Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:

Amino Acids 1

The amino acids are the building blocks for proteins - nearly all proteins studied are made from the twenty "standard" amino acids we will look at now. Other amino acids are also found in proteins, but most arise by modification from the twenty after they have been incorporated in the protein. All of the standard amino acids are alpha amino acids (except for proline, an imino acid). That is they have an amino group alpha to the carboxyl group (they are 2-amino acids). Thus all 20 of these amino acids share the basic structure below: [Figure 3.1]

Fischer and wedge structural diagrams of amino acids

At neutral pH (pH =7) both the acid and amine groups will be ionized to give the so-called zwitterion form. [Figure 3.1] Note that there is no pH at which the amino acid structure will have no ionized groups! Note the titration behavior of amino acids, and be able to draw the structure for an amino acid at each point in the curve. [Fig. 3.6]

With four different substituents on the central (alpha) carbon all of the amino acids except one, where R = H, will be chiral. All chiral protein amino acids are "L" as shown in the figure. (Recall the Fischer structure convention for drawing chiral molecules.) Most, but not all of the 20 amino acids are also "S." But since not all amino acids are the same configuration in the RS system, but still have the same relationships of the R- group, carboxyl group and amino group the DL system is used more frequently by biochemists.

Lets now look at the amino acid side chains as shown in the side chain handout in your packet [Models] Can group the side chain

3-D animated image showing aa isomers

D and L alanine space filling models

via Wikimedia Commons

s as nonpolar (hydrophobic or water hating) and polar (hydrophilic or water loving).

Hydrophobicity is a measure of relative solubilities of substances in water. Turns out to be the quantitatively most important weak force in biological systems. Often see term "hydrophobic bond" but really isn't a bond since force arises by exclusion from water - thus no attraction, as seen in bonds, takes place. Hydrophobic force has two components: 1) enthalpic (heat energy) due to the breaking of hydrogen bonds and dipole-dipole bonds etc. when nonpolar substances are inserted into water and disrupt its structure; 2) entropy due to the relative loss of mobility of water molecules forced into "cage" structures surrounding nonpolar molecules or groups inserted into water, as seen in our last lecture.

Nonpolar side chains: these will tend to be found on interior of protein, except that glycine and alanine are so small that they can fit into interior or on surface. Compare these amino acids: note how these side chains build in size from gly (glycine), ala (alanine), val (valine), to leu (leucine), then have two which have about same size but different shapes: ile (isoleucine) and met (methionine - met has a nearly identical shape to the linear analogue of leucine, norleucine). Met of course also has possibility of liganding metal ions through sulfur. Next have phe (phenylalanine) and trp (tryptophan). These are aromatic, which enables stacking interactions with other aromatic groups as well as being very hydrophobic. Trp also has an amine group which needs to form a hydrogen bond. Thus trp is often found with the -NH at the surface but with the remainder in a hydrophobic cleft. If trp is interior it will generally hydrogen bond with another functional group. Finally pro (proline) is also hydrophobic, but its main characteristic of interest is its tendency to put a near right angle in the direction of a peptide chain. It thus generally disrupts particular structural elements of proteins. As such it is often near the surface, since it forces structural elements to turn at the surface (defining the surface).*

*Just for your interest: You can briefly look at hydrophobicities of the nonpolar amino acids quantitatively by comparing their solubilities to glycine in a relatively "nonpolar solvent" such as ethanol or dioxane [values from Alan G. Marshall Biophysical Chemistry, Wiley (1978) pp 64-5]. The values in parenthesis are in cal/mole @ 25°C: Ala (-500), His (-500, uncharged), Met (-1300), Val (-1500), Leu (-1800), Tyr (-2300), Phe (-2500), Trp (-3400), and for comparison, Ser (+300). Plotting accessible surface area vs. hydrophobicity one finds that the hydrophobicities of the amino acid residues in proteins turn out to be about -2500 cal/mole/nm² of accessible surface.)

Uncharged Polar side chains: These side chains will generally occur on the surfaces of proteins because of their polarity and hydrogen-bonding characteristics. If they occur on the interior they must generally H-bond with other interior functional groups. The definition of "uncharged" is based on a pH of 7. There are four side-chains, ser (serine), thr (threonine), asn (asparagine), and gln (glutamine), which are neutral under all conditions of pH. (Note that asn and gln are simply the amide forms of asp and glu. It is thus often difficult to determine whether a given residue was a asp or asn etc. in chemical analysis of peptides, since the treatment breaking peptide bonds also will generally break the amide bonds of asn and gln.) Tyr (tyrosine) and cys (cysteine) are uncharged at pH 7, but both ionize at higher pH's (respective pK_a's = 9.5-10.9 & 8.3-8.6). Finally, his (histidine - imidazolium grp), has a pK_a of 6.4-7.0 and is thus partially charged (positive) at pH 7, and will be charged at low pH's.
Charged Polar side chains: These four side-chains will have very strong tendencies to be on the surface - it costs a great deal of energy to bury an ionic charge in a non-polar interior! It turns out the the sum of the acidic groups in a protein, asp (aspartate) + glu (glutamate), is usually equal to the sum of the sum of the basic groups, lys (lysine - amino grp) + arg (arginine - guanidinium grp). This is expected since we want a net neutral particle at its operating pH (usually around pH 7)

Amino Acid Chemistry

All aa's share two chemical functional groups, the carboxyl group and the amino group. Thus they will share the chemical reactions of these groups familiar from organic chemistry. Many of these reactions are exploited in the laboratory manipulation of amino acids, peptides, and proteins. Note that these reactions are also common to the side chains of asp, glu (-COOH), and lys (-NH₂). Another side-chain with important chemistry is cys (-SH). Biologically the most important reactions are those required for protein formation, particularly the peptide bond.

pK_a's:

Note that the pK_a's for carboxylic acids tend to have values of about 5, while the pK_a of the amino acid -COOH is around 2. What's going on? The shift in pK_a can be assigned to the nearby protonated amine. Recall that 'naked' charges are very unstable, while nearby counter-charges stabilize them. Also, from organic chemistry you may recall that negative charges can be stabilized by inductive effects of nearby electron withdrawing groups, such as a protonated, positively charged, nitrogen. Because of the extra intervening carbons the side chain -COOH's of asp and glu are not similarly stabilized, and thus have pK_a values closer to the expected 5. Of course we would also expect analogous effects of the negative charge on the carboxyl group on the protonated (charged) amine.