Biochemistry · MU Pleven

1. Three-Dimensional Structure of the Proteins. Super Secondary Domains: Leucine Type, Zn Fingers and Serpentine Type Domains.

Explains protein building blocks, then the four levels of protein structure: primary, secondary, tertiary and quaternary. Goes on to supersecondary motifs and the leucine zipper, zinc finger and serpentine domains, covering structure, DNA-binding or signalling roles and stabilisation. A summary table compares the three domain types.

Inside: 6 sections · 5 labelled pictures · 1 table · 22 flashcards · 6 min

Topic 1 of 76 in the MU Pleven syllabus for Biochemistry (Medicine, Year 2). The free AceMed note covers it in 6 sections, about 747 words (6 min of reading), with 22 flashcards.

In this note

  1. Three-Dimensional Structure of the Proteins.
  2. Protein building blocks
  3. Three-Dimensional Structure of Proteins
  4. Super-Secondary Structures (Motifs)
  5. Super Secondary Domains
  6. C. Serpentine Type Domain

Protein building blocks

  • Amino acids are compounds containing both, amino and carboxyl groups bonded to the same α-carbon, and 20 AA constitute the monomers of proteins. AA can be L or D, but only L are found in cells.
  • The combination of the carboxyl group (-COOH) and the amino group (-NH2) with the elimination of a water molecule forms a peptide bond.
  • In order to calculate the number of AA present in a protein we have divide the molecular mass of the
  • protein by 110, which is the average mass of an amino acid.
  1. 1. Molecular weight below 5000 Da: peptides
  2. 2. Molecular weight above 5000 Da: proteins
  3. 3. 1Da = 1,66 ×10^-27Kg

Three-Dimensional Structure of Proteins

The three-dimensional (3D) structure of a protein is the specific spatial arrangement of its atoms, which determines its biological function. Protein structure is organized in four hierarchical levels:

I. Primary Structure

  • Definition: The linear sequence of amino acids in a polypeptide chain, joined by peptide bonds.
  • Stabilized by: Covalent peptide bonds.
  • Importance: Determines all higher levels of structure because folding depends on the sequence.

II. Secondary Structure

  • Definition: Regular, repeating local arrangements of the polypeptide backbone.
  • Stabilized by: Hydrogen bonds between carbonyl oxygen and amide hydrogen.
  • Types:
  • α-helix: Right-handed coil; 3.6 amino acids per turn; stabilized by intrachain H-bonds.
  • β-pleated sheet: Formed by H-bonds between adjacent polypeptide chains (can be parallel or antiparallel).
  • β-turns (hairpins): Connect two strands of β-sheets, often containing glycine and proline.

III. Tertiary Structure

  • Definition: The overall 3D folding of a single polypeptide chain.
  • Stabilized by:
  • Hydrophobic interactions
  • Hydrogen bonds
  • Ionic bonds (salt bridges)
  • Disulfide bridges (covalent, between cysteines)
  • Importance: Creates functional domains and active sites for enzyme activity or ligand binding.

IV. Quaternary Structure

  • Definition: Association of two or more polypeptide subunits into a functional complex.
  • Example: Hemoglobin (α₂β₂ tetramer).
  • Stabilized by: Noncovalent interactions and sometimes disulfide bonds between subunits.

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