Amino Acids and R Group Biochemistry
The 20 amino acids found in proteins have a central carbon atom which is bonded to an R group. The R groups differ in size, shape, polarity and charge giving each amino acid distinct characteristics (Figure 2). These distinguishing features are what give proteins their unique properties.
Amino acids can be divided into three classes based on their R group pKa values. Amino acids that contain R groups that can donate hydrogen ions are called zwitterions.
Amino acids are the building blocks of proteins, which are the largest components (by mass) of living cells. Proteins are essential to all living systems, and it is widely believed that they played a critical role in the evolution of life on Earth.
Each amino acid has a central carbon atom that is bonded to an amino group (-NH2) and a carboxyl group (-COOH). Each amino acid also has a group of atoms on its side called the R group, which gives each amino acid unique characteristics.
The R groups can be divided into two categories, nonpolar and aromatic. The aliphatic amino acids (glycine, alanine, valine, leucine, isoleucine, and proline) have nonpolar hydrocarbon chains and are largely hydrophobic. The aromatic amino acids (phenylalanine, tyrosine, and tryptophan) have an aromatic functional group that makes them less hydrophobic but still relatively nonpolar. The amino acids can join to form short polymer chains called peptides or longer chains called proteins by condensation reactions.
Enzymes are proteins (though RNA molecules can also act as enzymes) that lower the activation energy required for chemical reactions to occur. They do this by changing shape and fitting tightly around the molecules they catalyze. Enzymes are reusable; they don’t degrade or disappear during the reaction.
All enzymes have a unique three-dimensional (3D) shape and a region, called an active site, that attracts other suitably shaped molecules to bind to them. This lock and key mechanism makes the process fast, efficient and highly precise.
Each enzyme has its own optimum temperature and pH range, above which they become inactive. If the temperature is too high, an enzyme can unfold and lose its shape, becoming denatured; if the pH is too low, an enzyme may no longer bind to a substrate and will become inactive.
The next level up from primary structure is secondary structure – the local folding of stretches of polypeptide into specific structural patterns (alpha helix, beta pleated sheet or random coil). Each of these structures holds its shape because of hydrogen bonds between the carbonyl oxygen of one amino acid and the amino hydrogen of another.
Secondary structure is characterized by a pattern of values for the phi and psi torsional angles in a particular region of the Ramachandran plot – this allows each secondary structure to be recognized. In addition, each protein has its characteristic circular dichroism spectral properties in the far UV region.
Computer programs can predict the likelihood that a sequence of amino acids will fold into a given secondary structure. For example, many programs can successfully predict the a-helix and b-sheet conformations of transmembrane stretches, although they are less successful with other secondary structures (e.g., helices or sheets without transmembrane stretches). These structural patterns are known as protein motifs.
The tertiary structure of a protein is the overall three-dimensional conformation that brings together different regions of secondary structures (alpha helices and b pleated sheets) to form a single globular protein. It may be stabilized by hydrogen bonds, salt bridges (ionic interactions between unlike electric charges on amino acid side chains), covalent disulfide bridges formed through oxidation of the sulfhydryl groups on cysteine residues, or other mechanisms.
Hydrophobic interactions between amino acid side chains also help determine tertiary structure. Most globular proteins have a core of nonpolar amino acids with a surface region rich in charged, hydrophilic residues. This allows for a high degree of structural stability and provides sites that can bind to specific molecules (biospecificity).
Most proteins are studied with X-ray crystallography, which gives very high resolution but does not provide any information about a protein’s dynamics. However, NMR is becoming a more common method of protein study because it can reveal time-dependent information about the conformational flexibility of a protein in solution.