4.1. Background and Terminology: Amino Acids
Amino acids are a class of bioorganic compounds that contain an amine group and a carboxylic acid. They are produced and/or used by every known organism and serve a variety of functions. To-date several hundred naturally occurring amino acids have been found, and several thousand “unnatural” (synthetic) amino acids have been synthesized.
Most organisms have a few dozen genes coding for only a handful of amino acids. Any amino acids the organism needs in order to live but does not synthesize for itself are referred to as “essential” amino acids. These are typically acquired by an organism through its diet.
This text will focus on the most common types of amino acids. Later, emphasis will be on their most recognizable application as parts of enzymatic proteins (see Chapter 6). However, it is important to recognize that proteins are used by cells for a much wider array of functions than enzymes alone AND that amino acids are used in many biological systems/cycles beyond only proteins.
4.1.1. Classification: Alpha- (α-), Beta- (β-), Gamma- (γ-) Amino Acids
Amino acids are broadly subdivided into categories based on where the amine group is relative to the carboxylic acid (Figure 4.1). The naming convention uses the same Greek letters as before (see Section 2.2) to describe the position of the amine with respect to the carbonyl of the carboxylic acid.
Figure 4.1 – Generalized Examples of α-, β-, and γ-Amino Acids.
By far the most common class of amino acids are the α-amino acids (alpha-amino acids). β-Amino acids (beta-amino acids) also occur in nature but are less common. With one notable exception, γ-amino acids (gamma-amino acids) and further (e.g. δ-amino acids, etc.) are rare in nature.
4.1.2. Trivial Names, Three-Letter Codes, and One-Letter Codes
Recall that trivial names are a form of slang, a specific word that refers to a compound that does not fall under the standard systematic IUPAC nomenclature rules but is so commonly used that they are recognized as alternatives. While the formal rules may be used to name these compounds, it is more common (and usually easier) to use the trivial name.
Trivial names for compounds are typically used when the compound is ‘common’, especially with bioorganic molecules. Most amino acids were identified and characterized before the IUPAC system was developed. As a result, the use of trivial names for them remains commonplace. For example, the compound 2-amino-3-methylbutanoic acid is more commonly referred to as valine (Figure 4.2).
Figure 4.2 – Trivial Name, Three-Letter Code, and One-Letter Code for 2-Amino-3-methylbutanoic acid.
Because amino acids are so commonly encountered in biological systems two other shorthand notations were developed for them. These are a three-letter and one-letter abbreviation. For valine these are simply abbreviations of the actual name but that is coincidental. Many other amino acids’ three- or one-letter codes are not abbreviations of their trivial names and are less intuitive.
4.1.3. The Twenty Common Amino Acids
Twenty amino acids are very common in organisms and merit special attention (Figure 4.3). Each has its own trivial name, three-letter code, and one-letter code.
Figure 4.3 – Trivial Name, Three-Letter Code, One-Letter Code, Structure, and pKa Values for The Twenty Common Amino Acids.
4.1.4. Amino Acids as Zwitterions
All amino acids contain at least one acid (the carboxylic acid) and at least one base (the amine). As a result, they do not normally exist as the typical neutral structures (viz. the structures in Figure 4.3). For example, analysis of a solution of glycine would show that the molecule exists as a charged species (Scheme 4.1).
Scheme 4.1 – Equilibrium Between the “Parent” Neutral Form of Glycine and its Zwitterionic Form.
A zwitterion is a molecule that contains an equal number of cationic and anionic functional groups. The overall charge of a zwitterion is zero, but there are cations and anions within the molecule.
In general, amino acids exist as their zwitterionic forms (ignoring the side chains) under physiological conditions. However, the actual protonation state (anionic, neutral, cationic) of each of the functional groups in an amino acid will depend on the specific pH of the solution (see Section 4.2.2).
4.1.5. Stereochemistry: D/L Notation and Fischer Projections
With the exception of glycine all of the common amino acids have at least one stereocentre. It is possible to describe the stereochemistry using the Cahn-Ingold-Prelog (CIP) system of R/S absolute configurations. However, for historical reasons the overwhelming majority of chemists and biochemists instead use a different notation system.
Amino acids were characterized before the CIP system was implemented. Instead of assigning absolute configuration(s), a relative description of the stereocentres is used. This relates the stereochemistry to an arbitrarily chosen standard (2,3-dihydroxypropanal [glyceraldehyde]) when drawn using a classical style of depicting molecules.
Fischer projections are a style of drawing for chemical structures developed before the widespread adoption of line-angle (skeletal) structures with hashed/wedged bonds. In a Fischer projection the molecule is drawn similar to a Lewis structure, flat and typically with 90° angles (Figure 4.4). However, the perspective is chosen to indicate stereochemistry by ‘projecting’ the three-dimensional structure down onto a two-dimensional image.
Figure 4.4 – Generalized Concept of a Fischer Projection.
This can be done for molecules such as (R)-2,3-dihydroxypropanal (R-glyceraldehyde) and (S)-serine (Figure 4.5). Note that part of drawing a Fischer projection involves reorienting the molecule such that the atom that would be numbered 1 in nomenclature is positioned at the top of the drawing (see Section 4.1.5.1).
Figure 4.5 – Generating Fischer Projections for (R)-2,3-Dihydroxypropanal (R-Glyceraldehyde) and (S)-Serine.
The Fischer projections of the enantiomers of glyceraldehyde (2,3-dihydroxypropanal) were arbitrarily chosen as the reference standard for the system (Figure 4.6). One has the alcohol of the stereocentre pointing “to the right” and is called D-glyceraldehyde (from the Latin “Dexter”, meaning “right”). The other has the alcohol of the stereocentre pointing “to the left” and is called L-glyceraldehyde (from the Latin “Laevus”, meaning “left”). The exact same D/L labels can be applied in the exact same way to other molecules, particularly amino acids (and carbohydrates, see Chapter 5).
Figure 4.6 – Origin of the D/L Notation for Relative Configuration to Glyceraldehyde (2,3-Dihydroxypropanal).
For those familiar with d/l notation from organic chemistry (optical rotation), it is important remember that these two systems are not related in any way.
The common amino acids are all L-amino acids. Although various naturally occurring D-amino acids have been characterized, the overwhelming majority of amino acids in nature are L-amino acids.
There is occasionally confusion about the relationship between this system and the CIP descriptors. The D/L notation is a relative descriptor that describes enantiomers by perspective. The D/L system does not directly translate to or from absolute configuration (Figure 4.7). Any apparent relationship is coincidental.
Figure 4.7 – Absolute Configuration and D/L Assignment for (S)-Serine and (R)-Cysteine.
4.1.5.1. How to Convert a Line-Angle Structure to a Fischer Projection for Amino Acids
Fischer projections are a classical style of drawing. While it is possible to generate Fischer projections for other types of molecules their use is only recommended for simple biomolecules, specifically amino acids and carbohydrates.
The process for converting a line-angle structure to a Fischer projection is straightforward but can be challenging when many stereocentres are present. Use of a molecular model is not required but may be helpful in some instances. There are two general approaches.
In the traditional approach:
1. Orient the line-angle structure. Identify and number the main carbon chain following the rules of the IUPAC naming process. Place all of the main-chain carbons in a row such that all other substituents face towards the “viewer’s perspective” for the Fischer projection. This includes hydrogens. You may change the conformation if needed. The resulting conformation may appear unusual but is required for the Fischer structure. Drawing in implied hydrogens is optional but is particularly helpful for introductory students.
2. Draw the Fischer projection backbone without adding any groups. Each numbered carbon is added as a point in the chain. You may choose to represent double bonds (non-tetrahedral geometry) now or add them in the next step. It is often helpful to number the carbons to keep track of what groups will go where. Orient the drawing so that position 1 is at the “top”.
3. Add substituents for each carbon. Depictions of non-tetrahedral geometries can be modified or used as-is. It may be helpful to visualize the hashed/wedged structure and/or imagine the hypothetical flattening of the molecule. It may be helpful to work systematically (e.g. add all groups for carbon 1, then carbon 2, etc.).
In the alternate approach:
1. Identify and number the main carbon chain following the rules of the IUPAC naming process. Assign R/S absolute configurations to all stereocentres.
2. Draw the Fischer projection backbone without adding any groups. Each numbered carbon is added as a point in the chain. You may choose to represent double bonds (non-tetrahedral geometry) now or add them in the next step. It is often helpful to number the carbons to keep track of what groups will go where. Orient the drawing so that position 1 is at the “top”.
3. Add substituents for each carbon. Depictions of non-tetrahedral geometries can be modified or used as-is. Add substituents to stereocentres arbitrarily and then check if the absolute configuration is correct. Re-draw if needed.
The alternative approach may or may not be faster depending on the number of stereocentres and the speed with which they can be assigned absolute configurations.
4.1.5.2. How to Assign D/L Notation to Amino Acids
Assignment of D/L to an amino acid is generally straightforward provided the Fischer projection is correct and in the proper orientation. Simply look for which side, left or right, the amine of the amino acid stereocentre (Position 2) in the molecule is.
1. Convert the line-angle structure to a Fischer projection (see Section 4.1.5.1). If a Fischer projection is provided ensure it is in the correct orientation (the numbered chain proceeds down). Rotating the Fischer projection clockwise or counterclockwise is acceptable. Flipping a Fischer projection is not acceptable and will produce the incorrect assignment.
2. Determine the left/right directionality of the highest priority group (the amine group) at amino acid stereocentre (Position 2) in the chain. If the group points to the left, it is the L-enantiomer of that compound. If the group points to the right, it is the D-enantiomer of that compound.
There are two potential issues.
If a Fischer projection is provided it may be manipulated by rotating clockwise or counterclockwise but not flipped. Flipping the image will generate the enantiomer and lead to an incorrect assignment.
The D/L system only classes which enantiomer is being described. For many amino acids this is straightforward. However, when there are multiple stereogenic centres present (some amino acids; almost all carbohydrates) this can be problematic.
