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Fundamentals of Biochemistry I - Structure and Catalysis

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Fundamentals of Biochemistry I - Structure and Catalysis

We explore the structure of the major classes of biomolecules, including proteins, lipids, nucleic acids, and carbohydrates. Next, we focus on their binding with other molecules, an emergent property of their structure. We then focus on additional functions of the bound complex, including diffusion and transport, catalysis and regulation. Finally, we integrate structure and function in a capstone chapter on cell signaling.

BiochemistryBiology
Author
Henry Jakubowski and Patricia Flatt
Publisher
LibreTexts
Source
LibreTexts
License
CC BY-SA
Language
EN
Category
Basic Sciences
Read online Download PDF (open licence)
Contents· 90 sections
  1. 01: The Foundations of Biochemistry
  2. 1.01: Cellular Foundations
  3. 1.02: Chemical Foundations
  4. 1.03: Physical-Chemical Foundations
  5. 1.04: Genetic Foundations
  6. 1.05: Chapter 1 Questions
  7. 02: Water and its Role in Life
  8. 2.01: The multiple roles of water
  9. 2.02: Weak Acids and Bases pH and pKa
  10. 2.03: Buffering against pH Changes in Biological Systems
  11. 2.04: Solubility in an aqueous world - noncovalent interactions in depth
  12. 2.05: Solubility in an aqueous world - The Hydrophobic Effect
  13. 2.06: Chapter 2 Questions
  14. 03: Amino Acids Peptides and Proteins
  15. 3.01: Amino Acids and Peptides
  16. 3.2: The Structure of Proteins- An Overview
  17. 3.3: Protein Purification
  18. 3.4: Analyses of Protein Structure
  19. 3.5: Extension - Antibodies in Quantitation and In Vivo Detection
  20. 3.6: Chapter 3 Questions
  21. 04: The Three-Dimensional Structure of Proteins
  22. 4.01: Main Chain Conformations
  23. 4.02: Secondary Structure and Loops
  24. 4.03: Tertiary and Quaternary Structures
  25. 4.04: Secondary Structural Motifs and Domains
  26. 4.05: Protein with Alpha Alpha-Beta Beta and Little Secondary Structure
  27. 4.06: Intrinsically Disordered Proteins
  28. 4.07: Fibrillar Proteins
  29. 4.08: Protein Folding and Unfolding (Denaturation) - Dynamics
  30. 4.09: Protein Stability - Thermodynamics
  31. 4.10: Protein Aggregates - Amyloids Prions and Intracellular Granules
  32. 4.11: Biomolecular Visualization - Conceptions and Misconceptions
  33. 4.12: Laboratory Determination of the Thermodynamic Parameters for Protein Denaturation
  34. 4.13: Predicting Structure and Function of Biomolecules Through Natural Language Processing Tools
  35. 4.14: Predicting Structure from Sequence and Sequence from Structure Function (New 10 24)
  36. 4.15: Chapter 4 Questions
  37. 05: Protein Function
  38. 5.01: Binding - The First Step Toward Protein Function
  39. 5.02: Techniques to Measure Binding
  40. 5.03: A. Oxygen-Binding Proteins and Allosterism
  41. 5.03: B. Other Allosteric Proteins
  42. 5.04: A. The Immune System - Antibodies B- cells T-cell receptors and T-cells
  43. 5.04: B. The Innate Immune System PAMPs and DAMPs and Inflammation
  44. 5.05: Protein Interactions Modulated by Chemical Energy- Actin Myosin and Molecular Motors
  45. 5.06: Binding - Conformational Selections and Intrinsically Disordered Proteins
  46. 5.07: Binding - Enzyme Linked Immunosorbant Assays (ELISAs)
  47. 5.8: Problems - Predicting Protein Structure and Function Using Machine Learning and AI Programs
  48. 5.9: Derivation of the MWC Equation
  49. 06: Enzyme Activity
  50. 6.01: How Enzymes Work
  51. 6.02: Kinetics without Enzymes
  52. 6.03: Kinetics with Enzymes
  53. 6.04: Enzyme Inhibition
  54. 6.05A: Enzyme Reaction Mechanisms - Arrow Pushing
  55. 6.05B: Quantitative Analysis of Enzyme Reaction Mechanisms - Serine Proteases
  56. 6.06: Enzyme and Protein Regulation
  57. 6.07: Ribozymes - RNA Enzymes
  58. 6.08: Cofactors and Catalysis - A Little Help From My Friends
  59. 07: Carbohydrates and Glycobiology
  60. 7.01: Monosaccharides and Disaccharides
  61. 7.02: Polysaccharides
  62. 7.03: Glycoconjugates - Proteoglycans Glycoproteins Glycolipids and Cell Walls
  63. 7.04: The Sugar Code and Lectin Decoding
  64. 7.05: Working with Carbohydrates
  65. 08: Nucleotides and Nucleic Acids
  66. 8.01: Nucleic Acids - Structure and Function
  67. 8.02: Nucleic Acids - RNA Structure and Function
  68. 8.03: Nucleic Acids - Comparison of DNA and RNA
  69. 8.04: Chromosomes and Chromatin
  70. 8.06: Enzymes for Genetic modifications
  71. 8.06: References
  72. 09: Investigating DNA
  73. 9.01: DNA Isolation Sequencing and Synthesis
  74. 9.02: Bioinformatics
  75. 9.03: Cloning and Recombinant Expression
  76. 9.04: DNA Microarrays
  77. 9.05: In Situ Hybridization
  78. 9.06: References
  79. 10: Lipids
  80. 10.01: Introduction to lipids
  81. 10.02: Lipids Aggregates in Water - Micelles and Liposomes
  82. 10.03: Membrane Bilayer and Monolayer Assemblies - Structures and Dynamics
  83. 10.04: Working with Lipids
  84. 10.05: Problems
  85. 11: Biological Membranes and Transport
  86. 11.01: Membrane and Membrane Proteins
  87. 11.02: Diffusion Across a Membrane - Passive and Facilitated Diffusion
  88. 11.03: Diffusion Across a Membrane - Channels
  89. 11.04: Diffusion Across a Membrane - Pores
  90. 11.05: Active Transport