Chapter 2 – Orientation for the Bio-Curious  29

or not, and whether or not the amino acid is hydrophobic. There are also other structural

features such as whether or not the side groups contain benzene-​type ring structures (termed

aromatic amino acids), or the side groups consist of chains of carbon atoms (aliphatic amino

acids), or they are cyclic (the amino acid proline).

Of the 23 natural amino acids, all but two of them are encoded in the cell’s DNA genetic

code, with the remaining rarer two amino acids called “selenocysteine” and “pyrrolysine”

being synthesized by other means. Clinicians and food scientists often make a distinction

between essential and nonessential amino acids, such that the former group cannot be

synthesized from scratch by a particular organism and so must be ingested in the diet.

Individual amino acids can link through a chemical reaction involving the loss of one

molecule of water via their amino and carboxyl group to form a covalent peptide bond. The

resulting peptide molecule obviously consists of two individual amino acid subunits, but still

has a free −NH2 and −COOH at either end and is therefore able to link at each with other

amino acids to form longer and longer peptides. When the number of amino acid subunits in

the peptide reaches a semiarbitrary 50, then the resultant polymer is termed a “polypeptide

or protein.” Natural proteins have as few as 50 amino acids (e.g., the protein hormone insulin

has 53), whereas the largest protein is found in muscle tissue and is called “titin,” possessing

30,000 amino acids depending upon its specific type or isomer. The median number of amino

acids per protein molecule, estimated from the known natural proteins, is around 350 for

human cells. The specific sequence of amino acids for a given protein is termed as “primary

structure.”

Since free rotation is permissible around each individual peptide bond, a variety of poten­

tial random coil 3D protein conformations are possible, even for the smallest proteins.

However, hydrogen bonding (or H-​bonding) often results in the primary structure adopting

specific favored generic conformations. Each peptide has two independent bond angles

called “phi” and “psi,” and each of these bond angles can be in one of approximately three

stable conformations based on empirical data from known peptide sequences and stable

phi and psi angle combinations, depicted in clusters of stability on a Ramachandran plot.

Hydrogen bonding results from an electron of a relatively electronegative atom, typically

either nitrogen −N or oxygen −O, being shared with a nearby hydrogen atom whose single

electron is already utilized in a bonding molecular orbital elsewhere. Thus, a bond can be

formed whose length is only roughly twice as large as the effective diameter of a hydrogen

atom (~0.2 nm), which, although not as strong a covalent bond, is still relatively stable over

the 20°C–​40°C temperatures of most living organisms.

As Figure 2.5b illustrates, two generic 3D motif conformations can result from the peri­

odic hydrogen bonding between different sections of the same protein primary structure,

one in which the primary structure of the two bound sections run in opposite directions,

which is called a “β-​strand,” and the other in which the primary structure of the two

bound sections run in the same direction, which results in a spiral-​type conformation

called an “α-​helix.” Each protein molecule can, in principle, be composed of a number

of intermixed random coil regions, α-​helices and β-​strands, and the latter motif, since

it results in a relatively planar conformation, can be manifest as several parallel strands

bound together to form a β-​sheet, though it is also possible for several β-​strands to bond

together in a curved conformation to form an enclosed β-​barrel that is found in several

proteins including, for example, fluorescent proteins, which will be discussed later (see

Chapter 3). This collection of random coil regions, α-​helices and β-​strands, is called the

protein’s “secondary structure.”

A further level of bonding can then occur between different regions of a protein’s sec­

ondary structure, primarily through longer-​range interactions of electronic orbitals between

exposed surface features of the protein, known as van der Waals interactions. In addition,

there may be other important forces that feature at this level of structural determination.

These include hydrophobic/​hydrophilic forces, resulting in the more hydrophobic amino

acids being typically buried in the core of a protein’s ultimate shape; salt bridges, which are

a type of ionic bond that can form between nearby electrostatically polar groups in a protein

of opposite charge (in proteins, these often occur between negatively charged, or anionic,

amino acids of aspartate or glutamate and positively charged, or cationic, amino acids of