TABLE OF CONTENTS

thoughtgreenpepperMechanics

Oct 27, 2013 (4 years and 11 days ago)

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TABLE OF CONTENTS


CHAPTER 1
. EQUILIBRIUM THERMODYNAMICS
.
Introduction








1.1 Chemical Potentials and Activities










1.1.1
Thermodynamic Preliminaries. The Electrochemical Potential




1.1.2
The Interphase Equilibrium Condition







1.1.
3
Electrochemical Potentials in Terms of Measurable Solution Variables: Introduction,
and the Effect of Electrostatic Potential





1.1.4
The Gibbs
-
Duhem Equation








1.1.5
Dependence of the Chemical Potential on Pressure






1.1.6
Dependence o
f the Chemical Potential on Composition





1.1.7
Units











1.1.8
Activity and Activity Coefficient








1.2 Ion Equilibrium across Membranes









1.2.1
The Nernst Equilibrium









1.2.2
Origin of the Nernst Potential







1.2.3
Spec
ific Ion Electrodes









1.2.4
Activity Coefficient Considerations







1.2.5
The Donnan Equilibrium









1.3 Chemical Equilibrium











Problems













CHAPTER 2. FREE DIFFUSION. Introduction








2.1 Free Diffusion of Nonelectroly
tes









2.1.1
The Teorell Equation









2.1.2
Integration of the Teorell Equation; Fick's First Law
; Solute Permeability



2.1.3
Unstirred Layers










2.1.4
Applications of Solution Theory








2.1.5
Fick's Second Law and Convective Diffu
sion






2.1.6 Justification of the Steady
-
State Assumption: Time Scales in Biological


Transport










2.2 Free Diffusion of Electrolytes









2.2.1
Differences between Electrolyte and Nonelectrolyte Diffusion




2.2.2
The Electrodiffusion Eq
uation








2.2.3
Integration of the Electrodiffusion Equation






2.2.4
Some Special Cases










Equilibrium


Uniform Composition


Diffusion Potential of a Bi
-
Ionic System


Active and Passive Exchange with a Closed Compartment


Equal Total Concent
rations on the Two Sides of the Membrane: The



Constant
-
Field Equation



2.2.5 Ionic Permeability and the Resting Potential of the Cell





2.2.6
Charged Membranes












2.2.7 Limitations of the Electrodiffusion Equation and Its
Solutions





Pr
oblems













CHAPTER 3. THE CELL
.
Introduction











2

3.1 Overview












3.2 The Structure of an Animal Cell










3.2.1

Composition and Structure of the Plasma Membrane








Heterogeneity of Cell Membranes


The Mosaic Model of the
Plasma Membrane


The Glycocalyx and Surface Charge

3.2.2 The Internal Structure of the Cell








3.3 Metabolism
: The Production of ATP








3
.4 Intracellular Transport










3.4.1
Intracellular
Diffusion









3.4.2

Protein Transport











Transport into the Nucleus


T
ransport into the Mitochondrion




3.4.3

Vesicular Transport












Endocytosis




Exocytosis, Secretion and Transcytosis

3.5 Cellular Motility and Locomotion








3.5.1

Actin
-
Based Movement and Chemotaxis






3.5
.2

Cilia and Flagella









Problems













CHAPTER

4
. FACILITATED DIFFUSION
: CHANNELS AND CARRIERS
.
Introduction


4.1 Mechanisms of Channels and Carriers







4.1.1
Hallmarks of Mediated Transport







4.1.2
Ion Selectivity of Channels







4.1.3
Energetics of Ion Selectivity, and Steric Effects





4.1.4
Ion Selectivity of Channels: Summary






4.1.5
The Structure of Ion Channels:
Selectivity
Filters, Gates
,

and Energy


P
rofiles










4.1.6
Regulation of the Gating Process







4.1.7
Classification of
Ion
Channels
. Aquaporins and Gap Junctions





4.1.8 Carrier Models









4.1.9
Carriers and Channels: Convergences and Differences




4.2 Kinetics of Facilitated Transport









4.2.1 Models
of
Ion Channel

Transport:
Over
view






4.2.2
Energy Barrier
and Binding
Models of Channel Transport





Ionic Independence: Absolute Rate Theory


Saturable Channels: Kinetic Analysis

4.2.3 The Patch Clamp and Two Applications







Acetylcholine Receptor Channel Kinetics


Voltage a
nd Current Sensitivity of a Voltage
-
Activated Sodium Channel

4.2.4
Stochastic Properties of Channels
:
Membrane Noise Analysis



4.2.5
The Simplest
Model of
Carrier

Transport
: Assumptions




4.2.6
The Simplest
Model of
Carrier

Transport
:

Equations




4.
2.7
Monosaccharide Transport

in the Erythrocyte





4.2.8 More Complex Carrier Models







4.2.9
Exchange
rs and Cot
ransporter
s







4.3 Inhibition of
Facilitated
Transport










3


4.3.1 Inhibition of Channel Transport: Channel Block






4.3.2 Inhi
bition of Carrier Transport







Problems












CHAPTER

5
. ACTIVE TRANSPORT. Introduction






.

5.1 Active Transport: General Considerations







5.1.1
Metabolic Coupling and Affinity







5.1.2
Classification of Active Transport Processes





5.1.3
Identification of Active Transport Processes




5.2 Mechanisms of Active Transport








5.2.1
Scalar Active Transport
:

Overview






5.2.2
Primary Scalar Transport








5.2.3
Secondary Scalar Transport








Cotransport


Countertranspor
t

5.2.4
Vectorial
Active Transport,
the Curie Theorem

and
Substrate






Activation









5.2.5
Sodium
-
Potassium Exchange







5.2.6 Pump
Selectivity and Other Properties

Shared with Passive Carriers


5.3 Kinetics of Active Transport








5.3.1
A Simple Secondary Scalar Transport Model: Assumptions



5.3.2
A Simple Secondary Scalar Transport Model: Equations




5.3.3
More Complex Symport Models
; the Sodium
-
Glucose Transporter



5.3.4
Primary Scalar Transport








5.3.5
Flux Equations for Pr
imary Scalar Transport





5.3.6
Relation between the Coupling Param
eter Γ and the Affinity of the


Metabolic Reaction








5.3.7
Vectorial Active Transport

and the Nature of Na
-
K Exchange





5.3.8
Pumps and Leaks











Pr
oblems











CHAPTER

6
. NONEQUILIBRIUM THERMODYNAMICS. Introduction




6
.1 The Basic
Phenomenological Equations







6.1.1 Con
jugate Forces and Fluxes







6.1.2
Phenomenological Coefficients and Linear Thermodynamics



6.1.3
Frictional Interpretation of the Phenomenological Equations



6.1.4
A Cautionary Note before Proceeding






6
.2 Nonequilibrium Thermodynamic Description of Passive Transport




6.2.1
Setting the Stage









6.2.2
The Chemical Potential of the Solvent






6.2.3
A New Set of Forces and Fluxes; Osmotic Pressure




6.2.4
The Kedem
-
Katchalsky Equations







6.2.5
Physical Significance of the Reflection Coefficient
: Semipermeable


Membranes and the Osmometer, Steric Effects and Sieving




6.2.6
Osmotic Pressure of Solutions; Donnan Osmotic Pressure
; Osmotic





Effects on Cells









6.2.7
Passive Trans
port of Multiple Nonelectrolytes





6.2.8
Passive Transport of Electr
olytes:

Electrokinetic Phenomena





4

6
.3 Nonequilibrium Thermodynamic Description of Active Transport




6.3.1
Definition of Active Transport







6.3.2
Coupling between Nonconjugate
Forces and Fluxes




6.3.3 Nonequilibrium Thermodynamics of Motor Proteins

and ATP Synthase

6.4
Limitations of Nonequilibrium Thermodynamics






6.4.1
Closeness to Equilibrium: A Limitation Intrinsic to Linearized


Nonequilibrium Thermodynamics






6
.4.2
The Concentration Dependence of the Phenomenological Coefficients


6.4.3
Closeness to Equilibrium in Biological Systems





6.4.4
The Information Content of Nonequilibrium Thermodynamics



6.4.5
Approximations in the Derivation of the Kedem
-
Katcha
lsky Equations



Problems












CHAPTER
7
.
MODELS OF TRANSPORT ACROSS CELL MEMBRANES
.

In
troduction


7
.1 Transport
A
cross the Lipid Bilayer of Cell Membranes







7.1.1
Evidenc
e for Nonelectrolyte Diffusion A
cross the Lipid Bilayer



7.1.2
A Simpl
e Model of Transbilayer Diffusion





7.1.3
Potential Barriers in the Bilayer







7
.2 Models of Transport
T
hrough Pores








7.2.1
Classification of Pore Transport Models






7.2.2
Hydraulic Conductivity of a Pore







7.2.3
Hindered Diffusion
;

Solute Permeability as a Probe of Pore Radius




7.2.4
Other Factors Affecting Estimated Pore Size; The Equivalent Pore




7.2.5
Hindered Convection (Sieving)
;
t
he Reflection Coefficient as a Probe of



Pore Radius









7.2.6 Combined Diffusion and
Convection through Pores




7.2.7
Single
-
File Transport through Pores






7.2.8
The Permeability Ratio of Larger Pores






7
.3 Electrical Analogs










7.3.1
Equivalent Circuit for the Passive Flux of a Single Ion




7.3.2
Equivalent Circuit for
the Passive Transport of
Multiple Ions



7.3.3
The Electrical Analog of a Rheogenic Pump






7.3.4
Some Final Remarks









Problems












CHAPTER 8. REGULATION AND FEEDBACK. Introduction







8.1 Regulation
of

Transport











8.1.1 Rece
ptor
-
Mediated Second Messenger Systems: Cyclic AMP and





Antidiuretic Hormone










8.1.2 Direct Hormonal Regulation without an Extracellular Receptor:




Aldosterone











8
.1.3 Calcium
-
Based Regulation










Maintenance of a Low Cytosolic
Calcium Concentration







Calcium Signaling











Calcium Handling in Cells and Compartmental Analysis





8.2 Feedback
in Transport Systems
: Insulin








8.3 Regulation
by
Transport











8.3.1 Regulation of Cell Volume









5



8.3.2 Regu
lation of Cell pH









Problems











Appendix 8.1 Nonequilibrium Binding in Compartmental Analysis





CHAPTER
9
. EXCITABLE CELLS. Introduction







9
.1 Nerve











9
.1.1. The Resting Neuron








9
.1.2. The Action Potential
:
Electrical A
spects







The Membrane Action Potential
: Resting State


Hodgkin and

Huxley's Equations for the Dependence of Conductance on



Membrane Potential


Excitation of the Membrane Action Potential


The Propagating Action Potential: Cable Theory


The Role of My
elin

9
.1.3. The Action Potential
:
Molecular Aspects







Hodgkin and Huxley's Channel Model


More Recent Models of the
Potassium and
Sodiu
m Channels of

Nerve

9
.1.4. Synaptic Transmission








9
.2 Muscle











9
.2.1. The Resting Muscle Fiber







9
.2.2. Excitation and Excitation
-
Contraction Coupling






Neuromuscular Transmission and Excitation:

the Acetylcholine Receptor



Excitation
-
Contraction Coupling

9
.2.3. Molecular Mechanisms of Muscle Contraction







Problems












CHAPTER
1
0
.
E
PITHELIAL
TRANSPORT. Introduction

1
0
.1
Organization of Epithelial and Endothelial Cell Layers and Some Consequences

1
0
.1.1 The Organization of Epithelial and Endothelial Cell Layers

1
0
.1.2

The Pathways across Leaky and Tight Epithelia

1
0
.1.3

Transport

in a Parallel Path System

1
0
.1.4

Coupling of Transepithelial Water Flow to Active Ion Transport

The Curran Model

The Standing Gradient Model

The Sodium Recirculation Model

The Cotransporter Hypothesis


1
0
.1.5

The Effect of Unstirred Layers on Trans
epithel
ial

Diffusion and Osmosis
:

Concentration Polarization

1
0
.1.6

Electrical Analogs of Cell Layers

1
0
.2 Examples of Epithelial and Endothelial Function

1
0
.2.1

Absorption

Absorption of Sugars in the Small Intestine

Transport of Water and Sodium in the Proximal

Tubule of the

Kidney

T
ransport of Water and Sodium in the Distal Tubule of the Kidney

1
0
.2.2

Secretion

1
0
.2.3

Filtration

Problems


Appendix 10.1 Convection, Diffusion and Mass Addition in Channel Geometries



6


CHAPTER 1
1
. GAS TRANSPORT. Introduction

1
1
.1

Partial Pressure and the Equations for Gas Flux

1
1
.2 Overview of the Gas Transport Process

11.3
Gas Exchange in the Lung

11.4
Oxygen

Transport in the Blood

11.5


Transport
from Red Blood Cells to Tissue


11.5.1 Reaction
-
Diffusion
Processes


11.5.2
The Krogh Tissue Cylinder

11.5.3
Modifications to the Basic Krogh Model



11.5.4 Beyond the Krogh Cy
l
inder


Problems