BCHM 102

Queen's

Course Overview

Lessons & Practice

1. Water, Weak Bonds, and the Generation of Order Out of Chaos

46min

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

1.2.1. The Nature of Acids and Bases15 min

1.3.1. Buffers4 min

2. Amino Acids

1.1hr

2.1.1. Amino Acids10 min

2.1.2. Example: Similar Amino Acids3 min

2.1.3. Example: Directed Mutagenesis3 min

2.2.1. Peptide Bond6 min

2.2.2. Peptide Bond Angles3 min

2.2.3. Example: Peptide Chain4 min

2.2.4. Example: Peptide Bond Angles2 min

2.2.5. Practice: Peptide Bond Resonance2 min

2.3.1. Acids-Base Definitions, pH, pKa5 min

2.3.2. pKa and Ionization State8 min

2.3.3. pKa of Amino Acids10 min

2.3.4. Amino Acid Isoelectric Point5 min

2.3.5. Practice: pKa of Side Chains4 min

2.Q. Amino Acids: Checkpoint Quiz7 Qns

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

2.P.2. Practice: Amino Acids

3. Protein Three-Dimensional Structure

1.4hr

3.1.1. α-helix3 min

3.1.2. Properties of α-helix5 min

3.1.3. Example: Properties of an Alpha Helix3 min

3.1.4. Example: Point Mutation in Alpha Helix4 min

3.1.5. Practice: Alpha-Helix3 min

3.2.1. β-Sheet4 min

3.2.2. β-turns and loops5 min

3.2.3. Example: Beta-Turns2 min

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

3.2.5. Example: Beta-Barrel Channels4 min

3.2.6. Practice: Stacked Beta-Sheets

3.3.1. Ramachandran Plot3 min

3.3.2. Example: Ramachandran Plot3 min

3.4.1. Anfinsen's Experiment8 min

3.4.2. Thermodynamics of Protein Folding7 min

3.4.3. Example: Urea2 min

3.4.4. Practice: Protein Folding2 min

3.5.1. Tertiary and Quarternary Protein Structure9 min

3.5.2. Example: Tertiary Structure (Motifs)3 min

3.5.3. Practice: Quaternary Structure3 min

3.6.1. Primary and Secondary Protein Structure5 min

3.6.2. Example: Point Mutation in Secondary Structure3 min

3.Q. Protein Structure: Checkpoint Quiz5 Qns

3.P.1. Practice: Hydrophobicity Scale

3.P.2. Practice: Thermophilic Proteins

4. Techniques in Protein Biochemistry

31min

4.1.1. Activity Assays7 min

4.1.2. Ammonium Sulfate Precipitation6 min

4.1.3. Specific Activity1 min

4.2.1. Methods of Determining Protein Sequence3 min

4.2.2. Protein Detection Techniques6 min

4.2.3. Mass Spectrometry2 min

4.2.4. Practice: Peptide Digest6 min

4.3.1. Protein Purification: Highlights

4.P.1. Practice: Peptide Digest

4.P.2. Ammonium Sulfate Precipitation

5. Structural Determination of Proteins

1hr

5.1.1. Predicting Protein Stucture3 min

5.1.2. Chou-Fasman Rules5 min

5.1.3. Applications of Chou-Fasman Rules5 min

5.1.4. Example: Predicting Tertiary Structure2 min

5.1.5. Example: Chou-Fasman Rules2 min

5.1.6. Practice: Predicting Structure from Chou-Fasman Parameters3 min

5.2.1. X-ray Crystallography2 min

5.2.2. Electron Microscopy2 min

5.2.3. Nuclear magnetic resonance (NMR)4 min

5.2.4. Infrared spectroscopy (IR)1 min

5.2.5. Circular Dichroism (CD)3 min

5.2.6. Example: Methods for Determining Protein Structure45 sec

5.2.7. Example: Determining Structure of Small Protein1 min

5.2.8. Practice: Match the Protein to the Technique2 min

5.2.9. Example: Affinity Tag Chromatography2 min

5.2.10. Example: Gel Filtration Chromatography2 min

5.2.11. Chromatography: Part II7 min

5.2.12. SDS-PAGE (Electrophoresis)6 min

5.2.13. Chromatography7 min

5.2.14. Mass Spectrometry2 min

5.Q. Structural Determination: Checkpoint Quiz4 Qns

5.P.1. Practice: Protein Structure Analysis in the Presence of Denaturant

6. Basic Concepts and Kinetics of Enzymes

41min

6.1.1. Post-translational Modifications7 min

6.2.1. Enzyme Classes7 min

6.2.2. Active Site3 min

6.2.3. Enzyme Mechanisms7 min

6.2.4. Cofactors/Coenzymes2 min

6.2.5. Chymotrypsin7 min

6.2.6. Example: Enzyme Classes58 sec

6.2.7. Example: Enzyme Mechanics1 min

6.2.8. Example: Coenzymes and Cofactors33 sec

6.2.9. Practice: Enzyme Catalyzed Reactions1 min

6.2.10. Chymotrypsin2 min

6.3.1. Protein Functions3 min

6.Q. Checkpoint Quiz4 Qns

7. Genetic Engineering of Proteins

38min

7.1.1. Basics of Genetic Engineering2 min

7.1.2. DNA Manipulation5 min

7.1.3. Plasmids7 min

7.1.4. Restriction Enzymes7 min

7.1.5. PCR8 min

7.1.6. Example: Palindromic Sequence2 min

7.1.7. Example: Cloning Process5 min

7.1.8. Practice: Cloning Plasmids2 min

7.Q. Genetic Engineering: Checkpoint Quiz6 Qns

8. Enzyme Assay (cont. Protein Purification and Identification)

14min

8.1.1. Pulldown Assays and Crosslinking6 min

8.1.2. ReporterAssays7 min

8.1.3. Example: Fluorescence Microscopy1 min

9. Lipids and Biological Membranes

56min

9.1.1. Introduction to Lipids2 min

9.1.2. Fatty Acids7 min

9.1.3. Triacylglycerols2 min

9.1.4. Glycerophospholipids3 min

9.1.5. Sphingolipids2 min

9.1.6. Cholesterol3 min

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

9.1.8. Example: Naming Fatty Acids3 min

9.1.9. Example: Identifying Lipids1 min

9.1.10. Practice: Fatty Acids1 min

9.2.1. The Lipid Bilayer6 min

9.2.2. Membrane Lipid Assembly3 min

9.2.3. Membrane Fluidity8 min

9.2.4. Membrane Lipid Dynamics2 min

9.2.5. Membrane Analysis6 min

9.2.6. Example: Membrane Fluidity1 min

9.2.7. Example: Cellular Membranes2 min

9.2.8. Practice: Transverse Diffusion of Lipids1 min

9.Q. Lipids and Membranes 4 Qns

10. Signalling

27min

10.1.1. Cell Signaling Overview3 min

10.1.2. Types of ligands1 min

10.1.3. Types of receptors1 min

10.1.4. Secondary Messengers2 min

10.1.5. GPCRs7 min

10.1.6. Receptor Tyrosine Kinase5 min

10.1.7. Signalling Lipids3 min

10.1.8. Practice: Secondary messenger2 min

10.1.9. Practice: G-Protein Coupled Receptors

10.1.10. Practice2: G-Protein Coupled Receptors

10.1.11. Practice3: G-Protein Coupled Receptors

10.1.12. Practice: Receptor tyrosine kinases

10.1.13. Practice2: Receptor tyrosine kinases3 min

10.1.14. Practice3: Receptor tyrosine kinases

11. Carbohydrate Metabolism

2.1hr

11.1.1. Glycolysis11 min

11.1.2. Glycolysis Regulation4 min

11.1.3. ATP production in Glycolysis1 min

11.1.4. Triose Phosphate Isomerase2 min

11.1.5. Glycolysis Regulation41 sec

11.1.6. Glycolysis1 min

11.1.7. Glycolysis: Cheatsheet

11.2.1. Gluconeogenesis6 min

11.2.2. Regulating Gluconeogensis5 min

11.2.3. Pyruvate Kinase Regulation59 sec

11.2.4. Gluconeogenesis1 min

11.2.5. Glycolysis and Gluconeogenesis30 sec

11.3.1. Glycogen Synthesis and Breakdown10 min

11.3.2. Example: Carbohydrate Metabolism- BIOCH22803 min

11.3.3. Example: Polysaccharide Structure-BIOCH22803 min

11.4.1. Pentose Phosphate Pathway-BIOCH22803 min

11.5.1. Pentose Phosphate Pathway3 min

11.6.1. Lactate Fermentation2 min

11.6.2. Alcohol Fermentation42 sec

11.6.3. Anaerobic Metabolism1 min

11.6.4. Lactate Formation55 sec

11.6.5. Anaerobic respiration30 sec

11.7.1. Structure of Mitochondria3 min

11.7.2. Pyruvate Dehydrogenase6 min

11.7.3. Citric Acid Cycle8 min

11.7.4. Pyruvate Dehydrogenase Complex38 sec

11.7.5. Regulation of PDC1 min

11.7.6. The Citric Acid Cycle1 min

11.7.7. The Citric Acid Cycle: Cheatsheet

11.8.1. Electron Transporters6 min

11.8.2. The Electron Transport Chain8 min

11.8.3. Electron Transport Inhibitors3 min

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

11.8.5. ATP Synthesis10 min

11.8.6. Electron Transporters49 sec

11.8.7. The electron transport chain1 min

11.8.8. Electron Transport Inhibitors42 sec

11.8.9. ATP production: Cheatsheet

11.9.1. Malate-Aspartate Shuttle5 min

11.Q. Checkpoint Quiz4 Qns

11.P.1. Gluconeogenesis and Glycolysis

11.P.2. Citric Acid Cycle

11.P.3. New Practice Question

11.P.4. New Practice Question1 min

11.P.5. Practice 1

11.P.6. Practice 3

11.P.7. New Practice Question

11.P.8. New Practice Question

11.P.9. New Practice Question

11.P.10. New Practice Question2 min

12. Photosynthesis

42min

12.1.1. Light-Dependent Reactions of Photosynthesis [detailed]10 min

12.1.2. Non-Cyclic and Cyclic Versions of Light-Dependent Reactions3 min

12.1.3. Calvin Cycle8 min

12.1.4. New Lesson2 min

12.1.5. New Lesson45 sec

12.1.6. New Lesson3 min

12.1.7. Wize Concept Check1 min

12.2.1. Photorespiration5 min

12.2.2. C4 Plants2 min

12.2.3. CAM Plants4 min

12.P.1. New Practice Question

12.P.2. New Practice Question

12.P.3. New Practice Question

12.P.4. Practice: Photosynthesis2 min

12.P.5. New Practice Question

12.P.6. New Practice Question

13. Fat metabolism, Lipoproteins & Ketogenesis

47min

13.1.1. Cholesterol Synthesis4 min

13.1.2. Lipoproteins5 min

13.1.3. Cholesterol Synthesis1 min

13.1.4. Lipoproteins1 min

13.1.5. Cholesterol1 min

13.2.1. Ketoneogenesis3 min

13.2.2. Diabetes4 min

13.2.3. Ketoneogenesis47 sec

13.2.4. Diabetes2 min

13.2.5. Ketoacidosis1 min

13.3.1. Fat Degradation (Beta Oxidation)11 min

13.3.2. Fat Catabolism1 min

13.3.3. Beta-oxidation51 sec

13.4.1. Fat Synthesis10 min

13.4.2. Fatty Acid Synthesis2 min

13.Q. Metabolic Processes5 Qns

13.P.1. Beta-oxidation

13.P.2. "Hitting the Wall"

14. DNA Replication and Repair

54min

14.1.1. Meselson-Stahl Experiment8 min

14.1.2. DNA Replication in Cells14 min

14.1.3. Example: Meselson-Stahl3 min

14.1.4. Example: DNA Replication3 min

14.1.5. Practice: DNA Replication

14.2.1. Telomerase & Telomeres4 min

14.2.2. New Practice Question2 min

14.3.1. Repair Mechanisms6 min

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

14.3.3. Example: Mutations4 min

14.3.4. Example: Recombination3 min

14.3.5. Practice: DNA Polymerase

14.Q. DNA Replication and Repair Checkpoint Quiz5 Qns

15. Prokaryotic Transcription

42min

15.1.1. Initiation8 min

15.1.2. Elongation7 min

15.1.3. Termination4 min

15.1.4. Prokaryotic Regulatory Proteins5 min

15.1.5. Example: mRNA Transcription4 min

15.1.6. Example: Transcriptional Repressors2 min

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

15.2.2. The Tryptophan (Trp) Operon5 min

15.2.3. Example: Negative Regulation3 min

15.Q. Transcription Checkpoint Quiz5 Qns

16. Cancer Biology

36min

16.1.1. Causes of Cancer14 min

16.1.2. How does cancer grow?7 min

16.1.3. Cancer Treatments9 min

16.1.4. Example: Cancer Causes3 min

16.1.5. Example: Cancer Treatment3 min

16.Q. Cancer Checkpoint Quiz5 Qns

17. Coordination of Metabolism

10min

17.1.1. Summary of Metabolism10 min

18. Intermolecular Forces + Properties of Water

46min

18.1.1. Types of Chemical Bonds 5 min

18.1.2. Practice 1

18.1.3. Practice 2

18.2.1. Intermolecular Forces: Hydrogen Bonding5 min

18.2.2. Example 2 min

18.2.3. Practice 12 min

18.2.4. Practice 22 min

18.2.5. Practice 33 min

18.3.1. Intermolecular Forces: Van der Waals Interactions 11 min

18.3.2. Practice 13 min

18.3.3. Practice 2

18.4.1. Important Elements that Make Up Life4 min

18.4.2. Unique Properties of Water6 min

18.4.3. Practice 12 min

18.4.4. Practice 22 min

19. Translation

1.1hr

19.1.1. Reading the Genetic Code (mRNA)8 min

19.1.2. tRNA and rRNA7 min

19.1.3. Translation into Proteins9 min

19.1.4. Translation: Protein Synthesis12 min

19.1.5. Example: Translation3 min

19.1.6. Example: Translation II5 min

19.1.7. Example: Translation III3 min

19.2.1. Initiation of Translation9 min

19.2.2. Elongation in Translation 5 min

19.2.3. Termination of Translation2 min

19.Q. Checkpoint Quiz2 Qns

20. Recombinant DNA and Sequencing

1.6hr

20.1.1. (Agarose) Gel Electrophoresis 3 min

20.1.2. Northern Blot2 min

20.1.3. Southern Blot2 min

20.1.4. Polymerase Chain Reaction10 min

20.1.5. Cloning and DNA libraries17 min

20.1.6. DNA Sequencing9 min

20.1.7. Microarrays 3 min

20.1.8. DNA Fingerprinting6 min

20.1.9. CRISPR [detailed]9 min

20.1.10. Example: Hybridization4 min

20.1.11. Example: Cloning 3 min

20.1.12. Example: DNA Transformation4 min

20.1.13. Example: DNA Fingerprinting3 min

20.2.1. DNA Sequencing10 min

20.2.2. Bioinformatics9 min

20.2.3. Example: Bioinformatics4 min

20.2.4. Practice: BLAST

20.Q. Checkpoint Quiz5 Qns

21. Buffers

20min

21.1.1. Introduction to Buffers6 min

21.1.2. Calculating the pH of a Buffer System4 min

21.1.3. Buffers Problem Type 16 min

21.1.4. Buffers Problem Type 22 min

21.1.5. Buffers Problem Type 32 min

22. Enzyme Catalysis

27min

22.1.1. Enzyme Kinetics3 min

22.1.2. Michaelis-Menten Equation5 min

22.1.3. Lineweaver-Burke Plot2 min

22.1.4. Example: Lineweaver Burke Plot1 min

22.1.5. Practice: Enzyme Kinetics52 sec

22.1.6. Enzyme Kinetics Practice Question2 min

22.2.1. Reversible/Irreversible Inhibition3 min

22.2.2. Competitive Inhibition2 min

22.2.3. Non-Competitive Inhibition3 min

22.2.4. Example: Enzyme Inhibition2 min

22.2.5. Cheatsheet: Summary of Inhibitors

22.3.1. Enzyme Regulation3 min

22.Q. Checkpoint Quiz4 Qns

23. Carbohydrate Structure

36min

23.1.1. Carbohydrates (Sugars)5 min

23.1.2. Carbohydrate Conformation and Annotation5 min

23.1.3. Carbohydrate Cyclization8 min

23.1.4. Complex Carbohydrates7 min

23.1.5. Polysaccharides5 min

23.1.6. Example: Simple Sugars2 min

23.1.7. Example: Glucose2 min

23.1.8. Example: Carbohydrate Structures1 min

23.1.9. Practice: Naming Carbohydrates1 min

23.1.10. Cheatsheet: Important Monosaccharides to Remember

23.Q. Checkpoint Quiz3 Qns

24. Nucleic Acid Structure + DNA Denaturation

40min

24.1.1. Review of DNA Structure10 min

24.1.2. DNA Packing4 min

24.1.3. RNA2 min

24.1.4. Chromosomes and Chromatin7 min

24.1.5. Example: Purine/Pyrimidine4 min

24.1.6. Example: Base Pairing4 min

24.2.1. Denaturation5 min

24.2.2. Denaturation vs. DNA Stability3 min

25. Fundamental Concepts of Biochemistry

18min

25.1.1. From Monomers to Polymers4 min

25.2.1. Gibbs Free Energy8 min

25.2.2. Example 2 min

25.3.1. The Central Dogma of Biology4 min

25.Q. Checkpoint Quiz6 Qns

26. Membrane Protein & Transporters

1.3hr

26.1.1. Proteins in the Lipid Bilayer1 min

26.1.2. Peripheral Membrane Proteins5 min

26.1.3. Integral Membrane Proteins5 min

26.1.4. Measuring Hydrophobicity7 min

26.1.5. Membrane Protein Folding2 min

26.1.6. Practice: Peripheral Membrane Proteins1 min

26.1.7. Practice: Integral Membrane Proteins1 min

26.1.8. Practice: Hydropathy49 sec

26.1.9. Practice: Integral Membrane Proteins55 sec

26.2.1. Membrane Proteins4 min

26.2.2. Practice: Membrane Proteins

26.3.1. Bacteriorhodopsin4 min

26.3.2. Porins2 min

26.3.3. Example: Bacteriorhodopsin1 min

26.3.4. Example: Membrane Proteins1 min

26.4.1. Introduction and Passive Transport7 min

26.4.2. Active Transport7 min

26.4.3. Transport Proteins: Ion Channels4 min

26.4.4. Example: Active vs. Passive Transport5 min

26.4.5. Practice: Potassium Ion Channels59 sec

26.5.1. Ion Channel Receptors2 min

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

26.5.3. Receptor Tyrosine Kinases (RTKs)5 min

26.5.4. Example: G-protein Coupled Receptors1 min

26.Q. Checkpoint Quiz4 Qns

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

26.P.2. Practice: Predicting transmembrane segments

27. Hormone Signalling

13min

27.1.1. Hormonal Metabolic Regulation: Catabolic6 min

27.1.2. Hormonal Metabolic Regulation: Anabolic4 min

27.1.3. Catabolic Horomone Signaling1 min

27.1.4. Insulin32 sec

27.1.5. Glucogenolysis45 sec

27.Q. Checkpoint Quiz2 Qns

28. Eukaryotic Transcription

2hr

28.1.1. Transcription In Eukaryotes9 min

28.1.2. General Transcription Factors (GTFs)5 min

28.1.3. Regulation of Eukaryotic Transcription12 min

28.1.4. Chromatin state and histone modifications7 min

28.2.1. RNA Maturation in Eukaryotes8 min

28.2.2. Eukaryotic Post-Transcriptional Regulation6 min

28.2.3. Nuclear Import and Export7 min

28.2.4. Example: mRNA Processing2 min

28.2.5. Example: mRNA Transcript2 min

28.3.1. Eukaryotic Transcription Initiation10 min

28.3.2. 5' Capping5 min

28.3.3. Poly(A) Tail5 min

28.3.4. Splicing and the Spliceosome6 min

28.3.5. Alternative Splicing12 min

28.3.6. mRNA Nuclear Export11 min

28.3.7. Cytoplasmic Processing of mRNAs13 min

29. Ligand-binding: Myoglobin and Hemoglobin

23min

29.1.1. Myoglobin1 min

29.1.2. Hemoglobin10 min

29.1.3. Dissorders in Hemoglobin2 min

29.1.4. Ligand Binding10 min

29.1.5. Hemoglobin Regulation

29.1.6. New Practice Question

29.1.7. Myoglobin

29.Q. Checkpoint Quiz3 Qns

30. Introduction to Metabolism: Redox Reactions

48min

30.1.1. Intro to Metabolism7 min

30.1.2. Gibbs Free Energy10 min

30.1.3. High Energy Intermediates9 min

30.1.4. Example: Gibbs Free Energy3 min

30.1.5. Free energy of ATP52 sec

30.1.6. Coupled Reactions1 min

30.2.1. Oxidation-Reduction Reactions6 min

30.2.2. Electrochemistry4 min

30.2.3. Cell Potentials and Gibbs Free Energy3 min

30.2.4. Example: Oxidation-Reduction Reactions3 min

30.Q. Checkpoint Quiz3 Qns

Mock Exam

ME.1. Final Exam - Mock Assessment72 Qns

ME.1 Final Exam - Mock Assessment

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