Goldfarb D. Biophysics DeMYSTiFied

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2 Biophysics DemystifieD

chemistry. This may be self-taught. Notice the or in physics or chemistry. If you

have one or the other, it should be enough to get you through this book.

Let’s see two examples. For our first example, take the equation

F 5 ma (1-1)

This should look somewhat familiar to you. It means that if you apply a force

F to an object of mass m, you will cause that object to accelerate with a rate of

acceleration a.

The equation also says that for any given force F on an object of mass m, the

acceleration rate will be exactly the rate that causes the product (mass 3 accel-

eration) to be equal to the force. This means, if we replace the object with a

more massive object so that m is larger and we apply the same force, then the

acceleration must be smaller (so that the mass times the acceleration will still

be equal to the force). Similarly, applying the same force to a less massive object

will cause the object to accelerate faster.

Let’s put this in concrete terms. Say we apply a force of 12 newtons (N) to an

object with a mass of 2 kilograms (kg). The object will accelerate at a rate of

6 meters per second per second (or 6 m/s

). That is, every second, the object will

be going 6 meters per second (or 6 m/s) faster than it was the previous second,

for as long as we continue to apply that force. If the object is standing still when

we first apply the force, then after 1 s, it will be moving at 6 m/s, after 2 s, it will

be moving 12 m/s, and after 3 s, 18 m/s [about 40 miles/hour (mi/h)].

But, if we now apply that same force, 12 N, to a more massive object, say 24 kg,

that object will accelerate much more slowly, only

m/s

(see Fig. 1-1).

To take this example a step further, we write Eq. (1-1) as

F 5 ma (1-2)

Notice that the F and a are now bold. This means that they are vectors. A vector

is a quantity that has not only a size but a direction as well. A force is always

Figure 1-1 • If we apply the same force to two

objects of different mass, the more massive object

accelerates slower. The product, force 5 mass 3

acceleration.

m = 2 kg

m = 24 kg

F = 12 N

a = 6 m/s

a = 0.5 m/s

Chapter 1 InTroduCTIon 3

applied in a specific direction. Acceleration also occurs in a specific direction,

and the acceleration will occur in the same direction as the force. The mass of

the object, however, is not a vector quantity, but is called a scalar: a quantity

that has only size.

All of this should sound familiar to you. By now you should at least be think-

ing, “Yes, I remember that. It’s all coming back to me.” (Unless you’re already

thinking, “I know this. When’s he going to get to the biophysics? I knew I should

have skipped this section.”)

Let’s take one more example. Consider the chemical reaction

1 H

O → sugar 1 O

(1-3)

The concept of a chemical reaction and this way of representing it needs to

be, if not familiar, at least something you can grasp quickly and become com-

fortable with. Equation (1-3) means that carbon dioxide and water can react

together to form sugar and oxygen. This is one of the most basic biological reac-

tions. It is how plants capture carbon and energy from the environment and

store that energy in a form (sugar) that we (and other animals) can later con-

sume and use to stay alive and to go about our daily business.

Strictly speaking, this reaction should have been written with a double arrow,

like this:

1 H

O ↔ sugar 1 O

(1-4)

The double arrow means that the reaction can occur in both directions. Going

from left to right, carbon dioxide and water combine to create sugar and oxy-

gen. This direction requires the input of energy. Plants get that energy from

sunlight and, through the process of photosynthesis, store some of that solar

energy in the chemical bonds of the sugar.

The reverse direction, from right to left, releases energy through the oxida-

tion or combustion of sugar. In living things this process is also known as respi-

ration. It is the way living things release stored energy that can be used for

moving around, growing, and so on.

To emphasize the fact that energy is required to combine the carbon dioxide

and water and that energy is released when the sugar is oxidized, we can also

show energy as part of the chemical reaction.

1 H

O 1 energy ↔ sugar 1 O

(1.5)

The preceding discussions of forces and chemical reactions should be some-

thing that you can feel comfortable with.

4 Biophysics DemystifieD

A Brief History of Biophysics

How old is biophysics? As a separate discipline, biophysics is a relatively new

science. In the big scheme of things, it is far, far younger than physics, mathe-

matics, chemistry, or biology, but somewhat older than genetic engineering or

computer science.

Although we find some physical studies of living things scattered through-

out history, biophysics as a discipline is only about 60 to 100 years old. The

first published use of the word biophysics was in 1892, in The Grammar of

Science by Karl Pearson. In the book, Pearson tells us that there is a need for

a new scientific discipline. In Pearson’s words, “The reader might conceive

that our classification [of the sciences] is now completed, but there still

remains a branch of science to which it is necessary to refer.” He explains that

there appears to be no link between the physical and biological sciences and

points out that “a branch of science is therefore needed dealing with the

application of the laws of inorganic phenomena, or Physics, to the develop-

ment of organic forms.” He proposes that the new branch of science be called

bio-physics.

Although Pearson coined the term, I like to mark the birth of biophysics with

the series of lectures given by Erwin Schrödinger in 1943. Schrödinger won the

1933 Nobel Prize in Physics for his work on quantum mechanics. In the 1930s

a small handful of physicists began turning their attention to the questions of

biology and biochemistry. Then in February 1943, Schrödinger gave his now

still struggling

If you lack the necessary prerequisites to be familiar with or to feel comfort-

able with the preceding discussion, then I highly recommend you begin with

Physics Demystified by Stan Gibilisco. Alternatively (or additionally) you may

prefer Chemistry Demystified by Linda Williams. If you have a strong preference

to start with physics or chemistry, then by all means go with your natural

inclination.

Chapter 1 InTroduCTIon 5

famous lecture series titled “What Is Life?” The Friday afternoon lectures were

so popular they had to be repeated on Monday for those unable to fit into the

lecture hall. A year later the lecture series was published as the book, What Is

Life? The Physical Aspects of the Living Cell.

The lecture series and book had a major impact on several notable scientists of

the time. Only a few years later, in 1946, the Medical Research Council of King’s

College in London established the Biophysics Research Unit of King’s College.

Their goal was to hire physicists and put them to work on questions of biological

significance. The physicist Maurice Wilkins and the physical chemist Rosalind

Franklin were among those who joined the unit to become biophysicists. There at

King’s College they used X-ray diffraction to investigate the structure of DNA.

The particle physicist Francis Crick at Cambridge University was also inspired

to turn his attention to biophysics. He was soon joined by the biologist James

Watson. In 1953 Watson and Crick made one of the most far-reaching discover-

ies of our time when they used Rosalind Franklin’s X-ray diffraction data to

discover the double helix structure of DNA.

In 1957 the Biophysical Society was founded, to encourage growth and dis-

semination of knowledge in biophysics. Since then, interest in biophysics has only

increased. By the early 1980s numerous universities offered graduate degrees in

biophysics, but only a few, if any, colleges offered undergraduate degrees. Today

over 60 colleges and universities offer undergraduate degrees in biophysics, and

the Biophysical Society has over 9000 members. Figure 1-2 shows a time line of

science and biophysics to put the age of biophysics in perspective.

The Scope and Topics of Biophysics

Biophysics is a very broad science, including a wide range of activities such as

Studying the forces between atoms that determine the shape of a protein

•

or DNA molecule

Developing algorithms for a computer to analyze and display a three-

•

dimensional image of the brain in real time during brain surgery

Investigating and comparing the mechanics of limb movements or blood

•

flow in various organisms

Researching the effects of radioactivity on the environment

•

There are many ways we can classify the long list of topics that make up the

field of biophysics. One very convenient and typical way to organize the broad

200015001000500

1700 1800 20001900

Pythagoras:

square of two

sides equals

square of

hypotenuse

Euclid:

mathematics

Archimedes:

hydrostatics,

levers,

compound

pulley

Bhaskara:

diameter

of the sun

Preparation of

chemicals: nitric

acid, etc

William of

Saliceto:

earliest

recorded

human

dissection

Copernicus:

planets orbit

the sun

Galileo:

thermometer,

falling

objects,

telescope

Leibniz,

Newton:

Calculus

Leibniz,

Newton:

Calculus

Newton:

mechanics,

gravity,

F = ma

Franklin:

experiments

with lightning

and electricity

Galvani:

experiments

with electrical

nature of

nerves

Schleiden

and

Schwann:

cell theory:

All organisms

are made of

cells

Mendeleyev:

Peridoc Table of

the Elements

Pearson:

proposes new

science called

biophysics

Rontgen:

X-Rays

Planck:

quantum theory

Ruska and

Knoll:

electron

microscope

Schrodinger: What

Is Life? The

Physical Aspects

of the Living Cell

Biophysics Unit at

King’s College

Pollard:

Biophysical

Society

founded

Boyer and

Cohen:

Recombinant

DNA and

Genetic

Engineering

Figure 1-2 • How old is biophysics?

Chapter 1 InTroduCTIon 7

scope of biophysics is according to the relative size of what we’re studying. For

example, are we studying molecules, cells, or whole organisms? Another com-

mon and useful way is according to technique employed and application. With

this in mind, and with some overlap, we will classify the many topics of bio-

physics into two broad classifications subdivided up into six categories.

Biophysical topics based on relative size of subject

•

1. Molecular and subcellular biophysics

2. Physiological and anatomical biophysics

3. Environmental biophysics

Biophysical techniques and applications

•

4. General biophysical techniques

5. Imaging biophysics

6. Medical biophysics

The next two chapters briefly describe many of the topics found in biophys-

ics, organized according to the two major classifications just given. The purpose

is to give you a broad overview of the scope of biophysics and to introduce

vocabulary specific to biophysics. This will aid in understanding the detailed

chapters that follow.

Throughout the book, vocabulary words that are important for you to learn

will be in italics when first defined and will appear in the glossary in the back

of the book.

8 Biophysics DemystifieD

Quiz

Refer to the text in this chapter if necessary. Answers are in the back of the

book.

1. An object of mass 3 kg is not moving. It is then pushed with a constant force of

12 N, causing it to accelerate at a rate of 4 m/s

. After 5 s how fast will the object

be going?

A. 12 m/s

B. 15 m/s

C. 20 m/s

d. 60 m/s

2. An average-size adult cheetah (50 kg) can accelerate from a standstill to 30 m/s in

just 3 s. If we approximate the forward thrust provided by the cheetah’s leg muscles

as a constant force, what force is necessary to cause this acceleration (10 m/s

A. 50 n

B. 150 n

C. 300 n

d. 500 n

3. If a cheetah accelerates from a standstill at a rate of 10 m/s

and reaches its top

speed in just 3 s, how far will the cheetah have traveled in that time?

A. 45 m

B. 30 m

C. 15 m

d. 10 m

Figure 1-3 • The cheetah is the fastest land animal. An average adult cheetah weighs about 110 pounds (lb). Its power-

ful leg muscles generate enough forward thrust to accelerate the cheetah from standing still to a top speed of about 70

mi/h in just 3 s.

Chapter 1 InTroduCTIon 9

4. A major source of energy for animals is carbohydrates (sugars) from plants

(grains, fruits, vegetables, etc.). Where does this energy primarily come from?

A. Plants use their roots to draw energy from the ground.

B. Potential energy was stored in the seed before the plant grew.

C. Plants breathe oxygen at night and carbon dioxide during the day.

d. Photosynthesis extracts energy from sunlight and stores it in chemical bonds.

5. A chemical equation is a symbolic representation of a chemical reaction. A dou-

ble arrow in a chemical equation indicates

A. we are not certain about the chemical reaction.

B. the chemical equation is balanced.

C. the reaction involves both physics and chemistry.

d. the reaction can occur in either direction.

6. Although Watson and Crick are credited with the 1953 discovery of the double-

helical structure of DNA, they were only able to do this with data obtained by

Rosalind Franklin at the Biophysical Research Unit of King’s College in London.

What kind of data did she obtain?

A. Temperature measurements of dnA crystals

B. Electron microscopic images

C. X-ray diffraction

d. Magnetic resonance

7. Biophysics is an interdisciplinary science; this means that

A. the internal aspects of living things are studied.

B. it takes a lot of discipline to be a biophysicist.

biophysics is less rigorous than other sciences such as physics and biology.

d. biophysics combines physics, chemistry, and biology into a single science.

8. Two common and convenient ways to classify the various branches of biophysics

are by

size of what is studied and by technique utilized.

B. size of what is studied and by whether mathematics is used.

technique used and by application.

d. technique used and by percentage of physics, chemistry, biology, and mathematics

used.

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In this chapter, we present an overview of the various topics of biophysics

according to the following three major divisions: molecular and subcellular

biophysics, physiological and anatomical biophysics, and environmental

biophysics.

CHAPTer OBJeCTiVeS

In this chapter, you will

Gain an understanding of the broad scope of biophysics.

•

acquire some vocabulary of biophysics, learning the most commonly used

•

terms and how they apply to the branches of biophysics.

learn to classify the topics of biophysics into the three major divisions of

•

Molecular and subcellular biophysics.

•

physiological and anatomical biophysics.

•

Environmental biophysics.

•

learn how the topic areas of biophysics are interrelated.

•

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Biophysical Topics