Proteins and Amino Acids: Videos & Practice Problems

Life on Earth is fundamentally built upon four major macromolecules: sugars, lipids, nucleic acids, and proteins. Among these, proteins play a crucial role, forming the structural and functional basis of nearly every component in the human body. To understand proteins, we first need to define them as polypeptides that serve a biological function. This distinction is essential; a polypeptide that does not contribute to any biological process is not classified as a protein.

To delve deeper, we must understand what a polypeptide is, starting with the concept of a peptide. A peptide is a polymer made up of monomeric units known as alpha amino acids. Each alpha amino acid consists of an amino group (a nitrogen atom bonded to hydrogen atoms), a carboxylic acid group, and a unique side chain referred to as the R group. The term "alpha" indicates the position of the amino group relative to the carbonyl group (C=O) in the molecule, specifically at the alpha carbon, which is adjacent to the carbonyl.

The 20 common alpha amino acids differ only in their R groups, which are carbon structures that define their unique properties. When amino acids link together, they form peptide bonds through a dehydration reaction, where a molecule of water is released. This bond connects the carbon of one amino acid to the nitrogen of another, creating a chain known as a peptide. The sequence of amino acids in this chain is referred to as the primary structure of a protein.

As amino acids join to form peptides, each dehydrated amino acid is termed a residue. For example, in a tripeptide composed of three amino acids, each amino acid that has lost water is called a residue. The nomenclature for peptides includes dipeptides (two amino acids), tripeptides (three amino acids), and oligopeptides (4 to 10 amino acids). A polypeptide is defined as a chain of 11 to 50 amino acids. While some sources may classify chains longer than 50 amino acids as proteins, the definitions can overlap, and the distinction is not always clear-cut.

Understanding these foundational concepts about amino acids, peptides, and polypeptides sets the stage for exploring the standard amino acids and their roles in protein structure and function in subsequent discussions.

Scientists have identified over 700 different molecules classified as amino acids in nature, but for practical purposes, we focus on the 20 most common amino acids that are integral to eukaryotic proteins, such as those found in multicellular organisms like humans. These amino acids are characterized primarily by their alpha amino acid structure and their chirality, specifically having an L configuration, which corresponds to an S configuration at the chiral center according to organic chemistry nomenclature.

To distinguish between standard and nonstandard amino acids, one can observe the presence of an amine group and a carboxylic acid group attached to the alpha carbon. Nonstandard amino acids, such as GABA (gamma-aminobutyric acid), may have their amine group attached to a different carbon, such as the gamma carbon, thus disqualifying them from being part of the standard 20 amino acids.

When determining the chirality of an amino acid, the R and S nomenclature is applied. The chiral center is identified, and the groups attached to it are prioritized based on atomic weight. The configuration is determined by tracing the path from the highest priority group to the lowest, while ensuring that the lowest priority group is positioned at the back. If the path is clockwise, it is classified as R; if counterclockwise, it is S. In biological contexts, S configuration is referred to as L amino acids, while R configuration is termed D amino acids.

It is essential to note that all standard amino acids exhibit the R group oriented towards the back, which can serve as a quick reference for identifying their configuration. Understanding these characteristics and the distinction between standard and nonstandard amino acids is crucial for further studies in biochemistry and molecular biology.