Amino Acids and Peptides

peptides play an important role in physiological processes such as blood pressure decreasing, anti-microbial properties and improving the immune system. They can also be derived from food and are listed in the Canadian Natural Health Products (NHP) database as “medicinal” ingredients.

The sequence of amino acid R-groups in a polypeptide chain is its primary structure. Bond lengths and angles are shown in the diagram below.

Amino Acids

Amino acids are organic starting molecules that are the building blocks of proteins and peptides. They are used in the body for vital functions, such as building cells and synthesis of hormones and neurotransmitters (brain chemicals). Amino acids are found naturally in foods, such as meat, fish and eggs, and also are available as dietary supplements. There are 20 amino acids that are considered essential in humans, meaning that they cannot be produced by the body and must be supplied from food or supplemental sources.

Peptide bonds are the vital links that connect amino acids to form polypeptide chains, which fold into functional proteins. These bonds are formed through a nucleophilic addition-elimination reaction and are characterized by their rigidity and planarity, thanks to resonance delocalization. They can be broken by hydrolysis, a process that can be nonspecific with strong acids or specific with proteolytic enzymes.

Unlike most other proteins, which contain carboxyl groups on their ends, peptides do not have carboxyl groups. Instead, they have an amide bond between the amino acid and the carbonyl group of another amino acid. This amide bond is formed by the covalent bonding of the peptide nitrogen and carboxyl oxygen atoms, which are placed in close proximity to each other.

Most amino acids have polar neutral side chains. However, there are two amino acids that are considered special: cysteine and glycine. These two amino acids have a thiol -SH group that can be oxidized to a disulfide bond, which is the other covalent bond in proteins besides the amide bond.

Peptides can be cyclized to create large-ring structures, such as cyclic peptides, which can be used for drug discovery. To accomplish this, the protected amino acid is reacted with an aryl iodide in solution. The resulting cyclic peptide is then dissolved in water and cleaved with a proteolytic enzyme to reveal the desired amino acid. This approach is particularly useful for generating peptides with complex side chains. For example, a cyclic peptide containing the proteinogenic amino acid meta-iodotyrosine was successfully reacted with 5-mol % Pd(OAc)2, AgBF4, and 2-nitrobenzoic acid in N,N-dimethylacetamide (0.03 M) to produce the corresponding peptide (58% yield).

Polypeptide Chains

A polypeptide chain is a sequence of amino acid residues joined together by peptide bonds. Polypeptide chains are formed through condensation reactions during protein synthesis, the process by which amino acids are coded for in the cell. Polypeptide chains are the primary structure of proteins, and they form the basis for describing protein conformation. The polypeptide chain is typically described as being oriented with its N- or amino terminus to the left and its C- or carboxyl terminus to the right. The N-terminus of a polypeptide is often referred to as the N-end, and the C-terminus as the C-end. Polypeptide chains have many properties that distinguish them from simple monomers, such as the presence of a peptide bond and an R-group.

The peptide bond is a covalent bond that connects the carbonyl oxygen of one amino acid to the amide hydrogen of another. Unlike the free rotation of single bonds in organic molecules, peptide bond rotation is constrained, and the peptide bond is nearly always found in the trans configuration. A rare exception is found when proline is present in a protein; this amino acid lacks a carbonyl oxygen and thus can form a cis bond only at higher concentrations.

Most of the R-groups on a typical amino acid are hydrophobic, and the peptide chain is driven by the attraction of its hydrophobic elements for water. This forces the polypeptide chain into a compact, dynamic, and functionally native state.

Once the polypeptide is in its native state, it can interact with other proteins through sets of weak noncovalent bonds. Depending on the pH of the solution and the nature of the binding site, the interaction can change the protein’s structure and activity.

The binding of two identical polypeptide chains at a specific site can also create a symmetrical complex of protein subunits, known as a dimer. Such symmetric complexes are common in the cell, and they allow different polypeptides to interact with each other or with other polypeptides to achieve specific biological functions. The cro repressor protein-a gene regulatory protein that binds to DNA and turns genes off in bacteria-is a good example. Each cro repressor protein subunit binds tightly to a corresponding polypeptide chain in the other dimer, in a “head-to-tail” arrangement that forms a closed ring (Figure 3-21).

Side Chains

The side chains of each amino acid are a crucial factor in the formation and folding of proteins. The polar side chains of the residues interact with each other and with the water molecules in the surrounding cellular aqueous environment, stabilizing the protein structure by Van der Waals forces and reducing its surface area. The hydrophobic interactions between non-polar residue side chains and the peptide backbone are also important in protein stability.

In the native state of a protein, the peptide bond geometry is nearly planar. The atoms of the peptide backbone (Calpha, Cb, Co, Nh, Oj) are co-planar and the peptide bond is usually in the trans configuration, although it can occur in the cis conformation for some residues, such as Pro and Phe, with lower free energy. This rigidity reduces the degrees of freedom that a peptide has in a protein structure, making it difficult to fold.

As a result of this limited degree of freedom, most proteins are folded in helices. The alpha helix has been shown to be the most stable form of a peptide, although beta sheets and tetramers have also been observed in some cases.

To stabilize an alpha helix, hydrogen bonds link the C=O and N-H groups of adjacent amino acids in the chain. This causes the chain to twist along its helix axis, with 3.6 residues per turn. In addition, the side chains of the amino acid residues orient away from the helix axis to prevent them from binding to each other.

Proteins are also formed in beta sheets and tetramers, with the helices of a protein often being parallel or antiparallel. The helices in a protein are referred to as its secondary structure, while the tertiary and quaternary structures are the final three-dimensional arrangement of a protein’s secondary elements.

It has been shown that a significant fraction of the protein’s overall free energy comes from inter-residue interactions, namely Fb-b and Ss interactions. These interactions are optimized in the native state at a significantly higher frequency than those between backbone atoms. Therefore, the Fb-b term should be the dominant contributor to the protein’s stabilizing potential.

Peptide Bonds

During the chemical reaction that joins amino acids into polypeptide chains, peptide bonds form. Each peptide bond connects the carboxylic acid end of one amino acid to the amino acid amine end using an amide group. The peptide bond is a rigid, planar structure that is stabilized by resonance between the amide groups of the a-carboxyl and a-amino acids (see Fig. 3-1). The peptide bond also limits the rotation of the carboxyl and a-amino acids in the backbone of the molecule, which provides stability to the polypeptide.

The amide bond in a peptide has mesomeric character, with two isomeric forms: the cis form and the trans form. In peptides, the peptide bond is mostly in the cis form, allowing less steric hindrance for adjacent amino acid side chains.

This rigid and planar nature of the peptide bond is essential to the stabilization of protein structures. In addition, the peptide bond has an energy barrier, which requires high activation energy to break. This makes it a very slow reaction. Only a long-time exposure to strong acids or bases at elevated temperature, or specific enzymes such as digestive enzymes, can break the peptide bond.

In order to synthesize a long chain of amino acids, each step in the synthesis must be carefully controlled to prevent cross-reactions. As a result, peptide production is time consuming and expensive. To reduce these costs, a new technique has been developed to speed up the synthesis of peptides. This process is called the Merrifield synthesis, named after its inventor R. Bruce Merrifield. It involves attaching the carboxyl ends of the amino acids to a polymeric solid that acts as an anchor, thus making it easy to separate and purify each peptide after forming a new amide bond.

The new synthesis method allows for the rapid development of bioactive peptides for use in health and wellness applications. However, the commercial application of these products is challenged by several factors including: insufficient understanding of their mechanisms of action, high gastro-intestinal digestibility and absorption rate, and a lack of well-designed clinical trials to prove their health claims.

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