Protein Science I

This is an introductory course in the science of proteins, aimed at undergraduate biochemistry majors at a research university. It will cover the composition, structure and function of proteins, as well as experimental methods for producing, purifying and studying proteins. Basic topics in chemistry, such as molecular bonds and interactions, will be touched upon as well.

This course falls within the Department of Biochemistry within the School of Biology.

Syllabus

Week 1: Molecules and molecular forces: putting the chemistry back into biochemistry

Daily lesson 1.1: The periodic table
Daily lesson 1.2: Electronegativity
Daily lesson 1.3: Chemical (covalent) bonds and ionic bonds
Daily lesson 1.4: Resonance stabilization
Daily lesson 1.5: Chemical reactions,
Daily lesson 1.6: Chemical reaction kinetics and free energy
Daily lesson 1.7: pH and pK_a

Week 2: Non-covalent molecular forces

Daily lesson 2.1: Titration curves
Daily lesson 2.2: pK_a shifts in molecules
Daily lesson 2.3: Charge, electrostatics, screening
Daily lesson 2.4: van der Waals interactions
Daily lesson 2.5: Hydrogen bonds
Daily lesson 2.6: Hydrophobic interactions
Daily lesson 2.7: Cation-pi and aromatic-aromatic interactions

Week 3: Amino acids, peptides, and proteins

Daily lesson 3.1: Overview of amino acids and their metabolism
Daily lesson 3.2: Hydrophobic amino acids (VILMA, FYW, CPG)
Daily lesson 3.3: Polar and charged amino acids (STNQ, DERKH)
Daily lesson 3.4: Peptide bond
Daily lesson 3.5: Peptides
Daily lesson 3.6: Proteins
Daily lesson 3.7: Disulfide bonds

Week 4: Protein primary structure

Daily lesson 4.1: Protein sequencing: Edman degradation and mass spectrometry
Daily lesson 4.2: Post-translational modifications
Daily lesson 4.3:
Daily lesson 4.4:
Daily lesson 4.5: Alignment of two sequences: BLAST, Needleman-Wunsch, Smith-Waterman
Daily lesson 4.6: Multiple sequence alignment and molecular evolution
Daily lesson 4.7: Multiple sequence alignment and homology modeling

Week 5: Protein secondary structure

Daily lesson 5.1: Definition of a dihedral angle
Daily lesson 5.2: Dihedral angles found in proteins
Daily lesson 5.3: Sidechain rotamers
Daily lesson 5.4: Backbone dihedrals: the Ramachandran map
Daily lesson 5.5: Alpha helices
Daily lesson 5.6: Beta sheets and turns
Daily lesson 5.7: Conformational stability of secondary structure in solution

Week 6:

Daily lesson 6.1:
Daily lesson 6.2:
Daily lesson 6.3:
Daily lesson 6.4:
Daily lesson 6.5:
Daily lesson 6.6:
Daily lesson 6.7:

Week 7:

Daily lesson 7.1:
Daily lesson 7.2:
Daily lesson 7.3:
Daily lesson 7.4:
Daily lesson 7.5:
Daily lesson 7.6:
Daily lesson 7.7:

Week 8:

Daily lesson 8.1:
Daily lesson 8.2:
Daily lesson 8.3:
Daily lesson 8.4:
Daily lesson 8.5:
Daily lesson 8.6:
Daily lesson 8.7:

Week 9:

Daily lesson 9.1:
Daily lesson 9.2:
Daily lesson 9.3:
Daily lesson 9.4:
Daily lesson 9.5:
Daily lesson 9.6:
Daily lesson 9.7:

Week 10:

Daily lesson 10.1:
Daily lesson 10.2:
Daily lesson 10.3:
Daily lesson 10.4:
Daily lesson 10.5:
Daily lesson 10.6:
Daily lesson 10.7:

Instructors

Prof. Bill Wedemeyer, from Michigan State University