BIOC 2580

University of Guelph

Course Overview

Lessons & Practice

1. Biological polymers; building blocks and hydrolyzable bonds. Amino acids, peptides and proteins

1.4hr

1.1.1. From Monomers to Polymers4 min

1.2.1. Important Elements that Make Up Life4 min

1.2.2. Unique Properties of Water6 min

1.2.3. Practice 12 min

1.2.4. Practice 22 min

1.3.1. Types of Chemical Bonds 5 min

1.3.2. Practice 1

1.3.3. Practice 2

1.4.1. Intermolecular Forces: Hydrogen Bonding5 min

1.4.2. Example 2 min

1.4.3. Practice 12 min

1.4.4. Practice 22 min

1.4.5. Practice 33 min

1.5.1. Intermolecular Forces: Van der Waals Interactions 11 min

1.5.2. Practice 13 min

1.5.3. Practice 2

1.6.1. Amino Acids10 min

1.6.2. Example: Similar Amino Acids3 min

1.6.3. Example: Directed Mutagenesis3 min

1.7.1. Peptide Bond6 min

1.7.2. Peptide Bond Angles3 min

1.7.3. Example: Peptide Chain4 min

1.7.4. Example: Peptide Bond Angles2 min

1.7.5. Practice: Peptide Bond Resonance2 min

1.Q. Checkpoint Quiz6 Qns

2. Amino acids, peptides and proteins (continued), Polarity and ionization of amino acids

48min

2.1.1. Introduction to Buffers6 min

2.1.2. Calculating the pH of a Buffer System4 min

2.1.3. Buffers Problem Type 16 min

2.2.1. Acids-Base Definitions, pH, pKa5 min

2.2.2. pKa and Ionization State8 min

2.2.3. pKa of Amino Acids10 min

2.2.4. Amino Acid Isoelectric Point5 min

2.2.5. Practice: pKa of Side Chains4 min

2.Q. Checkpoint Quiz8 Qns

3. Separation of amino acids and proteins by chromatography

14min

3.1.1. Chromatography7 min

3.1.2. Chromatography: Part II7 min

3.Q. Checkpoint Quiz3 Qns

4. More analytical methods; Polypeptides and proteins: structural hierarchy, sequence. Basis of reactivity and hydrolysis

6min

4.1.1. SDS-PAGE (Electrophoresis)6 min

4.Q. Checkpoint Quiz2 Qns

5. Sequence determination

17min

5.1.1. Methods of Determining Protein Sequence3 min

5.1.2. Protein Detection Techniques6 min

5.1.3. Mass Spectrometry2 min

5.1.4. Practice: Peptide Digest6 min

5.Q. Checkpoint Quiz2 Qns

6. Secondary structure: α-helix, β-sheet

1.2hr

6.1.1. Hydrogen Bonds4 min

6.1.2. Hydrophobic Interactions4 min

6.1.3. Electrostatic/Ionic Interactions3 min

6.1.4. Van der Waals Forces3 min

6.1.5. Disulfide Bond3 min

6.1.6. Example: Hydrogen Bonding3 min

6.1.7. Example: Non-Covalent Bonds4 min

6.1.8. Practice: Amino Acid Hydrophobicity5 min

6.2.1. Primary and Secondary Protein Structure5 min

6.2.2. Example: Point Mutation in Secondary Structure3 min

6.3.1. α-helix3 min

6.3.2. Properties of α-helix5 min

6.3.3. Example: Properties of an Alpha Helix3 min

6.3.4. Example: Point Mutation in Alpha Helix4 min

6.3.5. Practice: Alpha-Helix3 min

6.4.1. β-Sheet4 min

6.4.2. β-turns and loops5 min

6.4.3. Example: Beta-Turns2 min

6.4.4. Example: H-bonding in Beta-Sheets2 min

6.4.5. Example: Beta-Barrel Channels4 min

6.4.6. Practice: Stacked Beta-Sheets

6.Q. Checkpoint Quiz3 Qns

7. Principles of tertiary structure. Protein stability and function

1hr

7.1.1. Tertiary and Quarternary Protein Structure9 min

7.1.2. Example: Tertiary Structure (Motifs)3 min

7.1.3. Practice: Quaternary Structure3 min

7.2.1. Silk2 min

7.2.2. Keratins6 min

7.2.3. Collagen6 min

7.2.4. Collagen Example Problem3 min

7.2.5. Example: Keratins4 min

7.2.6. Practice: Fibers2 min

7.3.1. Hemoglobin10 min

7.3.2. Dissorders in Hemoglobin2 min

7.4.1. Globular Proteins: Myoglobin1 min

7.4.2. Ligand Binding10 min

7.Q. Checkpoint Quiz4 Qns

7.P.1. Hemeoglobin and anaeobic regulation

8. Binding and recognition of substrates and specificity of enzymes; The basis of chemical and enzymatic catalysis.

26min

8.1.1. Enzyme Classes7 min

8.1.2. Active Site3 min

8.1.3. Enzyme Mechanisms7 min

8.1.4. Cofactors/Coenzymes2 min

8.1.5. Example: Enzyme Classes58 sec

8.1.6. Example: Enzyme Mechanics1 min

8.1.7. Example: Coenzymes and Cofactors33 sec

8.1.8. Practice: Enzyme Catalyzed Reactions1 min

8.2.1. Protein Functions3 min

8.Q. Checkpoint Quiz3 Qns

9. Mechanism of action of chymotrypsin, Enzyme assay and detection

28min

9.1.1. Chymotrypsin7 min

9.1.2. Chymotrypsin2 min

9.2.1. Beer-Lambert Law5 min

9.2.2. Pulldown Assays and Crosslinking6 min

9.2.3. ReporterAssays7 min

9.2.4. Example: Fluorescence Microscopy1 min

9.Q. Checkpoint Quiz1 Qn

10. Enzyme kinetics

14min

10.1.1. Enzyme Kinetics3 min

10.1.2. Michaelis-Menten Equation5 min

10.1.3. Lineweaver-Burke Plot2 min

10.1.4. Example: Lineweaver Burke Plot1 min

10.1.5. Practice: Enzyme Kinetics52 sec

10.1.6. Enzyme Kinetics Practice Question2 min

10.Q. Checkpoint Quiz4 Qns

11. Enzyme inhibition and regulation

13min

11.1.1. Reversible/Irreversible Inhibition3 min

11.1.2. Competitive Inhibition2 min

11.1.3. Non-Competitive Inhibition3 min

11.1.4. Example: Enzyme Inhibition2 min

11.1.5. Cheatsheet: Summary of Inhibitors

11.2.1. Enzyme Regulation3 min

11.Q. Checkpoint Quiz5 Qns

12. Lipids: fatty acids, triglycerides and phospholipids

50min

12.1.1. Introduction to Lipids2 min

12.1.2. Fatty Acids7 min

12.1.3. Triacylglycerols2 min

12.1.4. Glycerophospholipids3 min

12.1.5. Sphingolipids2 min

12.1.6. Cholesterol3 min

12.1.7. Signalling Lipids (i.e., Steroids)3 min

12.1.8. Example: Naming Fatty Acids3 min

12.1.9. Example: Identifying Lipids1 min

12.1.10. Practice: Fatty Acids1 min

12.2.1. The Lipid Bilayer6 min

12.2.2. Membrane Lipid Assembly3 min

12.2.3. Membrane Fluidity8 min

12.2.4. Membrane Lipid Dynamics2 min

12.2.5. Example: Membrane Fluidity1 min

12.2.6. Example: Cellular Membranes2 min

12.2.7. Practice: Transverse Diffusion of Lipids1 min

12.Q. Checkpoint Quiz5 Qns

13. Carbohydrate Chemistry: simple sugars, rings and glycosides

36min

13.1.1. Carbohydrates (Sugars)5 min

13.1.2. Carbohydrate Conformation and Annotation5 min

13.1.3. Carbohydrate Cyclization8 min

13.1.4. Complex Carbohydrates7 min

13.1.5. Polysaccharides5 min

13.1.6. Example: Simple Sugars2 min

13.1.7. Example: Glucose2 min

13.1.8. Example: Carbohydrate Structures1 min

13.1.9. Practice: Naming Carbohydrates1 min

13.1.10. Cheatsheet: Important Monosaccharides to Remember

13.Q. Checkpoint Quiz3 Qns

14. Chemistry of nucleic acid bases, nucleotides & polynucleotides + DNA Double Helix

20min

14.1.1. Review of DNA Structure10 min

14.1.2. RNA2 min

14.1.3. Example: Purine/Pyrimidine4 min

14.1.4. Example: Base Pairing4 min

14.Q. Checkpoint Quiz4 Qns

15. ATP as Cellular Energy Currency

6min

15.1.1. ATP and the Proton Motive Force (PMF)6 min

15.Q. Checkpoint Quiz3 Qns

16. Introduction to Metabolism

41min

16.1.1. Intro to Metabolism7 min

16.1.2. Gibbs Free Energy10 min

16.1.3. High Energy Intermediates9 min

16.1.4. Oxidation-Reduction Reactions6 min

16.1.5. Example: Oxidation-Reduction Reactions3 min

16.1.6. Example: Gibbs Free Energy3 min

16.1.7. Free energy of ATP52 sec

16.1.8. Coupled Reactions1 min

16.Q. Introduction to Metabolism4 Qns

17. Fatty Acid Catabolism + Synthesis

24min

17.1.1. Fat Degradation (Beta Oxidation)11 min

17.1.2. Fat Catabolism1 min

17.1.3. Beta-oxidation51 sec

17.2.1. Fat Synthesis10 min

17.2.2. Fatty Acid Synthesis2 min

17.Q. Checkpoint Quiz4 Qns

18. Glycolysis + Pyruvate Dehydrogenase Complex

35min

18.1.1. Glycolysis11 min

18.1.2. Glycolysis Regulation4 min

18.1.3. ATP production in Glycolysis1 min

18.1.4. Triose Phosphate Isomerase2 min

18.1.5. Glycolysis Regulation41 sec

18.1.6. Glycolysis1 min

18.1.7. Glycolysis: Cheatsheet

18.2.1. Lactate Fermentation2 min

18.2.2. Alcohol Fermentation42 sec

18.2.3. Anaerobic Metabolism1 min

18.2.4. Lactate Formation55 sec

18.2.5. Anaerobic respiration30 sec

18.3.1. Pyruvate Dehydrogenase6 min

18.3.2. Pyruvate Dehydrogenase Complex38 sec

18.3.3. Regulation of PDC1 min

18.Q. Checkpoint Quiz6 Qns

19. The Citric Acid Cycle

13min

19.1.1. Structure of Mitochondria3 min

19.1.2. Citric Acid Cycle8 min

19.1.3. The Citric Acid Cycle1 min

19.1.4. The Citric Acid Cycle: Cheatsheet

19.Q. Checkpoint Quiz5 Qns

20. Oxidative Phosphorylation: The Electron Transport Chain + ATP synthase

27min

20.1.1. Electron Transporters6 min

20.1.2. The Electron Transport Chain8 min

20.1.3. ATP Synthesis10 min

20.1.4. Electron Transporters49 sec

20.1.5. The electron transport chain1 min

20.1.6. Electron Transport Inhibitors42 sec

20.1.7. ATP production: Cheatsheet

20.Q. Checkpoint Quiz7 Qns

Mock Exams

ME.1. Midterm - Mock Assessment7 Qns

ME.2. Final Exam - Mock Assessment68 Qns

ME.1 Midterm - Mock Assessment

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Midterm - Mock Assessment

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