Question

Describe what is meant by each of the following terms, using specific examples where appropriate: (a) $\alpha$ -amino acid; (b) zwitterion; (c) isoelectric point; (d) peptide bond; (e) tertiary structure.

Short answer

The $\alpha$-amino acid is a molecule with a –COOH and –NH2 group attached to the same carbon. A zwitterion is a neutral molecule with balanced positive and negative charges. The isoelectric point is the pH at which a molecule has no net charge. A peptide bond forms between two amino acids when one's carboxyl group reacts with another's amino group, releasing water. Lastly, the tertiary structure of a protein refers to the 3D arrangement of its polypeptide chain stabilized by R group interactions.

Step-by-step solution

Define $\alpha$-amino acid

An $\alpha$-amino acid is a molecule that contains both a carboxyl (–COOH) and an amino (–NH2) functional group. Specifically, they are attached to the same carbon in the molecule, which is the $\alpha$-carbon. An example is glycine, the simplest $\alpha$-amino acid.

Define Zwitterion

A zwitterion is a molecule that carries a positive and negative charge, but is overall neutral because the charges balance each other out. In the case of $\alpha$-amino acids, the carboxyl group can lose a proton (H+) and the amino group can gain a proton, resulting in a zwitterion.

Define Isoelectric Point

The isoelectric point (pI) is the specific pH at which a molecule carries no net electric charge. For $\alpha$-amino acids, it's the pH at which the amino acid forms a zwitterion.

Define Peptide Bond

A peptide bond is a chemical bond formed between two amino acids when the carboxyl group of one molecule reacts with the amino group of the other, releasing a molecule of water (H2O). This is a dehydration synthesis reaction.

Define Tertiary Structure

The tertiary structure of a protein is the three-dimensional (3D) shape formed when its polypeptide chain folds and bends in space. This structure is predominantly stabilized by interactions between the R groups of the amino acids, including hydrogen bonding, ionic interactions, and hydrophobic packing.

Key concepts

Amino Acids

Amino acids are the building blocks of proteins, essentially forming the "alphabet" of protein construction. Every amino acid contains a central carbon atom (the $\alpha$-carbon) that is bonded to four groups: a hydrogen atom, a carboxyl group ($-COOH$), an amino group ($-N{H}_2$), and a distinctive side chain or R-group that defines the type of amino acid. This structure allows them to link together in specific sequences to form proteins.

Amino acids are categorized into essential and non-essential. Essential amino acids cannot be synthesized by the body and must be acquired from diet, while non-essential amino acids can be synthesized by the organism. The unique properties of the side chains lead to the diverse characteristics of proteins in living systems.

Zwitterion

The concept of a zwitterion is fascinating as it reflects the dual nature of amino acids at certain pH levels. Zwitterions are compounds that contain both positive and negative charges but are net neutral. In the case of amino acids, the zwitterionic form occurs under physiological conditions. This happens when the amino group gains a proton, becoming $N{H}_3^{+}$, while the carboxyl group loses a proton, turning into $CO{O}^{-}$.

Due to this internal charge balance, zwitterions do not migrate in an electric field, a property that is pivotal in techniques like electrophoresis for separation and analysis of proteins and amino acids. Their zwitterionic nature accounts for many of the distinctive chemical properties of amino acids.

Isoelectric Point

The isoelectric point (pI) of an amino acid is a crucial concept that is often used in understanding protein solubility and reactions. It is the specific pH at which an amino acid has no net charge, staying in its zwitterionic form. Knowing the pI helps predict the behavior of amino acids in different environments. For instance, at pH levels below the isoelectric point, amino acids will be positively charged, whereas at pH levels above the isoelectric point, they will possess a negative charge.

This property is especially useful in protein purification methods where pH adjustments can help stabilize proteins or precipitate them for separation purposes. Each amino acid has a unique isoelectric point, which is determined by its specific side chain.

Peptide Bond

Peptide bonds are the core links that join amino acids in a protein chain. They form through a dehydration synthesis reaction, where the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water. This linkage results in a covalent bond known as a peptide bond, typically represented as $CO-NH$.

The formation of peptide bonds is critical in primary protein structure, determining the sequence and structure of polypeptides and proteins. These bonds are strong and confer resistance to degradation, requiring specific enzymes like proteases for their breakdown. Understanding peptide bonds is fundamental to biochemistry and molecular biology, underlying all processes related to protein synthesis.

Tertiary Structure

The tertiary structure of a protein refers to its overall three-dimensional shape, a result of various interactions between the side chains of amino acids. It emerges as the polypeptide chain folds upon itself, steered by hydrophobic forces, hydrogen bonds, ionic interactions, and van der Waals forces.

This structure is crucial for the protein's biological function, as it defines the specific spatial arrangement necessary for protein activity and interaction with other molecules. Binding sites, active sites, and structural domains are all consequences of a protein's tertiary structure. Any changes or mutations in this structure can significantly affect protein functionality, demonstrating the delicate complexity of molecular biology.