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By the end of this lesson, you will be able to:

  1. describe the general structure of an amino acid and be able to identify and draw the structural formula of a typical amino acid.
  2. explain the how the  functional groups found in proteins affect their function.
  3. describe the formation of peptide bonds (linkages) in forming polypeptides and be able to recognize them in a structural formula.
  4. describe the biophysical properties of the peptide linkage, what causes them and how they contribute to protein secondary structure.
  5. describe the structure of protein in terms of primary, secondary, tertiary and quaternary structure and the role of disulphide linkages, hydrogen bonds and hydrophobic interactions in forming and maintaining these structures.
  6. recognize, and be able to account for, the phenomenon of protein denaturation, with particular reference to the effects of pH, temperature and salinity.
  7. be able to analyze the 3-dimensional structure of carbohydrates (mono-, di- and polysaccharides) and lipids using a computer program/web using an application such as Chime, Ras-mol, etc

Proteins comprise more than 50% of a cell's dry weight and perform many functions in the body including regulation.  It is the structure of proteins that our DNA codes for.  Proteins, in turn, mediate the cell's, therefore the organism's, activities.  

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This lesson is about protein structure and it's impact on function. DNA codes for protein in the cell; proteins ensure that other macromolecules are synthesized. The monomers of proteins are amino acids. Condensation reactions result in peptide linkages which form polypeptide chains of many amino acids. This is the primary structure of proteins. They can (or not) fold into the secondary structures of alpha helices or beta pleated sheets. Protein function can only be realized once the tertiary structure has formed. Some, but not all proteins, aggregate together to become quaternary proteins.

Source: M O'Mahony, open source figures


Student note template to complete while watching the video


Source: M. O'Mahony, open source figures

Protein Folding Activity

This activity was shared on one of the list serves I belong to. You've done some of this, but the folding rules at the beginning of the "assignment" are good and I don't think I've given you anything written about it.


Source: Michal Kreiselman

Protein Folding Web-Interactive

The Concord Consortium has an excellent series of activities on Proteins at  

Their Protein Folding activity can be found at:



Molecular Workbench

Go to the site:

and select Proteins and Nucleic Acids

Lessons 1-6 are about Proteins.

This simulator requires Java.

Source: Molecular Workbench, The Concord Consortium

Protein Folding

Analysis questions for the 3D Molecular Designs manipulatives.


Source: 3D Molecular Designs

3D Molecular Designs Handout 1

Instructions for using the materials to make a protein.


Source: 3D Molecular Designs

3D Molecular Designs

Examining protein secondary structure using the manipulatives


Source: 3D Molecular Designs

How Life May Have First Emerged On Earth: Foldable Proteins in a High-Salt Environment

Short article (with processing questions) from Science Daily that examines the role of protein folding when the environment around the protein changes.
Straight forward reading.