8.0: Introduction

In which we consider the nature of proteins, how they are synthesized and assembled, how they get to where they need to go within the cell and within the organism, how they function, how their activities are regulated, and how mutations can influence their expression, stability, activity, and evolution.

We have mentioned proteins many times, since there are few biological processes that do not rely on them. Proteins act as structural elements, signals, regulators, and catalysts in a wide range of molecular machines. We have yet to say much about what they are, how they are made, and how they come to do what they do. The first scientific characterization of what are now known as proteins was published by the Dutch chemist, Gerardus Mulder (1802–1880).^[316] After an analysis of a number of different substances, he proposed that all proteins contain a common chemical core, with the molecular formula C₄₀₀H₆₂₀N₁₀₀O₁₂₀P₁S₁, and that the differences between proteins were primarily in the numbers of phosphate (P) and sulfur (S) atoms they contain. The name “protein”, from the Greek word πρώτα (“prota”), meaning “primary”, was suggested by Jons Berzelius (1779–1848) based on the presumed importance of these compounds in biological systems.^[317] As you can see, Mulder’s molecular formula is not very informative, it suggests that all proteins are fundamentally similar, which while true is confusing since they have so many different roles. Subsequent studies revealed that proteins could be dissolved in water or dilute salt solutions but formed insoluble aggregates when the solution was heated. As we will see this heat-induced aggregation was due to changes in protein structure. Mulder was able to break down proteins into amino acids through an acid hydrolysis reaction. Amino acids get their name from the fact that they contain both an amino (–NH₂) and a carboxylic acid (–COOH) group. While there many thousands of possible amino acids, only twenty (or rather twenty two, as we will see) were identified in hydrolyzed samples of proteins. Since their original characterization as a general class of compounds, we now understand that while proteins share a common basic polymer structure, they are remarkably diverse. Proteins are involved in roles from the mechanical strengthening of skin to the movement and control of the body, the building of shells and claws, the regulation of genes, the transport of oxygen, the capture of energy, the release of light, and the catalysis and regulation of essentially all of the chemical reactions that occur within cells and organisms.

With the introduction of various methods, it was discovered that different proteins were composed of distinct sets of polymers. Each polymer was an unbranched chain of amino acids, linked by -C-N- peptide bonds, with a specific amino acid sequence. These polymers are known generically as polypeptides. Specific proteins are composed of specific sets of polypeptides and each distinct polypeptide is encoded by a distinct gene. In addition many proteins contain other molecular components, known as co-factors or prosthetic groups. These co-factors can range from metal ions to various small molecules. A protein is a fully assembled and functional entity.

As you may recall a carbon atom (C) typically takes part in four covalent bonds. We can think of an amino acid as a modified form of methane (CH₄), with the C referred to as the alpha carbon (C_α). In an amino acid there is an H, an amino group (-NH₂), a carboxylic acid group (-COOH), and a variable (R) group attached to the alpha C_α atom. Different amino acids differ from one another by their R-groups, often referred to as "side-chains". Some R-groups are larger, some are small, some are hydrophobic, some are hydrophilic and some hydrophilic R-groups contain weak acidic or basic groups. The extent to which these weak acidic or basic groups are positively or negatively charged changes in response to environmental pH. Changes in side-group charge can (as we will see) influence the structure of the polypeptide/protein. The different R-groups provide proteins with a broad range of chemical properties that are further extended by the presence of co-factors.^[318]

The four groups attached to the α-carbon in an amino acid are arranged at the vertices of a tetrahedron (→). If four different groups attached to the α-carbon, as they are in all biological amino acids except glycine, the resulting amino acid can exist in two forms, known as L- and D- form enantiomeric stereoisomers. Enantiomers are mirror images of one another. Only L-type amino acids are found in proteins, even though there is no obvious chemical reason for why proteins could not have also been made using both types or only D-amino acids.^[319] It appears that the universal use of L-type amino acids in biological polypeptides found is an example of the evolutionary relatedness, a homologous trait presumably established in LUCA. Even though there are hundreds of amino acids known, only 22, the 20 common amino acids and selenocysteine and pyrrolysine, are found in proteins and presumably were present in LUCA.

As we noted for nucleic acids, a polymer is a chain of subunits. In a polypeptide, amino acid are linked together by peptide bonds. Under the conditions that exist inside the cell, this is a thermodynamically unfavorable dehydration reaction, and so polypeptide synthesis must be coupled to a thermodynamically favorable reaction, a nucleotide triphosphate hydrolysis reaction. A molecule formed from two amino acids, joined together by a peptide bond, is known as a dipeptide. A dipeptide has an N-terminal (amino) and a C-terminal (carboxylic acid) end. To generate a polypeptide, new amino acids are added sequentially to the polymer's C-terminal end – a reaction analogous to the synthesis of a polynucleotide, in which monomers are added only to one end of the growing polymer. A peptide bond forms between the amino group of the added amino acid and the carboxylic acid group of the polymer. The formation of a peptide bond is associated with the release of a water molecule (↓). The addition of an amino acid to the C-terminus of a polypeptide generates a new C-terminal carboxylic acid group. While some amino acids have a carboxylic acid group as part of their R-group, new amino acids are not added there. The result is that polypeptides are synthesized as unbranched, linear polymers. The process of amino acid addition can continue, theoretically without limit. Biological polypeptides range from the short (5-10) to the very long – hundreds to thousands of amino acids in length.^[320] The Titin polypeptide found in muscle cells can be more than 30,000 amino acids in length.^[321] Because there is no theoretical constraint on which amino acid occurs at a particular position within a polypeptide, there is a enormous number of possible polypeptides that can exist. In the case of a 100 amino acid long polypeptide, there are more than 20¹⁰⁰ possible different polypeptides that could, in theory, be formed.

---