Polypeptide

Polypeptide
n., plural: polypeptides
[ˌpɒlɪˈpɛptaɪd]
Definition: A polymer of amino acids joined together by peptide bonds. Image credit: CNX OpenStax

Polypeptide Definition Biology

What are polypeptides? A polypeptide is defined as a polymer of amino acids joined together by peptide bonds (Figure 1).

Larger polypeptides or more than one polypeptide that occur together are referred to as proteins. Proteins are polymers of amino acids that often bind to small molecules (e.g. ligands, coenzymes), to other proteins, or other macromolecules (DNA, RNA, etc.) Therefore, the building blocks of proteins are called amino acids. Proteins have a vital role in biology, functioning as the building blocks of muscles, bones, hair, nails as well as forming enzymes, antibodies, muscles, connective tissue, and much more. Peptides are shorter chains of amino acids (two or more), which distinguishes them from polypeptides that are much longer.

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Polypeptide Structure

A polymer produced by a living organism is called a biopolymer. There are four major classes of biopolymers: (1) polysaccharides, (2) polypeptides, (3) polynucleotides, and (4) fatty acids. Which polymers are composed of amino acids? A polypeptide is an unbranched chain of amino acids that are linked together by peptide bonds. The peptide bond links the carboxyl group of one amino acid to the amine group of the next amino acid to form an amide. What are peptides? Short polypeptides may be named based on the number of monomeric amino acids that comprise them. For instance, a dipeptide is a peptide consisting of two amino acids sub-units, a tripeptide is a peptide comprised of three amino acid sub-units, and tetrapeptide is a peptide comprised of four amino acid sub-units.

Amino Acid Definition Biology

The amino acids which make up polypeptides contain an alkali amino group (-NH2), an acidic carboxyl group (-COOH), and an R group (side chain). The R group is variable in its components and is unique to every amino acid. Each amino acid molecule contains a carbon atom (α-carbon). In most cases, the amino and carboxyl groups are attached to the α-carbon (figure 2).

Peptide Bond Definition

A peptide bond (amino acid bond) is the bond between amino acids. This forms the primary structure of a long polypeptide chain. Proteins are made up of one or several polypeptides that have interacted together to form the final, stable, working conformation.

Amino acids can either be α-amino acids are β-amino acids. Where both the carboxyl and amino group are attached to the central carbon, they are known as α-amino acids. In β-amino acids, the carboxyl and amino groups are attached to a different carbon molecule. Figure 3 shows an example of an α-amino acid and a β-amino acid.

There are 21 amino acids used by eukaryotes to generate proteins (protein synthesis). All vary by differences in their side chains. Humans and other vertebrate animals can make 12 of these, which are termed nonessential amino acids. The remaining 9 amino acids need to be ingested as they cannot be made in the body but are made by other organisms. These are termed essential amino acids.

Until recently, the list of amino acids was made up of 20. However, selenocysteine was added as the 21st amino acid in 1986. Selenocysteine is found in some rare proteins in bacteria and humans. Even more recently, it was suggested that pyrrolysine should be named the 22nd amino acid. However, pyrrolysine is not used in human protein synthesis. Table 1 shows the lists of essential and nonessential amino acids. Figure 4 illustrates the structure of 21 amino acids.

Polypeptide Formation

The variation of the R group side chains alters the chemistry of the amino acid molecule. Most amino acids have side chains that are non-polar (do not have positive and negative poles). Others have positively or negatively charged side chains. Some have polar side chains that are uncharged. The chemistry of the side-chain affects how the amino acids bond together when forming the final protein structure.

If the amino acids have charged side chains, they can form ionic bonds. If the side chains are hydrophobic, they can join with van der Waals interactions. Polar amino acids can join with hydrogen bonds. Therefore, side-chain interactions of a long chain of amino acids, and their order in the chain would determine how the protein molecule is formed, i.e. where it folds together. More information regarding the different bonds and interactions between the amino acids will be discussed later in this section.

Proteins have 4 levels of structure: the primary structure, the secondary structure, the tertiary structure, and the quaternary structure.

1. Primary Structure

What is a polypeptide sequence? In simple terms, polypeptides are chains of amino acids. The primary structure of a protein begins with peptide bond formation between amino acids resulting in the creation of a peptide.

What is a peptide bond? Peptide bonds exist between the α-carboxyl group of amino acids and the α-amino group of different amino acids. This forms a stable two-dimensional structure with side chains extending out from the polypeptide chain. This allows the side chains to interact with other molecules. This act of joining smaller units together to create a longer polymer is known as polymerization. How are peptide bonds formed? The reaction of two amino acids joining is a condensation reaction. This is because a hydrogen and oxygen molecule is lost from the carboxyl group of 1 amino acid, and a hydrogen molecule is lost from the amino group of another amino acid. This produces a water molecule (H₂O), hence the term condensation reaction.

2. Secondary Structure

The secondary structure forms when hydrogen bonds arise between atoms in the backbone of the polypeptide (this does not include the side chains). Two common patterns arising from repeated folding via hydrogen bonding are the α-helix and the β-pleated sheet.

In the α-helix secondary structure, the coil is right-handed, and the hydrogen bonds are found between every fourth amino acid. α-keratin is an example of a protein composed of α-helices. This protein is found in hair and nails.

The β-pleated sheet is the other common secondary structure. This occurs when two polypeptide chains lie next to each other and hydrogen bonds form between them. There are two types of β-pleated sheets; these are the parallel β-pleated sheet and the antiparallel β-pleated sheet. At the end of a polypeptide, there is either a free carboxyl group or a free amino group.

In a parallel β-pleated sheet, the two polypeptide chains are running in the same direction with the same group at each end. In an anti-parallel β-pleated sheet, the polypeptides are running in different directions. Figure 6 illustrates an anti-parallel β-pleated sheet and an α-helix.

A less commonly known secondary structure is the β-barrel. In this case, the polypeptides run anti-parallel to each other but have also coiled into a barrel shape with hydrogen bonds between the first and last amino acid (figure 7).

Although hydrogen bonds in the amino acids are weak, the combination of all the hydrogen bonds together gives the structure stability allowing it to keep its shape.

3. Tertiary Structure

The tertiary structure of the polypeptide is defined as the 3-dimensional structure. The protein begins further folding resulting from side chain (R group) interactions in the primary sequence. This is via hydrophobic bonds, hydrogen bonds, ionic bonds, disulfide bonds, and Van der Waals interactions.

• Hydrophobic bonds – side chains that are non-polar and the hydrophobic groups together. They remain on the inside of the protein leaving hydrophilic side chains on the outside that are in contact with water.
• Hydrogen bonds – occur between an electrically negative atom and a hydrogen atom that is already bound to an electrically negative atom. They are weaker than covalent bonds and ionic bonds but stronger than Van der Waals interactions.
• Ionic bonds – a positively charged ion forms a bond with a negatively charged ion. [a]These bonds are stronger on the inside of a protein where water is excluded as water can dissociate these bonds.
• Van der Waals interactions – this refers to electrical interactions between close atoms or molecules. These interactions are weak, however, if there are a number of these interactions in a protein, it can add to its strength.
• Disulphide Bond – this is a type of covalent bond and is also the strongest bond found in proteins. It involves the oxidation of 2 cysteine residues resulting in a sulfur-sulfur covalent bond. Almost one-third of eukaryotic synthesized proteins contain disulfide bonds. These bonds provide stability to the protein. Figure 8 shows the different bonds involved in the tertiary structure of a protein.

4. Quaternary Structure

In the quaternary structure, chains of polypeptides begin to interact together. These protein subunits bind together via hydrogen bonds and van der Waals interactions. Their arrangement allows the specific functionality of the final protein. Changes in conformation can be detrimental to their biological actions. Hemoglobin is an example of a protein with a quaternary structure.[b] It is made up of 4 subunits.

It is worth noting that not all proteins have a quaternary structure, many proteins only have a tertiary structure as their final conformation.

Are polypeptides proteins? In some cases, the word polypeptide is used interchangeably with the word protein. However, a protein may consist of more than 1 chain of polypeptides so using the term polypeptide for all proteins is not always correct.

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Polypeptide Functions with Examples

Polypeptides and their resulting proteins are found throughout the body. What is the function of a polypeptide? The roles of polypeptides are dependent on the amino acid content. There are over 20 amino acids, and the average length of a polypeptide is around 300 amino acids. These amino acids can be arranged in any given sequence. This allows for a massive number of possible protein variations. However, not all these proteins would have a stable 3D conformation. The proteins found in cells are not only stable in their conformation but also unique to one another.

What are examples of polypeptides? The most important examples of proteins include transporters, enzymes, hormones, and structural support.

Transporters

There are protein transporters and peptide transporters. Peptide transporters are found in the peptide transporter family (PTR). Their function is to act as membrane proteins in a cell to take up small peptides (di- or tri-peptides). There are 2 main types of peptide transporters, PEPT1 and PEPT2. PEPT1 is found in intestinal cells and aids the uptake of di- and tripeptides. PEPT2 on the other hand is found largely in the kidney cells and aids reabsorption of di- and tripeptides.

Enzymes

Polypeptides also make up enzymes. Enzymes initiate (catalyze) or speed up biochemical reactions. They are biomolecules that aid in the synthesis as well as the breakdown of molecules. All living organisms use enzymes, and they are vital to our survival. It is believed that enzymes catalyze around 4000 different biochemical reactions in life. All enzymes are named with the ending -ase. There are 6 functional groups of enzymes: oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. Lactase, for example, is a hydrolase that causes the hydrolysis (breakdown reaction with water) of lactose (milk sugar) into galactose and glucose monomers (figure 10). Lactase is found in humans and animals and has the function of aiding the digestion of milk. It is also found in some microorganisms.

Hormones

Hormones can be either steroid-based or peptide-based. Polypeptide and protein hormones vary in their size with some consisting of only a few amino acids whereas others are large proteins. They are made in cells in the rough endoplasmic reticulum (RER) and then move to the Golgi apparatus. They are then placed into vesicles until they are needed/stimulated for secretion outside the cell.

Insulin is an example of a protein hormone. It is 51 amino acid residues in length and is composed of 2 polypeptide chains known as chain A and chain B. The beta cells in the pancreas synthesize this hormone. Insulin helps the body to regulate blood sugar levels by removing excess glucose from the blood and allowing it to be stored for later use (figure 11).

Structural Support

Finally, structural proteins provide shape and support to living organisms. For example, they may provide support in a cell wall. They are also found in connective tissue, muscle, bone, and cartilage. Actin is an example of a structural protein found in cells. It is the most abundant protein found in eukaryotic cells. In muscle cells, they help to support muscle contraction. They also form the cytoskeleton of cells helping them keep their shape. Additionally, actin is involved in cell division, cell signaling, and organelle movement.

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