Goldfarb D. Biophysics DeMYSTiFied
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x BIOPHySICS DeMYSTiFieD
Atomic Force Microscopy 48
Optical Tweezers 48
Voltage Clamp
48
Current Clamp 49
Patch Clamp 49
Calorimetry
50
Quiz 52
chapter 4 Energy and Life 55
The First Law of Thermodynamics 56
Simplifying Assumptions 59
Enthalpy
60
Entropy 65
Gibbs Energy 68
The Second Law of Thermodynamics
69
The Gibbs Function as the Driver of Biophysical
Processes 70
Quiz 72
chapter 5 Statistical Mechanics 75
What Is Statistical Mechanics? 76
Statistical Mechanics: A Simple Example 78
Permutations
79
Boltzmann Distribution 93
Gibbs Energy and the Biophysical Partition
Function 101
Quiz 103
chapter 6 Forces Affecting Conformation
in Biological Molecules 105
Chemical Bonds 107
Forces That Affect Conformation in Biomolecules 113
Charge-Charge Forces
114
Dipole Forces 117
Hydrogen Bonds and Water 124
Aromatic Ring Structures: Cation-Pi Interactions
and Stacking 127
Dispersion Forces 130
Steric Interactions
131
Hydrophobic Interactions 132
Hydrophilic Interactions 134
Quiz 136
Contents xi
chapter 7 Biomolecules 101 139
Classes of Biomolecules 140
Functional Groups 143
Carbohydrates
148
Lipids 150
Proteins 155
Nucleic Acids
158
Quiz 170
chapter 8 The Cell 173
What Is a Cell? 174
Cell Structure 175
The Cell Membrane
179
Cell Organelles 181
Cell Life Cycle 192
Quiz
195
chapter 9 Protein Biophysics 197
Protein Folding 198
Factors Influencing Protein Structure 204
Membrane Proteins
209
Analysis of Polypeptide Backbone
Bond Angles 210
Common Protein Secondary Structures
211
Quiz 218
chapter 10 Nucleic Acid Biophysics 221
Introduction 222
DNA Secondary Structure 222
DNA Melting
231
DNA Tertiary Structure 252
Quiz 262
chapter 11 Membrane Biophysics 265
Membrane Functions 266
Phospholipid Behavior and Self-Assembly 267
Lipid Bilayer Energetics and Permeability
271
Fluid Mosaic Model 273
Phase Transitions in Phospholipid Bilayers 274
Membrane Growth
277
Membrane Permeability and Transport 278
Quiz 291
xii BIOPHySICS DeMYSTiFieD
chapter 12 Physiological and Anatomical Biophysics 293
The Scope of Physiological and Anatomical Biophysics 294
Jumping in the Air 294
Pumping Blood
299
Hummingbird Hovering 307
Quiz 313
Final Exam 315
Answers to Quizzes and Final Exam 341
Appendix: Units, Conversions, and Constants 343
Glossary
347
Index 371
xiii
Preface
Biophysics is a fascinating and relatively new science. After centuries of
studying the physical properties and behavior of inanimate objects, we finally
got the idea to use physics to study living things. The hope is to reveal the most
basic principles of life, in much the same way that physics has illuminated fun-
damental principles of matter and energy.
This is an introductory textbook. Ideally we would cover the entire field of
biophysics. You will certainly agree, as you read this book, that a thorough cov-
erage of the entire field of biophysics is just not possible in a single volume.
However, what you can gain from this book is a solid foundation, and a knowl-
edge of biophysical principles and how they are applied. Once gained, that
foundation will be easy to build on.
The book is organized as follows. The first three chapters give a broad over-
view of and introduction to the science of biophysics. In Chap. 1 you will learn
to define biophysics, understand the prerequisites needed to study Biophysics
Demystified
®
, and learn about the brief history of biophysics. You will also get
to know the major divisions of biophysics and how the various topics in bio-
physics are categorized into these major divisions.
Chapters 2 and 3 then provide a broad overview of the science of biophysics.
There are several reasons to gain a broad understanding of the field before get-
ting into the details. First, you will need to build up some vocabulary, that is, the
“language of biophysics.” Understanding the most commonly used terms from
the outset will be a help later on. Second, the various topics of biophysics are
interconnected. Although each can be studied independently, a broad overview
will give you the ability to understand the context of each topic as you learn its
details. Similarly, knowing the interconnections will underscore the importance
and usefulness of each branch of biophysics to the others. Finally, the broad
overview of Chaps. 2 and 3 will enable us to cover a lot of topics that may not
be covered in great detail later in the text, so at least you will understand how
they fit into the whole. This will be part of your foundation for later learning.
Chapters 4 through 8 teach the principles of physics, biology, and chemistry
that are necessary for a journey into biophysics. The focus is on aspects of these
sciences that apply most directly to biophysics. This includes, in Chaps. 4 and 5,
an understanding of free energy, the laws of thermodynamics, entropy, and
statistical mechanics. Next, Chaps. 6 and 7 delve into the physical forces that
come into play at the molecular level, again paying special attention to those
that are most relevant to living things. We then review the major categories of
biomolecules—what they are made of and aspects of their structure and
function—sort of a quick overview of biochemistry from a biophysical point of
view. Chapter 8 provides an overview of the living cell, its structures, and what
these structures do.
In Chaps. 9 through 11 the focus is on subcellular biophysics. This is the most
common and largest branch of biophysics, and so we go into it in more detail.
This branch includes protein biophysics, DNA biophysics, and membrane bio-
physics. Finally, Chap. 12 explores some aspects of anatomical biophysics, in-
cluding blood flow and winged flight in animals.
You can use this book as a self-teaching guide, to lay the foundation for fur-
ther study or just to satisfy your immediate curiosity. It can also be used as a
classroom supplement, explaining and clarifying topics that are not as simple
in other texts. My hope is that in reading this book you will truly find “hard
stuff made easy.”
Daniel Goldfarb
xiv BIOPHySICS DeMYSTiFieD
xv
Acknowledgments
Thanks to Judy Bass, my editor at McGraw-Hill, for the opportunity to write
this book, and for her advice and guidance throughout; to Dr. Kenneth Breslauer,
a role-model biophysicist, for coming to my aid on short notice and helping me
find a good technical reviewer; and to Pragati Sharma, for her great job
in finding errors, and for her valuable suggestions for clarity in many places. I
especially thank my wife, Sora Rivka, for her sound advice, her encouragement,
helping schedule time for me to write, and everything else she did to help make
this project possible. Finally, I thank my children for their exceptional curiosity,
and for always being there (when I was trying to write).
xv
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Biophysics
DeMYSTiFieD®
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1
What is Biophysics?
Plain and simple, biophysics is the physics of biology, just as astrophysics is the
physics of astronomy and nuclear physics is the physics of atomic nuclei.
What does this mean? What is the physics of biology? Physics is the study of
matter and energy. Biophysics tries to understand how the laws of matter and
energy are at work in living systems. Another way to say this is that biophysics
uses of the principles, theories, and methods of physics to understand biology.
Biophysics is an interdisciplinary science. One could say it is the place where
physics, chemistry, biology, and mathematics all meet. In practice, most
biophysicists study things at the molecular level, but biophysics also includes
physiological, anatomical, and even environmental approaches to the physics
of living things.
Prerequisites for Biophysics
Biophysics is an advanced science. It requires some basic knowledge of biology,
physics, chemistry, and mathematics. However, since this book is meant as an
introduction to biophysics, to demystify biophysics, then as much as possible along
the way, I will introduce or review the necessary background information.
Still, I do need to make some assumption as to your level of understanding in
the physical sciences. For this purpose I will assume that you have had at least an
introductory college-level (or advanced high school–level) course in physics or
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Introduction