Primary Structure of Proteins: Composition, Sequence, and Biological Importance

Primary Structure of Proteins

Definition and Formation

The primary structure of a protein refers to the unique sequence of amino acids linked together by peptide bonds to form a polypeptide chain. This sequence determines the protein's identity and function.

• Peptide bond: A covalent bond formed between the carboxyl group of one amino acid and the amino group of another.

• Amino acid residue: An amino acid that is part of a polypeptide chain.

• Composition: The types and numbers of amino acids in a chain.

• Sequence: The specific order of amino acids from the N-terminus (amino end) to the C-terminus (carboxyl end).

Example: The primary structure of a protein can be represented as a linear sequence of amino acids, such as Gly–Ala–Ser–Leu.

Key Features of Primary Structure

• Linear sequence: Each protein has a unique order of amino acids.

• Directionality: The sequence is always written from the N-terminus to the C-terminus.

• Peptide bonds: The backbone of the polypeptide is formed by repeating units of –N–C–C–.

Formula for peptide bond formation:

$\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Practice and Application

• Identifying sequence: Use 1-letter or 3-letter codes to represent amino acids in a sequence.

• Recognizing α-carbons: The α-carbon is the central carbon atom in each amino acid residue.

• Functional importance: The primary structure determines higher levels of protein structure (secondary, tertiary, quaternary).

Example: Cleavage of peptide bonds by drugs or enzymes directly affects the primary structure.

Importance of Primary Structure

• Protein diversity: The sequence of amino acids encodes the protein's unique properties and function.

• Mutation effects: Changes in the primary structure (mutations) can alter protein function and lead to disease.

• Hierarchy of structure: The primary structure is the foundation for secondary, tertiary, and quaternary structures.

Practice Questions and Examples

• Sequence identification: Given a peptide, fill in the blanks with the correct amino acid codes and circle the α-carbons.

• Structure analysis: Determine which amino acid residue is responsible for a peptide's function at a specific pH.

• Drug action: Identify the primary level of structure affected by a drug that cleaves peptide bonds.

Table: Levels of Protein Structure

Level	Description	Bond Types
Primary	Linear sequence of amino acids	Peptide bonds
Secondary	Local folding (α-helix, β-sheet)	Hydrogen bonds
Tertiary	3D folding of a single polypeptide	Hydrogen, ionic, hydrophobic, disulfide bonds
Quaternary	Assembly of multiple polypeptides	Same as tertiary (between subunits)

Additional info: The notes and questions provided focus on the identification and analysis of primary protein structure, including practical exercises with peptide sequences and the impact of chemical modifications. This foundational knowledge is essential for understanding protein biochemistry and its applications in medicine and biotechnology.