Goldfarb D. Biophysics DeMYSTiFied

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173

We want to dig deeper into the physics of biomolecules. In order to do so, we

must first understand the context in which biomolecules function. That context

is almost always the cell. We also want to lay a foundation to study the physics

of the cell itself. With this in mind, in this chapter we review the main struc-

tures of living cells and give you a basic understanding of the relationship

between cell structures and the biomolecules they are made of.

CHAPTer OBJeCTIVeS

In this chapter, you will

learn the basic concepts of cell theory.

•

learn the structures of the cell and their functions.

•

learn the relationship between biomolecules and cell structures.

•

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The Cell

174 Biophysics DemystifieD

What Is a Cell?

So what is a cell? A cell is a pouch or sack of biomolecules that is (or was) alive.

A cell is the smallest unit of an organism that can be considered alive. If you

break the cell into anything smaller, it’s just a bunch of biomolecules and not

considered alive. The pouch or sack is part of the cell itself and is called the cell

membrane.

So what do we consider alive? Something is alive if it can take in matter and

energy and use that matter and energy to do work on its surroundings, to grow, and

to reproduce itself.

This definition leaves out certain things, about which scientists are still

debating whether they should be considered organisms. For example, a virus is

a DNA molecule surrounded by a protein coat. Should it be considered alive?

Viruses reproduce, but they do not grow. And viruses only reproduce with the

aid of a cell they’ve infected. Without a host cell a virus can’t do much of any-

thing. So for now, for our purposes, we will consider living things to be only

those things that meet our definition’s criteria concerning matter and energy

and growing and reproducing. (Note: This definition of alive is not meant to

exclude individual organisms or individual cells that may be at some phase of

life lacking in one of these features. E.g., an adult human being stops growing

in terms of their body height, but their cells are still growing and reproducing,

so the person is alive. Or, e.g., an individual cell may stop reproducing, while

other cells in the same organism are still reproducing and the individual cell

that has stopped is still otherwise functioning—taking in matter and energy to

do work—and so that individual cell is alive.)

Cell theory was formally developed in 1839 by M. J. Schleiden and T. Schwann.

The theory was based not only on Schleiden’s and Schwann’s own microscopic

observations, but also the observations and ideas expressed by others going as far

back as the mid- to late-1600s, when scientists including Robert Hooke and

Antonie van Leeuwenhoek began using microscopes to examine living things.

Cell theory says (1) all living things are made of cells and (2) all cells come

from preexisting cells.

A quick note regarding the second point: many people have tried unsuccess-

fully to create a living cell from biomolecules. As of this writing, it is still the

case that all living cells we know of came from previously existing cells. The

process by which cells come from preexisting cells is called cell division. In cell

division, a cell replicates its DNA and then splits into two daughter cells. Each

of the daughter cells gets a copy of the replicated DNA.

chapter 8 The cell 175

An organism can be single cellular, that is, made up of a single cell (like an

amoeba) or multicellular (like people). Cells themselves can grow, by taking in

matter and energy to build up their internal structures and increase their mem-

brane size. Organisms can grow too (obviously). Single-cell organisms grow as

a cell grows. Multicellular organisms grow primarily by adding cells to them-

selves through cell division.

Cells can be large or small. Most cells are too small to see with the naked eye.

However, a modest microscope is usually sufficient to visualize most kinds of

cells. In some cases cells can be quite large. For example, an egg is a single cell.

The eggs of many organisms are too small to see without a microscope, whereas

the eggs of others are big enough to eat for breakfast.

There are many different types of cells. The cells of different organisms can be

very different from one another. But even within the same organism cells special-

ize to carry out different functions. For example, nerve cells are long and thin like

wires to carry nerve impulses throughout the body. Muscle cells can contract to

provide movement. Skin cells are flat and strong to protect the body. And bone

marrow cells manufacture blood cells which carry oxygen through the blood. The

process of a young cell maturing to specialize and become a particular type of

cell is known as differentiation. Figure 8-1 shows some examples of various types

of cells. For the most part, however, in the remainder of this chapter we will

concern ourselves mainly with those things that cells have in common.

Cell Structure

All cells are surrounded by a lipid bilayer membrane that encloses and contains

the contents of the cell. We already learned that many lipids are amphipathic,

having both hydrophobic and hydrophilic parts on the same molecule. In an

aqueous or polar environment these molecules arrange themselves in com-

plexes (aggregates of molecules) that place their hydrophobic parts inside, away

from the water, and their hydrophilic parts on the outside, facing the water.

One such complex is a lipid bilayer as shown in Fig. 8-2. The bilayer forms a

membrane around the cell. The polar, hydrophilic portions of lipid molecules

face the aqueous environments on both the inside and outside of the cell. The

nonpolar, hydrophobic parts lie in the center of the bilayer and form a barrier

that blocks many molecules from crossing the membrane. This keeps the inside

of the cell on the inside and the outside on the outside. The cell membrane is

in fact selectively permeable, meaning that certain types of molecules can pass

through the membrane, whereas others cannot.

176 Biophysics DemystifieD

The inside of the cell is called the cytoplasm. It contains all the biomolecules

we have discussed so far, and more. This is where these molecules do the work

of keeping the cell alive.

There are two major categories of cells, and all organisms are made up

entirely of one of these two categories of cells. Some cells contain a central,

membrane-bound compartment called the nucleus which contains most or all

of the cell’s genetic material. Cells that have a nucleus are called eukaryotic

FIgure 8-1 • Microscopic images of various cell types, clockwise from top left: blood,

onion, nerve, and cholera bacteria. (Courtesy of Wikimedia Commons.)

chapter 8 The cell 177

cells, and the organisms that contain these cells are called eukaryotes. Cells that

lack a nucleus are called prokaryotic cells, and organisms made of prokaryotic

cells are called prokaryotes.

There are some important distinctions between eukaryotes and prokaryotes.

Eukaryotes, in addition to a nucleus, have other membrane-bound, internal

structures called organelles. These organelles compartmentalize some of the func-

tions of the cell. For example, an organelle called a mitochondrion carries out the

role of generating ATP molecules for use as energy currency throughout the cell

(see Chap. 7). Some of these organelles are shown in Fig. 8-3, which highlights

the structures of prokaryotic and eukaryotic cells.

In contrast to a eukaryotic cell, a prokaryotic cell is one large compartment.

All of the cell’s functions are carried out in this one compartment. However,

like a one-room apartment, various functions tend toward certain locations

FIgure 8-2 • A lipid bilayer, the foundation of cell

membranes, separates the cytoplasm (the inside of the cell)

from the extracellular environment.

FIgure 8-3 • Eukaryotic versus prokaryotic cells.

178 Biophysics DemystifieD

within the cell. For example, in prokaryotes, protein synthesis occurs for the

most part near the edge of the cytoplasm, just inside the cell membrane. And

DNA and its functions are found mostly toward the center of the cell.

There are two main divisions of prokaryotes: bacteria and archaea. Prokary-

otes were originally thought of as unicellular plants, because of similarities they

have with plant cells. However, with the advent of detailed genetic analysis

(analysis of the organism’s nucleic acid sequence), it now makes sense to clas-

sify bacteria and archaea into domains of their own, separate and apart from

plants and animals. Prokaryotic organisms are almost exclusively unicellular;

however, many can form multicellular colonies that have properties resembling

multicellular organisms. Eukaryotes are for the most part multicellular organ-

isms, such as plants and animals. But unicellular eukaryotes exist as well

(e.g., the amoeba).

Table 8-1 summarizes some of the differences between eukaryotes and

prokaryotes.

TABLE 8-1 Eukaryotes and prokaryotes compared.

Eukaryotes Prokaryotes

Nucleus and other membrane-bound

organelles compartmentalize the cell.

No nucleus. Genetic material and all

biomolecules are all together in the

cytoplasm.

Mostly multicellular; some

unicellular.

Unicellular (some have colonial or

multicellular stage of life).

Slower division rates. Rapid division rates. Can adapt

quickly to drastic changes in

environment.

Can carry out more complex and

more efficient biochemical reactions,

because reactions can be isolated in

membrane-bound compartments

where reactants can be brought

closer together.

Biochemical reactions are simpler,

and must all occur in the cytoplasm

where more complex reactions might

interfere with each other. Also, less

efficient in bringing reactants

together.

Tend to be larger, since able to

ingest nutrients actively and process

those nutrients with a wide variety of

reactions for efficient growth and

maintenance.

Typical size is 10 to 100 µm across.

Tend to be smaller. Nutrients obtained

inefficiently, primarily through

diffusion, and processed with only a

simple set of biochemical reactions.

Typical size is 0.1 to 10 µm across.

Plants and animals. Bacteria and archaea.

chapter 8 The cell 179

The Cell Membrane

As mentioned, all cells are surrounded by a lipid membrane, which keeps the

insides in and the outsides out. The cell membrane is also called the plasma

membrane. In addition to lipids, cell membranes contain a variety of molecules

embedded in, or connected to, the lipid bilayer. These include proteins, carbo-

hydrates, glycoproteins (proteins with carbohydrate attached), and glycolipids

(lipids with carbohydrate attached). These molecules are often classified in

terms of how deep they are within the membrane. If such a molecule is embed-

ded deep into the membrane, we call it integral, for example, integral mem-

brane protein. Those that are just on the surface (but are still fundamentally

part of the membrane) are called peripheral. If a molecule is embedded all the

way through the membrane, sticking out on both sides, it is called transmem-

brane. Figure 8-4 illustrates these, and some other, features of cell membranes.

Membrane Transport

Both the inside and outside of the cell are typically aqueous environments. In

order for a molecule to dissolve in an aqueous environment such as blood or

cytoplasm, the molecule must be polar or hydrophilic. But for a molecule to

penetrate the membrane’s lipid barrier, the molecule must be lipid soluble, that

is, nonpolar or hydrophobic. So the hydrophobic portion of the membrane acts

as a barrier to keep molecules from passing through. Some small molecules are

able to pass through the membrane, for example. water or carbon dioxide,

because their interactions with the lipids are minimal.

FIgure 8-4 • Cell membrane.

180 Biophysics D emystifieD

Although the membrane acts to protect the cell from larger outside mole-

cules, intruders, or environmental hazards, the cell does need to somehow get

nutrient molecules in and waste molecules out. The cell has a variety of ways

to transport molecules through the membrane when it needs to. The physics of

membrane transport is discussed in Chap. 11. Here we outline the various

transport methods, and some of the molecules involved.

One method is via membrane transport proteins. These are transmembrane

proteins that assist other molecules in getting through the membrane. They

may simply provide a channel or tunnel for the molecule to pass through. Or

they may bind the other molecule and then undergo a conformational change

that essentially pulls the other molecule through the membrane.

Two other methods are endocytosis and exocytosis. See Fig. 8-5. In endocyto-

sis, a portion of the cell membrane folds in toward the cell. At the same time,

this portion of membrane engulfs some molecule or molecules from outside the

cell. This portion of membrane then breaks off from the membrane and carries

the engulfed contents into the cell. Exocytosis is the opposite process and is

used by cells to secrete materials or to eliminate waste. In exocytosis a small

membrane pouch of material merges with the cell membrane, releasing its

contents outside the cell.

Receptors

A receptor is a molecule in the membrane (such as a protein, glycoprotein,

glycolipid, or carbohydrate) that has at least a portion of itself on the surface of

the membrane. This portion of the molecule on the surface of the membrane

has specificity for some other molecule. This means that only one particular type

of molecule can bind to the receptor. For example, a particular receptor may

FIgure 8-5 • Endocytosis and exocytosis. (Courtesy of

Biochemistry Demystified.)

chapter 8 The cell 181

bind a specific amino acid. The binding of a specific molecule to its receptor is

often a signal for the cell to do something. For example, binding of a certain

molecule to a receptor might signal to the cell that it should increase its pro-

duction of a certain enzyme. It might be a signal to the cell to begin endocyto-

sis of some foreign object; this is the case for example when a white blood cell

engulfs and destroys a virus particle.

Sometimes receptors are also transport proteins. If the receptor is also a

transport protein, it may then pull that bound molecule through the cell mem-

brane into the cell. Sometimes receptors signal the need to transport another

molecule. For example, the hormone insulin (a small protein) binds to insulin-

specific receptors in the cell membrane. This signals glucose transport proteins

elsewhere in the membrane to allow glucose into the cell.

Cell Walls

Some cells have a protective layer on the outside surface of the membrane

called a cell wall. Cell walls are commonly found in plants and many prokary-

otes such as bacteria, but are not usually found in animal cells. The cell wall is

a relatively stiff structure, enabling the cell to maintain a specific shape even

under a certain amount of external or internal pressure.

In plants the cell wall is commonly made from cellulose, a polymerized car-

bohydrate. In other organisms cell walls may be made from glycoproteins or a

variety of polysaccharides. Although cell walls are somewhat flexible, they are

more rigid than the cell membrane. This additional rigidity means that organ-

isms with cell walls are usually not capable of endocytosis and exocytosis.

Instead they rely heavily on membrane transport proteins. Some bacteria, called

gram-negative bacteria, have an extra membrane on the outside surface of the

cell wall. (The term gram-negative comes from the fact that this extra mem-

brane prevents the cell from absorbing Gram stain. Gram staining is a technique

for highlighting and visualizing certain differences among cells and the structures

inside them. The technique was developed by H. C. Gram in 1882.)

Cell Organelles

We now list and describe the major internal structures, or organelles, found

inside a cell. For the most part, with the exception of the cell nucleus, there

may be several or many instances of each of these organelles. Also, the following

list is not exhaustive, but is just intended to introduce you to the more impor-

tant organelles of the cell.