Biology C2005 Lecture 4 Unlike the catch-all category of LIPIDS, NUCLEIC ACIDS are biopolymers par excellence. There are 2 types, DNA and RNA, the monomers are nucleotides, that have nitrogen-containing rings and 5-carbon sugars. There are four types of monomers in each polymer. We will discuss them in detail, but not for a few weeks yet. ::Proteins: Amino acids are the monomers (20):: PROTEINS. These are the most important class of macromolecules in the cell, and we will discuss them now in detail. The monomers that make up proteins are the amino acids, of which there are 20. The same 20 in E. coli and in elephants and in tomatoes. The general structure of an amino acid is: Note the central carbon atom, to which 4 different groups are attached: an amino group (drawn by convention at the left), a carboxylic acid group (put at the right side), a hydrogen, and a side chain, or R-group. Only the R-group varies among the 20 different amino acids. This is the side chain, and so there are 20 different side chains. Look at the amino acids and peptides handout for some of the side chains. Your texts and hard copy handout show al l 20, and you should examine all 20. Out of laziness, I drew the general amino acid incorrectly: Actually at neutral pH, the molecule is charged, because the carboxylic acid group is an acid, and the amine group is a base, so more accurately: (also see 3-D picture) Let's take this opportunity to discuss the charge on organic molecules a bit more. In living systems, the carboxylic acid group is mostly charged and the amine is mostly charged, but that is a pH7, the cellular pH under most circumstances. Is an acid always charged in aqueous solution? No. It depends on the pH of the environment. In the laboratory we do not have to keep things at pH 7, as it is in the cell. We can vary the environment at will, adding strong acids such as hydrochloric acid as a source of hydrogen ions (lowering the pH), or a strong base such as sodium hydroxide (raising the pH). The strength of an acid is a measure of how readily it gives up a proton. Carboxylic acids are always in equilibrium with the hydrogen ions (protons) in the solution, so if the hydrogen ion concentration is high (acidic) then the equilibrium will shift toward the protonated (uncharged) species. At pH 3 an amino acid carboxyl group is protonated about half the time; for each pH unit this proportion of protonated species will drop by a factor of 10, so very little of the carboxyl group is protonated at the neutral pH of 7 found in most cells. A similar situation pertains to the amine base end: at a very low H+ ion concentration (e.g., 10-11M H+, a high pH of 11), it will tend to lose its extra proton, but at pH y,it will mostly remain protonated, with a positive charge. ly. high pH . So at pH7, most amino acids are neutral (no net charge), but they are highly charged nonetheless. Now, what are some of these 20 different side groups? Here are 2 charged side group, e.g.: asp: R= -CH2-COO- , there is a second carboxyl group on this amino acid) lys: R= -CH2-CH2-CH2-CH2-NH3+ , there's a second amine on lysine, so lysine will have 3 charged groups, and a net charge of +1 (two +'s and one -) at pH7. There is a convention for numbering amino acid carbons; actually it's a lettering. It starts from the central carbon, called alpha: so lys has (count with me) an alpha, beta, gamma, delta, EPSILON-amino group as well as an alpha-amino group (and an alpha-carboxyl). The average molecular weight of an aminoacid is ~120,but the range is from 75 to 203. The smallest amino acid (a.a.) is glycine (gly), MW = 75. Here the side chain is merely hydrogen. The largest is tryptophan (trp), MW = 203 [-CH2- bridge to a 5-membered ring containing a N + a fused 6-membered ring] and fairly hydrophobic. Look over the structures of the 20 amino acids in the textbook. It is the properties of the functional groups on the 20 different side chains of the 20 different amino acids that determine the function of a protein, so they are all-important. The handout shows all 20 aa's, but without indicating the ionization of the acidic and basic groups. We will discuss many of the side chains within the context of the discussion as we go along. There are a couple that deserve special mention: arginine contains a functional group that is not on your list; it is -NH-CH2(NH2)NH2, called the guanido group. The guanido group is a strong base, even stronger than an ordinary amine, so it is positively charged at pH7 (like lysine). Proline has a side chain that folds back and forms a covalent bond to the amine nitrogen of the amino acid, thus producing a ring structure. You should be able to recognize the properties of the side chains as polar or non-polar, charged or not charged. You will not be responsible for recalling a specific amino acid structure from the English name or vice versa, but given the structure you should know how it behaves. {Q&A}. ::Stereoisomers:: Now let's consider the structure of an amino acid in 3 dimensions: When carbon forms 4 single bonds, it makes them spaced equally apart from each other in space, in the form of a tetrahedron as in this representation of glycine [a model with 2 white groups is shown]. Now consider this other molecule of an amino acid [again with 2 white groups], with 2 H's of glycine, e.g. Are these the same molecule, that is, are they distinguishable or are they indistinguishable? They are indistinguishable, since I can rotate them and superimpose their atoms. But now suppose I make this alanine instead of glycine. I replace one H with a [blue] -CH3 group on each molecule [I am being sure to make them stereoisomers]. I can no longer superimpose them. They are both alanine, as they have the same four groups attached to the central carbon. But in three dimensions they are actually mirror images of each other. See [Purves6ed 2.21a]. We call one D-ala and one L-ala. See [Purves6ed 2.21b]. This one is D, or is it this one... ? I can't remember .. it's not too important here. What is important is that in general, you have this situation, the possibility of two stereoisomers, whenever there is what is called an ASYMMETRIC carbon atom in a molecule, that is, a carbon with four different groups attached. These stereo isomers are sometimes called optical isomers, since the two forms, in solution, will bend a beam of polarized light one way or the other. Thus the D designation originally meant dextro, or to the right), whereas L stood for levo, to the left. All amino acids except glycine have an asymmetric carbon, which is the alpha-carbon. So we can draw 19 of the amino acids in 2 stereoisomeric forms. So do we really have 39 a.a.'s? No. All the stereoisomeric forms of the amino acids in proteins are L-amino acids, so we only have to worry about 20. Note that the sugars we discussed, like glucose, have several asymmetric carbon atoms. Aside from L and D designations, the sugar stereoisomers are given different English names (e.g., D-glucose, D-mannose, L-rhamnose, etc.). ::Polypeptides, peptide bond:: Polymerization of aa's OK, now let's string these L-amino acids together, polymerize them. The bond that connects two amino acids is an AMIDE bond (-CO-NH-) between the carboxyl of one amino acid and the amino group of the next. Once again, a molecule of water is removed in the formation of the connecting bond: In the special case of proteins, this amide bond is called a PEPTIDE BOND, and the resulting product a PEPTIDE, a dipeptide (or we could go on to a tri-peptide, oligo-peptide, or finally, POLY-PEPTIDE). (See also polypeptide handout). Also see [Purves6ed 3.4], and another picture. By convention, the amino group is written on the left for an amino acid and also for a peptide. In the tripeptide in the diagram, note the peptide bond (boxed), and the repeating unit, or aa "residue" [circled]. Residue refers to what's left of the amino acid monomer after it ahs been incorporated into a polypeptide, which is most of it: it just lacks one H at what was the amino end and one OH at what used to be the carboxyl end. Note also that the charged amine and carboxyl groups no longer exist inside the polypeptide, having been replaced by the amide, an uncharged functional group. Almost all polypeptides have 2 ends, the amino end and the carboxyl end, which do remain charged at pH7. . The "backbone" of the polypeptide is defined as all of the atoms except the side chains. The only free amino and carboxyl atoms of the backbone are at the 2 ends. The side chains then, stick out of this backbone (also see polypeptide handout). The length of polypeptides is commonly 100-1000 amino acids, but smaller and larger ones also can be found. Each and every protein molecule in the cell has an identity defined by its particular sequence of amino acids. Each E. coli cell contains about 3 million polypeptide molecules, but only about 3000 different ones. Each of these individual protein types has a name to go along with its chemical identity. Some examples of polypeptides, taken not from E. coli, but from more familiar organisms include: hemoglobin, which carries oxygen in red blood cells; egg albumin, a nutrient in the white of a hen's egg; keratin, providing toughness in skin, fingernails, and wool; collagen, providing a strong connection between cells in tendons; beta-galactosidase, which helps digest the milk sugar lactose. ::Primary (1o)= linear sequences of AAs:: Each of these proteins contains a polypeptide with a particular sequence of amino acids, usually all 20 are represented, although not at all equally. Unlike polysaccharides, this sequence usually exhibits no obvious regularity, or repeating subsequence:      This linear sequence of amino acids is called the primary (1o) structure of a protein. ::Methods: Paper chromatography, electrophoresis, fingerprinting:: I will discuss a bit now some methodology used in the purification of amino acids and proteins. We bring in some selected lab methods from time to time for two reasons: First, the behavior of molecules in experimental situations helps you to understand their behavior in nature; and second, the methodology is interesting in its own right as an example of how science is done. Our first topic of methodology is directed at the question of how we get to know this primary structure, this sequence of amino acids in a polypeptide? One way to determine the sequence of a polypeptide is to chemically degrade it in a stepwise fashion, starting at the carboxyl end. First you must purify the polypeptide in question away from the other 3000 polypeptides in the cell; we will discuss that process a little later. The degradation of the polypeptide back to its free monomer aa's is a form of HYDROLYSIS, a reverse of the dehydration that accompanied the formation of the peptide bond. The controlled hydrolysis of amino acid residues from the carboxyl end of a polypeptide is a form of enzymatic hydrolysis; an enzyme, called carboxypeptidase, itself a polypeptide, catalyzes this hydrolysis; it does not happen by itself. We will learn more about enzymes next week. After the carboxypeptidase is mixed with a peptide, hydrolysis begins: all the trillions of molecules release their C-terminal amino acid in unison, synchronously, so that in the first wave the last (original c-terminal) amino acid is released. If the reaction is stopped at this point and the released amino acid is separated from the main peptide and identified. By letting the reaction proceed for increasing amounts of time, the time that amino acids are released can be correlated with their distance form the C-terminal end. You can get the sequence of perhaps 20 amino acids from the carboxyl terminal in this way, before the process breaks down. Since most polypeptides are greater than 20 amino acids in length, you first need to chop the polypeptide into manageable pieces and then sequence each piece by subjecting it to hydrolysis by carboxypeptidase. Here I want to concentrate on the chemical analysis problem of separating and identifying the different amino acids that are released by this carboxypeptidase hydrolysis. How do you know which amino acid came off when? Amino acids will behave sufficiently differently from each other under certain conditions to allow the complete separation of all 20 species from a mixture. We will discuss two methods for separation and identification here. One way is based on the migration of amino acids in an electric field. In PAPER ELECTROPHORESIS, an amino acid mixture is spotted onto a sheet of filter paper, the paper is wet with a buffer salt solution and placed between two electrodes and a high voltage (e.g., 2000 volts) applied. At neutral pH, the acidic amino acids (asp and glu) will have a net negative charge and will migrate toward the ANODE (+ pole) while the basic amino acids (arg and lys) will migrate toward the CATHODE (- pole). {Q&A} Electrically neutral amino acids will not migrate much, unless the pH is made acidic or basic. A more versatile separation method is PAPER CHROMATOGRAPHY. This method is based on the differential solubility of the different amino acids in organic (non-polar) solvents, which in turn is determined by the nature of the side group. The amino acid mixture is spotted onto a filter paper; one edge of the paper is immersed in a mixture of aqueous and non-aqueous solvents. The liquid will be drawn up the paper by capillary action. As it rises the water in the liquid mixture is bound by the paper (cellulose, with its many OH groups), forming a stationary water layer, or stationary phase. The organic solvent (e.g., propanol) moves up without as much interaction with the solid cellulose; it is considered the mobile phase. The amino acids will be constantly equilibrating between being in the mobile organic phase or the stationary water phase. The more polar the side chain, the more time the amino acid will spend in the stationary phase. The more hydrophobic the side chain, the more time it spend in the mobile organic phase. By using a series of different solvents, all 20 amino acids can be separated in this way. It works for many other organic molecules as well. Small PEPTIDES [I emphasize peptides here, oligopeptides, not polypeptides] can also be separated by both of these techniques; the properties of the peptides will be a COMPOSITE of the properties of the constituent amino acids. {Q&A}. One of the most famous examples of the use of these methods to analyze peptides rather than single amino acids was in the study of sickle cell disease. Sickle cell disease is caused by an abnormal hemoglobin protein. Hemoglobin is made up of several components, one of which is a polypeptide called alpha-globin. The sequence of amino acids in beta-globin from sickle cell hemoglobin differs from that of normal alpha-globin. The nature of that difference can be determined by chopping up the sickle cell alpha-globin into small peptides and then first separating them along one edge of a filter paper sheet by paper electrophoresis. The sheet is then turned 90 degrees and subjected to paper chromatography. The result is a series of spots (after staining to visualize their positions) representing all the sub-peptides. One peptide migrates differently in sickle cell globin compared to normal globin. This peptide can then eluted from the paper and sequenced. Comparison with the normal counterpart shows that the sickle cell globin carries a single amino acid substitution. In place of glutamic acid, it has a valine at one position in the peptide. How could such a small change have such a large effect? The answer lies in the 3-dimensional shape of proteins, to which we will turn next. Most proteins can be separated into characteristic patterns of spots this way. The procedure is called FINGERPRINTING a protein, since the migration patterns are so characteristic. Protein 3-dimensional structure Now let us return to polypeptide structure. Each polypeptide has a particular sequence of amino acids. Thus if we could examine several molecules of the protein albumin we might find: Molecule #1: N-met-leu-ala-asp-val-val-lys-.... Molecule #2: N-met-leu-ala-asp-val-val-lys-... Molecule #3: N-met-leu-ala-asp-val-val-lys-... etc. So they have the same primary structure. But as always, we must consider structure in 3-dimensional space for a real picture of the molecule. While the linear structure is the same, the 3-d structure for each molecule must surely be different in solution, no? After all, thermal motion will be buffeting this rope of strung-together amino acids all about, so that each molecule will be expected to take on a random configuration, no? Look at this scale model of a POLYPEPTIDE OF 500 amino acids, a CLOTHES LINE. The dimensions are about right, but the side chains have been left out. I have put colored parts of the rope red to indicate polar side chains, the white parts being apolar or hydrophobic [board]. At 37 degrees, you might imagine this clothesline in a Jacuzzi, constantly taking on new shapes, with its hydrophilic side chains constantly forming new hydrogen bonds to water. This is the wrong picture. A more appropriate picture is a bundled up rope, folded into a compact structure that withstands this thermal motion at body temperatures [bundled rope].. red on outside ...white hydrophobic on inside (which makes sense based onthe weak bond behavior we discussed). OK, maybe this molecule could collapse on itself .. after all the hydrophobic side chains will tend to aggregate. But if we took another molecule, another linear chain, it would probably fold a different way, after all, 500 amino acids, there must be many many ways to get the hydrophobics inside. I could stuff the white parts of the rope together and put them on the inside in many different ways. But if we look for a second folded up example of this molecule, it looks like this [second rope bundle], exactly the same as the first (note loop count, etc.). Protein molecules exist as precisely defined 3-dimensional structures in solutions, each molecule like the next, superimposable. That is, a typical polypeptide chain, having some 10,000 atoms linked together, is folded up so that these 10,000 atoms all have the same relative position in each and every molecule you examine. This still amazes me. How could this be? Well, what is holding the molecule in this shape? The four weak bond types we discussed earlier, plus one new bond to be described in a few minutes. Let's consider how this folding looks in more detail: First, the flexible rope was not a good representation of even the backbone, because the peptide bond itself imposes some constraint on structure. The peptide bond itself has a property that influences all polypeptides regardless of the side chains. Because of the electronegativity difference between C and O or N, there is a partial separation of charge, one you could have predicted. What you may not have realized is that the partial + charge on the C and the partial - charge on the adjacent N, imparts a partial extra bond between those 2 atoms, and thus a partial double bond character to the C-N bond. This partial double bond is sufficient to stop free rotation about the C-N bond. Thus the backbone is not free to rotate around all connections, but rather each repeat contains 6 atoms confined to one plane: The polypeptide can be visualized as having a series of planes, each able to rotate about one another. So a chain would be a better representation than a rope. ::Secondary (2o)= alpha-helix, beta sheet:: This partial separation of charge also means that the O and the NH of the peptide bond can hydrogen bond... to water for example. Since the NH is a hydrogen donor and the O is a hydrogen acceptor for a hydrogen bond, we should consider the possibility that these groups can H-bond to each other. But H-bonds require a linear orientation of the 3 atoms involved, so certainly the NH of the very next residue cannot H-bond to a C=O preceding it. But what about the next residue? No, still can't make it. But by the fifth residue down you are able to line up an NH to the O: -C=O..H-N-. i.e., there are 3 complete residues 3 in between. So the C=O of #1 can H-bond to the HN of #5. But then also the C=O of #2 should be able to H-bond to the HN of #6, and so on. This twisting and H-bonding can hold the backbone in a HELIX, the so-called alpha-helix. The alpha-helix is an example of secondary structure, which is (my definition): structure produced by regular repeated interactions between atoms of the backbone. We might expect all the amino acid backbone atoms to be in an alpha-helical conformation, but we have left out consideration of the side chains, which can greatly influence the folding, as we will see in a minute. The alpha-helix is not the only form of secondary structure, there is another, the beta-pleated sheet. In this case we once again have the C=O and the NH of the backbone forming H-bonds to each other, but in this case two sections of the polypeptide are aligned side by side: Several sections of polypeptide can line up like this, to produce a sheet of strands. The chains are usually anti-parallel, but parallel alignments are also possible. See text for better pictures. B:49 & [Purves6ed3.5a]. Once again, side chain interactions play a major role in allowing or disallowing such secondary structures to form. But in fact, most proteins do have extensive regions folded into alpha-helices and beta-pleated sheets. Secondary structure consists mostly of these 2 structures. Tertiary structure means the overall 3-dimensional folding of a single polypeptide chain. We will continue with this most important level of structure next time. (C) Copyright 2001  Lawrence Chasin and Deborah Mowshowitz   Department of Biological Sciences   Columbia University   New York, NY Clickable pictures are from Purves, et. al., Life, 5th Edition, Sinauer-Freeman's Images of Life 5.0. A production of the Columbia Center for New Media Teaching and Learning