# 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:
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* Daily lesson 6.6:
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### Week 7:

* Daily lesson 7.1:
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### Week 8:

* Daily lesson 8.1:
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### Week 9:

* Daily lesson 9.1:
* Daily lesson 9.2:
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* Daily lesson 9.6:
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### Week 10:

* Daily lesson 10.1:
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* 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