THE STRUCTURE AND PROPERTY OF AMINO ACIDS

Proteins are polymers of the bifunctional monomer, amino acids. The twenty common naturally-occurring amino acids each contain an a-carbon, an a-amino group, an a-carboxylic acid group, and an a-side chain or side group. These side chains (or R groups) may be either nonpolar, polar and uncharged, or charged, depending on the pH and pKa of the ionizable group. Two other amino acids occasionally appear in proteins. One is selenocysteine, which is found in Arachea, eubacteria, and animals. Another just recently found is pyrrolysine, found in Arachea. Shultz et al. have gone one step farther. They have engineered bacterial to incorporate two new amino acids, O-methyl-tyrosine and p-aminophenylalanine. More recently, they (Chin et al.) have engineered the yeast strain Saccharomyces cerevisiae to incorporate five new unnatural amino acid (using the TAG nonsense codon and new, modified tRNA and tRNA synthetases) with keto groups that allow chemical modifications to the protein. We will concentrate only the 20 abundant, naturally-occurring amino acids.
Amino acids form polymers through a nucleophilic attack by the amino group of an amino acid at the electrophilic carbonyl carbon of the carboxyl group of another amino acid. The carboxyl group of the amino acid must first be activated to provide a better leaving group than OH^-. (We will discuss this activation by ATP latter in the course.) The resulting link between the amino acids is an amide link which biochemists call a peptide bond. In this reaction, water is released. In a reverse reaction, the peptide bond can be cleaved by water (hydrolysis).
When two amino acids link together to form an amide link, the resulting structure is called a dipeptide. LIkewise, we can have tripeptides, tetrapeptides, and other polypeptides. At some point, when the structure is long enough, it is called a protein. There are many different ways to represent the structure of a polypeptide or protein. each showing differing amounts of information. .

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Proteins are polymers of twenty naturally occurring amino acids. In contrast, nucleic acids are polymers of just 4 different monomeric nucleotides. Both the sequence of a protein and it's total length differentiate one protein from another. Just for an octapeptide, there are over 25 billion different possible arrangement of amino acids. Compare this to just 65536 different oligonucleotides of 8 monomeric units (8mer). Hence the diversity of possible proteins is enormous.
Please consult the great Chime Site on the web dealing with amino acids. Please learn the 3 letter code for the amino acids.
The amino acids are all chiral, with the exception of glycine, whose side chain is H. As with lipids, biochemists use the L and D nomenclature. All naturally occuring proteins from all living organisms consist of L amino acids. The absolute stereochemistry is related to L-glyceraldehyde, as was the case for triacylglycerides and phospholipids. Most naturally occurring chiral amino acids are S, with the exception of cysteine. As the diagram below shows, the absolute configuration of the amino acids can be shown with the H pointed to the rear, the COOH groups pointing out to the left, the R group to the right, and the NH3 group upwards. You can remember this with the anagram CORN.
Why do Biochemistry still use D and L for sugars and amino acids? This explanation (taken from the link below) seems reasonable.
"In addition, however, chemists often need to define a configuration unambiguously in the absence of any reference compound, and for this purpose the alternative (R,S) system is ideal, as it uses priority rules to specify configurations. These rules sometimes lead to absurd results when they are applied to biochemical molecules. For example, as we have seen, all of the common amino acids are L, because they all have exactly the same structure, including the position of the R group if we just write the R group as R. However, they do not all have the same configuration in the (R,S) system: L-cysteine is also (R)-cysteine, but all the other L-amino acids are (S), but this just reflects the human decision to give a sulphur atom higher priority than a carbon atom, and does not reflect a real difference in configuration. Worse problems can sometimes arise in substitution reactions: sometimes inversion of configuration can result in no change in the (R) or (S) prefix; and sometimes retention of configuration can result in a change of prefix.
It follows that it is not just conservatism or failure to understand the (R,S) system that causes biochemists to continue with D and L: it is just that the DL system fulfils their needs much better. As mentioned, chemists also use D and L when they are appropriate to their needs. The explanation given above of why the (R,S) system is little used in biochemistry is thus almost the exact opposite of reality. This system is actually the only practical way of unambiguously representing the stereochemistry of complicated molecules with several asymmetric centres, but it is inconvenient with regular series of molecules like amino acids and simple sugars. "
If I told you to draw the correct stereochemistry of a molecule with 1 chiral C (S isomer for example) and I gave you the substituents, you could do so easily following the R, S priority rules you learned in organic. However, how would you draw the correct isomer for the L isomer of the amino acid alanine? You couldn't do it without prior knowledge of the absolute configuration of the related molecule, L glyceraldehyde, or unless you remembered the anagram CORN. This disadvantage, however, is more than made up for by the fact that different L amino acids with the same absolute stereochemistry, might be labeled R or S , which makes this nomenclature unappealing to biochemists.
Monomeric amino acids have an alpha amino group and a carboxyl group, both of which may be protonated or deprotonated, and a R group, some of which may be protonated or deprotonated. When protonated, the amino group has a +1 charge, and the carboxyl group a 0 charge. When deprotonated the amino group has no charge, while the carboxyl group has a -1 charge. The R groups which can be protonated/deprotonated include Lys, Arg and His, which have a + 1 charge when protonated, and Glu and Asp (carboxylic acids), Tyr and Ser (alcohols) and Cys (thiol), which have 0 charge when protonated. Of course, when the amino acids are linked by peptide bonds (amide link), the alpha N and the carboxyl C are in an amide link, and are not charged. However, the amino group of the N -terminal amino acid and the carboxyl group of the C-terminal amino acid of a protein may be charged. The Henderson Hasselbach equation gives us a way to determine the charge state of any ionizable group knowing the pKa of the group. Write each functional group capable of being deprotonated as an acid, HA, and the deprotonated form as A. The charge of HA and A will be determined by the functional group. The Ka for the reaction is:
This is the (in)famous Henderson-Hasselbach (HH) equation.
The properties of a protein will be determined partly by whether the side chain functional groups, the N terminal, and the C terminal are charged or not. The HH equation tells us that this will depend on the pH and the pKa of the functional group.

• If the pH is 2 units below the pKa, the HH equation becomes, -2 = log A/HA, or .01 = A/HA. This means that the functional group will be about 99% protonated (with either 0 or +1 charge, depending of the functional group).
  
• If the pH is 2 units above the pKa, the HH equation becomes 2 = log A/HA, or 100 = A/HA. Therefore the functional group will be 99% deprotonated.
  
• If the pH = pka, the HH equation becomes 0 = log A/HA, or 1 = A/HA. Therefore the functional group will be 50% deprotonated
  

From these simple examples, we have derived the +2 rule. This rule is used to quickly determine protonation, and hence charge state, and is extremely important to know (and easy to derive). Titration curves for Gly (no ionizable) side chain, Glu (carboxlic acid side chain) and Lys (amine side chain) are shown below. You should be able to associate various sections of these curves with titration of specific ionizable groups in the amino acids.

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The Henderson-Hasselbach equation is also useful in calculating the composition of buffer solutions. Remember that buffers are composed of a weak acid and its conjugate base. Consider the equilibrium for a weak acid, like acetic acid, and its conjugate base, acetate:
If the buffer solution contains equal concentrations of acetic acid and acetate, the pH of the solution is:
A look at the titration curve for the carboxyl group of Gly (see above) shows that when the pH = pKa, the slope of the curve (i.e. the change in pH with addition of base or acid) is at a minimum. As a general rule of thumb, buffer solution can be made for a weak acid/base in the range of +/- 1 pH unit from the pKa of the weak acids. At the pH -= pKa, the buffer solution best resists addition of either acid and base, and hence has its greatest buffering ability. The weak acid can react with added strong base to form the weak conjugate base, and the conjugate base can react with added strong acid to form the weak acid (as shown below) so pH changes on addition of strong acid and base are minimized.

• addition of strong base produces weak conjugate base: CH₃CO₂H + OH^- --> CH₃CO₂^- + H₂O
  
• addition of strong acid produces weak acid: H₃O⁺ + CH₃CO₂^---> CH₃CO₂H + H₂O
  

There are two simples ways to make a buffered solution. Consider an acetic acid/acetate buffer solution.

• make equal molar solution of acetic acid and sodium acetate, and mix them, monitoring pH with a pH meter, until the desired pH is reached (+/- 1 unit from the pKa).
  
• take a solution of acetic acid and add NaOH at substoichiometric amounts until the desired pH is reached (+/- 1 unit from the pKa). In this method you are forming the conjugate base, acetate, on addition of the weak base: