amino acid residue side chains that interact with the ion. We’ll zoom in on that region here:
MetalBinding

You can see that the positively charged metal ion is being held in place by several side-chain oxygens. I’ve labeled some of them (two aspartic acids, “D,” and one glutamic acid, “E”). There are others.

Now, I’m going to add in the substrate, 2-phosphoglycerate. I’ll make it solid, and I’ll highlight a couple of side chains that interact with it, Lysine 345 (K345) and glutamic acid 211 (E211). At the other end of 2-phosphoglycerate, you may see how close the metal ion is to the oxygens of the carboxyl end. The electron-poor magnesium ion is right up against that electron-rich oxygen. Now, normally, oxygen wins the battle for electrons easily...and it does here too. But the whole structure draws electrons away from a bond with a hydrogen at position 2.
ActiveSite


Below is a schematic of the reaction of enolase to form PEP.
EnolaseMechanism

The arrows in the diagram represent moving electron pairs. Here’s what happens:
The metal ion, which is 2+, is withdrawing electrons from the two oxygens, there on the left (this version of enolase has two magnesium ions). Lysine has a basic nitrogen. You see the lone pair depicted on the nitrogen. This makes the H attached to Carbon 2 behave like an acidic proton…not normally the case. However, the proton leaves carbon 2 and gets the electrons in the lone pair on lysine’s nitrogen, the electrons that were in the C-H bond move over and form a double bond with C1. That makes it an “alkene.” The electrons from the double bond of the C=O will flip out to that oxygen, making it negative. The carboxyl of Glu211 is making a hydrogen bond with the OH on C3.
In the second panel, the OH from position 3 will combine with the acidic proton from Glu 211 to form water. The elections from the other carboxyl oxygen will form a double bond, the electrons from the 1-2 double bond will move to the 2-3 position. The product, PEP, is released (Phosphoenolpyruvate). The extra H from the amine of lysine 345 (picked up from carbon 2 in the second panel) transfers over to Glu211 regenerating the enzyme in its starting configuration.

See…kind of cool.

Intro Enzyme Kinetics

Enzyme Kintetics


Most of the images for this article were taken from the Wikipedia entry on Enzyme kinetics. You can read that here. It gets a little intense, even for our purposes.
Some Words:
Enzyme: a biocatalyst that acts to speed up the rate of a reaction, often by many orders of magnitude (that is, many factors of ten). Most enzymes are protein, though some important ones are RNA.
Substrate:
the starting material acted upon by the enzyme to make the product.
Active site: the site in the enzyme in which the substrate binds. It is the site at which the catalysis takes place.
Saturation Kinetics
We’ll call the above graph, “fig 1.”
Notice firstly that the graph is determined from a series of kinetic experiments and that Y axis is a rate (usually in mol/L*s that is change in concentration over change in time). So, each point is from an experiment in which you had an initial concentration of substrate and then measured the change in that concentration versus change in time (the initial rate). The points on this Fig.1 are each the initial slope of one experiment from Fig. 2, below.
The image below was taken from Campbell’s website.
EnzymeRatesFig 2
It represents three experiments tracking a reaction where A B and following the rate of disappearance of A. The three experiments have different initial concentrations and different initial rates. The slope of each of those lines becomes a point on Fig 1. The sign of the slope is changed so that it is positive (remember from chemistry that Δ[B]/Δt = -Δ[A]/Δt).
Experiment 1 above might be one of the high points on Fig 1. Experiment 3 would be at lower concentration.
Saturation Kinetics:
The pattern seen in Fig. 1 is called saturation kinetics for reasons that should be obvious.
Please Note: the flat part of Fig 1 is not when the rate of the reaction is zero.
It shows that above a certain concentration of "A," the initial rate no longer increases. The reason for this is that all the enzyme molecules are occupied. Adding more substrate just adds to the “line” of substrate waiting, so to speak (see the “Starbucks Model below). Saturation kinetics are also called “Michaelis-Menten” kinetics after the people who first explained it. You should know that almost no enzymes follow this model exactly. It also deals with a single substrate...but can be adapted to deal with more. Nevertheless, it is an important model that helps explain a lot. The idea is that there are at least two steps to the overall reaction: Binding of substrate to enzyme; and catalysis.
You can think of the process of catalysis as proceeding in at least two steps (there are usually more): a binding step and a catalytic step.

Fig.3EnzymeSteps
“E” is enzyme, “S” is substrate, “ES” is enzyme bound to substrate and “P” is product.
There is an “on” rate and an “off” rate (k
1 and k-1) indicating that a substrate molecule can bind and then come off again. The second step is determined by something internal to the enzyme: its catalytic constant. Note that if I blocked the second step, the binding step would come to equilibrium, with substrate binding and releasing at equal rates. Under those conditions, I could calculate a “KD,” for “dissociation constant,” which would be k1/k-1. This would represent the concentration at which you would see ½ maximal binding.

Important Points on Figure 1.


There are two important points on Fig. 1. We have already talked about the first, V
max. That is, the maximum velocity, or rate, of the reaction once all of the enzyme molecules are busy.
The other point is a substrate concentration known as “K
M,” which is the concentration at which the rate is ½ of the Vmax. Note that if the catalytic step is fast and we are still in the linear portion of the graph, the KM is approximately equal to the KD.

High or Low Substrate concentrations.


Imagine two situations, one in which substrate concentration is low and one in which it is high.

EnzymeCartoonFig 4.

In the first case, the slow step (rate-determining step) is the binding (first) step. The catalysis step may seem instantaneous, by comparison. This gives us the steep initial portion of Fig. 1. The rate is determined by the rate of binding.
In the latter case, essentially all the enzyme molecules are occupied. No enzymes are sitting around idle. Thus, the reaction is going at its maximum velocity (V
max), the (nearly) horizontal portion of the graph at the top. At that point, the overall rate is governed by the catalytic step, give by k2.

The Starbuck’s Model


Think of the reaction being catalyzed as production of cappuccini at Starbucks. The enzyme is the “Barista” and the customers are the substrate. If you count cappuccini per hour, you get a rate. If there is a low concentration of coffee drinkers wandering in front of the store, you get a slow rate. If you increase their numbers, the rate of cappuccino production increase. The rate is ‘diffusion limited,’ that is, set by the number of coffee drinkers that wander into the store…until a line forms. At that point, the Barista is working at maximum rate (saturation kinetics) and the rate of cappuccino production is limited by the catalytic rate, how fast the Barista can work. The only way to increase the rate is to add more enzyme…in this case, just open another Starbuck’s 100 meters away).
Inhibitors
Let’s consider two types of inhibitors: one that purely inhibits the first step (binding) and one that alters the enzyme so that it is not as good at catalysis (the second step), but otherwise has no effect on binding.
Competitive: Enzyme-Inhibitor (E-I) complex or Enzyme Substrate (E-S)
Inhibitor1Fig 5.
The substrate does not bind the E-I complex and the inhibitor does not bind the E-S complex. Shown here the two are actually binding to the same site. Inhibitor physically blocks access of the substrate to the enzyme. This could be the idiot who gets to the front of the line at Starbuck’s and cannot think of what he wants to order, but just stands there and won’t let others order.

The substrate will have its binding constant (approximately K
M) and the inhibitor with have its binding constant (lets call that KI). Note that the second step governed by k2 in Fig. 3 is NOT affected by the presence of the inhibitor (The Barista works at the same rate…he’s just not able to get working). If the substrate binds, it will be catalyzed at the same rate as it would if the inhibitor were not in solution. It’s just that fewer substrate molecules get to bind.
Since both the inhibitor and the substrate have an “off rate,” I can assume that even in the presence of the inhibitor, substrate will have some opportunity to get access to the enzyme when the inhibitor comes off.
Let’s assume a simple case in which the inhibitor and the substrate have similar binding constants for the enzyme. Then, if I had equal amounts of each, I would expect at any given time that half the enzyme will have substrate bound and half will have inhibitor bound. If I increase the concentration of substrate, I would be able to get more of it to bind (out-compete the inhibitor for the site) and the enzyme would be able to do its job as normal. At a great enough excess substrate concentration, the probability of substrate binding is much higher than that of inhibitor binding; so most enzymes would have substrate bound. I could eventually get the rate up to the V
max. But, the KM becomes much higher...you need much more substrate to get the enzyme to work at half the max rate.
So, a competitive inhibitor raises the Km, but does not affect the Vmax.

Note:
while the mechanism of competition strictly results in inhibition, the other types of interactions described below could just as easily activate the enzyme, or increase, the rate.

Non-competitive: Lower the rate “k2.”
Another type of inhibitor does not affect binding of substrate. Instead, it alters the rate of the catalytic step. How can it do that? Remember that these are proteins. A small shift tertiary structure caused by the binding of inhibitor could change the ability of the enzyme to catalyze the reaction.
This effect where binding of a regulator (inhibitor or activator) changes the shape of the enzyme and alters its rate are call
“Allosteric effects.” Allosteric just means binding somewhere else and not directly interfering with substrate binding.
In that case, I’d get binding at the same rate. So, K
M would not change. However, since k2 is lower, I have a lower Vmax.
Easy. This would be the girl behind the counter who is really “into” the Barista and is chatting to him non-stop. That slows down his catalytic rate, but doesn’t affect the rate at which customers wander in.
All non-competitive inhibition is allosteric. However, not all allosteric effectors show non-competitive inhibition. Some are even activators.

Regulation
You may notice that I have more steps for my enzyme than the book has. The substrate has a binding constant, what about the product? Wouldn’t I expect the product to have some binding affinity for the enzyme? And, the product has to leave the binding pocket in order for new substrate to fill it. In effect, the product can act as a competitive inhibitor of the enzyme that produced it. This is the very simplest form of “feedback inhibition,” an important concept we will talk more about. We refer to the combined rates for the steps of catalysis and releasing product as an enzyme’s “turnover rate.” That is, how fast it is available to do its job again.

Much of the time, I don’t want an enzyme to work at full speed. One very important way of regulating an enzyme is feedback inhibition, as in the simple product competitive inhibition mentioned above. Suppose I have a pathway requiring 3 enzyme steps.
Pathway
Once I have enough D, I don’t want the pathway to be running at full speed. Maybe “A” is also needed for another pathway (not at all unlikely) and once I have enough D, I want to divert A down that other pathway.
One real world example would be if "A" were glucose. Sometimes I want to use my glucose to get energy right now. Sometimes I want to store glucose in glycogen for later use. Which path I choose would depend on changing conditions. A well-evolved system should adjust to needs.
One way to regulate this is if D is an inhibitor of enzyme 1. It may be competitive or non-competitive.

Allosteric
activation is common as well.

This sounds magical, until you remember that we are talking about proteins, composed of helices and sheets arranged in specific tertiary structure. Couldn't the binding of some activator on one face of the protein cause to helices to shift relative to each other? Of course. Couldn't the shift slide a helix out of the way of the active site, allowing better access? Sure.
The possibilities for regulation seem endless, really. And every possibility I've ever thought of and about 100x more that I never thought of can be found operating in nature.

Pumps and Gradients

Gradients


As we said, the membrane is impermeable to most dissolved solutes. Gases can pass freely through the membrane, so oxygen and CO2 can be traded as necessary. But things dissolved in the water that surrounds the cell and is inside the cell generally are hydrophilic. As such, they cannot pass through the membrane directly.
For this reason, there are transport proteins that are responsible for moving all of the small molecules, ions and even fairly large molecules across the membrane. We will talk a little bit later about the protein that allows water to move across the membrane. For right now we will talk about transport in terms of several overlapping concepts shown in the diagram.


transportImage from www.physiologyweb.com

Passive diffusion


all forms of passive diffusion are "down gradient." That is to say, one side of the membrane has more of the solute while the other side has less. Given any pathway through which the solute can move it will tend to distribute more evenly. I can divide this further into simple diffusion for molecules that can diffuse again across the membrane directly, passive diffusion for molecules that pass through a channel protein (which is just what it sounds like, a protein that forms a channel through the membrane), and facilitated diffusion, where the solute is carried by a protein from one side of the membrane to the other, sort of like a shuttle. The important thing to remember is that all three of these are diffusion down gradient and require no input energy. No work needs to be done for molecules to diffuse. In fact as we will see later, a gradient can be used to do work.

Active transport.


All forms of active transport require the expenditure of energy at some point in the overall pathway and result in even greater disparities in concentration between the two sides of the membrane. That is, something moves from an area where there is a low concentration to an area where there is already a high concentration of that solute.
Active transport can be separated further into "pumps," which directly expend energy in a cycle to move solutes from one side of the membrane to the other, and "co-transport." Co-transport uses a gradient that was established by a pump or exists for some other reason to drive transport of some other molecule up its own gradient. This is one of those things that is hard to explain in writing. However the diagram below does a pretty good job of showing it.
Symport is when the molecule that is moving down gradient is moving in the same direction as the molecule you want to move up gradient.
SucroseTransportimage from your textbook, Campbell Biology ninth edition

In the diagram, we see that ATP is expended to pump protons to the external side of the cell membrane.Those protons, given a pathway, would diffuse down their gradient back into the cell. The trick here is to use a pathway (that is to say, a protein in the membrane) that will only allow protons to diffuse down gradient if a sucrose molecule accompanies it.
You can think of it sort of as a revolving door that will allow protons to enter but will only revolve if sucrose is there also.
The other related concept is the "antiporter." you can think of this as a revolving door where the two players have to enter opposite sides in order for the door to turn. In either case one molecule or ion diffuses down its gradient (passive diffusion) while the other molecule moves up its gradient (active transport).

Ion pumps and the electrochemical gradient


In order to carry out co-transport, one needs to have a gradient established of one or more ions. This is generally achieved by proteins that we call "pumps." While there are many that are crucial to cell function, one has an outsized role in establishing what we call the "electrochemical gradient."That protein is the sodium-potassium pump. Sometimes you will hear it called the sodium-potassium antiporter ( which makes sense because sodium and potassium ions are moving in opposite directions – but is misleading since both will move up gradient against the direction favored by diffusion.) Another name you may hear is the sodium/potassium ATPase.
Here is a moderately
amusing GIF based on Drake's music video of a couple years ago.
Here is the gist of it: the pump can bind two potassium ions when it is open to the outside, but cannot find sodium ions at all. When open to the inside it will no longer bind potassium ions, but can bind three sodium ions. ATP is hydrolyzed to force the switch between the two states (open to the inside versus open to the outside). The net result of this is that as it goes through a cycle two potassium ions are pumped into the cell and three sodium ions are pumped out. This results in a gradient of potassium (high on the inside, low on the outside) and sodium ions (high on the outside, low on the inside). This is the "chemical" part of the gradient. Because two positive ions are pumped in for every three that are pumped out, there is also an electrical component to the gradient. The inside of the cell ends up being negatively charged overall to a level of about -70 mV.

I would like you to read David G’s really nice blog on the pump. I think you will find some of the numbers, frankly, shocking. Also, understanding the way this works will help you with other proteins we consider.
For example, some may be interested in proton pumps in the cells of the stomach that make the stomach acidic...it works like this protein, as David explains.

Proceeding from specific to general:

The Pump


  • This protein has binding sites for ions. Below is an image of two ions bound. In this case, the protein crystallographers have used a trick and bound Rubidium+ to the sites. But, it works similarly. What would bind a positive ion? Well, you should hold it between negative ions, like deprotonated acid side chains. What are the acid side chains in amino acids?: Aspartic Acid (D) and Glutamic Acid (E). Look at the image below:

  • IonBindinginPump
  • D804, E327 and E779 (the numbers correspond to the residue number in the amino acid sequence, or primary structure) all come together to make a really nice pocket that binds the ions (greenish). That makes sense. There are others I didn’t label. All three residues that bind the cation are on different helices. If you slide those helices relative to each other, the components of the binding site move closer or farther away from each other. Now, check out the ionic radii of Na+ and K+ at the wikipedia page. K+ is 30% bigger than Na+ (Rb+ is only slightly larger than K+). So, by sliding the helices, I can change the sized of the pocket and whether K+ or Na+ is favored.
  • ATP hydrolysis transfers a phosphate to a serine on the pump (Serine 33 on our pump), causing the helices to shift. This opens the pump to the outside and changes the shape of the binding pocket so that Na+ cannot really be held tightly anymore and K+ fits in well.
  • The Binding of K+ changes the shape a little more. This favors hydrolysis of the phosphate from the serine, shifts the helices back to be open inside the cell and makes the pocket too small for K+, but allows Na+ back in. Of course, I didn’t explain exactly, but the three Na+ sites only reconstruct 2 K+ sites once the helices move.

This type of pump could be modified to pump other cations.


  • As Goodsell points out, this same mechanism can be used to pump protons. You just have to change the size of the binding pocket. That probably just involves some shifting of the positions of the acidic residues.

Gradients are useful


  • Once you establish a gradient, you can use it to do stuff. The pump establishes an electrochemical gradient. Every cell at “resting potential” has more K+ on the inside and more Na+ on the outside. The inside is also more negative. Maybe I could use that gradient to do something.
  • For example, suppose I had a protein that would allow Na+ to come back in...but it would only do that if there was also a glucose molecule bound. I could use the gradient to transport glucose into the cell.
  • Suppose I had a channel that I opened in response to some signal...maybe something binding to the channel, and that channel would allow sodium to pass through it. All the sodium ions would start racing into the cell, down their chemical gradient. But that would also make the inside positively charged...that would be a dramatic effect. It get’s even more complicated, but that’s the start of an action potential in nerve cells.
  • Or...what if I stacked a whole bunch of cells on top of one another and made a little battery of cells, each with a small voltage across the membrane...then released all of them at once. That would be really interesting.
  • Phosphorylation and interactions with other molecules change the shape of proteins

  • A more general mechanism exists by which any protein could have a set of possible shapes, each favored under different conditions. Imagine a protein that binds to microtubules, for example. Maybe you could come up with a series of shapes that change depending on whether ATP is bound, or ADP is bound, or the protein is bound to tubulin or not... Could you imagine a series of steps like: Bind ATP and Release from tubulin; hydrolyze ATP and move forward; bind again, release ADP....what would that look like?

Cells intro

First, a fun science meme

Ran across this meme and thought might be both funny and educational.

21462937_1124277061041083_731827351515322829_n

All living things are made of cells


Why? Because I said so. Well, not because
I said so. This is something called the “cell theory of life” and it builds into our definition of life the requirement for cells. There are a lot of ways in which this makes sense. However, there are many biological entities, most notably, viruses, which are not cellular and at least fulfill many of the other requirements for being alive.
There is a pretty
good interactive site here.

Components

of a cell
We looked at diagrams of “generic” animal and plant cells (by generic, I really mean cells that don’t look like any real cells.
I want you to know the names and general descriptions of the major organelles.

  1. Nucleus: large structure that houses the chromosomes (DNA). All RNA for the cell is made there, using the DNA as a template. It is encased by a double membrane. That is, two complete lipid bilayers. There are pores, or holes, for the transport of stuff out. These are cleverly named "nuclear pores."
  2. Nucleolus: dense structure in the nucleus. It is the site of ribosome assembly. Ribosomes are then transported to the cytoplasm through the pores. Some scary numbers: a single mammalian cell may have 10,000,000 ribosomes and about 10,000,000,000 protein molecules (numbers form British Society for Cell Biology).
  3. Rough endoplasmic reticulum: Membrane stack near the nucleus. Site of synthesis of proteins that either end up in membranes or are secreted out of the cell (secreted merely means transported out of the cell). They are “rough” because they are dotted with ribosomes. Note: ribosomes are not ALL here. Most make proteins that stay inside the cell and work in the cytoplasm, not the ER membrane.
  4. Smooth endoplasmic reticulum (Lacks ribosomes): Has many varied functions depending on cells. Is the site of phospholipid synthesis, steroid synthesis and used to manage calcium ion concentrations in cells that really use a lot of that (such as muscle cells).
  5. Golgi apparatus: Stacks of membranes that are between the rough ER and the plasma membrane. Proteins are transported from the ER to the Golgi in spheres of membrane called “vesicles.” In the Golgi, proteins are processed (usually meaning sugar molecules are added to specific amino acid residues).
  6. Plasma membrane or cell membrane: the lipid bilayer that keeps the outside out and the inside in. It also has many proteins in it, which may function, for example, as channels allowing transport of nutrients, or allow cells to grab other surfaces or detect the presence of various molecules.
  7. Lysosomes: Spherical membranes that derive from the plasma membrane. Imagine them as pinching off from the membrane and taking in with the membrane any proteins in the area that pinches off. They are sites for “recycling” components of proteins.
  8. All together, numbers 3-6 (actually starting at the nuclear envelope) make up sort of one continuous super-organelle comprising a system of membranes. If I were to make radioactive lipids and put them in the cell, so I could detect the radiation where ever it was, I would find the “hot” lipids show up first in the smooth ER next the nuclear nuclear envelope, and then later would be detected in each of the other places as time passed.
  9. Mitochondria: these are the sites in which the high energy molecules from your food are broken down to low energy products (water and CO2) and the released free energy is captured in other high-energy molecules such as ATP, used to help run many reactions in your body. Mitochondria have their own chromosome (circular, like bacteria), their own ribosomes and their own tRNA. The function of all these components resembles that of bacteria. It is thought that ribosomes derived evolutionarily from bacterial cells that became part of a larger cell.
  10. Cytoskeleton: worst representation ever in the diagrams. We will look more at this later. It is a network of fibers made of the proteins actin (microfilaments), tubulin (microtubules) and Keratin (intermediate filaments…actually, there are many forms of each of these proteins). Microfilaments and microtubules are constantly changing. Microfilaments are usually involved when cells are migrating, are found more at the edges of the cell and at points where cells are attached to surfaces. Microtubules all grow out of centrioles or similar structures (generically known as “microtubule organizing centers” or MTOC). In a generic cell, that usually is the centriole, near the nucleus. However, the tail of sperm and many other things that stick out of cells and allow them to move (wag like the tail of sperm…called either “flagella” or “cilia” are made of microtubules and they each require their own set of centriole-like structures). Intermediate filaments are more permanent and are used to link cells together in very strong tissues (like skin). You only find them in cells that aren’t going any where anytime soon.
Unique to plants:

Cell wall: cellulose-based structure that provides rigid “box” around cell.
Vacuole: large, fluid-filled region of the cell, surrounded by membrane. Used to maintain pressure in the cell, keeping the cell pressed out against the cell wall.
Chloroplast: site of photosynthesis. Like the mitochondria, these have their own DNA, ribosomes and tRNA. They also appear to have been bacterial in origin…long ago.
“Higher” plants (all the plants you know well…except maybe kelp, don’t have true centrioles. This is really a distinction without a difference. They have MTOCs, but lack the clear cylindrical tubes that we call centrioles.
Plasmodesmata: holes in the cell wall that allow direct diffusion of medium-sized things between cells (we will see that animal cells have smaller pores between them called "gap junctions").
Peroxosome: similar role to lysosome.

Below I’m including some real micrographs of what the components of cells look like. I can explain the technique in great detail later, if you like. But, for now, just know that we have tools that allow us to make any structure we want “fluoresce” or “glow” in a special microscope. These are not the best images. But you get the idea.
CellPhotos

Nucleic Acids 1

Lambda_repressor_1LMB
Wikipedia wikimedia commons image of a Short stretch of DNA bound by a protein called “Lambda Repressor.” DNA bases are shown in “stick model” form, sugar-phosphate backbone as red or blue pipes. Protein is shown in “ribbon” form, backbone only (no sidechains).
This is one of the ways that genes are turned “off” and “on.” In this case, it’s for a gene found in a virus that infects bacteria. But, many of the same principles will apply all over.
The Double Helix
This is a really beautiful structure. Unfortunately, the beauty lies in just how much it explained when it was first proposed, and is therefore, perhaps, hard for you to see. To me, it is astonishing. I’ll run down a few features.
Basic Structure (image also from Wikimedia Commons):
514px-DNA_chemical_structure
And a more detailed view:
340px-DNA_Structure+Key+Labelled.pn_NoBB
  1. There are two strands. Each is defined by a polymer of sugar-phosphate moieties (yes, that’s a word similar in meaning to “functional group”). Each subunit is linked from the number 3 carbon of one deoxyribose, to a phosphate, then to the number 5 carbon of the next deoxyribose. Instead of calling them 3 and 5, we call them 3’ (pronounced 3-prime) and 5’. The “prime” tells you that the number refers to the carbons in the sugar, as opposed to a carbon in the rings of the “base.”
  2. Thus, each strand has a chemical polarity. What I mean is that each strand has a 5’ end and a 3’ end, just as protein has an amino end and a carboxyl end. That, it turns out, is not a coincidence.
  3. The strands are aligned “anti-parallel.” The 5’ end of one strand of the double helix is aligned with the 3’ end of the other.
  4. The information is encoded by the “bases,” which protrude from the polymer backbone. This is really one of the key points: DNA is a code. The sequence of bases stands for something else. The main thing a DNA sequence stands for is the sequence of amino acids in a protein. A good first definition of “Gene” is: a stretch of DNA that encodes a protein.
  5. The information takes the form of hydrogen bonds. This is more profound than it seems: information is energy. Adenine has a much greater ability to bond to Thymine than to Cytosine; Guanine bonds much more tightly cytosine. Thus, we have A-T pairs and G-C pairs. Each base “complements” the one it pairs with in terms of hydrogen bonds it can make. We use the term “complementarity” to describe this.
  6. Now, for some interesting stuff: DNA is redundant. I only have to see one strand to know what the sequence of the other is. Each stand has all the information needed to specify its opposite strand. When there is damage to one strand, the other strand tells you how to fix it. To replicate, each strand directs the synthesis of its mate.
  7. The information is in the hydrogen bonds...and it’s a code that specifies the primary sequence of proteins (among other things). Yes, I am aware that I too am being redundant. It’s important. The DNA and the peptide sequence are “co-linear.” The 5’ end of a gene corresponds to the amino end of the peptide chain. The 3’ end of the gene corresponds to the carboxyl end of the protein. Each group of three bases in a gene is a “codon,” specifying what amino acid goes in the corresponding place of the protein...Obviously, some fascinating machine and lots of regulation must go into that. I could go on and on...but I won’t just yet.

RNA

  • ATP
  • This is ATP (adenosine triphosphate). You’ve heard of it in terms of an “energy source” for your body. That’s true, as far as it goes. However, It is also one of the four bases that are the building blocks of RNA. The difference between this and dATP (“d” for “deoxy”) is the presence of that oxygen on the 2’ carbon. (Note, when I draw it, I usually have the protons removed from the phosphates. It’s an acid and will deprotonate under most conditions in the cell. this diagram I lifted happens to have the phosphates protonated).
  • Here are three important differences between RNA and DNA:
  • There is the extra oxygen.
  • RNA is almost always single stranded, but that strand can fold back to form stretches of helix. Remember that if you fold a strand back, the arrangement is antiparallel, which is the way nucleic acids align when pairing.
  • The rules for base-paring are the same…except that a different pyrimidine, “Uracil” or “U” stands in for Thymine. It’s pairing is no different. It just lacks a methyl group on the pyrimidine ring.
  • All RNAs in the cell are made by making a copy of DNA. That is, there is DNA in the cell that corresponds to all the types of RNA we have. This will expand our definition of “Gene” a little.
  • There are three main types of RNA in the cell (that’s a lie…there are more). But, the three main types for now are:
  • mRNA: the message form of the code. The mRNA will look just like the coding strand of DNA, except it will have uracil instead of thymine (and have the 2’ oxygen). The machine that translates the code into a protein sequence does not read the DNA directly. mRNA is sort of a "buffer" copy of the information. DNA, in this analogy, is the permanent "archival" copy of the gene.
  • rRNA: The structure of the machine that reads the code and synthesizes protein. This machine is called the “ribosome” and actually includes proteins as well. It is the RNA that is the major player.
  • tRNA: transfer RNA is the “adapter” molecule. It is an RNA and therefore can “read” the code using base-pair rules. But, at one end of it, there is a specific amino acid. So, the tRNA that reads the codon UGG in messenger RNA will have a phenylalanine attached to the end of it, because UGG is a “codon” for phenylalanine (phe, or simply “F”).
  • Below is the structure of the Phenylalanine tRNA.
  • 220px-TRNA-Phe_yeast_1ehz
  • Notice that it has a detailed structure, not unlike a protein. In this case, the “secondary structure” is mediated by base-pairing. Where protein has helices and sheets, RNA has “stems” and “loops.” I’m pretty sure you can see in the cartoon to the lower right of the structure what a stem and loop is. The stems are regions of base pairing and loops have free, non-base-paired bases. That blue loop at the bottom is the “anticodon loop.” In the gray section it has the sequence 5’ CCA, so that it reads the 5’UGG codon. It may seem more natural to write the anticodon as ACC to show that it pairs with UGG. However, I will almost always write 5’ to 3’.
  • It also has tertiary structure, folding up in the “L” shape you see. That is also mediated by base pairing and other interactions.
  • You know it’s funny, you would think looking at this structure that we would have guessed that RNA like this could have protein-like functions. I mean…it has structure and functional groups (the most important ones, I"ve told you). Well, nobody guessed it (except Francis Crick). But, it turns out to be true. I’ll talk more about that later.
  • The wikipedia entry has some nice, simple pictures of translation--the making of proteins using the mRNA sequence as a guide. We’ll cover that later. But, if you want to take a look.