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Lecture 1 Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

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Page 1: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Lecture 1Lecture 1

Rob PhillipsCalifornia Institute of Technology

(Block et al.)

(Wuite et al.)

Page 2: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Gibbs and the Calculus of Gibbs and the Calculus of EquilibriumEquilibrium

Page 3: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

ATP and ADPATP and ADP

Page 4: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

The Statistical Mechanics of The Statistical Mechanics of DNA/Protein InteractionsDNA/Protein Interactions

Page 5: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Schrodinger’s Great QuestionSchrodinger’s Great Question

“A physics that has no place for life is as impoverished as would be a biologynot informed by chemistry.” F. Harold

Our mission: build up simplequantitative models at the biology/physics/chemistryinterface.

Page 6: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

X-Ray Crystallography of ProteinsX-Ray Crystallography of Proteins

Page 7: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

PDB Structures and PDB FilesPDB Structures and PDB Files

Page 8: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

NMR of Macromolecules: A Step NMR of Macromolecules: A Step Towards DynamicsTowards Dynamics

Page 9: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Case Studies in Molecular Biology: Case Studies in Molecular Biology: Polymerase Chain ReactionPolymerase Chain Reaction

Page 10: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Case Studies in Molecular Biology: Case Studies in Molecular Biology:

CloningCloning

Genomic libraries constructed by chopping up DNA of interest with restriction enzymes and then gluing these fragments into the phage genome and then infecting cells with the modified phage.The phage DNA circularizes within E. coli and is then propagated from one generation of E. coli to the next and carries with it copies of the original genome.Visit the Stratagene website.

www.stratagene.com

Page 11: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

The Tools of Single Molecule The Tools of Single Molecule

ScienceScience

Optical Tweezers

AFM

FRET

Page 12: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Optical Microscopy and Fluorescent Optical Microscopy and Fluorescent Dyes: The CytoskeletonDyes: The Cytoskeleton

Huge advances have taken place in microscopy which allow for the real time examination of biological structures and their temporal evolution – the cell is teeming with activity.This slide: staining of the cytoskeleton.

Actin filaments Microtubules Intermediate Filaments

Page 13: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Laser Tweezers: The Manipulation Laser Tweezers: The Manipulation of Single Moleculesof Single Molecules

Concept: Attach optical beads (micron size) to molecules of interest. Use laser light to apply force through radiation pressure.Molecular velcro – biotin/streptavidin complex.

The setup: optical microscope with a laser port and a digital camera.

(Bennink et al.)

(Prost group)

Page 14: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Optical Tweezers in Action: Optical Tweezers in Action: Transcription by RNA PolymeraseTranscription by RNA Polymerase

(Wang et al.)

(Gelles et al.)

Page 15: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

ATPase: Observations of a Rotary ATPase: Observations of a Rotary Motor in ActionMotor in Action

ATPase: Rotary molecular factory which exploits proton gradient to produce ATP.Rotary Assay: Actin filament attached to ATP rotary head and then the rotation of the stained actin filament is observed.

Page 16: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Single Molecule Experiments with Single Molecule Experiments with the AFMthe AFM

(Fernandez et al.)

Concrete example of dynamical force spectroscopy in the case of the giant muscle protein titin.Key modeling challenge: the precise details of the force/extension curve.Note that by performing mutations on the titin molecule, the force/extension signature can be altered.

Page 17: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Biological Structure: Spatial Biological Structure: Spatial HierarchyHierarchy

Structure exists at many length scales → structural hierarchiesBond lengths: ~1-3ÅAmino Acids: ~1nmProteins: 2-5nmMacromolecular assemblies: 5-50nmOrganelles: 50-1000nmCells: microns and beyondTissues

Page 18: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Biological Structure: Spatial Biological Structure: Spatial HierarchyHierarchy

Structure exists at many length scales → structural hierarchies.Each of these scales in the hierarchy is amendable to modeling.Not surprisingly, all of the usual multiscale challenges are presence with a vengeance because often different levels in the hierarchy cannot be isolated.

Page 19: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Amino Acids and Proteins Amino Acids and Proteins

Amino Acids are the building blocks of Proteins

Page 20: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Biological Structure: Protein Biological Structure: Protein StructureStructure

Structural LevelsPrimary (amino acid sequence)Secondary (α-helices, β-strands)Tertiary (domains)Quaternary (active sites)

Page 21: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Case Studies in Protein Structure: Case Studies in Protein Structure: Protein Diversity Protein Diversity

Proteins come in a variety of shapes and sizes. Enzymes are usually huge in comparison with the molecules for which they catalyze reactions (i.e. their substrates).Question: Is there a simple scaling of protein size with the number of amino acid residues?Close packing leads to:

Random walk description of polymer leads to:

Page 22: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Somes: The Biologists OnsSomes: The Biologists Ons

Macromolecular AssembliesMacromolecular Assemblies

Physicists characterize collective excitations as ONS (phonons, magnons, excitons, etc…)Biologists also consider collective phenomena in the form of interacting macromolecular complexes.

Replisome

Proteosome

Ribosome

Page 23: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Collections of Molecules - Collections of Molecules - OrganellesOrganelles

Page 24: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Structure of VirusesStructure of Viruses

Page 25: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Viruses and Their HostsViruses and Their Hosts

Page 26: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Procaryotic Cells - BacteriaProcaryotic Cells - Bacteria

Page 27: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Eucaryotic CellsEucaryotic Cells

Yeast cells

Page 28: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Collections of Cells - TissuesCollections of Cells - Tissues

Page 29: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

C Elegans – a worm with 959 cellsC Elegans – a worm with 959 cells

Page 30: Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

Biological Processes: Temporal Biological Processes: Temporal HierarchyHierarchy

Processes exists at many time scales → hierarchies of processes.Not surprisingly, all of the usual multiscale challenges are presence with a vengeance because often different levels in the hierarchy cannot be isolated.

(Chan and Dill)


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