SC/BIOL 2020 4.00

York U

Course Overview

Lessons & Practice

1. Introduction, chemical bonds

28min

1.1.1. Hydrogen Bonds4 min

1.1.2. Hydrophobic Interactions4 min

1.1.3. Electrostatic/Ionic Interactions3 min

1.1.4. Van der Waals Forces3 min

1.1.5. Disulfide Bond3 min

1.1.6. Example: Hydrogen Bonding3 min

1.1.7. Example: Non-Covalent Bonds4 min

1.1.8. Practice: Amino Acid Hydrophobicity5 min

2. Water acids and bases, buffers

19min

2.1.1. The Nature of Acids and Bases15 min

2.2.1. Buffers4 min

3. Amino Acids

1.1hr

3.1.1. Amino Acids10 min

3.1.2. Example: Similar Amino Acids3 min

3.1.3. Example: Directed Mutagenesis3 min

3.2.1. Peptide Bond6 min

3.2.2. Peptide Bond Angles3 min

3.2.3. Example: Peptide Chain4 min

3.2.4. Example: Peptide Bond Angles2 min

3.2.5. Practice: Peptide Bond Resonance2 min

3.3.1. Acids-Base Definitions, pH, pKa5 min

3.3.2. pKa and Ionization State8 min

3.3.3. pKa of Amino Acids10 min

3.3.4. Amino Acid Isoelectric Point5 min

3.3.5. Practice: pKa of Side Chains4 min

3.Q. Amino Acids: Checkpoint Quiz7 Qns

3.P.1. Practice: Role of Amino Acids in an Active Site

3.P.2. Practice: Amino Acids

4. Protein Structure

1.4hr

4.1.1. α-helix3 min

4.1.2. Properties of α-helix5 min

4.1.3. Example: Properties of an Alpha Helix3 min

4.1.4. Example: Point Mutation in Alpha Helix4 min

4.1.5. Practice: Alpha-Helix3 min

4.2.1. β-Sheet4 min

4.2.2. β-turns and loops5 min

4.2.3. Example: Beta-Turns2 min

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

4.2.5. Example: Beta-Barrel Channels4 min

4.2.6. Practice: Stacked Beta-Sheets

4.3.1. Ramachandran Plot3 min

4.3.2. Example: Ramachandran Plot3 min

4.4.1. Anfinsen's Experiment8 min

4.4.2. Thermodynamics of Protein Folding7 min

4.4.3. Example: Urea2 min

4.4.4. Practice: Protein Folding2 min

4.5.1. Tertiary and Quarternary Protein Structure9 min

4.5.2. Example: Tertiary Structure (Motifs)3 min

4.5.3. Practice: Quaternary Structure3 min

4.6.1. Primary and Secondary Protein Structure5 min

4.6.2. Example: Point Mutation in Secondary Structure3 min

4.Q. Protein Structure: Checkpoint Quiz5 Qns

4.P.1. Practice: Hydrophobicity Scale

4.P.2. Practice: Thermophilic Proteins

5. Protein Purification

31min

5.1.1. Activity Assays7 min

5.1.2. Ammonium Sulfate Precipitation6 min

5.1.3. Specific Activity1 min

5.2.1. Methods of Determining Protein Sequence3 min

5.2.2. Protein Detection Techniques6 min

5.2.3. Mass Spectrometry2 min

5.2.4. Practice: Peptide Digest6 min

5.3.1. Protein Purification: Highlights

5.P.1. Practice: Peptide Digest

5.P.2. Ammonium Sulfate Precipitation

6. Protein Function & Enzymes

1.1hr

6.1.1. Protein Functions3 min

6.2.1. Post-translational Modifications7 min

6.3.1. Silk2 min

6.3.2. Keratins6 min

6.3.3. Collagen6 min

6.3.4. Collagen Example Problem3 min

6.3.5. Example: Keratins4 min

6.3.6. Practice: Fibers2 min

6.4.1. Enzyme Classes7 min

6.4.2. Active Site3 min

6.4.3. Enzyme Mechanisms7 min

6.4.4. Cofactors/Coenzymes2 min

6.4.5. Chymotrypsin7 min

6.4.6. Example: Enzyme Classes58 sec

6.4.7. Example: Enzyme Mechanics1 min

6.4.8. Example: Coenzymes and Cofactors33 sec

6.4.9. Practice: Enzyme Catalyzed Reactions1 min

6.4.10. Chymotrypsin2 min

6.Q. Checkpoint Quiz4 Qns

7. Glycolysis and gluconeogenesis

1.9hr

7.1.1. Glycolysis11 min

7.1.2. Glycolysis Regulation4 min

7.1.3. ATP production in Glycolysis1 min

7.1.4. Triose Phosphate Isomerase2 min

7.1.5. Glycolysis Regulation41 sec

7.1.6. Glycolysis1 min

7.1.7. Glycolysis: Cheatsheet

7.2.1. Glycogen Synthesis and Breakdown10 min

7.2.2. Example: Carbohydrate Metabolism- BIOCH22803 min

7.2.3. Example: Polysaccharide Structure-BIOCH22803 min

7.3.1. Pyruvate Dehydrogenase6 min

7.3.2. Pyruvate Dehydrogenase Complex38 sec

7.3.3. Regulation of PDC1 min

7.4.1. Pentose Phosphate Pathway3 min

7.5.1. Lactate Fermentation2 min

7.5.2. Alcohol Fermentation42 sec

7.5.3. Anaerobic Metabolism1 min

7.5.4. Lactate Formation55 sec

7.5.5. Anaerobic respiration30 sec

7.6.1. Structure of Mitochondria3 min

7.6.2. Pyruvate Dehydrogenase6 min

7.6.3. Citric Acid Cycle8 min

7.6.4. Pyruvate Dehydrogenase Complex38 sec

7.6.5. Regulation of PDC1 min

7.6.6. The Citric Acid Cycle1 min

7.6.7. The Citric Acid Cycle: Cheatsheet

7.7.1. Electron Transporters6 min

7.7.2. The Electron Transport Chain8 min

7.7.3. Electron Transport Inhibitors3 min

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

7.7.5. ATP Synthesis10 min

7.7.6. Electron Transporters49 sec

7.7.7. The electron transport chain1 min

7.7.8. Electron Transport Inhibitors42 sec

7.7.9. ATP production: Cheatsheet

7.Q. Checkpoint Quiz4 Qns

8. Oxidation of pyruvate, citric acid cycle

13min

8.1.1. Structure of Mitochondria3 min

8.1.2. Citric Acid Cycle8 min

8.1.3. The Citric Acid Cycle1 min

8.1.4. The Citric Acid Cycle: Cheatsheet

9. Oxidative phosphorylation and electron transport

30min

9.1.1. Electron Transporters6 min

9.1.2. Electron Transport Chain7 min

9.1.3. Electron Transport Inhibitors3 min

9.1.4. ATP Synthesis10 min

9.1.5. Electron Transporters49 sec

9.1.6. The electron transport chain1 min

9.1.7. Electron Transport Inhibitors42 sec

9.1.8. ATP Synthesis1 min

9.1.9. ATP production: Cheatsheet

9.P.1. Mitochondria

9.P.2. P/O ratios

10. Metabolism of fatty acids

24min

10.1.1. Fat Degradation (Beta Oxidation)11 min

10.1.2. Fat Catabolism1 min

10.1.3. Beta-oxidation51 sec

10.2.1. Fat Synthesis10 min

10.2.2. Fatty Acid Synthesis2 min

10.Q. Metabolic Processes2 Qns

10.P.1. Beta-oxidation

10.P.2. "Hitting the Wall"

11. Metabolism of amino acids

12. Nucleotides and nucleic acids

31min

12.1.1. Example: Purine/Pyrimidine4 min

12.1.2. Example: Base Pairing4 min

12.1.3. DNA Packing4 min

12.1.4. Review of DNA Structure10 min

12.1.5. Chromosomes and Chromatin7 min

12.1.6. RNA2 min

12.Q. Checkpoint Quiz4 Qns

13. DNA replication, and Repair

54min

13.1.1. Meselson-Stahl Experiment8 min

13.1.2. DNA Replication in Cells14 min

13.1.3. Example: Meselson-Stahl3 min

13.1.4. Example: DNA Replication3 min

13.1.5. Practice: DNA Replication

13.2.1. Telomerase & Telomeres4 min

13.2.2. New Practice Question2 min

13.3.1. Repair Mechanisms6 min

13.3.2. Repair of DNA Strand Breaks [detailed]9 min

13.3.3. Example: Mutations4 min

13.3.4. Example: Recombination3 min

13.3.5. Practice: DNA Polymerase

13.Q. DNA Replication and Repair Checkpoint Quiz5 Qns

14. RNA transcription and processing + Regulation of Gene Transcription

42min

14.1.1. The Lac Operon & Glucose Regulation [detailed]5 min

14.1.2. The Tryptophan (Trp) Operon5 min

14.1.3. Example: Negative Regulation3 min

14.2.1. Initiation8 min

14.2.2. Elongation7 min

14.2.3. Termination4 min

14.2.4. Prokaryotic Regulatory Proteins5 min

14.2.5. Example: mRNA Transcription4 min

14.2.6. Example: Transcriptional Repressors2 min

14.Q. Transcription Checkpoint Quiz5 Qns

15. Coordination of metabolism

10min

15.1.1. Summary of Metabolism10 min

16. Intermolecular Forces + Properties of Water

46min

16.1.1. Types of Chemical Bonds 5 min

16.1.2. Practice 1

16.1.3. Practice 2

16.2.1. Intermolecular Forces: Hydrogen Bonding5 min

16.2.2. Example 2 min

16.2.3. Practice 12 min

16.2.4. Practice 22 min

16.2.5. Practice 33 min

16.3.1. Intermolecular Forces: Van der Waals Interactions 11 min

16.3.2. Practice 13 min

16.3.3. Practice 2

16.4.1. Important Elements that Make Up Life4 min

16.4.2. Unique Properties of Water6 min

16.4.3. Practice 12 min

16.4.4. Practice 22 min

17. Translation

1.1hr

17.1.1. Reading the Genetic Code (mRNA)8 min

17.1.2. tRNA and rRNA7 min

17.1.3. Translation into Proteins9 min

17.1.4. Translation: Protein Synthesis12 min

17.1.5. Example: Translation3 min

17.1.6. Example: Translation II5 min

17.1.7. Example: Translation III3 min

17.2.1. Initiation of Translation9 min

17.2.2. Elongation in Translation 5 min

17.2.3. Termination of Translation2 min

17.Q. Checkpoint Quiz2 Qns

18. Recombinant DNA and Sequencing

1.6hr

18.1.1. (Agarose) Gel Electrophoresis 3 min

18.1.2. Northern Blot2 min

18.1.3. Southern Blot2 min

18.1.4. Polymerase Chain Reaction10 min

18.1.5. Cloning and DNA libraries17 min

18.1.6. DNA Sequencing9 min

18.1.7. Microarrays 3 min

18.1.8. DNA Fingerprinting6 min

18.1.9. CRISPR [detailed]9 min

18.1.10. Example: Hybridization4 min

18.1.11. Example: Cloning 3 min

18.1.12. Example: DNA Transformation4 min

18.1.13. Example: DNA Fingerprinting3 min

18.2.1. DNA Sequencing10 min

18.2.2. Bioinformatics9 min

18.2.3. Example: Bioinformatics4 min

18.2.4. Practice: BLAST

18.Q. Checkpoint Quiz5 Qns

19. Buffers

20min

19.1.1. Introduction to Buffers6 min

19.1.2. Calculating the pH of a Buffer System4 min

19.1.3. Buffers Problem Type 16 min

19.1.4. Buffers Problem Type 22 min

19.1.5. Buffers Problem Type 32 min

20. Enzyme Catalysis

27min

20.1.1. Enzyme Kinetics3 min

20.1.2. Michaelis-Menten Equation5 min

20.1.3. Lineweaver-Burke Plot2 min

20.1.4. Example: Lineweaver Burke Plot1 min

20.1.5. Practice: Enzyme Kinetics52 sec

20.1.6. Enzyme Kinetics Practice Question2 min

20.2.1. Reversible/Irreversible Inhibition3 min

20.2.2. Competitive Inhibition2 min

20.2.3. Non-Competitive Inhibition3 min

20.2.4. Example: Enzyme Inhibition2 min

20.2.5. Cheatsheet: Summary of Inhibitors

20.3.1. Enzyme Regulation3 min

20.Q. Checkpoint Quiz4 Qns

21. Carbohydrate Structure

36min

21.1.1. Carbohydrates (Sugars)5 min

21.1.2. Carbohydrate Conformation and Annotation5 min

21.1.3. Carbohydrate Cyclization8 min

21.1.4. Complex Carbohydrates7 min

21.1.5. Polysaccharides5 min

21.1.6. Example: Simple Sugars2 min

21.1.7. Example: Glucose2 min

21.1.8. Example: Carbohydrate Structures1 min

21.1.9. Practice: Naming Carbohydrates1 min

21.1.10. Cheatsheet: Important Monosaccharides to Remember

21.Q. Checkpoint Quiz3 Qns

22. Nucleic Acid Structure + DNA Denaturation

40min

22.1.1. Review of DNA Structure10 min

22.1.2. DNA Packing4 min

22.1.3. RNA2 min

22.1.4. Chromosomes and Chromatin7 min

22.1.5. Example: Purine/Pyrimidine4 min

22.1.6. Example: Base Pairing4 min

22.2.1. Denaturation5 min

22.2.2. Denaturation vs. DNA Stability3 min

23. Fundamental Concepts of Biochemistry

18min

23.1.1. From Monomers to Polymers4 min

23.2.1. Gibbs Free Energy8 min

23.2.2. Example 2 min

23.3.1. The Central Dogma of Biology4 min

23.Q. Checkpoint Quiz6 Qns

24. Membrane Protein & Transporters

1.3hr

24.1.1. Proteins in the Lipid Bilayer1 min

24.1.2. Peripheral Membrane Proteins5 min

24.1.3. Integral Membrane Proteins5 min

24.1.4. Measuring Hydrophobicity7 min

24.1.5. Membrane Protein Folding2 min

24.1.6. Practice: Peripheral Membrane Proteins1 min

24.1.7. Practice: Integral Membrane Proteins1 min

24.1.8. Practice: Hydropathy49 sec

24.1.9. Practice: Integral Membrane Proteins55 sec

24.2.1. Membrane Proteins4 min

24.2.2. Practice: Membrane Proteins

24.3.1. Bacteriorhodopsin4 min

24.3.2. Porins2 min

24.3.3. Example: Bacteriorhodopsin1 min

24.3.4. Example: Membrane Proteins1 min

24.4.1. Introduction and Passive Transport7 min

24.4.2. Active Transport7 min

24.4.3. Transport Proteins: Ion Channels4 min

24.4.4. Example: Active vs. Passive Transport5 min

24.4.5. Practice: Potassium Ion Channels59 sec

24.5.1. Ion Channel Receptors2 min

24.5.2. G-Protein Coupled Receptors (GPCRs)7 min

24.5.3. Receptor Tyrosine Kinases (RTKs)5 min

24.5.4. Example: G-protein Coupled Receptors1 min

24.Q. Checkpoint Quiz4 Qns

24.P.1. Practice: G-Protein Coupled Receptors

24.P.2. Practice: Predicting transmembrane segments

25. Hormone Signalling

13min

25.1.1. Hormonal Metabolic Regulation: Catabolic6 min

25.1.2. Hormonal Metabolic Regulation: Anabolic4 min

25.1.3. Catabolic Horomone Signaling1 min

25.1.4. Insulin32 sec

25.1.5. Glucogenolysis45 sec

25.Q. Checkpoint Quiz2 Qns

26. Eukaryotic Transcription

2hr

26.1.1. Transcription In Eukaryotes9 min

26.1.2. General Transcription Factors (GTFs)5 min

26.1.3. Regulation of Eukaryotic Transcription12 min

26.1.4. Chromatin state and histone modifications7 min

26.2.1. RNA Maturation in Eukaryotes8 min

26.2.2. Eukaryotic Post-Transcriptional Regulation6 min

26.2.3. Nuclear Import and Export7 min

26.2.4. Example: mRNA Processing2 min

26.2.5. Example: mRNA Transcript2 min

26.3.1. Eukaryotic Transcription Initiation10 min

26.3.2. 5' Capping5 min

26.3.3. Poly(A) Tail5 min

26.3.4. Splicing and the Spliceosome6 min

26.3.5. Alternative Splicing12 min

26.3.6. mRNA Nuclear Export11 min

26.3.7. Cytoplasmic Processing of mRNAs13 min

27. Introduction to Metabolism: Redox Reactions

48min

27.1.1. Intro to Metabolism7 min

27.1.2. Gibbs Free Energy10 min

27.1.3. High Energy Intermediates9 min

27.1.4. Example: Gibbs Free Energy3 min

27.1.5. Free energy of ATP52 sec

27.1.6. Coupled Reactions1 min

27.2.1. Oxidation-Reduction Reactions6 min

27.2.2. Electrochemistry4 min

27.2.3. Cell Potentials and Gibbs Free Energy3 min

27.2.4. Example: Oxidation-Reduction Reactions3 min

27.Q. Checkpoint Quiz3 Qns

28. Ligand-binding: Myoglobin and Hemoglobin

23min

28.1.1. Myoglobin1 min

28.1.2. Hemoglobin10 min

28.1.3. Dissorders in Hemoglobin2 min

28.1.4. Ligand Binding10 min

28.1.5. Hemoglobin Regulation

28.1.6. New Practice Question

28.1.7. Myoglobin

28.Q. Checkpoint Quiz3 Qns

Mock Exams

ME.1. Midterm 1 - Mock Assessment7 Qns

ME.2. Midterm 2 - Mock Assessment42 Qns

ME.3. Final Exam - Mock Assessment78 Qns

ME.1 Midterm 1 - Mock Assessment

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