Question

What is a polypeptide linkage? In a polypeptide, what do the terms 'Nterminal' and 'C-terminal' refer to?

Short answer

A polypeptide linkage is a peptide bond between amino acids in a chain. 'N-terminal' refers to the start of the chain with a free amino group, while 'C-terminal' refers to the end with a free carboxyl group.

Step-by-step solution

Understanding Polypeptides

A polypeptide is a polymer consisting of many amino acids linked together by amide bonds known as peptide bonds. These peptide bonds form between the carboxyl group of one amino acid and the amino group of another, leading to the release of a molecule of water. This continuous chain of amino acids is termed a polypeptide.

Defining a Peptide Bond

A peptide bond, also known as an amide bond, is the covalent bond that forms between the amino group (NH_2) of one amino acid and the carboxyl group (COOH) of another amino acid. The reaction is a condensation reaction, releasing water and forming the link: \[ \text{O} |\text{C} - \text{NH} | \] This bond is termed a polypeptide linkage.

Understanding N-terminal and C-terminal Ends

In a polypeptide chain, the 'N-terminal', also known as the amino terminus, is the end of a polypeptide chain with a free amino group (NH_3^+). Conversely, the 'C-terminal', also known as the carboxyl terminus, is the end of the polypeptide with a free carboxyl group (COO^-). These terminal groups define the chain directionality, starting from the N-terminal to the C-terminal.

Key concepts

Amino Acids

Amino acids are the building blocks of proteins. They are organic compounds composed of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. Each amino acid has a central carbon atom (also known as the alpha carbon) bonded to:

• An amino group (\(\text{-NH}_2\))
• A carboxyl group (\(\text{-COOH}\))
• A hydrogen atom
• A distinctive side chain known as an R-group, which varies among different amino acids

The diversity of the R-group gives each amino acid unique properties and influences how they interact with one another.
While there are hundreds of amino acids in nature, only 20 standard amino acids are encoded by the genetic code and play a crucial role in making proteins. These 20 amino acids vary in size, structure, and function, allowing for the wide variety of proteins seen in biology.
Understanding amino acids is fundamental in grasping how they link to form peptides and proteins, ultimately determining an organism's traits and abilities.

Peptide Bond

A peptide bond is a special type of covalent bond that connects amino acids in a protein. It is formed through a dehydration synthesis reaction between the carboxyl group of one amino acid and the amino group of another, effectively removing a molecule of water (\(\text{H}_2\text{O}\)).
Here's how it works:

• The carboxyl group (\(-COOH\)) of one amino acid loses an OH group.
• The amino group (\(-NH_2\)) of the second amino acid loses a hydrogen atom.
• A water molecule (\(\text{H}_2\text{O}\)) is released, and the two amino acids are joined by a peptide bond, creating a dipeptide.

This bond forms the backbone of a polypeptide chain, linking together long sequences of amino acids. The resulting chain, being a polypeptide, can fold into specific three-dimensional structures critical for protein function.
Peptide bonds have unique chemical stability that allows proteins to maintain their structure under a variety of conditions. This stability is due to the resonance of the peptide bond, which means electrons are shared between the atoms involved, leading to a partially double-bond characteristic.

N-terminal and C-terminal

The structure of a polypeptide chain is uniquely defined by its two ends: the N-terminal and the C-terminal.

• The N-terminal, or amino terminus, is the start of the polypeptide and contains a free amino group (\(-NH_3^+\)). It marks the beginning of a protein sequence and is conventionally written on the left when representing protein sequences.
• The C-terminal, or carboxyl terminus, is the end of the polypeptide, featuring a free carboxyl group (\(\mathrm{COO}^-\)). It is typically depicted on the right side of the sequence.

The directionality from the N-terminal to the C-terminal is crucial, as it reflects the direction in which the protein is synthesized by ribosomes in the cell. This order also influences how the protein folds and functions.
Each polypeptide chain is synthesized starting from the N-terminal and ending at the C-terminal, corresponding to the order in which amino acids are added to the growing chain during protein synthesis. Therefore, the N-terminal and C-terminal help establish the framework for understanding protein structure and function, as well as providing the signals for subsequent biological processes that the protein may engage in.