Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online





Learning Goals/Objectives for Chapter 2C:  After class and this reading, students will be able to

  • describe the differences between primary, secondary, supersecondary, tertiary, quaternary and domain protein structure
  • explain the basis of CD measurements for secondary structure
  • describe the similarities between torsion angles and an energy vs torsion angle plot for the rotation of the C2-C3 torison angle with phi/psi angles of peptide bonds and the 2D plots off allowed conformations around a given amino acid in a protein (Ramachandran plot).
  • (from reading give explanation for observed propensities of amino acids for different secondary structure)

C5.  Structual Clases of Proteins

 Proteins can be divided into 3 classes of protein, depending on their characteristic secondary structure. Click below for Chime structures showing examples of these proteins.

 Jmol:  Updated cytochrome B562  Jmol14 (Java) |  JSMol  (HTML5)

 Jmol:  Updated met-myoglobin  Jmol14 (Java) |  JSMol  (HTML5)    

Jmol: Updated  triose phosphate isomerase Jmol14 (Java) |  JSMol  (HTML5) 

  Jmol: Updated  hexokinase Jmol14 (Java) |  JSMol  (HTML5) 

 Jmol:  Updated   superoxide dismutase Jmol14 (Java) |  JSMol (HTML5) 

Jmol: Updated   human IgG1 antibodyJmol14 (Java) |  JSMol (HTML5)    

 Jmol: Updated   retinol binding proteinJmol14 (Java) |  JSMol (HTML5)

 fatty acid binding proteins; Peptide-N(4)-(N-Acetyl-b-D-Glucosaminyl) Asparagine Amidase  (PNGase F) - under construction.

A more complete classification of protein structure has been developed based on the following hierarchy of organization: Class, Architecture, Topology, and Homologous Superfamilies - CATH.

Structural Biology Knowledge Base

Here are some 3D structures resources, accessible through a sequence or ID-based search. and collated in Nature's Structural Biology Knowledge Base.


Return to Chapter 2C: Understanding Protein Conformation Sections

Return to Biochemistry Online Table of Contents

Archived version of full Chapter 2C:  Understanding Protein Conformation


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Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.