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The Fundamentals of Biochemistry: Interactive Tutorials


10th Edition

  1. Introduction
    1. Orientation
      1. The Basics
      2. The Toolbar
      3. Scripting in JSmol
    2. Methane and Cyclohexane
    3. Glucose and Its Anomers
    4. The Double Helix
  2. Fundamentals
    1. Water: The Realm of Biochemistry
      1. Water and Ice
      2. The Hydrophobic Effect
        1. Introduction
        2. Hydration of Methane
        3. Janus Molecules I
        4. Janus Molecules II
      3. Amphiphilic Molecules
    2. Noncovalent Interactions
      1. Van der Waals Interactions
      2. Ionic Interactions
        1. Ionic Bonds
        2. Ion-Dipole Interactions I
        3. Ion-Dipole Interactions II
      3. Molecular Recognition
        1. Hydrogen Bonds and Coulombic Interactions
        2. Pi-Based Interactions
  3. Nucleic Acids
    1. Molecular Complementarity
      1. Nucleotides
      2. Watson-Crick Base Pairs
    2. DNA Architecure
      1. From A to Z
      2. Nucleic Sugars
    3. DNA and RNA Aptamers
      1. Introduction
      2. Backbone Flexibility
      3. Oligonucleotide Conformations
      4. Case Studies
    4. Homo-DNA and Nature's Choice of Pentose
    5. Transfer RNA
    6. Pseudoknots in RNA
  4. Protein-Nucleic Acid Interactions
    1. An active site of the ribosome: The structure of the ribosomal protein L11 complex with 23 S ribosomal RNA
    2. Tonicity-response enhancer binding protein (TonEBP)
    3. trp RNA-binding attenuation protein (TRAP)
  5. Amino Acids and Peptides
    1. Amino Acids
      1. Overview
      2. Glycine, Alanine and Proline
      3. Branched-Chain
      4. Aromatic
      5. Polar (Charged)
      6. Polar (Uncharged)
      7. Sulfur-Containing
      8. Flash Cards
    2. Peptides and the Peptide Bond
    3. The Disulfide Bond
  6. Protein Architecture
    1. Secondary Structure
      1. The Alpha Helix
        1. Introduction
        2. The α-Helix
        3. Amphipathic α-Helices
        4. Proline and the α-Helix
        5. Summary
      2. Beta Sheets and Turns
        1. Beta Strands and Antiparallel Sheets
        2. Beta Turns
        3. Parallel Beta Sheets
      3. The Beta Helix
    2. Tertiary Structure
      1. All-Beta Proteins
      2. All-Alpha Proteins
        1. Lambda Repressor
        2. HIV-1 p17
      3. Alpha/Beta Proteins
  7. Quaternary Structure of Proteins
    1. Introduction
    2. Hydrophobic Interfaces
      1. Association via Hydrophobic Surfaces
      2. Interfaces with Buried Hydrogen Bonds
        1. Protein Kinase C Inhibitor
        2. Met Repressor
      3. Interface with Interchain Salt Bridges
    3. Protein Symmetry
      1. Transthyretin
      2. Protein Misfolding Diseases
    4. Heteromeric Proteins
      1. αVβ3 Integrin
      2. Angiogenin-RNase Inhibitor Complex
    5. Domains and Modular Proteins
      1. Domains and Protein Evolution
      2. KIX, pKID and c-Myb
    6. Supercoiled Protein Motifs
      1. The Collagen Triple Helix
      2. Coiled-Coil Proteins
        1. GCN4 Leucine Zipper
        2. Surfactant Protein D
        3. Vitamin D3 Storage Protein
        4. Tetrabrachion
        5. Thermostable Proteins
  8. Local Electrostatic Interactions
    1. Cation-pi and pi-pi Interactions
      1. Gallery of cation-pi interactions
      2. Cation-pi interactions at protein-DNA interfaces
      3. pi-pi interactions
      4. Vaccinia methyltransferase (VP39)
      5. Glucoamylase: A cation-pi "cocoon" for lysine 108
    2. Salt Bridges in Proteins
      1. Interchain salt bridges in human triose phosphate isomerase
      2. Salt bridges in tetrabrachion: an electrostatic belt
      3. Buried salt bridges in carbonic anhydrase
  1. Functional Diversity of Proteins
    1. Oxygen Transport
      1. Myoglobin
        1. The Globin Fold
        2. The Oxygen-Binding Pocket
        3. Helix Crossing
        4. O2 Binding
        5. Changes in Heme Iron
      2. Hemoglobin – An Allosteric Protein
        1. Quaternary Structure
        2. Ion Pairs in Deoxyhemoglobin
        3. BPG Binding
    2. Protein Evolution
      1. Lamprey α vs. human α chain
      2. Human hemoglobin: α vs. β chain
      3. Structural alignment of neuroglobin and myoglobin
      4. Sickle cell hemoglobin
    3. Molecular Recognition
      1. The active site is located in a canyon that closes around the ligand
      2. Glutamate recognition involves a network of eleven H-bonds
      3. Kainate is a glutamate mimic
    4. Molecular Chaperones
      1. The GroE Chaperonin
        1. The GroEL-GroES Chaperone
        2. Chaperonin 60: ATP Binding and Allostery
        3. Anfinsen's Cage
        4. The Bullet Complex
      2. The Thermosome
    5. Lipoproteins
      1. High density lipoprotein (HDL)
      2. Human apolipoprotein A1
      3. Molecular belt model for nascent HDL
    6. Surfactant Proteins
      1. Surfactant protein C
      2. Surfactant protein D
  2. Enzymes
    1. Lessons from lysozyme
    2. The aspartate proteases
      1. Pepsin–An aspartate protease
      2. Pepsinogen
      3. Pepstatin: A transition state analog
      4. HIV protease
    3. The serine proteases
      1. The oxyanion hole
      2. Lessons from trypsin
      3. The specificity pocket of trypsin
      4. Enteropeptidase
      5. The trypsin and subtilisin families
    4. Adenylate kinase: A Venus flytrap
      1. Monitoring the ATP/ADP ratio
      2. Phosphoryl transfer occurs via an in-line mechanism
      3. Substrate binding induces domain closing
      4. Conserved salt bridges ensure juxtaposition of ATP and AMP
    5. Human hexokinases
      1. Brain hexokinase: domain structure
      2. Regulation of hexokinase A
      3. Glucokinase (hexokinase D)
    6. Transketolase
      1. Role of thiamine pyrophosphate
      2. Tertiary and quaternary structure
      3. The active site
      4. Why TPP binds in the V conformation
    7. Citric acid cycle enzymes
      1. Citrate synthase
      2. Aconitase: an iron-sulfur protein
      3. Isocitrate dehydrogenase from E. coli
        1. Introduction
        2. The hydride transfer path
        3. Why a Mg2+ ion is essential for IDH activity
  3. Membrane Lipids
    1. Lessons from crystals of POPC
    2. Cholesterol
    3. Sphingolipids
  4. Integral Membrane Proteins
    1. β-barrel outer membrane proteins
      1. OmpF porin: A trimeric transmembrane channel
      2. TolC: A microbial pump for toxic compounds
    2. Helix packing in transmembrane proteins
      1. Bacteriorhodopsin: A light-driven proton pump
      2. Glycophorin: The GXXXG association motif
      3. The alanine coil
    3. Lipid-Protein Interactions
      1. ADP-ATP exchanger
      2. The Membrane Rotor of V-ATPase
    4. Cytochrome bc1
      1. Cytochrome bc1, a bifunctional enzyme
      2. The bc1 core subcomplex
    5. Mitochondrial Processing Peptidase (MPP)
      1. MPP is a homodimer
      2. β-MPP evolved by gene duplication
      3. β-MPP is a Zn-dependent endopeptidase
      4. MPP and the core proteins of cytochrome bc1 are related
  5. Ion Transport Across Membranes
    1. Ionophores
      1. Gramicidin
      2. Valinomycin
    2. The bacterial potassium ion channel KcsA
      1. Ion channels are transmembrane proteins
      2. Quaternary structure of KcsA channel
      3. The selectivity filter
  6. ATP Synthase
    1. Introduction
    2. The quaternary structure of mitochondrial F1-ATPase
    3. Opening and closing of the catalytic site
    4. Rearrangement of side chains in the catalytic site
    5. E. coli ATP synthase: Siggi Engelbrecht's model
  7. Photosynthesis
    1. A photosynthetic reaction center
    2. Bacteriochlorophyll A Protein
    3. Light-harvesting complex LH2
    4. Ribulose bisphosphate carboxylase (rubisco)
  8. Supramolecular Assemblies
    1. The Bacterial Ribosome
      1. Binding of K+ and Mg2+ to 23S rRNA
      2. Secondary structure of 23S rRNA
      3. The kissing loop motif
      4. Binding sites for mRNA and tRNA on the bacterial ribosome
      5. The 16S rRNA decoding A-site
    2. The Nucleosome
      1. Core histones
      2. Special features of the nucleosome
      3. Tetranucleosome