Learning Objectives
Exam II

Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure
 

•Know amino acid structures including all twenty side chains, properties

•Understand pKa's and pH effects on weak acids and bases (esp. -COO^-, -NH³⁺)

•Know approx. pKa’s of side chains (for those that can be acids/bases)

•Use Henderson-Hasselbach equation for ratios, concentrations of species

•Describe the peptide bond and its formation

•Describe primary structure of proteins

•Use sequencing data (protease cutting and Edman degradation) to determine protein primary structure

•Be familiar with the concepts: DNA->RNA->protein, protein synthesis, and post-translational modification of proteins

•Know techniques and principles for protein purification, sequencing, synthesis of polypeptides
 
 

Chapter 6: Protein 3D Structure
 

•Levels of protein structure: primary, secondary, tertiary, quaternary

•Describe covalent and noncovalent forces involved at each level

•Describe H-bonding for a-helix and b-pleated sheet

•Give the likely effects of amino acid substitutions on 3D structure

•Be familiar with typical fibrous and globular protein structures

•Understand disulfide bonding

•Know techniques and principles for spectroscopy and subunit determination

Chapter 7: Protein Function and Evolution
 

•Know the differentiated roles of myoglobin and hemoglobin

•Know the mechanism of oxygen binding to heme

•Understand cooperativity and allosterism

•Know some of the changes in hemoglobin upon oxygen binding

•Understand the four models for allosterism: Sequential (KNF), Concerted (MWC), Multi-State, and Protein Dynamic

•Know the effects of other ligands and hemoglobin: the Bohr effect, carbamate reaction, bisphosphoglycerate

•Understand mechanism of mutation and effect on resultant protein

•Know some hemoglobin variants, properties (eg., fetal Hb, sickle-cell Hb)

•Understand how immunoglobulins work

•Understand genetics of immunoglobulins and how that results in variablility

•Know how HIV causes AIDS (Find a cure and get an A, and the Nobel Prize!)

Chapter 8: Proteins in Motion: Contractile and Motile Systems
 

•Understand actin-myosin contractile systems:

•Structure of actin, structure of myosin

•Assembly of structures in muscle

•Mechanism of contraction: the sliding filament model

•Roles of calcium, ATP

•Be familiar with non-muscle actin and myosin

•Understand microtubule systems for motility:

•Motions of cilia and flagella

•Intracellular transport: dynein, kinesin

•Microtubules and mitosis

•Understand mechanism for rotating protein in bacteria