In this section, we will cover:

• What are peptides?
• Why are peptides important?
• What is an amino acid?
• How do amino acid structures influence peptide properties?
• Understanding amino acid notations
• What are amino acid derivatives?

What are peptides?

Peptides are small chains of amino acids that share a similar composition with proteins. The key difference lies in their length: peptides typically consist of 2–100 amino acids, although some definitions place the upper limit at 50 amino acids. Proteins, on the other hand, are generally longer, consisting of more than 100 amino acids. It’s worth noting that the distinction between peptides and proteins can be somewhat arbitrary, with varying definitions depending on the context.

Imagine peptides as chains of uniquely shaped “pearls,” where the “pearls” represent the 20 proteinogenic amino acids commonly found in nature. These amino acids can be arranged in countless combinations, with the ability to repeat at any frequency. For example, in collagen—a critical structural protein in the skin, cartilage, and tendons—the amino acid glycine (Gly) appears in every third position of the chain: …-Xaa (commonly proline (Pro))-Yaa-Gly-…

Why are peptides important?

Aside from water and fat, proteins make up almost the entire composition of our bodies. Despite their shared structural principles, proteins serve an extraordinary variety of functions and are essential to our diet.

This diversity is achieved through variations in the type and number of amino acid building blocks, enabling peptides and proteins to possess a vast range of properties. Many peptides exhibit remarkable biological activity, such as those found in hormones and toxins. In fact, most hormones are peptides of varying lengths:

• TRH (thyrotrophin-releasing hormone): A tripeptide consisting of three amino acids.
• LHRH (gonadotropin-releasing hormone, GnRH): A decapeptide with 10 amino acids.
• Calcitonin: Contains 32 amino acids.
• PTH (parathormone): Composed of 84 amino acids, almost qualifying as a protein.
• Insulin: Made up of two peptide chains containing 30 and 21 amino acids, linked by disulfide bridges.

In general, peptide hormones are produced by specialized cells then released into the bloodstream and transported to the target organ. The cells to be stimulated possess receptors — specialized proteins embedded in the cell membrane — that recognize and specifically bind the peptide hormones. This binding of the hormone to the cellular receptors creates a signal that triggers the desired biological effect.

Peptides are often classified based on their length:

• Two amino acids = dipeptide 
• Three amino acids = tripeptide 
• Four amino acids = tetrapeptide 
• Five amino acids = pentapeptide etc. 
• A few (2–20) amino acids = oligopeptide

An enormous number of combinations are possible even for short peptides. For example, 3.2 million different pentapeptides may be formed from the 20 proteinogenic amino acids, without even considering non-proteinogenic and modified amino acids!

Even dipeptides can be biologically active. For instance, Leu-Trp* and other dipeptides lower blood pressure, while N-acetyl-Asp-Glu (NAAG) is an important neurotransmitter that mediates the transmission of signals between nerve cells. The peptides found in the body are usually obtained by enzymatic splitting or “cleavage” of proteins.

Introduction to amino acids

What are amino acids?

The amino acids most commonly found in nature are known as α-amino acids. These molecules have four different substituents attached to a central carbon atom, called the α-C atom:

• Amino group (NH₂, abbreviated as “H-” in the three-letter code).
• Carboxylic acid group (COOH, abbreviated as “-OH” in the three-letter code).
• Side chain (R, which varies significantly and determines the properties of the amino acid and, ultimately, the peptide).
• Hydrogen atom (H).

The α-C atom’s attachment to these four distinct groups gives it unique chemical properties, which play a critical role in determining the behavior and characteristics of amino acids and peptides (refer to Fig. 1 and Table 2).

Figure 1: An α-amino acid, showing the α-C atom with four different substituents.

How do amino acid structures influence peptide properties?

Cells synthesise proteins using 20 proteinogenic amino acids, which differ only in their side chain (R group). Beyond these, nature provides other α-amino acids that exist either freely, as metabolic by-products, or as components of peptides and proteins. Examples include:

• Hydroxyproline (Hyp): Found in collagen.
• Ornithine (Orn): Detected in urine.

Some amino acids, like norleucine (Nle), have only been synthesized chemically. At Bachem, we refer to these non-proteinogenic amino acids as “unusual amino acids,” even though they are often called “unnatural amino acids” regardless of their natural occurrence.

Biological activity of amino acids

Amino acids can exhibit biological activity, such as:

• Tryptophan (Trp) and glutamic acid (Glu), play key roles in metabolic processes.

The R group, or side chain, defines the unique properties of amino acids. These groups may:

• Be simple: A hydrogen atom, as in glycine (Gly).
• Include additional acids: Examples include aspartic acid (Asp) and glutamic acid (Glu).
• Carry basic groups: Arginine (Arg), lysine (Lys), or histidine (His).
• Contain polar groups: Such as serine (Ser) or threonine (Thr).
• Be non-polar hydrocarbons: Alanine (Ala), phenylalanine (Phe), or valine (Val).
• Contain sulfur: As seen in cysteine (Cys) and methionine (Met).

Beyond α-Amino acids

Bachem offers a broad range of amino acids beyond the α-amino acids used in peptide and protein synthesis. These include β-amino acids and γ-amino acids, where the amino group is bonded to a carbon atom other than the α-carbon. This diversity allows for incredible versatility in peptide and protein design.

The role of L- and D-amino acids

The four substituents of the α-C atom are arranged at the corners of a tetrahedron, with the α-C atom at the centre (see Fig.3). This arrangement allows two forms of the amino acid molecule to exist as mirror images, similar to left and right hands. These mirror-image forms are called “stereoisomers” or “enantiomers.”

Biological importance of enantiomers

While enantiomers have nearly identical chemical and physical properties, their biological effects can differ significantly. The shape of a molecule is crucial for its interaction with biological targets. One enantiomer may bind effectively to a target and produce a positive effect, while the other may fail to bind or, in some cases, cause a negative effect. In solution, enantiomers rotate the plane of polarized light in opposite directions.

Figure 3: Arrangement of the substituents around the α-C atom (gray).

Optical activity in nature

Compounds exhibiting this behavior are referred to as “optically active.” Optical activity is widespread in nature. Unlike glycine (R = H), whose image and mirror image are identical, all proteinogenic amino acids display optical activity. Similarly, glucose (a sugar) and DNA, along with its building blocks, also rotate plane-polarized light—a property often used to measure the concentration of glucose solutions.

L- and D-enantiomers of amino acids

All proteinogenic amino acids, except glycine, are L-enantiomers (L, from laevus, Latin for “left”), such as L-alanine. Their mirror images, the D-amino acids (D, from dexter, Latin for “right”), are far less common in nature.

L and D refer to the specific arrangement of the four substituents around the α-C atom. However, these designations do not indicate the direction of optical rotation. For L-amino acids, the rotation can be positive or negative, but it will always be opposite to that of their corresponding D-amino acid.

Figure 4: Absolute configurations of the L- and D-enantiomers of amino acids.

Rotation values of amino acids

The rotation value, denoted as [α], is a characteristic property often listed on Bachem Analytical Data Sheets for amino acids and their derivatives. This value is also commonly measured for peptides.

Examples:

• L-alanine: +14.3°
• D-alanine: −13.9°
• L-tryptophan: −31.8°
• D-tryptophan: +30.7°

Discrepancies in the absolute values of L- and D-enantiomers fall within the method’s range of accuracy.

A 1:1 mixture of the two enantiomers is called a “racemate”. In this case, the rotations of the l- and d-enantiomers cancel each other out. In the Bachem notation, the l-form is not explicitly indicated because of its ubiquity (e.g., l-alanine = H-Ala-OH). Only the less common d-form (e.g., d-alanine = H-d-Ala-OH) and the racemate, which is shown as dl, are designated as such.

Understanding amino acid notations

If the name of an amino acid is written out in full, the enantiomeric form is usually shown as well, e.g., l-alanine and d-alanine. In the case of a racemate — as is common in organic chemistry — the DL is routinely omitted. Amino acids and peptides are often represented by their three-letter codes (usually the first three letters of the name, see Table 3).

In addition, there is also a one-letter code that is sometimes preferred, especially for longer peptides and proteins.

Examples: 

L-alanine → Ala, l-Ala, H-Ala-OH (3-letter), A (1-letter)

L-arginine → Arg, l-Arg, H-Arg-OH (3-letter), R (1-letter)

Bachem notation: 

H-Ala-OH, H-Arg-OH

This notation signifies that it is the l-form and that the amino and carboxyl groups are free.

The abbreviations for the 20 proteinogenic amino acids are listed in Table 3. The one-letter code is reserved for these 20 amino acids, while for d-amino acids, lower-case letters are typically used (e.g., f = D-Phe). Many non-proteinogenic amino acids also have established three-letter codes, such as Hyp (L-trans-hydroxyproline), Nle (L-norleucine), and Orn (L-ornithine). However, not all abbreviations found in the literature are used by Bachem. In some cases, the full name is preferred, such as l-thiazolidine-4-carboxylic acid (sometimes abbreviated as Thz).

What are amino acid derivatives?

In organic chemistry, the term “derivatives” refers to compounds derived from a parent molecule. Derivatives of an amino acid are created by modifying the amino group, carboxyl group, or side chain. If the modification can be reversed without altering the amino acid itself, it serves as a “protecting group,” shielding reactive parts of the amino acid while other modifications are made, such as attaching additional amino acids. These protected derivatives are useful building blocks for peptide synthesis. For example, some simple protected derivatives of H-Ala-OH include:

• Ac-Ala-OH (amino group blocked)
• H-Ala-NH2 (carboxyl group blocked)
• Fmoc-Ala-OH (amino group blocked)

Fmoc can be selectively removed under mild conditions, making it a suitable protecting group for peptide synthesis.

What are unusual amino acids?

α-Amino acids bearing unusual side-chain functionalities and turn mimetics are useful tools for peptide design. Bachem offers an exceptional range of unusual amino acids. Most of these are available as Nα-protected derivatives from stock, so they can be inserted into your peptide without delay (see Table 4).

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