Biology

Douglas Wilkin, Ph.D.

Niamh Gray-Wilson

Say Thanks to the Authors

Click http://www.ck12.org/saythanks
(No sign in required)
www.ck12.org

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.

CK-12 Foundation is a non-profit organization with a mission to

reduce the cost of textbook materials for the K-12 market both in
the U.S. and worldwide. Using an open-source, collaborative, and
web-based compilation model, CK-12 pioneers and promotes the
creation and distribution of high-quality, adaptive online textbooks
that can be mixed, modified and printed (i.e., the FlexBook®
textbooks).

Copyright © 2016 CK-12 Foundation, www.ck12.org

The names “CK-12” and “CK12” and associated logos and the
terms “FlexBook®” and “FlexBook Platform®” (collectively
“CK-12 Marks”) are trademarks and service marks of CK-12
Foundation and are protected by federal, state, and international
laws.

Any form of reproduction of this book in any format or medium,

in whole or in sections must include the referral attribution link
http://www.ck12.org/saythanks (placed in a visible location) in
addition to the following terms.

Except as otherwise noted, all CK-12 Content (including CK-12

Curriculum Material) is made available to Users in accordance
with the Creative Commons Attribution-Non-Commercial 3.0
Unported (CC BY-NC 3.0) License (http://creativecommons.org/
licenses/by-nc/3.0/), as amended and updated by Creative Com-
mons from time to time (the “CC License”), which is incorporated
herein by this reference.

Complete terms can be found at http://www.ck12.org/about/

terms-of-use.

Printed: August 15, 2016

iii
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

iv
www.ck12.org Contents

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

v
4.5. Enzymes and Metabolism www.ck12.org

4.5 Enzymes and Metabolism

• Explain the importance of enzymes to living organisms.

FIGURE 4.20

Metabolism

Metabolism is the name given to the collection of, the lump sum of, chemical reactions performed by an organism
to survive.
The study of metabolism is divided into two broad categories, or types, of metabolic reactions:
(1) Anabolism: These are reactions that synthesize, or build up molecules/materials from simpler ingredients/reactants.
Most anabolic reactions are endergonic, the name given to reactions that require cells to expend energy to build more
complex molecules from simpler ones. Endergonic reactions are not considered as spontaneous reactions, energy
must be inputted for the reaction to proceed. These types of reactions are indicated with a positive number for "energy
going in" (+G). A common anabolic pathway is the synthesis of starch/polymers from smaller sugar/monomers.
(2) Cataboism: These are reactions that breakdown, break apart, complex molecules/materials into simpler molecules-
usually releasing energy to complete these reactions. These reactions are exergonic reactions, the name given to
reactions that break down molecules and release energy in the process. This category of reactions generate energy,
and are indicated with a negative number for "energy being released" (-G).

Enzymes are catalysts for chemical reactions- enzymes control and catalyze (i.e accelerate) , biochemical reactions
of an organism. A catalyst is a substance that causes a chemical reaction to happen more quickly.
Anotherwords: ENZYMES make an organism’s METABOLIC reactions go faster, speed up.

140
www.ck12.org Chapter 4. Biological Molecules

What is a biological catalyst?

This super fast train can obviously reach great speeds. And there’s a lot of technology that helps this train go fast.
Speaking of helping things go fast brings us to enzymes. Life could not exist without enzymes. Essentially, enzymes
are biological catalysts that speed up biochemical reactions.

Enzymes

Enzymes and Biochemical Reactions

Most chemical reactions within organisms would be impossible under the conditions in cells. For example, the
body temperature of most organisms is too low for reactions to occur quickly enough to carry out life processes.
Reactants may also be present in such low concentrations that it is unlikely they will meet and collide. Therefore,
the rate of most biochemical reactions must be increased by a catalyst. A catalyst is a chemical that speeds up
chemical reactions. In organisms, catalysts are called enzymes. Essentially, enzymes are biological catalysts.
How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by lowering
the activation energy of chemical reactions. Activation energy is the energy needed to start a chemical reaction.
This is illustrated in Figure below . The biochemical reaction shown in the figure requires about three times as
much activation energy without the enzyme as it does with the enzyme.

141
4.5. Enzymes and Metabolism www.ck12.org

FIGURE 4.21

Enzymes are extremely efficient in speeding up reactions. They can catalyze up to several million reactions per
second. As a result, the difference in rates of biochemical reactions with and without enzymes may be enormous.
A typical biochemical reaction might take hours or even days to occur under normal cellular conditions without an
enzyme, but less than a second with an enzyme.
Cellular processes consist of many chemical reactions that must occur quickly in order for the cell to function
properly. Enzymes catalyze most of the chemical reactions that occur in a cell. A substrate is the molecule or
molecules on which the enzyme acts. In the urease catalyzed reaction, urea is the substrate. The Figure below
diagrams a typical enzymatic reaction.

FIGURE 4.22

Enzymes, an overview of these proteins, can be viewed at http://www.youtube.com/watch?v=E90D4BmaVJM&f

eature=related (9:43).

MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/203

142
www.ck12.org Chapter 4. Biological Molecules

As you view Enzymes, focus on these concepts:

1. the role of enzymes in nature,

2. other uses of enzymes.

Importance of Enzymes

Enzymes are involved in most of the chemical reactions that take place in organisms. About 4,000 such reactions
are known to be catalyzed by enzymes, but the number may be even higher.
In animals, an important function of enzymes is to help digest food. Digestive enzymes speed up reactions that
break down large molecules of carbohydrates, proteins, and fats into smaller molecules the body can use. Without
digestive enzymes, animals would not be able to break down food molecules quickly enough to provide the energy
and nutrients they need to survive.

Summary

• Enzymes are biological catalysts. They speed up biochemical reactions.

• Enzymes are involved in most of the chemical reactions that take place in organisms.

Practice

Use this resource to answer the questions that follow.

• http://www.hippocampus.org/Biology ! Biology for AP* ! Search: Enzymes as Catalysts

1. What are enzymes?

2. What are substrates? What is the enzyme-substrate complex?
3. How do enzymes work?
4. What happens to the enzyme during a reaction?

Review

1. What are enzymes?

2. Explain why organisms need enzymes to survive.

143
4.6. Nucleic Acids - Advanced www.ck12.org

4.6 Nucleic Acids - Advanced

• Describe the structure and function of nucleic acids.

• Name the components of a nucleotide.
• Compare DNA to RNA.
• Describe the structure and function of ATP.

You may have heard that "it’s in your DNA." What does that mean?

Nucleic acids. Essentially the "instructions" or "blueprints" of life. Deoxyribonucleic acid, or DNA, is the unique
blueprints to make the proteins that give you your traits. Half of these blueprints come from your mother, and half
from your father. And they come in different combinations every time. In fact, every couple - every man and woman
that has every lived - together has over 64,000,000,000,000 combinations of their chromosomes, which is where the
DNA is found. Therefore, every person that has ever lived - except for identical twins - has his or her own unique
set of blueprints - or instructions - or DNA.

Nucleic Acids

Nucleic acids are organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. They are
made of smaller units called nucleotides. Nucleic acids are named for the nucleus of the cell, where some of them
are found. Nucleic acids are found not only in all living cells but also in viruses. Types of nucleic acids include
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Structure of Nucleic Acids

A nucleic acid consists of one chain (in RNA) or two chains (in DNA) of nucleotides held together by chemical
bonds. Each individual nucleotide unit consists of three parts:

144
www.ck12.org Chapter 4. Biological Molecules

• a base (containing nitrogen)

• a sugar (ribose in RNA, deoxyribose in DNA)
• a phosphate group (containing phosphorus)

The sugar of one nucleotide binds to the phosphate group of the next nucleotide. Alternating sugars and phosphate
groups form the backbone of a nucleotide chain, as shown in Figure 4.23. The bases, which are bound to the sugars,
protrude from the backbone of the chain. In DNA, pairs of bases-one from each of two nucleotides-form the middle
section of the molecule.

FIGURE 4.23
Part of a Nucleic Acid (DNA). This small
section of a nucleic acid shows how phos-
phate groups and sugars alternate to form
the backbone of a nucleotide chain. The
bases that jut out to the side from the
backbone are adenine, thymine, cytosine,
and guanine. Hydrogen bonds between
complementary bases, such as between
adenine and thymine, hold the two chains
of nucleotides together.

MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/198

RNA consists of a single chain of nucleotides, and DNA consists of two chains of nucleotides. Bonds form between
the bases on the two chains of DNA and hold the chains together (Figure 4.23). There are four different types of
bases in a nucleic acid molecule: cytosine (C), adenine (A), guanine (G), and either thymine (T) (in DNA) or uracil
(U) (in RNA). Each type of base bonds with just one other type of base. Cytosine and guanine always bond together,
and adenine and thymine (or uracil) always bond with one another. The pairs of bases that bond together are called
complementary bases.

145
4.6. Nucleic Acids - Advanced www.ck12.org

The binding of complementary bases allows DNA molecules to take their well-known shape, called a double helix.
Figure 4.24 shows how two chains of nucleotides form a DNA double helix. A simplified double helix is illustrated
in Figure 4.25. It shows more clearly how the two chains are intertwined. The double helix shape forms naturally
and is very strong. Being intertwined, the two chains are difficult to break apart. This is important given the
fundamental role of DNA in all living organisms.

FIGURE 4.24
DNA Molecule. Hydrogen bonds between
complementary bases help form the dou-
ble helix of a DNA molecule. The letters
A, T, G, and C stand for the bases ade-
nine, thymine, guanine, and cytosine. The
sequence of these four bases in DNA is a
code that carries instructions for making
proteins. Shown is a representation of
how the double helix folds into a chro-
mosome. In this double-stranded nucleic
acid, complementary bases (A and T, C
and G) form hydrogen bonds that hold
the two nucleotide chains together in the
shape of a double helix. Notice that
A always bonds with T and C always
bonds with G. The hydrogen bonds help
maintain the double helix shape of the
molecule.

FIGURE 4.25
Simple Model of DNA. In this simple
model of DNA, each line represents a
nucleotide chain. The double helix shape
forms when the two chains wrap around
the same axis.

MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/200

146
www.ck12.org Chapter 4. Biological Molecules

Role of Nucleic Acids

The order of bases in nucleic acids is highly significant. The bases are like the letters of a four-letter alphabet. These
"letters" can be combined to form "words." Groups of three bases form words of the genetic code. Each code word,
called a codon, stands for a different amino acid. A series of many codons spells out the sequence of amino acids
in a polypeptide or protein (Figure 4.26). In short, nucleic acids contain the information needed for cells to make
proteins. This information is passed from a body cell to its daughter cells when the cell divides. It is also passed
from parents to their offspring when organisms reproduce.

How RNA codes for Proteins

FIGURE 4.26
The letters G, U, C, and A stand for the
bases in RNA, specifically mRNA or mes-
senger RNA. Each group of three bases
makes up a codon, and each codon rep-
resents one amino acid (represented here
by a single letter, such as V (valine), H
(histidine), or L (leucine)). A string of
codons specifies the sequence of amino
acids in a protein.

DNA and RNA have different functions relating to the genetic code and proteins. Like a set of blueprints, DNA
contains the genetic instructions for the correct sequence of amino acids in proteins. RNA uses the information in
DNA to assemble the amino acids and make the proteins. More about the genetic code and the role of nucleic acids
will be discussed in Concept Molecular Biology (Advanced).

Adenosine Triphosphate

Adenosine Triphosphate (ATP), or Adenosine-5’-triphosphate, is another important nucleic acid. ATP is described
as the "energy currency" of the cell or the "molecular unit of currency." One molecule of ATP contains three
phosphate groups, and it is produced by ATP synthase from inorganic phosphate and adenosine diphosphate (ADP)
or adenosine monophosphate (AMP). The structure of ATP consists of the purine base adenine, attached to the
1’ carbon atom of the pentose sugar ribose. Three phosphate groups are attached at the 5’ carbon atom of the
pentose sugar. It is the removal of these phosphate groups that convert ATP to ADP (adenosine diphosphate) and to
AMP (adenosine monophosphate). ATP is produced during cellular respiration, and will be further discussed in the
Cellular Respiration (Advanced) concepts.
ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and lipids, as
well as by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP (cAMP). The
ratio between ATP and AMP determines the amount of available energy. This regulates the metabolic pathways
that produce and consume ATP. Apart from its roles in energy metabolism and signaling, ATP is also incorporated
into DNA and RNA by polymerases during both DNA replication and transcription. When ATP is used in DNA
synthesis, the ribose sugar is first converted to deoxyribose by ribonucleotide reductase.

147
4.6. Nucleic Acids - Advanced www.ck12.org

FIGURE 4.27
ATP. The ATP molecule clearly shows the
three phosphate groups.

Summary

• Nucleic acids are organic compounds that consist of carbon, hydrogen, oxygen, nitrogen, and phosphorus.
• DNA, RNA and ATP are important nucleic acids.
• DNA and RNA are made up of repeating units called nucleotides. They contain genetic instructions for
proteins, help synthesize proteins, and pass genetic instructions on to daughter cells and offspring.

Review

1. What is a nucleic acid?

2. Identify the three parts of a nucleotide.
3. What is the structure of DNA?
4. Bases in nucleic acids are represented by the letters A, G, C, and T (or U). How are the bases in nucleic acids
like the letters of an alphabet?
5. Describe the role and structure of ATP.

148
www.ck12.org Chapter 4. Biological Molecules

4.7 Chemical Reactions - Advanced

• Describe what happens in a chemical reaction, and identify types of chemical reactions.

Understanding chemistry is essential to fully understand biology. Why?

A general understanding of chemistry is necessary to understand biology. Essentially, our cells are just thousands of
chemicals — made of elements like carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur — in just the right
combinations. And these chemicals combine through chemical reactions.

What Are Chemical Reactions?

A chemical compound may be very different from the substances that combine to form it. For example, the element
chlorine (Cl) is a poisonous gas, but when it combines with sodium (Na) to form sodium chloride (NaCl), it is no
longer toxic. You may even eat it on your food. Sodium chloride is just table salt. What process changes a toxic
chemical like chlorine into a much different substance like table salt?
A chemical reaction is a process that changes some chemical substances into other chemical substances. The
substances that start a chemical reaction are called reactants. The substances that form as a result of a chemical
reaction are called products. During the reaction, the reactants are used up to create the products. For example,
when methane burns in oxygen, it releases carbon dioxide and water. In this reaction, the reactants are methane
(CH4 ) and oxygen (O2 ), and the products are carbon dioxide (CO2 ) and water (H2 O).

149
4.7. Chemical Reactions - Advanced www.ck12.org

Chemical Equations

A chemical reaction can be represented by a chemical equation. Using the same example, the burning of methane
gas can be represented by the equation:
CH4 + 2 O2 ! CO2 + 2 H2 O.
The arrow in a chemical equation separates the reactants from the products and shows the direction in which the
reaction occurs. If the reaction could also occur in the opposite direction, then two arrows, one pointing in each
direction, or one arrow pointing in both directions, would be used. On each side of the arrow, a mixture of chemicals
is indicated by the chemical symbols joined by a plus sign (+). The numbers preceding some of the chemical symbols
(such as 2 O2 ) indicate how many molecules of the chemicals are involved in the reaction. (If there is no number in
front of a chemical symbol, it means that just one molecule is involved.)
In a chemical reaction, the quantity of each element does not change. There is the same amount of each element at
the end of the reaction as there was at the beginning. This is reflected in the chemical equation for the reaction. The
equation should be balanced. In a balanced equation, the same number of atoms of a given element appear on each
side of the arrow. For example, in the equation above, there are four hydrogen atoms on each side of the arrow.

Types of Chemical Reactions

In general, a chemical reaction involves the breaking and forming of chemical bonds. In the methane reaction above,
bonds are broken in methane and oxygen, and bonds are formed in carbon dioxide and water. A reaction like this, in
which a compound or element burns in oxygen, is called a combustion reaction. This is just one of many possible
types of chemical reactions. Other types of chemical reactions include synthesis, decomposition, and substitution
reactions.

• A synthesis reaction occurs when two or more chemical elements or compounds unite to form a more complex
product. For example, nitrogen (N2 ) and hydrogen (H2 ) unite to form ammonia (NH3 ):

N2 + 3 H2 ! 2 NH3 .

• A decomposition reaction occurs when a compound is broken down into smaller compounds or elements.
For example, water (H2 O) breaks down into hydrogen (H2 ) and oxygen (O2 ):

2 H2 O ! 2 H2 + O2 .

• A substitution reaction occurs when one element replaces another element in a compound. For example,
sodium (Na+ ) replaces hydrogen (H) in hydrochloric acid (HCl), producing sodium chloride (NaCl) and
hydrogen gas (H2 ):

2 Na+ + 2 HCl ! 2 NaCl + H2 .

Redox Reactions

Reduction-oxidation reactions, or redox reactions include all chemical reactions in which atoms have their oxidation
state changed. This can be either a simple redox process, such as the oxidation of carbon into carbon dioxide or the
reduction of carbon by hydrogen into methane, or a complex process such as the oxidation of glucose through a
series of complex electron transfer processes during cellular respiration. Oxidation is the loss of electrons or an
increase in oxidation state by a molecule, atom, or ion. Reduction is the gain of electrons or a decrease in oxidation
state by a molecule, atom, or ion.

150
www.ck12.org Chapter 4. Biological Molecules

Redox Reactions in Biology

Many important biological processes involve redox reactions, which frequently store and release energy. For
example, photosynthesis involves the reduction of carbon dioxide into glucose and the oxidation of water into
oxygen. This process stores the energy of sunlight in the bonds of sugars. The reverse reaction, cellular respiration,
converts the energy in glucose into ATP. Cellular respiration involves the oxidation of glucose to carbon dioxide and
the reduction of oxygen gas to water. This process depends on the reduction of NAD+ to the electron carrier NADH,
and the reverse oxidation of NADH to NAD+ . The reduction of NAD+ leads to the formation of a proton (H+ )
gradient, which drives the synthesis of ATP. NADH (nicotinamide adenine dinucleotide) and NADPH (Nicotinamide
adenine dinucleotide phosphate) are electron carriers in biological systems. The term redox state is often used to
describe the balance between NAD+ /NADH and NADP+ /NADPH (Nicotinamide adenine dinucleotide phosphate).

MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/165496

Summary

• A chemical reaction is a process that changes some chemical substances into others. It involves breaking and
forming chemical bonds.
• Types of chemical reactions include synthesis reactions and decomposition reactions.

Review

1. Identify the roles of reactants and products in a chemical reaction.

2. Describe each type of chemical reaction.
3. What is wrong with the following chemical equation? How could you fix it? CH4 + O2 ! CO2 + 2H2 O
4. What type of reaction is represented by the following chemical equation? Explain your answer. 2Na + 2HCl
! 2NaCl + H2

151
4.8. Solutions - Advanced www.ck12.org

4.8 Solutions - Advanced

• Define solution, and describe water’s role as a solvent.

• State how water is used to define acids and bases.
• Identify the pH ranges of acids and bases.
• Describe a neutralization reaction.
• Give examples of acids and bases in organisms.

Acids and bases. Why are these important in biology?

It comes back to a number of biological and biochemical processes. For example, some enzymes work best at
specific pH levels of acids. Other biochemical reactions need a relatively neutral environment to function properly.
Take your stomach, a very acidic environment. The enzyme pepsin that works best in that acidic environment could
not work in your mouth. What would your food taste like if your mouth was also a very acidic environment? Other
biochemical reactions need a relatively neutral environment to function properly.

Solutions

Water is one of the most common ingredients in solutions. A solution is a homogeneous mixture composed of two
or more substances. In a solution, one substance is dissolved in another substance, forming a mixture that has the
same proportion of substances throughout. The dissolved substance in a solution is called the solute. The substance
in which it is dissolved is called the solvent. An example of a solution in which water is the solvent is salt water. In
this solution, a solid—sodium chloride—is the solute. In addition to a solid dissolved in a liquid, solutions can also
form with solutes and solvents in other states of matter. Examples are given in Table 4.4.

152
www.ck12.org Chapter 4. Biological Molecules

TABLE 4.4: Solutions and Three States of Matter

Gas Liquid Solid
Gas Oxygen and other gases in
nitrogen (air)
Liquid Carbon dioxide in water Ethanol (an alcohol) in Sodium chloride in water
(carbonated water) water (salt water)
Solid Hydrogen gas in metals Mercury in silver and Iron in carbon (steel)
other metals (dental fill-
ings)

The ability of a solute to dissolve in a particular solvent is called solubility. Many chemical substances are soluble in
water. In fact, so many substances are soluble in water that water is called the universal solvent. Water is a strongly
polar solvent, and polar solvents are better at dissolving polar solutes. Many organic compounds and other important
biochemicals are polar, so they dissolve well in water. On the other hand, strongly polar solvents like water cannot
dissolve strongly nonpolar solutes like oil. Did you ever try to mix oil and water? Even after being well shaken, the
two substances quickly separate into distinct layers.

Acids and Bases

Water is the solvent in solutions called acids and bases. To understand acids and bases, it is important to know more
about pure water, in which nothing is dissolved. In pure water (such as distilled water), a tiny fraction of water
molecules naturally breaks down, or dissociates, to form ions. An ion is an electrically charged atom or molecule.
The dissociation of pure water into ions is represented by the chemical equation:
2 H2 O ! H3 O+ + OH .
The products of this reaction are a hydronium ion (H3 O+ ) and a hydroxide ion (OH ). The hydroxide ion is
negatively charged. It forms when a water molecule donates, or gives up, a positively charged hydrogen ion. The
hydronium ion, modeled in Figure 4.28, is positively charged. It forms when a water molecule accepts a positively
charged hydrogen ion (H+ ).

Acidity and pH

Acidity refers to the hydronium ion concentration of a solution. It is measured by pH. In pure water, the hydronium
ion concentration is very low. Only about one in ten million water molecules naturally dissociates to form a
hydronium ion in pure water. This gives water a pH of 7. The hydronium ions in pure water are also balanced
by hydroxide ions, so pure water is neutral (neither an acid nor a base).
Because pure water is neutral, any other solution with the same hydronium ion concentration and pH is also
considered to be neutral. If a solution has a higher concentration of hydronium ions and lower pH than pure water,
it is called an acid. If a solution has a lower concentration of hydronium ions and higher pH than pure water, it is
called a base. Several acids and bases and their pH values are identified on the pH scale, which ranges from 0 to 14,
in Figure 4.29.
The pH scale is a negative logarithmic scale. Because the scale is negative, as the ion concentration increases, the
pH value decreases. In other words, the more acidic the solution, the lower the pH value. Because the scale is
logarithmic, each one-point change in pH reflects a ten-fold change in the hydronium ion concentration and acidity.
For example, a solution with a pH of 6 is ten times as acidic as pure water with a pH of 7.

153
4.8. Solutions - Advanced www.ck12.org

FIGURE 4.28
A hydronium ion has the chemical formula
H3 O+ . The plus sign (+ ) indicates that the
ion is positively charged. How does this
molecule differ from a water molecule?

Acids

An acid can be defined as a hydrogen ion donor. The hydrogen ions bond with water molecules, leading to a higher
concentration of hydronium ions than in pure water. For example, when hydrochloric acid (HCl) dissolves in pure
water, it donates hydrogen ions (H+ ) to water molecules, forming hydronium ions (H3 O+ ) and chloride ions (Cl ).
This is represented by the chemical equation:
HCl + H2 O ! Cl + H3 O+ .
Strong acids can be harmful to organisms and damaging to materials. Acids have a sour taste and may sting or burn
the skin. Testing solutions with litmus paper is an easy way to identify acids. Acids turn blue litmus paper red.

Bases

A base can be defined as a hydrogen ion acceptor. It accepts hydrogen ions from hydronium ions, leading to a lower
concentration of hydronium ions than in pure water. For example, when the base ammonia (NH3 ) dissolves in pure
water, it accepts hydrogen ions (H+ ) from hydronium ions (H3 O+ ) to form ammonium ions (NH4 + ) and hydroxide
ions (OH ). This is represented by the chemical equation:
NH3 + H2 O ! NH4 + + OH .
Like strong acids, strong bases can be harmful to organisms and damaging to materials. Bases have a bitter taste and
feel slimy to the touch. They can also burn the skin. Bases, like acids, can be identified with litmus paper. Bases
turn red litmus paper blue.

Neutralization

What do you think would happen if you mixed an acid and a base? If you think the acid and base would “cancel each
other out,” you are right. When an acid and base react, they form a neutral solution of water and a salt (a molecule

154
www.ck12.org Chapter 4. Biological Molecules

FIGURE 4.29
Acidity and the pH Scale. Water has a
pH of 7, so this is the point of neutrality
on the pH scale. Acids have a pH less
than 7, and bases have a pH greater
than 7. Approximate pHs of examples are
depicted.

composed of a positive and negative ion). This type of reaction is called a neutralization reaction. For example,
when the base sodium hydroxide (NaOH) and hydrochloric acid (HCl) react, they form a neutral solution of water
and the salt sodium chloride (NaCl). This reaction is represented by the chemical equation:
NaOH + HCl ! NaCl + H2 O.
In this reaction, hydroxide ions (OH ) from the base combine with hydrogen ions (H+ ) from the acid to form water.
The other ions in the solution (Na+ ) and (Cl ) combine to form sodium chloride.

155
4.8. Solutions - Advanced www.ck12.org

Acids and Bases in Organisms

Enzymes are needed to speed up biochemical reactions. Most enzymes require a specific range of pH in order to do
their job. For example, the enzyme pepsin, which helps break down proteins in the human stomach, requires a very
acidic environment in order to function. Strong acid is secreted into the stomach, allowing pepsin to work. Once the
contents of the stomach enter the small intestine, where most digestion occurs, the acid must be neutralized. This is
because enzymes that work in the small intestine need a basic environment. An organ near the small intestine, called
the pancreas, secretes bicarbonate ions (HCO3 ) into the small intestine to neutralize the stomach acid.
Bicarbonate ions play an important role in neutralizing acids throughout the body. Bicarbonate ions are especially
important for protecting tissues of the central nervous system from changes in pH. The central nervous system
includes the brain, which is the body’s control center. If pH deviates too far from normal, the central nervous system
cannot function properly. This can have a drastic effect on the rest of the body.

MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/163563

Summary

• A solution is a homogeneous mixture in which a solute dissolves in a solvent. Water is a very common solvent,
especially in organisms.
• The ion concentration of neutral, pure water gives water a pH of 7 and sets the standard for defining acids and
bases. Acids have a pH lower than 7, and bases have a pH higher than 7.

Review

1. What is pH?
2. Define solution, and give an example of a solution.
3. What is the pH of a neutral solution? Why?
4. What type of reaction is represented by this chemical equation: KOH + HCl ! KCl + H2 O? Defend your
answer.
5. What is pepsin and give an example of how the body neutralizes its environment?

156
www.ck12.org Chapter 4. Biological Molecules

4.9 How Enzymes Speed Up the Chemical Re-

actions
Enzyme Function

Do cells have one enzyme with lots of functions, or many enzymes, each with just one function?
Enzymes. Magical proteins necessary for life. So how do enzymes work? How do they catalyze just one specific
biochemical reaction? In a puzzle, only two pieces will fit together properly. Understanding that is one of the main
steps in understanding how enzymes work.
How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by lowering
the activation energy of chemical reactions. Activation energy is the energy needed to start a chemical reaction.
This is illustrated in Figure 4.30. The biochemical reaction shown in the figure requires about three times as much
activation energy without the enzyme as it does with the enzyme.
As you view Enzyme Animation, focus on this concept:
1. how enzymes function.
Enzymes generally lower activation energy by reducing the energy needed for reactants to come together and react.
For example:

• Enzymes bring reactants together so they don’t have to expend energy moving about until they collide at
random. Enzymes bind both reactant molecules (called the substrate), tightly and specifically, at a site on the
enzyme molecule called the active site.
• By binding reactants at the active site, enzymes also position reactants correctly, so they do not have to
overcome intermolecular forces that would otherwise push them apart. This allows the molecules to interact
with less energy.
• Enzymes may also allow reactions to occur by different pathways that have lower activation energy.

Enzyme Animation

This animation of how enzymes work is a basic rundown of enzyme functions and illustrates what enzymes do.

157
4.9. How Enzymes Speed Up the Chemical Reactions www.ck12.org

FIGURE 4.30
The reaction represented by this graph
is a combustion reaction involving the re-
actants glucose (C6 H12 O6 ) and oxygen
(O2 ). The products of the reaction are
carbon dioxide (CO2 ) and water (H2 O).
Energy is also released during the reac-
tion. The enzyme speeds up the reaction
by lowering the activation energy needed
for the reaction to start. Compare the
activation energy with and without the en-
zyme.

MEDIA
Click image to the left or use the URL below.
URL: https://www.ck12.org/flx/render/embeddedobject/165503

Watch the video at: https://www.youtube.com/watch?v=CZD5xsOKres

158
www.ck12.org Chapter 4. Biological Molecules

4.10 References

1. Mariana Ruiz Villarreal (LadyofHats), modified by CK-12 Foundation. . Public Domain

2. Caroline Davis. . CC BY 2.0
3. User:Booyabazooka/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Saccharose.svg . Pub-
lic Domain
4. Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
5. Seeds: Lebensmittelfotos; Olives: Steve Jurvetson; Nuts: Petr Kratochvil. Seeds: http://pixabay.com/en
/barley-grain-cereals-whole-wheat-74247/; Olives: http://www.flickr.com/photos/jurvetson/454873761/; Nut
s: http://www.publicdomainpictures.net/view-image.php?image=424&picture=nuts . Seeds: Public Domain;
Olives: CC BY 2.0; Nuts: Public Domain
6. Wolfgang Schaefer (User:WS62/Wikimedia Commons). http://commons.wikimedia.org/wiki/File:Fat_trigl
yceride_shorthand_formula.PNG . Public Domain
7. User:YassineMrabet/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:AminoAcidball.svg .
Public Domain
8. Courtesy of the National Human Genome Research Institute. http://commons.wikimedia.org/wiki/File:Prote
in_primary_structure.svg . Public Domain
9. Hana Zavadska, based on image from the National Human Genome Research Institute. CK-12 Foundation .
CC BY-NC 3.0
10. Image copyright ynse, 2014. http://www.shutterstock.com . Used under license from Shutterstock.com
11. Marianna Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
12. Marianna Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.0
13. User:Honeymane/Wikimedia Commons and User:LucasVB/Wikimedia Commons. http://commons.wikim
edia.org/wiki/File:Double_Helix.png . Public Domain
14. Madeleine Price Ball (User:Madprime/Wikimedia Commons), modified by CK-12 Foundation. http://commo
ns.wikimedia.org/wiki/File:Genetic_code.svg . Public Domain
15. User:NEUROtiker/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Adenosintriphosphat_proto
niert.svg . Public Domain
16. User:Bensacoount/Wikipedia. http://commons.wikimedia.org/wiki/File:Hydronium.png . Public Domain
17. Hana Zavadska and Marianna Ruiz Villarreal (LadyofHats). CK-12 Foundation . CC BY-NC 3.0
18. Hana Zavadska. How enzyme changes activation energy .

159