Rucete ✏ Lehninger Principles of Biochemistry In a Nutshell
3.4 The Structure of Proteins: Primary Structure
This chapter introduces the concept of protein primary structure—the unique linear sequence of amino acids in a polypeptide chain—and explains its central role in determining protein structure, function, and evolutionary relationships.
Levels of Protein Structure
• Protein structure is organized into four levels: primary (amino acid sequence and covalent bonds), secondary (local stable arrangements), tertiary (overall 3D folding), and quaternary (spatial arrangement of subunits in multisubunit proteins).
• The primary structure is the sequence of amino acids linked by peptide (and sometimes disulfide) bonds; it dictates higher-order structure and function.
Importance and Determination of Primary Structure
• The unique amino acid sequence of each protein determines its 3D shape and specific biological function.
• Variations in sequence—ranging from single residue changes to large deletions—can dramatically affect function and are the basis for many genetic diseases.
• Functionally similar proteins in different species often show similar sequences, especially in essential regions (conserved regions).
• Most modern sequence data come from genome databases and mass spectrometry, but classical methods like Edman degradation and chemical labeling remain useful for sequencing and analyzing protein fragments.
• Proteases and chemical reagents are used to cleave proteins at specific residues for sequencing and functional studies.
Peptide Synthesis and Sequence Analysis
• Small peptides can be chemically synthesized, often by automated solid-phase synthesis, allowing stepwise addition of amino acids while anchored to a resin.
• Mass spectrometry (MALDI, ESI, MS/MS) can determine molecular mass, sequence, and identify proteins in complex mixtures or whole proteomes.
• Sequence information can be used to infer protein structure, function, modifications, and cellular localization signals.
Protein Sequence Comparison and Evolution
• Comparing protein sequences reveals families of homologous proteins with shared ancestry and similar functions (homologs: orthologs from different species, paralogs within the same species).
• Bioinformatics tools align sequences and identify conserved regions, consensus sequences, and signature motifs linked to specific biological functions.
• Sequence alignment and analysis can be used to infer evolutionary relationships and construct phylogenetic trees, revealing how proteins and species have diverged over time.
• Sequence logos provide a visual summary of conserved and variable positions in protein families.
In a Nutshell
• The primary structure—the amino acid sequence—uniquely defines each protein, determines its structure and function, and underlies both health and disease.
• Protein sequences can be determined by DNA sequencing and mass spectrometry, and analyzed to explore protein function, modification, and evolution.
• Sequence comparison and bioinformatics allow researchers to trace evolutionary history, discover protein families, and identify functionally critical regions in proteins.