Biology

Douglas Wilkin, Ph.D.

Niamh Gray-Wilson

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AUTHORS
Douglas Wilkin, Ph.D.
To access a customizable version of this book, as well as other
Niamh Gray-Wilson
interactive content, visit www.ck12.org
CONTRIBUTOR
Jean Brainard, Ph.D.

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Contents www.ck12.org

Contents

1 Cell 1
1.1 The Cell Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 Discovery of Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.4 Cell Size and Shape - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.5 Common Parts of Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
1.6 Cell Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.7 Two Types of Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.8 The Nucleus - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
1.9 The Mitochondria - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
1.10 Ribosomes - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
1.11 Endoplasmic Reticulum - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
1.12 The Golgi Apparatus - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
1.13 Vesicles and Vacuoles - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
1.14 Other Structures of Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
1.15 Plant Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
1.16 The Cytoplasm and Cytoskeleton - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
1.17 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

2 Cell Cycle 58
2.1 Cell Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
2.2 Mitosis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
2.3 Genetic Variation - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
2.4 Meiosis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
2.5 Significance of Mitosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
2.6 Significance of Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
2.7 Genetic Disorders - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
2.8 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

3 Transport Mechanisms 90
3.1 The Cell Membrane: A Semi-Permeable Barrier . . . . . . . . . . . . . . . . . . . . . . . . . . 91
3.2 Cell Transport - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
3.3 Diffusion - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
3.4 Facilitated Diffusion - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
3.5 Osmosis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
3.6 Active Transport - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
3.7 Exocytosis and Endocytosis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
3.8 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

4 Biological Molecules 115

4.1 Biological Molecules (organic compounds) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4.2 Carbohydrates - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

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4.3 Lipids - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

4.4 Proteins - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
4.5 Enzymes and Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
4.6 Nucleic Acids - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
4.7 Chemical Reactions - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
4.8 Solutions - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
4.9 How Enzymes Speed Up the Chemical Reactions . . . . . . . . . . . . . . . . . . . . . . . . . 157
4.10 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

5 Energy Transformation 160

5.1 Energy Transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
5.2 Energy Carrying Molecules - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
5.3 Autotrophs vs. Heterotrophs - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
5.4 Photosynthesis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
5.5 The Photosynthesis Reaction - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
5.6 The Chloroplast - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
5.7 The Light Reactions - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
5.8 The Calvin Cycle - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
5.9 Chemosynthesis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
5.10 Cellular Respiration - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
5.11 Cellular Respiration Overview - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
5.12 Glycolysis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
5.13 The Mitochondria in Cellular Respiration - Advanced . . . . . . . . . . . . . . . . . . . . . . . 222
5.14 The Krebs Cycle - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
5.15 The Electron Transport Chain - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
5.16 Anaerobic Respiration - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234
5.17 Lactic Acid Fermentation - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
5.18 Alcoholic Fermentation - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
5.19 Aerobic vs. Anaerobic Respiration - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
5.20 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249

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C HAPTER
3 Transport Mechanisms
Chapter Outline
3.1 T HE C ELL M EMBRANE : A S EMI -P ERMEABLE BARRIER
3.2 C ELL T RANSPORT - A DVANCED
3.3 D IFFUSION - A DVANCED
3.4 FACILITATED D IFFUSION - A DVANCED
3.5 O SMOSIS - A DVANCED
3.6 ACTIVE T RANSPORT - A DVANCED
3.7 E XOCYTOSIS AND E NDOCYTOSIS - A DVANCED
3.8 R EFERENCES

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3.1 The Cell Membrane: A Semi-Permeable

Barrier
• Describe the structure and properties of a phospholipid and a phospholipid bilayer.
• Distinguish between hydrophilic and hydrophobic.

How is a cell membrane like a castle wall?

The walls of a castle, like the cell membrane, are designed to keep out dangerous things. Whether you’re concerned
about an enemy army or a disease-causing bacteria, you don’t want to allow everything to enter! However, in order
to survive, there are some things that the cell (or the castle) does need to let in.

Introduction to Cell Transport

Cells are found in all different types of environments, and these environments are constantly changing. For example,
one-celled organisms, like bacteria, can be found on your skin, in the ground, or in all different types of water.
Therefore, cells need a way to protect themselves. This job is done by the cell membrane, which is also known as
the plasma membrane.

Controlling the Cell Contents

The cell membrane is semipermeable, or selectively permeable, which means that only some molecules can pass
through the membrane. If the cell membrane were completely permeable, the inside of the cell would be the same as
the outside of the cell. It would be impossible for the cell to maintain homeostasis. Homeostasis means maintaining
a stable internal environment. For example, if your body cells have a temperature of 98.6 F, and it is freezing outside,

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your cells will maintain homeostasis if the temperature of the cells stays the same and does not drop with the outside
temperature.
How does the cell ensure it is semipermeable? How does the cell control what molecules enter and leave the cell?
The composition of the cell membrane helps to control what can pass through it.

Composition of the Cell Membrane

Molecules in the cell membrane allow it to be semipermeable. The membrane is made of a double layer of
phospholipids (a "bilayer") and proteins (Figure below). Recall that phospholipids, being lipids, do not mix with
water. It is this quality that allows them to form the outside barrier of the cell.
A single phospholipid molecule has two parts:

1. A head that is hydrophilic, or water-loving.

2. A tail that is hydrophobic, or water-fearing.

FIGURE 3.1
The cell membrane is made up of a phos-
pholipid bilayer, two layers of phospholipid
molecules.

There is water found on both the inside and the outside of cells. Since hydrophilic means water-loving, and they
want to be near water, the heads face the inside and outside of the cell where water is found. The water-fearing,
hydrophobic tails face each other in the middle of the cell membrane, because water is not found in this space. The
phospholipid bilayer allows the cell to stay intact in a water-based environment.
An interesting quality of the plasma membrane is that it is very "fluid" and constantly moving, like a soap bubble.
Due to the composition of the cell membrane, small molecules such as oxygen and carbon dioxide can pass freely
through the membrane, but other molecules cannot easily pass through the plasma membrane. These molecules need
assistance to get across the membrane. That assistance will come in the form of transport proteins.

Vocabulary

• cell membrane: Lipid barrier that surrounds the cell; also known as the plasma membrane.
• homeostasis: Ability of an organism to maintain stable internal conditions, such body temperature, regardless
of outside conditions.
• hydrophilic: Can combine with water (water-loving).

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• hydrophobic: Does not combine with water (water-fearing).

• phospholipid: Lipid molecule with a hydrophilic ("water-loving") head and two hydrophobic ("water-hating")
tails; makes up the cell membrane.
• semipermeable: Allowing only certain materials to pass through; characteristic of the cell membrane.
• transport protein: Protein that assists molecules entering or leaving the cell.

Summary

• The cell membrane is selectively permeable, meaning only some molecules can get through.
• The cell membrane is made of a double layer of phospholipids, each with a hydrophilic (water-loving) head
and a hydrophobic (water-fearing) tail.

Explore More

Use the resources below to answer the following questions.

Explore More I
• Active and Passive Transport at http://www.youtube.com/watch?v=kfy92hdaAH0 (6:13)

MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/57349

1. How is passive transport different from active transport?

2. What are three types of passive transport? What do these all have in common?
3. What does the body use iodine for? What kind of transport is necessary to transport this molecule into a cell?
4. What happens to the receptor complex in receptor mediated endocytosis?

Explore More II
• Membrane tutorial at http://www.bio.davidson.edu/people/macampbell/111/memb-swf/membranes.swf

1. Can proteins in the plasma membrane move around the membrane? Why is this characteristic beneficial to the
cell?
2. What are five functions of the membrane in cells?
3. What types of lipids are found in plasma membranes? What characteristics do these types of lipids share?

Review

1. Why is the plasma membrane considered selectively permeable? Why is this important?
2. Explain the composition of the cell membrane.
3. Explain the arrangement of phospholipids in the membrane.

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3.2 Cell Transport - Advanced

• Describe the importance of cell transport.

What is cell transport?

It is the movement of substances across the cell membrane either into or out of the cell. Sometimes things just move
through the phospholipid bilayer. Other times, substances need the assistance of a protein, like a channel protein or
some other transmembrane protein, to cross the cell membrane.

Cell Transport

Cell transport refers to the movement of substances across the cell membrane. Probably the most important feature of
a cell’s phospholipid membranes is that they are selectively permeable. A membrane that is selectively permeable,
or semipermeable, has control over what molecules or ions can enter or leave the cell, as shown in Figure 3.2. This
feature allows a cell to control the transport of materials, as dictated by the cell’s function. The permeability of a
membrane is dependent on the organization and characteristics of the membrane lipids and proteins. In this way,
cell membranes help maintain a state of homeostasis within cells (and tissues, organs, and organ systems) so that an
organism can stay alive and healthy.

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FIGURE 3.2
A selectively permeable, or semiperme-
able, membrane allows certain molecules
through, but not others.

Transport Across Membranes

The molecular make-up of the phospholipid bilayer limits the types of molecules that can pass through it. For
example, hydrophobic (water-hating) molecules, such as carbon dioxide (CO2 ) and oxygen (O2 ), can easily pass
through the lipid bilayer, but ions such as calcium (Ca2+ ) and polar molecules such as water (H2 O) cannot. The
hydrophobic interior of the phospholipid bilayer does not allow ions or polar molecules through because they are
hydrophilic, or water loving. In addition, large molecules such as sugars and proteins are too big to pass through
the phospholipid bilayer. Transport proteins within the membrane allow these molecules to cross the membrane into
or out of the cell. This way, polar molecules avoid contact with the nonpolar interior of the membrane, and large
molecules are moved through large pores.
Every cell is contained within a membrane punctuated with transport proteins that act as channels or pumps to let in
or force out certain molecules. The purpose of the transport proteins is to protect the cell’s internal environment and
to keep its balance of salts, nutrients, and proteins within a range that keeps the cell and the organism alive.
There are four main ways that molecules can pass through a phospholipid membrane. The first way requires no
energy input by the cell and is called simple diffusion. This type of transport includes passive diffusion and osmosis.
No assistance by a transport is necessary in simple diffusion. Facilitated diffusion, does involve the assistance of
transport proteins. The third way, called active transport, requires that the cell uses energy to pull in or pump out
certain molecules and ions. Active transport involves proteins known as pumps. The fourth way is through vesicle
transport, in which large molecules are moved across the membrane in bubble-like sacks that are made from pieces
of the membrane. Vesicular transport includes exocytosis and endocytosis.

Homeostasis and Cell Transport

Homeostasis refers to the balance, or equilibrium, within the cell or a body. It is an organism’s ability to keep a con-
stant internal environment. Keeping a stable internal environment requires constant adjustments as conditions change
inside and outside the cell. The adjusting of systems within a cell is referred to as homeostatic regulation. Because
the internal and external environments of a cell are constantly changing, adjustments must be made continuously to
stay at or near the normal proportions of all internal substances. This involves continual adjustments in transport of
substances across the cell membrane. Homeostasis is a dynamic equilibrium rather than an unchanging state. The
cellular processes discussed in the cell transport (passive and active transport) concepts all play an important role in

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homeostatic regulation.

Summary

• The cell membrane is selectively permeable, allowing only certain substances to pass through.
• Cell transport may require assistance by a protein/pump.
• Cell transport may require energy.
• Some transport involves vesicles.

Review

1. What is meant by cell transport? Why is cell transport important?

2. List types of cell transport.
3. Explain how cell transport helps an organism maintain homeostasis.

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3.3 Diffusion - Advanced

• Define diffusion.

What will eventually happen to these dyes?

They will all blend together. The dyes will move through the water until an even distribution, or equilibrium, is
achieved. The process of moving from areas of high amounts of a substance to areas of low amounts of the same
substance is called diffusion.

Diffusion

Passive transport is a way that small molecules or ions move across the cell membrane without input of energy by
the cell. The three main kinds of passive transport are diffusion (or simple diffusion), osmosis, and facilitated diffu-
sion. Simple diffusion and osmosis do not involve transport proteins. Facilitated diffusion requires the assistance of
proteins.
Diffusion is the movement of molecules from an area of high concentration of the molecules to an area with a lower
concentration. For cell transport, diffusion is the movement of small molecules across the cell membrane. The
difference in the concentrations of the molecules in the two areas is called the concentration gradient. The kinetic
energy of the molecules results in random motion, causing diffusion. In simple diffusion, this process proceeds
without the aid of a transport protein. it is the random motion of the molecules that causes them to move from an
area of high concentration to an area with a lower concentration.
Diffusion will continue until the concentration gradient has been eliminated. Since diffusion moves materials from
an area of higher concentration to the lower, it is described as moving solutes "down the concentration gradient."
The end result of diffusion is an equal concentration, or equilibrium, of molecules on both sides of the membrane.
At equilibrium, movement of molecules does not stop. At equilibrium, there is equal movement of materials in both
directions.

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If a molecule can pass freely through a cell membrane, it will cross the membrane by diffusion (Figure 3.3). The
inside of the plasma membrane is hydrophobic, so certain molecules cannot easily pass through the membrane.
Recall the semipermeable nature of the lipid bilayer. Molecules that cannot easily pass through the bilayer include
ions and small hydrophilic molecules, such as glucose, and macromolecules, including proteins and RNA. Examples
of molecules that can easily diffuse across the plasma membrane include carbon dioxide and oxygen gas. These
molecules diffuse freely in and out of the cell, along their concentration gradient. Though water is a polar molecule,
it can also diffuse through the plasma membrane. The diffusion of water through the cell membrane is of such
importance to the cell that it is given a special name, osmosis.

FIGURE 3.3
Molecules move from an area of high
concentration to an area of lower concen-
tration until an equilibrium is met. The
molecules continue to cross the mem-
brane at equilibrium, but at equal rates in
both directions.

MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/183323

Summary

• The cell membrane is selectively permeable, allowing only certain substances to pass through.
• Passive transport is a way that small molecules or ions move across the cell membrane without input of energy
by the cell. The three main kinds of passive transport are diffusion, osmosis, and facilitated diffusion.
• Diffusion is the movement of molecules from an area of high concentration of the molecules to an area with a
lower concentration.

Review

1. What is diffusion? What is the main difference between simple diffusion and facilitated diffusion?
2. What is a concentration gradient?

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3. What happens at equilibrium?

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3.4 Facilitated Diffusion - Advanced

• Describe facilitated transport mechanisms.

• Define ion channels.
• Identify the role of ion channels in facilitated diffusion.

Can you help me move?

What is one of the questions no one likes to be asked? Sometimes the cell needs help moving things as well, or
facilitating the diffusion process. And this would be the job of a special type of protein.

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Facilitated Diffusion

Facilitated diffusion is the diffusion of solutes through integral membrane transport proteins. Facilitated diffusion
is a type of passive transport. Even though facilitated diffusion involves transport proteins (and is essentially a
transport process), it can still be considered passive transport because the solute is moving down the concentration
gradient, and no input of energy is required. Facilitated diffusion utilizes proteins known as uniporters. A uniporter
can be either a channel protein or a carrier protein.
As was mentioned earlier, small nonpolar molecules can easily diffuse across the cell membrane. However, due to
the hydrophobic nature of the phospholipids that make up cell membranes, polar molecules and ions cannot do so.
Instead, they diffuse across the membrane through transport proteins. A transport protein completely spans the
membrane, and allows certain molecules or ions to diffuse across the membrane. Channel proteins, gated channel
proteins, and carrier proteins are three types of transport proteins that are involved in facilitated diffusion.
A channel protein, a type of transport protein, acts like a pore in the membrane that lets water molecules or small
ions through quickly. Water channel proteins allow water to diffuse across the membrane at a very fast rate. Ion
channel proteins allow ions to diffuse across the membrane.
A gated channel protein is a transport protein that opens a "gate," allowing a molecule to pass through the
membrane. Gated channels have a binding site that is specific for a given molecule or ion. A stimulus causes
the "gate" to open or shut. The stimulus may be chemical or electrical signals, temperature, or mechanical force,
depending on the type of gated channel. For example, the sodium gated channels of a nerve cell are stimulated by
a chemical signal which causes them to open and allow sodium ions into the cell. Glucose molecules are too big to
diffuse through the plasma membrane easily, so they are moved across the membrane through gated channels. In
this way glucose diffuses very quickly across a cell membrane, which is important because many cells depend on
glucose for energy.
A carrier protein is a transport protein that is specific for an ion, molecule, or group of substances. Carrier proteins
"carry" the ion or molecule across the membrane by changing shape after the binding of the ion or molecule. Carrier
proteins are involved in passive and active transport. A model of a channel protein and carrier proteins is shown in
Figure 3.4.

FIGURE 3.4
Facilitated diffusion through the cell mem-
brane. Channel proteins and carrier pro-
teins are shown (but not a gated-channel
protein). Water molecules and ions move
through channel proteins. Other ions or
molecules are also carried across the cell
membrane by carrier proteins. The ion or
molecule binds to the active site of a car-
rier protein. The carrier protein changes
shape, and releases the ion or molecule
on the other side of the membrane. The
carrier protein then returns to its original
shape.

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MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/254

Ion Channels

Ions such as sodium (Na+ ), potassium (K+ ), calcium (Ca2+ ), and chloride (Cl ), are important for many cell
functions. Because they are polar, these ions do not diffuse through the membrane. Instead they move through
ion channel proteins where they are protected from the hydrophobic interior of the membrane. Ion channels allow
the formation of a concentration gradient between the extracellular fluid and the cytosol. Ion channels are very
specific as they allow only certain ions through the cell membrane. Some ion channels are always open, others are
"gated" and can be opened or closed. Gated ion channels can open or close in response to different types of stimuli
such as electrical or chemical signals.

Summary

• Facilitated diffusion is the diffusion of solutes through transport proteins in the plasma membrane.
• Channel proteins, gated channel proteins, and carrier proteins are three types of transport proteins that are
involved in facilitated diffusion.

Review

1. Compare and contrast simple diffusion and facilitated diffusion. For each type of diffusion, give an example
of a molecule that is transported.
2. Explain the three types of transport proteins involved in facilitated diffusion.

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