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Single-Molecule Cellular Biophysics

Book Description

Recent advances in single molecule science have presented a new branch of science: single molecule cellular biophysics, combining classical cell biology with cutting-edge single molecule biophysics. This textbook explains the essential elements of this new discipline, from the state-of-the-art single molecule techniques to real-world applications in unravelling the inner workings of the cell. Every effort has been made to ensure the text can be easily understood by students from both the physical and life sciences. Mathematical derivations are kept to a minimum whilst unnecessary biological terminology is avoided and text boxes provide readers from either background with additional information. 100 end-of-chapter exercises are divided into those aimed at physical sciences students, those aimed at life science students and those that can be tackled by students from both disciplines. The use of case studies and real research examples make this textbook indispensable for undergraduate students entering this exciting field.

Table of Contents

  1. Coverpage
  2. Single-Molecule Cellular Biophysics
  3. Title page
  4. Copyright page
  5. Dedication
  6. Contents
  7. Preface
  8. 1 Once upon a (length and) time (scale). . .
    1. 1.1 Introduction
    2. 1.2 There are already many informative ‘multi-molecule’ methods
    3. 1.3 American versus European coffee
    4. 1.4 Scales of length, force, energy, time and concentration
    5. 1.5 Some basic thermodynamics of life
    6. 1.6 The concept of ‘functionality’
    7. 1.7 Test tube or cell?
    8. The gist
    9. References
    10. Questions
  9. 2 The molecules of life – an idiot’s guide
    1. 2.1 Introduction
    2. 2.2 The atomic components of single biological molecules
    3. 2.3 Cell structure and sub-cellular architecture
    4. 2.4 Amino acids, peptides and proteins
    5. 2.5 Sugars
    6. 2.6 Nucleic acids
    7. 2.7 Lipids
    8. 2.8 Miscellaneous ‘small’ molecules
    9. 2.9 The ‘central dogma’ of molecular biology
    10. 2.10 Molecular simulations
    11. 2.11 Importance of non-covalent forces
    12. The gist
    13. References
    14. Questions
  10. 3 Making the invisible visible: part 1 – methods that use visible light
    1. 3.1 Introduction
    2. 3.2 Magnifying images
    3. 3.3 Generating optical contrast using scattered light or fluorescence
    4. 3.4 Organic dyes, FlAsH/ReAsH, fluorescent amino acids and quantum dots
    5. 3.5 Fluorescent proteins, SNAP/CLIP-Tags and HaloTags
    6. 3.6 Illuminating and detecting fluorescent tags
    7. 3.7 Fluorescence correlation spectroscopy (FCS)
    8. 3.8 Fluorescence lifetime imaging (FLIM)
    9. 3.9 ‘Super-resolution’ techniques
    10. 3.10 ‘Multi-dimensional’ imaging
    11. The gist
    12. References
    13. Questions
  11. 4 Making the invisible visible: part 2 – without visible light
    1. 4.1 Introduction
    2. 4.2 Scanning probe microscopy
    3. 4.3 Electron microscopy
    4. 4.4 Ionic currents through nanopores
    5. 4.5 Raman spectroscopy
    6. 4.6 Interference-based detection
    7. The gist
    8. References
    9. Questions
  12. 5 Measuring forces and manipulating single molecules
    1. 5.1 Introduction
    2. 5.2 Optical tweezers
    3. 5.3 Magnetic tweezers
    4. 5.4 Atomic force spectroscopy
    5. 5.5 Using force spectroscopy to explore non-equilibrium processes
    6. 5.6 Electric dipole induction in polarizable particles for torque and trapping
    7. The gist
    8. References
    9. Questions
  13. 6 Single-molecule biophysics: the case studies that piece together the hidden machinery of the cell
    1. 6.1 Introduction
    2. 6.2 What makes a ‘seminal’ single-molecule biophysics study?
    3. 6.3 Carving up the cell into a few sensible themes
    4. The gist
    5. References
    6. Questions
  14. 7 Molecules from beyond the cell
    1. 7.1 Introduction
    2. 7.2 Receptor molecules and ligands in the cell membrane
    3. 7.3 Endocytosis and exocytosis
    4. 7.4 Viral invasion
    5. The gist
    6. References
    7. Questions
  15. 8 Into the membrane
    1. 8.1 Introduction
    2. 8.2 Molecular transport via pores, pumps and carriers in membranes
    3. 8.3 Rotary motors – the rise of the (bionano) machines
    4. 8.4 Energizing the cell
    5. 8.5 Architecture and shape of the cell surface
    6. The gist
    7. References
    8. Questions
  16. 9 Inside cells
    1. 9.1 Introduction
    2. 9.2 Free, hindered and driven molecular diffusion in the cytoplasm
    3. 9.3 Chromosomes and DNA: their architecture and replication
    4. 9.4 Translating, transcribing and splicing the genetic code
    5. The gist
    6. References
    7. Questions
  17. 10 Single-molecule biophysics beyond single cells and beyond the single molecule
    1. 10.1 Introduction
    2. 10.2 Single-molecule biophysics in complex organisms
    3. 10.3 Bionanotechnology and ‘synthetic’ biology
    4. 10.4 The outlook for single-molecule cellular biophysics
    5. The gist
    6. References
    7. Questions
  18. Index