Fundamentals of molecular structural biology:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
London ; San Diego, CA
Academic Press
[2020]
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xxi, 495 Seiten Illustrationen, Diagramme |
| ISBN: | 9780128148556 |
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Datensatz im Suchindex
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| adam_text | Contents About the Author......................................................................................................... xv Preface....................................................................................................................... xvii Acknowledgments......................................................................................................xxi CHAPTER 1 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 1.12 1.13 1.14 1.15 CHAPTER 2 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 Introduction—A historical perspective...........................1 Biology begins as natural history................................................... 1 Nature of matter............................................................................... 1 Microscope reveals internal structure of livingorganisms........... 2 Cell theory....................................................................................... 2 Theory of natural selection and laws of heredity.........................3 Gene and genetics...........................................................................4 Nature of “physical objects” in the cell...................................... 4 DNA as the genetic material........................................................ 5 Biology turns molecular—natural science becomes unified..............................................................................................5 Deeper into the structure of matter.............................................. 6 Molecular biology endowed with structures................................7 Structural complexity)
disentangled........................................... 8 Molecular structural biology confronts humandisease................8 From gene to genome.................................................................... 9 In lieu of a conclusion................................................................... 9 References and Further Reading................................................. 10 Mathematical tools................................................................ 11 Measurements: Standards and units............................................11 Algebraic functions.......................................................................13 Trigonometric functions...............................................................15 Exponential and logarithm........................................................... 17 Complex numbers......................................................................... 18 Vector.............................................................................................20 Matrix.............................................................................................21 Calculus......................................................................................... 23 2.8.1 Differentiation.....................................................................23 2.8.2 Integration...........................................................................24 2.8.3 Multivariate function......................................................... 25 2.8.4 Applications........................................................................27 2.8.5
Vector operators.................................................................28
Contents CHAPTER 2.9 Series and transform..................................................................29 Sample questions...................................................................... 32 References and further reading................................................ 33 3 Physical basis of chemistry............................................35 3.1 Classical mechanics.................................................................. 35 3.1.1 Matter and motion.......................................................... 35 3.1.2 Fundamental forces of nature......................................... 36 3.1.3 Newton’s laws................................................................ 37 3.1.4 Circular motion and angular momentum........................38 3.1.5 Work and energy............................................................ 39 3.1.6 Oscillatory systems......................................................... 40 3.2 Wave motion.............................................................................41 3.2.1 Mechanical waves........................................................... 41 3.2.2 Electromagnetic wave.................................................... 42 3.2.3 Interference of light waves............................................. 43 3.3 Kinetic theory of gases.............................................................44 3.4 Thermodynamics.......................................................................45 3.5 Quantum physics.......................................................................46 3.5.1 Light as
photons............................................................. 47 3.5.2 Matter as waves..............................................................48 3.5.3 Schrödinger equation...................................................... 49 3.5.4 Barrier tunneling by free electron.................................. 51 3.5.5 Bound electron—Hydrogen atom.................................. 52 3.6 Some elements of statistics.......................................................54 3.6.1 Microscopic versus macroscopic.................................... 54 3.6.2 Normal distribution......................................................... 55 3.6.3 Boltzmann distribution................................................... 56 Sample questions...................................................................... 57 References and further reading................................................ 59 CHAPTER 4 4.1 4.2 Chemical basis of biology..................................................61 From atoms to molecules..........................................................61 4.1.1 Electron configuration of atoms..................................... 61 4.1.2 Atomic interactions—Chemical bonds.......................... 62 4.1.3 Electron sharing principles—Electronegativity..............63 4.1.4 Polarity of bond—Molecular dipole.............................. 64 Bonding theories.......................................................................65 4.2.1 Valence bond theory....................................................... 65 4.2.2 Molecular orbital
theory................................................. 66
Contents 4.3 4.4 4.5 CHAPTER 5 5.1 5.2 5.3 CHAPTER 6 6.1 Noncovalent interactions.............................................................67 4.3.1 Ion-ion interactions............................................................ 68 4.3.2 Ion-dipole interactions.......................................................68 4.3.3 Ion-induced dipole interactions........................................ 69 4.3.4 Van der Waals interactions—Leonard-Jones potential..............................................................................69 4.3.5 Hydrogen bond and water structure................................. 72 Chemical thermodynamics—Free energy..................................73 Chemical kinetics......................................................................... 76 4.5.1 Rate law—Arrhenius equation......................................... 76 4.5.2 Collison theory.................................................................. 77 4.5.3 Transition state theory.......................................................78 4.5.4 Quantum tunneling............................................................79 4.5.5 Nucleophilic-electrophilic—SN2 reaction........................79 Sample questions..........................................................................81 References and further reading...................................................81 Biomacromolecules.........................................................83 Nucleic acids................................................................................ 83 5.1.1
Nucleotides.........................................................................83 5.1.2 The DNA double helix......................................................84 5.1.3 DNA superhelicity.............................................................93 Proteins..........................................................................................93 5.2.1 Amino acids....................................................................... 93 5.2.2 Peptide bond...................................................................... 95 5.2.3 Secondary structures..........................................................96 5.2.4 Supersecondary and tertiary structures.......................... 101 5.2.5 Quaternary structure........................................................ 110 5.2.6 Protein flexibility and dynamics.................................... 113 Carbohydrates.............................................................................115 Sample questions........................................................................116 References and further reading................................................. 116 Structure analysis and visualization.........................119 X-ray 6.1.1 6.1.2 6.1.3 6.1.4 6.1.5 crystallography................................................................. 119 Scattering of X-rays by atoms.........................................120 Diffraction from a crystal................................................ 122 The phase problem.......................................................... 125 Temperature
factor.......................................................... 127 Refinement........................................................................ 127 IX
x Contents 6.2 Nuclear magnetic resonance (NMR)........................................ 127 6.2.1 Basic principles..................................................................127 6.2.2 Chemical shift....................................................................129 6.2.3 7-Coupling.........................................................................130 6.2.4 Nuclear overhausereffect (NOE)..................................... 131 6.2.5 Structure computation....................................................... 131 6.3 Cryo-electron microscopy...........................................................132 6.3.1 Physical principles............................................................ 132 6.3.2 Problem of imaging biomolecules..................................133 6.3.3 Three-dimensional electron microscopy........................ 134 6.4 Representation of structures.......................................................136 6.4.1 Structural data................................................................. 136 6.4.2 Line representation.........................................................137 6.4.3 Spheres—CPK representation....................................... 138 6.4.4 Ribbon representation.....................................................138 6.4.5 DNA................................................................................. 141 6.4.6 Surface representation....................................................142 6.4.7 Surface hydrophobicity and charge...............................143 6.4.8 Volume
representation....................................................144 6.4.9 Occupancy.......................................................................145 6.4.10 Temperature factor......................................................... 146 Sample questions.........................................................................146 References and further reading..................................................147 CHAPTER 7 Protein folding........................................................................149 7.1 The protein folding problem.......................................................149 7.2 Physical forces in protein folding.............................................. 150 7.3 Protein energy landscape............................................................ 151 7.4 Folding in cellular environment................................................ 152 7.5 Some model chaperones.............................................................153 7.5.1 Trigger factor.................................................................... 153 7.5.2 Spy..................................................................................... 157 7.5.3 Hsp60................................................................................. 160 7.5.4 Chaperonin containing TCP1.......................................... 164 Sample questions........................................................................ 168 References and further reading..................................................168 CHAPTER 8 8.1 8.2 DNA synthesis:
Replication................................................171 Thermodynamics of DNA synthesis.........................................171 Mechanism of DNA synthesis................................................... 173 8.2.1 Structural and functional diversity..................................173
Contents 8.3 8.4 8.5 8.6 8.7 CHAPTER 9 9.1 9.2 9.3 9.4 8.2.2 Common architecture of DNA polymerases..................175 8.2.3 Primertemplate DNA-binding toenzyme...................... 177 8.2.4 Formation of E:p/t:dNTP ternarycomplex..................... 180 8.2.5 Phosphoryl transfer reaction............................................182 Cellular context...........................................................................185 Initiation of bacterial DNA replication.................................... 187 8.4.1 Melting of the DNA—Replicatorand initiator............... 187 8.4.2 Unwinding of the DNA—Helicase and helicase loader................................................................................ 190 8.4.3 Priming DNA synthesis—Primase and SSB..................193 Bacterial replicase.......................................................................196 8.5.1 The polymerase.................................................................197 8.5.2 The processivity clamp.................................................... 199 8.5.3 The clamp loader............................................................. 201 8.5.4 Proofreading..................................................................... 204 Disentanglement of replication products..................................206 A glimpse of eukaryotic replication......................................... 209 8.7.1 Initiation of replication....................................................210 8.7.2 Multiple polymerases at work........................................ 211 Sample
questions........................................................................215 References and further reading.................................................216 Transcription......................................................................... 217 Basic requirements for transcription........................................ 217 Bacterial transcription................................................................218 9.2.1 Bacterial RNA polymerase............................................. 218 9.2.2 Promoter............................................................................222 9.2.3 Initiation: Holoenzyme-DNA interactions.....................224 9.2.4 Elongation.........................................................................230 9.2.5 Termination...................................................................... 234 Eukaryotic transcription.............................................................237 9.3.1 RNA polymerase II..........................................................237 9.3.2 Promoter............................................................................240 9.3.3 General transcription factors...........................................241 Transcriptional regulation..........................................................249 9.4.1 Prokaryotic regulation.....................................................250 9.4.2 Eukaryotic regulation......................................................263 Sample questions....................................................................... 274 References and further
reading.................................................274 XI
Contents CHAPTER 10 RNA processing............................................................... 277 10.1 RNA Pol II CTD......................................................................... 277 10.2 5 -End capping............................................................................. 278 10.3 З -End polyadenylation................................................................287 10.4 10.5 10.3.1 CFI................................................................................... 287 10.3.2 CPSF................................................................................ 290 10.3.3 CstF.................................................................................. 292 10.3.4 CPU.................................................................................. 293 RNA splicing...............................................................................294 10.4.1 Chemistry.........................................................................294 10.4.2 Spliceosome dynamics.................................................. 295 RNA editing................................................................................. 303 10.5.1 Site-specific deamination.............................................. 303 10.5.2 Guide RNA-directed editing......................................... 305 Sample questions.........................................................................308 References and further reading................................................. 308 CHAPTER 11 Translation.........................................................................311
11.1 Transfer of genetic information—From mRNA to protein ....311 11.1.1 Protein synthesis.............................................................311 11.1.2 Messenger RNA—Genetic code....................................311 11.1.3 Transfer RNA—Means ofinformation transfer............313 11.1.4 Aminoacyl-tRNA synthetase—Activation of tRNA...317 11.1.5 The ribosome—Multicompartmental reaction vessel................................................................................326 11.2 Initiation of translation............................................................... 330 11.2.1 Prokaryotic...................................................................... 330 11.2.2 Eukaryotic....................................................................... 333 11.3 Translation elongation.................................................................338 11.3.1 Decoding......................................................................... 338 11.3.2 Peptidyl transfer.............................................................. 340 11.3.3 Translocation.................................................................. 341 11.4 Translation termination...............................................................342 Sample questions........................................................................ 345 References and further reading................................................. 345 CHAPTER 12 DNA damage and repair................................................347 12.1 Structural chemistry of DNA damage........................................ 347 12.1.1
Spontaneous reactions................................................... 347 12.1.2 Chemical damage...........................................................347
Contents 12.1.3 Radiation damage..........................................................351 12.2 Mismatch repair......................................................................... 352 12.3 Direct reversal of damage..........................................................358 12.4 Base excision repair...................................................................361 12.5 Nucleotide excision repair.........................................................365 12.6 Translesion synthesis.................................................................. 373 Sample questions....................................................................... 375 References and further reading.................................................375 CHAPTER 13 Recombination........................... 377 13.1 Homologous recombination.......................................................377 13.1.1 Initiation of recombination: Resection and recombinase loading...............................................378 13.1.2 Homologous DNA pairing and strand exchange....... 385 13.1.3 Branch migration and Holliday junction resolution ...390 13.2 DNA rearrangements.................................................................. 395 13.2.1 Conservative site-specific recombination....................396 13.2.2 Transpositional recombination..................................... 399 Sample questions....................................................................... 403 References and further reading................................................ 403 CHAPTER 14 Membrane structure and
function............................. 405 14.1 14.2 14.3 14.4 Composition of the membrane................................................. 405 Membrane structure...................................................................406 Membrane dynamics..................................................................408 Transport across membranes.................................................... 410 14.4.1 Passive transport............................................................410 14.4.2 Active transport............................................................. 412 14.4.3 Transport in vesicles......................................................414 14.4.4 Signal transduction........................................................416 Sample questions....................................................................... 419 References and further reading................................................ 419 CHAPTER 15 Fundamentals of structural genomics........................421 15.1 15.2 15.3 Genome sequencing...................................................................421 15.1.1 Sanger-automated sequencing...................................... 421 15.1.2 Next-generation sequencing......................................... 422 Genome annotation....................................................................425 Structural genomics/proteomics............................................... 426 15.3.1 Experimental structure determination..........................426 15.3.2 Computational structure prediction..............................427
XIV Contents 15.4 15.5 Function prediction......................................................................429 Structural genomics initiatives...................................................430 Sample questions......................................................................... 430 References and further reading..................................................431 CHAPTER 16 Cell signaling and systemsbiology................................ 433 16.1 16.2 16.3 Cell signaling............................................................................... 433 16.1.1 Pathway as signal amplifier.......................................... 433 16.1.2 Signaling by phosphorylation........................................ 433 16.1.3 МАРК pathway.............................................................. 434 Structural basis of immune response.........................................440 Structural systems biology..........................................................444 Sample questions.........................................................................447 References and further reading..................................................448 CHAPTER 17 Macromolecular assemblies........................................... 449 17.1 Molecular self-assembly.............................................................449 17.1.1 Principles of self-assembly............................................ 449 17.1.2 Biomacromolecular complexes.....................................450 17.1.3 Viral capsids................................................................... 450 17.1.4
Ribosome assembly........................................................453 Single-particle cryo-electron microscopy................................. 457 Sample questions........................................................................ 462 References and further reading................................................. 462 17.2 CHAPTER 18 Computational molecular biology..................................465 18.1 Modeling and simulation............................................................ 465 18.2 Molecular dynamics....................................................................466 18.2.1 Basic theory.................................................................... 467 18.2.2 Simulation of a cellular process....................................471 18.3 Drug design..................................................................................472 18.3.1 Hemoglobin and sickle cell disease............................. 472 18.3.2 Enzyme inhibitors as drugs...........................................473 18.3.3 HIV protease as drug target..........................................474 18.3.4 Targeting interaction networks......................................476 18.3.5 Computational drug screening.......................................478 Sample questions........................................................................ 479 References and further reading................................................. 480 Index.......................................................................................................................... 481
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| spelling | Pal, Subrata Verfasser aut Fundamentals of molecular structural biology Subrata Pal London ; San Diego, CA Academic Press [2020] xxi, 495 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Zelle (DE-588)4067537-3 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Molekularbiologie Zelle (DE-588)4067537-3 s Molekularbiologie (DE-588)4039983-7 s b DE-604 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=031428821&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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| title | Fundamentals of molecular structural biology |
| title_auth | Fundamentals of molecular structural biology |
| title_exact_search | Fundamentals of molecular structural biology |
| title_full | Fundamentals of molecular structural biology Subrata Pal |
| title_fullStr | Fundamentals of molecular structural biology Subrata Pal |
| title_full_unstemmed | Fundamentals of molecular structural biology Subrata Pal |
| title_short | Fundamentals of molecular structural biology |
| title_sort | fundamentals of molecular structural biology |
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