Quiz Discussion

I'm still working on a way to embed this here. But, this is the link to a shared document in which any of you can ask and answer questions as you study. I will also contribute, of course.
Here is the link.

Protein Structure

Protein Structure: Overview


Amino Acids


You should know the basic structure of one, identify the amine, the alpha carbon, the “R” side chain and the carboxyl group (acid). You don’t need to name and recognize side chains. However, given an example, I would like you to be able to identify whether it is hydrophobic or what other important functional groups it has. Example: presented with serine:
Serine
you should be able to spot that the side-chain has an OH on it (It's at the top). You could guess that it is a decent H-bond donor. You might also ask whether that OH ever chemically attacks a phosphate (it does, quite often).

Primary structure

Primary structure is nothing other than the sequence of amino acids that make up the proteins. While I don’t want you to sit and memorize the structures (well, I kind of do, but it’s a lot of memorization), I do want you to get to know the categories as they are identified in the book or at wikipedia. We haven’t gone into that yet. So far we have ignored the “R” groups.
Primary structure just gives you one long chain, like the chain of magnetic beads.
You should understand the chemistry of how amino acids connect to form peptides (dehydration synthesis). At typical peptide will include hundreds of amino acids…and maybe 1000s. Notice that there is an
amino terminus and a carboxyl terminus. There are no actual amino acids left after peptide bond formation (the former carboxyl end has lost an OH and is now just a carbonyl, the former amine has lost one of it's Hs). They are then often called “amino acid residues.”

Secondary Structure

Secondary structure is the first step of how the chain of amino acids folds. This does not directly involve the R groups, though, they will have an impact. The secondary structure will be due to hydrogen bonds between the carbonyl oxygen and the amine hydrogen of another residue. Those are part of the backbone.
For our purposes, there are two main secondary structures:
ɑ helices and β sheets (often called “beta pleated sheets,” by non biochemists).
Alpha helices will be like the small helices we built with the magnet spheres. There will not be enough space in the center of the helix for other molecules, even water, to fit. They are “right handed” screws. Looking down the spiral from either direction, the spiral runs clockwise away from you.
When we used the yellow models, we saw three main features:
  • The helix is held together by backbone hydrogen bonds between a carbonyl carbon and the amino group of the fourth amino acid along the chain.
  • This structure is fairly rigid.
  • This repeating structure places all the “R” side chains on the outside (they couldn’t fit in the center anyway). A subtle result of this is that residues 1, 4, 8 etc will be on the same side of the helix.
Here is a close up of a helix in the estrogen receptor
untitled
Notice the dotted lines indicating hydrogen bonds between a carbonyl in the backbone (little red sphere for oxygen) and the hydrogen of the amine on the loop in front of it.

Why do some amino acids form helices and some not?


The other common form of secondary structure is called a “beta sheet” or “beta pleated sheet.” (See below) Why do some chains form helices and some form sheets?

Dihedral angles:


Phi Psi Angles 1These angles, also known as the “phi/psi” angles denote the rotation around the N-Carbon-alpha bond (phi, ϕ) or the rotation around the Carbon-alpha-Carboncarbonyl bond (psi, ѱ)
The key thing to know is that, while the atoms are free to spin around the single bonds, there is a preferred dihedral angle. That is generally dictated by the nature of the R side chain. You can force any amino acid (except proline) into the correct angles for an alpha helix. But, some are better at it than others. Alpha helices form because they are strings of amino acids that prefer the correct phi/psi angles. If you have a run of these alpha-helix-preferring residues, they form quickly into the correct structure.
Beta sheets are made up of residues that prefer a slightly different dihedral angle. Again, any amino acid except proline can fit into a beta sheet. But, some residues are better at it.
Beta sheets will be like those flat sheets we made, or, at least the two strands we made, with the magnet spheres. As with the spheres, the sheet can be made either of antiparallel strands or of parallel ones. Also like the spheres, the details of the structure will be different in parallel and antiparallel sheets. However, the wonderful beads breakdown as a nearly perfect model at this point.

Levels of structure:



ProteinFolding1

Folding of proteins and structure:


Recap: proteins are made as one long strand of hundreds of amino acid residues (the largest know has over 33,000 residues). Given that the average mass of an amino acid is 110 Daltons, a “typical” protein might have a mass of 50,000-60,000 daltons and a really big one in the several million Daltons, We actually use “KiloDalton,” 1000 Daltons, as the unit of choice. So, 50,000 Dalton would be 50KD.
They are in a line and the sequence of residues is known as the primary structure. There is an amino-terminus and a carboxyl terminus. But, there are no actual amino acids left, since water was removed when the peptide bond was formed between each residue.
Secondary structure, for A.P. bio, is simplified to be alpha helices and beta sheets. There are more subtle things I want you to know. Or rather, I want you to know that there are more subtle things. Just know that alpha helix and beta sheet are not the only possible folded secondary structures.
My wife recently solved one that is a “beta propeller.” It’s a cool variant on a beta sheet.
betapropeller
Secondary structure is mediated by the backbone carbonyls interacting with backbone amines.
The last thing about secondary structure I mentioned was that an alpha helix is easy to make with one side hydrophobic and the other hydrophilic by incorporating residues with hydrophobic side-chains in every fourth position. This is called an amphipathic helix. Beta sheet have side-chains that alternate Up/down along each strand.
Structures with lots of alpha helices tend to be soluble in water. Beta sheets, not so much.
Remember that, while the “R” groups or side-chains of amino acids are not directly involved in secondary structure, they influence the dihedral angles and thereby indirectly determine what will form.

Tertiary structure:


This is the first aspect of structure that is mediated directly by the “R groups” or side-chains. The side chains influence the preferred dihedral angles and therefore influence secondary structure. But tertiary structure results from how helices and sheets come together in a 3-D shape.
ProteinFolding
Tertiary structure may be mediated by hydrophobic interactions, leaving the hydrophilic faces on the surface if the protein is found in water. But, there may also be “salt bridges” formed by interactions between negatively charged (Acid) side chains on one section with a positive (Basic) side-chain on another.
There also are covalent interactions, where to Sulfhydryl-containing side chains form a disulfide link. Two cysteine residues that may be very far apart in the primary structure may fold so that the structures in which they reside come close together. They can then form a covalent link:
Disulfide2
This is an oxidation, as two electrons are removed. It looks like you would get hydrogen gas out. But, usually, the electrons go somewhere else.

Quaternary Structure:


This is when two or more folded polypeptide chains interact to form a larger structure. These are mediated by the same interaction as found in tertiary structure.

Lipids

Outline

  1. You must know the classes of lipids, how to spot saturated and unsaturated fatty acids, trans and cis double bonds and know how those things affect the interactions among fatty acids. You must be able to read a “shorthand” structure (applies to proteins and sugars too). You must be able to identify a mono, di or triglyceride (really "mono, di or triacylglyceride). Among diacylglycerides, identify a phospholipid and describe how they form a lipid bilayer. You should know that the fatty acids become attached to glycerol via a dehydration synthesis step, similar to what happens with both peptide bonds and glycosidic link. You must know that the membrane of the cell, the plasma membrane, is made of phospholipids, primarily (it also includes lots of proteins, cholesterol and other stuff). Phospholipids are probably the most important class for our purposes. We will talk about them again when we do membranes.
  2. Note, most images below are taken from Wikicommons. The others were constructed with the program “chemdoodle.”
  3. Lipids

  4. We break lipids into two classes that don’t look a lot alike, but are both hydrophobic. The first are called sterols, which are based on this structure. There are four carbon rings, three of which have six carbons and one with five. There is hydroxyl at the end. That’s what makes it an alcohol (ol ending).
  5. The most well known of the sterols and most abundant in you is cholesterol, which looks like this:
Pasted Graphic 1 While you have heard that cholesterol is bad in your diet, it actually is an important molecule you need to live. You make it in your body, as do all animals. In addition to cholesterol, all the steroid hormones are based on the sterol molecule (for example, testosterone and estradiol).
That’s pretty much all you need to know about sterols. When we talk about hormones later on, we will revisit them.




CisFA

Fatty Acid-based lipids


As noted above, those structures are Fatty acids. These are the components of the other class of lipid. They comprise a chain of hydrocarbon with a carboxyl (acid) group at the end. We start counting carbons at the carboxyl group. The one above has 18, as noted.

Saturated or Unsaturated


These terms originally referred to whether a fat could accept more hydrogens into its structure. However, what that means structurally is whether it has any double bonds. Recall that carbon must make four bonds total. At the site of the double bond (carbons 9 and 10) in the middle of those structures above, the two carbons have only one H each. If we break the double bond, we would have to add one more hydrogen atom to each. So, that bond is “unsaturated.” This would be known as a monounsaturated fatty acid. In the popular media, that’s usually shortened, incorrectly, to “monosaturated.”
In contrast, a saturated fatty acid has no double bonds.

Cis and Trans


Cis and Trans
ONLY apply to positions where there are double bonds…that is, unsaturated bonds.
Note that the bottom structure has a big kink in it whereas the other one is fairly straight, like a saturated chain.
Pasted Graphic 3
That’s because the carbons cannot rotate around the double bond and you therefore have two different ways to arrange the bond: the long carbon chains on the same side (both down in this case) of the double bond. That’s known as “cis” and results in the kink.
Or, the long chain on one side goes “up” and the one on the other goes “down.” That is known as “trans” (opposite directions) and results in a fairly straight molecule.
Trans fatty acids are not found in biology. The Cis fatty acids are important because of the kink. The kink keeps the fatty acids from sticking together as well and lowers the melting point of the fat. Plant oils (not from the tropics) tend to have CIS unsaturated bonds and are liquids at room temp. Animal fats and tropical plant fats tend to have saturated fatty acids and be solid.
Trans fats occur almost any time you chemically treat (or even heat) fatty acids with double bonds.

Mono-, Di- and Triglycerides


These are all fatty acids attached to glycerol, a three-carbon chain with an OH on each carbon.

The Mono, di and tri refer not to the number of glycerols, but the number of fatty acids stuck to the glycerol. I know…dumb naming scheme.
Once the bond is formed, since an OH is taken off the acid and an H of the hydroxyl, it is no longer a fatty acid (it’s a fatty ester).
The synthesis is another example of dehydration synthesis.
Pasted Graphic 12
This is a triglyceride, also known as a “Fat.” It’s primarily for storing fatty acids for use in membranes or for energy. In this case, there are three very different fatty acids on the glycerol. You can also see the alternate numbering of the “alpha” and “omega” carbon. But, again, don’t worry about that.
One misleading thing in this structure is that the double bonds are Cis, but the person drawing it has left out the kinks.

Phospholipids


These are the main components of the cell membrane, and any membrane within the cell. They allow us to build cells with an outside and an inside, as well as internal compartments, transport vesicles (that weird “bag” the Kinesin molecule was dragging in the movie).
They comprise glycerol with two fatty-ester chains. On the end position of the glycerol, there is a phosphate, which is then in turn connected to some other hydrophilic group (such as the amino acid, serine or the ionic structure, choline). The thing below is phosphatidylcholine:
Phopshoplipid
You see the two fatty acid (ester) chains going to the right and angled to the right. You should see the phosphate.

The key point is this: the part on the left is VERY attracted to water and the fatty acids avoid water at all costs. If you get a bunch of things like this together, they will arrange in the only way that allows each part to be where it wants. They will line up in two layers, fatty acid tails pointing toward each other and lined up alongside, with the hydrophilic part out. T


This depiction from Wikipedia LipidBilayer
is a good one because it shows how thick the membrane is. It is bad because it doesn’t tell you what comes after the phosphate. Remember, though, I told you that varies all over the place. It just has to be hydrophilic. The completely hydrophobic (dehydrated) area is about 3.5nm thick. A nm (nanometer) is 1/1,000,000 of a millimeter. The membrane is about 35 carbon atoms thick.

Water and pH

Most biochemistry takes place in water


There are proteins that work in lipid layers, but the interaction with water is critical to the way biology works. It is the medium in which all the biochemistry takes place, but is also an important chemical player in reactions.
I think you get the first part: the molecules of life are, for the most part, floating in water. Yes, there are some in membranes, but even that depends on the water being on each side of the membrane (remember it is the interaction of the hydrophilic heads of the phospholipid with water and the avoidance of water by the hydrophobic tails that lead to the formation of the lipid bilayer).
Also, you seem to get the idea of how surface tension works, and cohesion and adhesion.
What about the chemistry?
We just learned about dehydration synthesis and hydrolysis. Obviously, the chemistry of water plays a huge role in that. Another main role of water is in acid/base chemistry. pH greatly affects how easily certain reactions proceed and also the shape and function of many proteins.

The central equilibrium:


Water equilib

The big points:
  • There is very little H3O+ and OH- in pure water. The concentration of both is 10-7 Mol/liter.
  • The product of the concentrations of H3O+ and OH- is always 10-14. That is called the "Kw" and is really just an equilibrium constant.
  • For our purposes, acids and bases act by changing the equilibrium position of this equation.
The law of Mass Action says that if I change the concentrations of any one of the components of the equilibrium, the reaction will shift to adjust so that the product of the concentrations of H3O+ and OH- is 10-14. Acids act by adding H+ to the solution, increasing the amount of H3O+ and decreasing the amount of OH-. Bases act by soaking up available H+, which increases the concentration of OH-.
So, if I dissolve HCl in water to a concentration of 0.01 (10
-2 molar) the concentration of H3O+ becomes 10-2 molar (called pH 2) and the concentration of OH- shifts to 10-12 molar (the product of the two is 10-14).
This is what happens in the stomach, for example, where the pH is about 2.
A carboxyl group would release it's H+, doing resulting in the same sort of change as with HCl. An amine could steal an H+ from an H
3O+ and make the pH go up.
Here is a scale I liked that I stole from another website:
http://crescentok.com/staff/jaskew/isr/chemistry/class21.htm

phscale


Buffers:


I didn't get to talk about this in class. A buffer is anything that is a weak acid or base (preferably both) that will give up an H
+ if the pH is above a certain point (different for each buffer) or absorb an H+ if the pH is lower than that point. The result of this is that a solution of water that contains a buffer resists change in pH. Your blood, for example is not pH 5.5 like the water in the room, it is pH 7.4 +/- 0.5 pH units. It is tightly controlled by multiple buffers, including a carbonate buffer system.

Polysaccharides

Polymers of sugar

or, polysaccharides.
A monomer of sugar, with the empirical formula CH2O, is called a simple sugar. For our purposes, hexoses including glucose and fructose are most important here. Pentoses such as ribose in RNA and deoxyribose in DNA will be dealt with later.
Sugars have a carbonyl on one carbon and hydroxyls on the others. The carbonyl can be on the end (an aldose such as glucose), or not on the end (A ketose, such as fructose). We often draw them as a linear form. But, in water, they are not.

Sugar Cyclization.



Here is the linear form of glucose:
Pasted Graphic 8
and another view in ball-and-stick model.
Pasted Graphic 9
Carbon 1 is on the right, the carbonyl.
The cyclization is just a rearrangement of the atoms in the molecule. No atoms are lost (e.g. water is not released).
The dashed-line bonds are bonds that would go slightly back into the page and the dark wedge-shaped bonds would come forward out of the page, as indicated in the 3-d view.
The chemistry of the interaction, if you care, is that the carbonyl carbon is very electron poor (the brutish oxygen is stealing it’s electrons). The lone pairs on any of the alcohol (OH) group oxygens could in principle initiate a reaction with the carbonyl carbon (alcohols and aldehyde often react...so when you put sugar in solution, it reacts with itself). The most stable ring is formed when the OH on Carbon 5 attacks the carbonyl carbon. As the bonds are exchanging, that oxygen ends up bridging carbon 1 and carbon 5 AND having a hydrogen bonded to it….This intermediate is unstable. Both the oxygen and Carbon 1 are making too many bonds, which cannot stay. So carbon 1 has to lose one bond to what had been the carbonyl oxygen. That leaves the carbon looking good, but we have one oxygen (in the ring) with 1 too many bonds (+1 formal charge) and the other on carbon one with not enough bonds (-1 formal charge). The more stable structures trades the hydrogen off the ring oxygen on (originally from carbon 5) to the former carbonyl carbon on carbon 1.
For those keeping score, this adds one more asymmetric carbon (carbon 1) and one more possible isomer, which we call the alpha and beta form, as we see in either starch or cellulose.
It seems like such a small thing: does the OH on carbon 1 stick straight out of the plane of the ring (called “axial”) as below:
Pasted Graphic 7
Or does it stick out more in plane with the ring (“equatorial”), as it does in this form:
Pasted Graphic 10

But, it is a big deal. The top form is called alpha and the bottom is called beta.

Polymerization


Polymerization is carried out by an enzyme that joins the joins carbon 1 of one ring with carbon 4 of another. It’s a dehydration synthesis, resulting in the OH from carbon 4 leaving with an H from the hydroxyl on the carbon 1 to form water. The bond can be hydrolyzed by a different enzyme. I said, animals lack the enzymes to deal with the beta form of glucose…But, actually, I was wrong about that, to some extent. We do have a (poor) beta glucosidase…in our tears. It’s called “lysozyme” and it’s part of our defense against bacteria. Also, a sugar similar to glucose (another hexose/aldose with the formula C
6H12O6) called galactose pairs in its beta form with glucose to form a disaccharide called Lactose (perhaps you’ve heard of it?). At least as infants, we make a beta galactosidase protein called “lactase.” Most of us don’t make that when we get older and so we have some level of lactose intolerance.

But, in general, we deal poorly with beta forms of glucose in polymers.

Pasted Graphic 3
This is a representation of cellulose (also known as “Fiber”) from Wikipedia, the same one we looked at today. It is a main structural component of plants, in what is known as the “cell wall”. Note that there are four VERY short chains linked through the oxygens in a beta 1-4 link. The actual chains would be much longer.
Notice that the oxygen on carbon 1 (right-hand carbon in each ring) is sticking out to the side of the ring. The net result of this is that the sugars alternate orientation. You can see this best by looking at the carbon 6, which is sticking out of the rings, either up or down, alternating.
As a result of this, there are hydrogen bonds both within each chain (from each sugar to the next) and to the chain running along side of it. Seems like a recipe for something fairly strong, but flexible (chains can slide along each other under stress, simply making new hydrogen bonds).
This is a great example of how details of the fine structure explain the behavior of the larger structure. Wood is essentially made of single fibers all cross-linked in many directions that allows at least some sliding, and therefore bending.

Compare it to this, which is starch (we can digest that).

Pasted Graphic 5
In this case, you see the O off carbon 1 sticking down, out of the plane of the ring. This leads to all the sugars more or less orienting the same way, no great ability for hydrogen-bond cross linking, and sort of a slow, spiraling of the strand.

Key properties of polysaccharides for AP:
  1. Cellulose and Starch (and the slightly branched “amylopectin”) are made by plants.
  2. Glycogen is made in animals (mainly in the liver).
  3. Starch, pectin and glycogen all use alpha glucose and are mainly storage forms of glucose. Your body, for example, will either make or hydrolyze glycogen to take up or release glucose to your blood.
  4. Cellulose is the beta form of glucose and used primarily to provide structure.
  5. Though a strand of polysaccharide is joined from carbon 1 of a glucose to carbon 4 of the next, you can have branching where a long strand will attack carbon 6 (the one outside the ring) with its carbon 1.
  6. Cellulose has no branching; starch (amylose) has no branching and pectin a little branching. Glycogen is highly branched.

Here are some things I would like you to know at this point or very soon.
  1. What are polymers? How are monomers assembled into polymers? Explain hydrolysis and dehydration synthesis.
  2. Identify the number of the carbons in a monosaccharide both in linear and ring form.
  3. What is the difference between an aldose and a ketose sugar?
  4. What’s the difference between a triose sugar and a trisaccharide? (or hexose versus hexasaccharide).
  5. How do sugars form the ring structure. Show that no atoms are gained or lost.
  6. What is wrong with this sentence commonly found in biology texts “cells obtain energy by breaking the bonds in sugar molecules.” ? Students who had me in chemistry may have a leg-up on that one.
  7. Explain the key differences and similarities between glycogen, starch and cellulose. What makes cellulose a good “structural” polysaccharide? (you just read the answer).

Energy Review

Why do things happen?
When you think about it, this is one of those fundamental questions. Historically, answers have ranged from religious or superstitious to mechanistic. We, predictably, will try to come up with mechanistic rules. And, our answer will be tied up with the idea of energy. Things in a high-energy state will tend to move to a lower energy state, so that energy will become more evenly distributed. All of biology will follow the rules of thermodynamics. Energy rules. So, we must talk about what energy is.
This is pretty much my intro about "capacity to cause pain."
Things in a high-energy state will tend to move to a lower energy state, so that energy will become more evenly distributed.
Remember that.
Read More…

Molecules and stuff

This has links to a screencast and some other stuff, as well as some text on molecules and functional groups.
I would like you to review the bonding basics (25 minute screencast) and read about functional groups and molecular shorthand (all in the body of this blog).
Most of this can be found in the first three of chapters of Campbell. This will be enough to get us started on our discussion and the have us able to do the lab.
Read More…

You Are Here

This is a graphic of the “tree of life” based on comparisons of ribosomes...the machine that makes protein. It was compiled a long time ago by Norman Pace. I’ve modified it slightly.
It’s not the most up to date complete. But, it give you the idea.Pace Tree of Life

This is the most "up-to-date" tree of life, published last year:


nmicrobiol201648-f1.jpg

If you are wondering where we are on it, the line labeled Opisthokonta, found at the lower right, includes all animals and fungus.