4.4. Background and Terminology: Peptides
Amino acids are very commonly joined together with another amino acid(s) by combining the amine of one with the carboxylic acid of another (Figure 4.22).
Figure 4.22 – Generalized Combination of Two α-Amino Acids Highlighting the Linkage via an Amide Bond.
The resulting functional group linking the two amino acids is an amide. However, for historical reasons the overwhelming majority of chemists and biochemists instead refer to amide bonds between two amino acids as peptide bonds.
Confusingly, molecules that are multiple amino acids connected through amide/peptide bonds are also often called “peptides” (Figure 4.23). Functionally, a molecule with “peptide” bonds is called a “peptide” as a slang name to indicate that it comes from the combination of two or more amino acids connected this way.
Figure 4.23 – Generalized Examples of Peptide Bonds and Peptide.
To emphasize the functional group involved this text will avoid using the term “peptide bond” to refer to amide bonds between amino acids. As the usage is very common it is extremely likely to be encountered in other sources. Conversely, as there is no other convenient description this text will use the shorthand term “peptide” to refer to molecules made from multiple connected amino acids.
4.4.1. Monomers, Polymers, and Biopolymers
A polymer is a compound, typically a chain, that is made of connected repeating parts (sometimes called subunits). The term “polymer” derives from Greek and translates as “many parts”; polymers are generally large molecules made by combining many molecules (parts) together.
The individual subunit of the polymer is referred to as a monomer (“one part”; Figure 4.24). Similar terms can be used for short chains of subunits: dimer (“two parts”), trimer (“three parts”), and tetramer (“four parts”). While there are terms for other short chains (pentamer, hexamer, etc.) in general after more than four units are connected together the molecule is simply referred to as a polymer. Rarely, longer polymers are described using the number of subunits and a “mer’ suffix (e.g. 23-mer).
Figure 4.24 – Generalized Examples of a Monomer, Dimer, Trimer, Tetramer, and Polymer.
Polymers can be a single long chain or have special subunits connected to multiple chains, causing branching to occur (Figure 4.25).
Figure 4.25 – Generalized Examples of a Linear Polymer and a Branched Polymer.
There are many synthetic polymers used for a variety of applications (e.g. polystyrene (styrofoam), polyvinylchloride (PVC plastics), nylon (textiles), teflon (non-stick pans), etc.). At the same time, there are many naturally occurring polymers in biological systems used for a variety of applications. These are occasionally called “biopolymers”, though the distinction is not necessary. Many of the most famous biomolecules are polymers (Figure 4.26): amino acid monomers combine to make polymers (peptides); carbohydrate monomers combine to make polymers (sugars, starches, etc.; see Chapter 5); nucleic acid monomers (as nucleotides) combine to make polymers (DNA and RNA; see Chapter 7).
Figure 4.26 – Generalized Examples of Biopolymers from Amino Acids, Carbohydrates, and Nucleotides.
4.4.2. Peptide Terminology: N-Terminus and C-Terminus
Peptides are typically made from a combination of many different amino acids. Often the exact sequence (the order that they are connected in) is important. To avoid ambiguity a naming convention for peptide chains was established.
The end of the chain that would contain the last amine from an amino acid of the sequence is called the N-terminus (Figure 4.27). The sequence is read starting from this amino acid. The end of the chain that would contain the last carboxylic acid from an amino acid of the sequence is called the C-terminus. The sequence is read ending at this amino acid. The orientation and/or perspective of the drawing is irrelevant, the chain is always read from the N-terminus to the C-terminus.
Figure 4.27 – Generalized Examples of Reading Amino Acid Sequences in Peptide Chains from N-Terminus to C-Terminus Regardless of Drawing Orientation/Perspective.
The N-terminus does not have to be the parent primary amine functional group; the C-terminus does not have to be the parent carboxylic acid functional group (Figure 4.28). Peptide chains that have been modified and/or that are in a different protonation state are still read from the N-terminus to the C-terminus. The functional group itself may be modified, including to amides formed with non-amino acid compounds.
Figure 4.28 – Generalized Examples of Reading Amino Acid Sequences in Peptide Chains from N-Terminus to C-Terminus Regardless of Amine or Carboxylic Acid Derivatization.
4.4.3. Peptide Nomenclature: Describing Peptide Chains
Under the IUPAC rules the peptide sequence may be expressed in several different ways. However, two simple methods are commonly used (Figure 4.29). These express the sequence of amino acids in order from N-terminus to C-terminus using either the three- or one-letter codes for the amino acids. Generally, the three-letter codes are used for short peptide chains while the one-letter codes are used for longer chains. This is only a convention and not a rule; the use of either approach is technically valid for any peptide chain of any length. Individual amino acids may or may not be separated by hyphens when using the one-letter codes.
Figure 4.29 – Examples of Naming Amino Acid Sequences for Two Trimers/Tripeptides.
If the chain has been modified in a straightforward way then the modification is often included in the name. However, at an introductory level it is often difficult to know when/how to describe modifications. This text will avoid examples using these variations but they may be encountered in other sources.
In the resonance form that is normally drawn the nitrogen of an amide appears to be tetrahedral (sp3 hybridized; Figure 4.30). However, because the amide has other contributing resonance forms the actual geometry of the nitrogen is trigonal planar (sp2 hybridized). The carbon and oxygen of the amide are also trigonal planar. As a result, the entire amide and its attached groups are flat with the amino acid side chains pointing above and below the plane of the amide.
Figure 4.30 – Resonance Forms and Geometry of Ala-Ala Dipeptide.
Recall that resonance structures are an imperfect way of attempting to approximate the ‘real’ distribution of electron density in the molecule. The molecule does not look like one form one second and the other the next. The molecule looks like a weighted superposition of all resonance forms at once. As a result, the bond from the nitrogen to the carbon of the carbonyl is not a single bond, not a double bond, but something in-between. This can be approximated using dotted bonds, though this approach is discouraged (Figure 4.31). The electron distribution for the pi (π) system of the amide is better visualized as a probability distribution made from the p orbitals of all three atoms of the amide (the O, the C, and the N). This is useful for seeing how the electron density is spread over the entire set of atoms involved but can be challenging for students to draw at an introductory level.
Figure 4.31 – Visualizations of the Pi Electron Distribution of the Amide of Ala-Ala Dipeptide.
Recall that the two sides of a sigma (σ) bond can rotate independently without affecting the bond, creating different rotational arrangements called conformations (Figure 4.32). Barring outside factors all σ bonds are capable of rotations like this.
Figure 4.32 – 60° Rotations Around the Carbon-Carbon σ Bond of Ethane and the Resulting Conformations.
One of the ‘outside factors’ that inhibits rotation is a pi (π) bond. Rotation around a π bond is heavily disfavoured; during rotation the π bond would have to be broken. As a result, the two forms are permanent, do not easily interconvert, and are instead configurations (Figure 4.33).
Figure 4.33 – Lack of Rotation Around the Carbon-Carbon σ Bond of But-2-ene as a Result of the π Bond.
The bond between the nitrogen and the carbon of the carbonyl in an amide, as normally drawn, looks like a single σ bond but is actually something in between a single and double bond. Consider the resonance structures of the two conformations from rotation around this bond (Scheme 4.15). Rotation around this C-N bond is heavily disfavoured because during the rotation the “π bond” between the nitrogen and the carbon (the conjugation and resonance stabilization) would be lost. The bond behaves like a double bond rather than a single bond. The two forms are technically conformations but they do not readily interconvert (like configurations).
Scheme 4.15 – Inhibited Rotation Around the C-N Bond of an Amide in a Peptide.
Because the disfavoured interconversion is similar to that of a double bond they are given special names relating them to the (relative) configurations of alkenes (Figure 4.34). The conformation with the two large groups on opposite sides of the “double bond” is called the s-trans conformation. The conformation with the two large groups on the same side of the “double bond” is called the s-cis conformation. The “s” prefix is used to show that these not actually configurations: they are two conformations around a bond that appears to be only a sigma (σ) bond but is not purely a single or double bond.
Figure 4.34 – s-Cis/s-Trans Conformations of a Dipeptide and Relationship to Cis/Trans Configurations of But-2-ene.
Steric interactions between large groups in the s-cis conformation raise the energy of this conformation. When one of the groups attached to the nitrogen of the amide is significantly smaller than the others (e.g. one of the groups is a hydrogen) then the s-trans conformation is heavily favoured because it has fewer steric interactions (>99:1; Scheme 4.16). This means that almost all amides in peptide chains will heavily favour the s-trans conformation.
Scheme 4.16 – Steric Strain and Preference for s-Trans for Amides with a Hydrogen on Nitrogen Contrasted with No Preference for Amides with Proline.
However, when there is less of a difference in size between groups the difference in steric interactions between the two conformations becomes much smaller. In these instances the s-cis and s-trans conformations are roughly equal in energy and the amide can adopt either shape. This has significant consequences for one of the common amino acids: amides in peptide chains made using the nitrogen of proline can adopt either s-cis or s-trans conformations.
The large preference for s-trans conformations has a significant impact on the three-dimensional shapes of large peptide chains (see Sections 4.5.2.1 and 4.5.2.2). Conversely, the special nature of amide bonds with proline is taken advantage of for other structural features (see Section 4.5.2.4).
4.4.5. Representations of Large Peptides
Long peptide polymers (sometimes called polypeptides) have complex three-dimensional shapes. This has far reaching consequences for the polymer’s eventual biological function(s). Because of the importance of these molecules in bioorganic chemistry, biochemistry, and biology there are a variety of ways to depict these three-dimensional structures depending on the focus and/or background of the source.
For convenience, the following depictions all show the same polypeptide from the same perspective. The only difference is the style of drawing.
In organic chemistry a common approach is to use differently coloured ellipsoids (spheres) to represent different atoms (Figure 4.35). Bonds are typically represented using lines or cylinders connecting the spheres. These models are sometimes called Ball-and-Stick and are meant to approximate seeing a molecular model. Most representations use the same colours to refer to the same elements. However, this is only a convention and not a rule. For example, this computer-generated image coloured the carbon atoms green, but a standard molecular model kit will have black balls for carbon atoms.
Figure 4.35 – Ball-and-Stick Model of Thioredoxin 1 (TCF52B).
These representations may show all of the atoms or omit hydrogen atoms. The style makes it easier to see certain kinds of interactions and structural features (Figure 4.36). However, because there are many amino acids there are many atoms; the images rapidly become crowded and confusing. It is typically challenging to see what the function of the peptide may be and what individual parts may do/make it up.
Figure 4.36 – Ball-and-Stick Model of Thioredoxin 1 (TCF52B) with Highlighted Examples of Structural Features and Non-Covalent Interactions.
A slightly less common approach is to display the electron clouds of the different atoms or the molecule itself (Figure 4.37). Several different versions of this style exist depending on which surface is being focused on (van der Waals radii, electron density, electrostatic potential, etc.). These models are sometimes called Space-Filling and are meant to approximate the actual physical size occupied by the atoms and their electrons. Depending on the exact style the colours may correspond to elements, density, structural features, etc. As a result, these images must be interpreted carefully.
Figure 4.37 – Two Examples of Space-Filling Models of Thioredoxin 1 (TCF52B).
These representations may show all of the atoms, omit hydrogen atoms, or focus on surfaces that do not distinguish individual atoms. The style sometimes makes it easier to see certain kinds of physical features (Figure 4.38). However, regardless of what surface is being shown the images are often crowded and confusing, with the interior space(s) obscured. In general, this style is reserved for enzymes or other proteins to identify “pockets” for other molecules to bind to. At an introductory level it is typically not feasible to look for these places unassisted.
Figure 4.38 – Example of a Space-Filling Model of Thioredoxin 1 (TCF52B) Showing a Potential Binding Site and Bound Molecule.
In bioorganic chemistry and biochemistry the standard approach is to use a cartoon-style image to represent common structural features (Figure 4.39). Individual atoms, bonds, and amino acids are not shown, only regularly recurring structural patterns (see Section 4.5.2 and subsections therein). These models are sometimes called Ribbons and are meant to convey the general shapes and areas making up the peptide’s structure. Most representations use colours to highlight the different features. However, there are no standardized rules for this. Any given representation may, or may not, divide structural components by colour and/or use the same colour(s) for the components themselves.
Figure 4.39 – Ribbon Model of Thioredoxin 1 (TCF52B).
The style makes it very easy to see certain kinds of common structural features (Figure 4.40). Because these features are present in many different peptide chains they often behave and interact with other nearby areas similarly. As a result, this may make it easier to see what the function of the peptide may be and what individual parts may do/make it up. However, because the amino acids are not expressly shown the images lose specific details and may make it challenging to identify the precise amino acid side chains involved in catalysis.
Figure 4.40 – Ribbon Model of Thioredoxin 1 (TCF52B) with Highlighted Examples of Common Structural Features.
