3.2 Peptide bonds and primary structure of proteins

Proteins are made of amino acids linked by peptide bonds, forming long chains called polypeptides. These bonds create a backbone that gives proteins their unique shape and function. Understanding peptide bonds is key to grasping how proteins work in our bodies.

The primary structure of a protein is its specific sequence of amino acids. This sequence is like a code that determines how the protein will fold and function. Knowing the primary structure helps scientists understand protein behavior and design new drugs.

Peptide Bonds and Polypeptides

Formation and Structure of Peptide Bonds

• Peptide bonds form through a condensation reaction between the carboxyl group of one amino acid and the amino group of another amino acid
• This reaction releases a water molecule (H2O) as a byproduct
• The resulting covalent bond between the carbon atom of the carboxyl group and the nitrogen atom of the amino group is called a peptide bond
• Peptide bonds have a partial double bond character due to resonance stabilization
  • This partial double bond character restricts rotation around the peptide bond, resulting in a planar structure

Polypeptide Chains and the Peptide Backbone

• When multiple amino acids are joined together by peptide bonds, they form a polypeptide chain
• A polypeptide is a linear chain of amino acids connected by peptide bonds
• The peptide backbone refers to the repeating sequence of atoms along the polypeptide chain, consisting of the amino nitrogen, alpha carbon, and carbonyl carbon of each amino acid residue
• The side chains of the amino acids extend outward from the peptide backbone
• The peptide backbone is also known as the main chain of the polypeptide

Protein Termini

N-terminus and Its Properties

• The N-terminus of a polypeptide chain refers to the end of the polypeptide that has a free amino group (NH2)
• It is the end where protein synthesis begins, with the first amino acid being added to the growing polypeptide chain
• The N-terminus is conventionally written on the left side of a polypeptide sequence
• The amino acid at the N-terminus can undergo chemical modifications, such as acetylation, which can affect the stability and function of the protein

C-terminus and Its Properties

• The C-terminus of a polypeptide chain refers to the end of the polypeptide that has a free carboxyl group (COOH)
• It is the end where protein synthesis terminates, with the last amino acid being added to the growing polypeptide chain
• The C-terminus is conventionally written on the right side of a polypeptide sequence
• The amino acid at the C-terminus can also undergo chemical modifications, such as amidation, which can affect the stability and function of the protein

Primary Structure

Definition and Significance of Primary Structure

• The primary structure of a protein refers to the linear sequence of amino acids in a polypeptide chain
• It is determined by the genetic code, which specifies the order in which amino acids are incorporated into the polypeptide during protein synthesis
• The primary structure is the foundation for the higher levels of protein structure (secondary, tertiary, and quaternary)
• Changes in the primary structure, such as mutations or post-translational modifications, can significantly impact the folding, stability, and function of the protein

Amino Acid Sequence and Its Determination

• The amino acid sequence is the specific order in which amino acids are arranged in a polypeptide chain
• It is typically represented using the one-letter or three-letter abbreviations for each amino acid (e.g., Ala or A for alanine)
• The amino acid sequence can be determined experimentally using techniques such as Edman degradation or mass spectrometry
• Advances in DNA sequencing technologies have also enabled the prediction of amino acid sequences from the corresponding gene sequences
• The amino acid sequence is unique to each protein and determines its specific structure and function