CELL AND

MOLECULAR
BIOLOGY FOR
ENVIRONMENTAL
ENGINEERS
 CELL AND
MOLECULAR
BIOLOGY FOR
ENVIRONMENTAL
ENGINEERS

RYAN ROGERS, PhD

MOMENTUM PRESS, LLC, NEW YORK

Cell and Molecular Biology for Environmental Engineers

Copyright © Momentum Press®, LLC, 2018.

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This is for all of my students, past and present. I am constantly inspired
and motivated by their curiosity.
 Abstract

Understanding the molecular underpinnings of life is a task requiring

insight from multiple disciplines. In that likeness, biologists have moved
toward a systemic approach drawing from the expertise of computational
scientists, chemists, engineers, and mathematicians. This collabora-
tive approach requires translation of biological semantics into common
language so that the molecular mechanisms can be decoded to promote
health, design devices, and preserve environmental homeostasis. This
book provides context for biological forms and functions by starting at
the molecular level then building outward to include trends in biomedi-
cal technology, evolutionary impact, and the lasting implications for our
biosphere. In that likeness, biological concepts underlie most wastewater
treatment and provide foundation for the hazardous waste treatment being
done today. Furthermore, the relationship between biology and geology is
starting to emerge as a key relationship for self-healing concrete and rein-
forcement protection within concrete. Together, the information presented
in this book will provide a resolved understanding of biology that will
complement the Environmental Engineering collection.

KEYWORDS

cell biology, genetics, molecular biology

 Contents

List of Figures xi
List of Tables xix
Acknowledgments xxi
Introduction xxiii
1 Classification of Macromolecules 1
1.1  Composition of Biomolecules 1
1.2  Nucleotide Structure 1
1.3  Protein Structure and Function 5
1.4  Lipid Structure and Function 9
1.5 Carbohydrate Structure and Function 13
2 Cellular Structures 17
2.1  Cell Theory 17
2.2  Prokaryotic Cells 18
2.3  Eukaryotic Cells 22
3 Cellular Energy Production and Utilization 31
3.1  Biochemical Reactions 31
3.2 Enzymes 32
3.3 Photosynthesis 34
3.4  Aerobic Cellular Respiration 39
3.5  Anaerobic Respiration 45
4 The Cell Cycle and Cell Division 47
4.1  Cell Stages 47
4.2  Maintenance of Ploidy 47
4.3 Interphase 49
x  •   Contents

4.4 Mitosis 50
4.5 Other Methods of Cellular Replication 53
5 Meiosis and the Formation of Gametes 55
5.1  The Meiotic Process 55
5.2  Meiosis I 55
5.3  Meiosis II 58
5.4 Genetic Diversity as a Result of Meiosis 58
6 Gene Expression and Mutation 61
6.1 Genes 61
6.2  Gene Structure 62
6.3 Transcription in Prokaryotic Organisms 63
6.4  Eukaryotic Transcription 65
6.5 Translation 70
6.6 Mutations 75
6.7 Genetic Engineering and Recombinant DNA Technology 76
7 Evolution Patterns and Processes 79
7.1  Descent with Modification 79
7.2 Evolution as a Result of Natural Selection 80
7.3  Factors in Evolution 80
7.4  Speciation and Phylogeny 81
7.5  Conservation of Species 83
References 85
Glossary 87
About the Author 101
Index 103
 List of Figures

Figure 1.1.   Synthesis and hydrolysis of biological molecules.

(a) Dehydration synthesis reactions result in the
formation of covalent bonds between monomers to
build larger macromolecules. (b) Hydrolysis reactions
introduce a water m ­ olecule to break covalent bonds
between polymers. 2
Figure 1.2. The structure of nucleotides. (a) Nucleotides are ­
carbon-based ­macromolecules that comprise nucleic
acids. Each nucleotide is comprised of a pentose
sugar attached to a nitrogenous base on the 1′
carbon and a ­phosphate group on the 5′ carbon.
(b) There are five common nitrogenous bases
found attached to the 1′ carbon of nucleotides.
Pyrimidines ­(cytosine, thymine, and ­uracil) are single
ringed; whereas, purines (adenine and ­guanine) are ­­
double-ringed.2
Figure 1.3.  The structural variations between RNA and DNA.
(a) RNA is comprised of ribonucleotides, each
­consisting of ribose sugar, a nitrogenous base (adenine,
guanine, cytosine, or uracil) and a phosphate group.
(b) DNA is comprised of deoxyribonucleotides, each of
which contains deoxyribose, a nitrogenous base (adenine,
guanine, cytosine, or thymine), and a phosphate group.
Structurally both form phosphodiester bonds between
the 3′ hydroxyl of one nucleotide and the 5′ carbon of
another.4
Figure 1.4. The structure of adenosine triphosphate (ATP). ATP is
a nucleoside triphosphate. 5
Figure 1.5. The structure of amino acids. Amino acids are
carbon-based monomers of proteins. Each amino acid
xii  •   List of Figures

contains a central carbon bound to a hydrogen atom, a

carboxyl group, an amino group, and a distinct functional
(R) group. There are 20 different amino acids, each
differentiated by the variable R group. 6
Figure 1.6. Peptide bonds. Peptide bonds (arrow) form as a result of
dehydration synthesis reactions between the amino
groups and carboxyl groups of different amino acids. 6
Figure 1.7.  Protein folding. The process of protein folding can be
characterized by four distinct structures. The primary
protein structure is characterized by the formation of
peptide bonds between amino acids to form a
polypeptide chain. The secondary structure is driven
by hydrogen bonding between carboxyl and amino
groups giving rise to the formation of either alpha-helices
or beta pleated sheets. The tertiary structure forms as
a result of bonding between R-groups g­ iving rise to a
3-dimensional shape. The quaternary structure forms
when two or more polypeptides bond to form a final
functional protein. 7
Figure 1.8.  The many roles of proteins. The diversity of shapes
exhibited by proteins leads to a vast array of functions.
In each case the function of the protein is directly
related to its function. 8
Figure 1.9.  The structure of Lipids. Lipids are carbon-based
hydrophobic ­macromolecules. They exist either as
(a) hydro­carbon chains attached to a g­ lycerol molecule
or (b) as c­ onnected ring structures. 9
Figure 1.10. Saturated and unsaturated fatty acids. (a) Saturated
fatty acids contain only single bonds. (b) Unsaturated
fatty acids contain at least one double bond. Unsaturated
fatty acids with one double bond are characterized
as ­monounsaturated; whereas, fatty acids containing
more than one double bond are characterized as
polyunsaturated.10
Figure 1.11. The structure and function of phospholipids. (a, b)
Phospholipids consist of two hydrophobic fatty acid tails
attached to a glycerol and a hydrophilic phosphate group
with an associated choline. (c) Icon representation of a
phospholipid with the circle r­ epresenting the hydrophilic
region and the lines representing the hydrophobic
regions. (d) Organization of phospholipid bilayer. In
 List of Figures  •   xiii

this conformation, hydrophobic fatty acid tails extend

toward each other and the hydrophilic head regions
extend toward water. 12
Figure 1.12. Carbohydrate structure and properties. (a) Monosac­-
charides are monomers of carbohydrates. They
are characterized based upon the position of the carbonyl
along the hydrocarbon backbone. The monosaccharide
can be classified as an aldehyde, or aldose sugar if the
carbonyl group is found at the end of the molecule. If
the carbonyl group is within the hydrocarbon backbone,
it is classified as a ketone or a ketose sugar. (b) Glucose
and fructose are isomers because they have the
same chemical formula but differ in properties.
(c) ­Polysaccharides are comprised of monosaccharides
linked together by g­ lycosidic linkages as a result of
dehydration synthesis reactions. 14
Figure 2.1. Prokaryotic cell structures. Prokaryotic cells are
considered the simplest forms of life. They
lack a membrane-bound nucleus and internal
compartmentalization; however, they do possess
ribosomes for protein s­ ynthesis. The labels in the
schematic are as follows: (A) inclusion vesicle,
(B) nucleoid, (C) cell membrane, (D) cell wall,
(E) plasmid, (F) flagella, (G) pilus, and (H) fimbriae. 19
Figure 2.2. Animal cell structures. Animal cells are eukaryotic cells.
They are encapsulated by a semipermeable phospholipid
­membrane and have substantial internal organization
due to the p­ resence of ­membrane-bound organelles.
Animal cells have a distinct m ­ embrane-bound nucleus,
which holds the DNA and nucleolus. The labels in
the schematic are as follows: (A) cell membrane,
(B) nuclear envelope, (C) mitochondria, (D) smooth ER,
(E) rough ER, (F) peroxisome, (G) Golgi apparatus,
(H) vesicles, (I) lysosome, (J) centrosome, (K) ­centrioles,
(L) ribosomes, (M) nucleolus, and (N) nuclear pore. 22
Figure 2.3. Plant cell structures. Plant cells are eukaryotic cells
surrounded by a cell wall and a semipermeable
phospholipid membrane. Specialized pores span
the cell wall allowing for cell–cell communication.
Plant cells have a membrane-bound nucleus, and
specialized membrane-bound organelles. Chloroplasts
xiv  •   List of Figures

are photosynthetic organelles surrounded by a double

membrane. Vacuoles are primarily used for storage;
however, in some plants, they contain hydrolases,
associated with metabolic recycling. The labels in
the schematic are as follows: (A) ribosomes, (B)
plasmodesmata, (C) cell membrane, (D) nuclear
envelope, (E) nucleolus, (F) nuclear pore, (G) Golgi
apparatus, (H) mitochondria, (I) ­peroxisome, (J) vacuole,
(K) chloroplast, (L) rough ER, (M) smooth ER, and
(N) cell wall. 27
Figure 2.4. Fungal hyphae. Fungi grow as tubular, elongated, ­
thread-like structures called hyphae. Hyphae divided
into cells by internal cross-walls are called septate
hyphae. Hyphae that are not compartmentalized are
classified as coenocytic hyphae. 29
Figure 3.1. Enzymatic reactions. (a) Enzymes have distinctively
shaped active sites that correspond to specific substrate(s).
Enzymes bind to the substrate to form the enzyme-
substrate complex. A conformational change, known as
induced fit, will reposition the substrate (s) to catalyze
the reaction. Once the reaction is complete, products
are released and the enzyme cycles back to catalyze the
next reaction. (b) Enzymes can be regulated. Substrates
binding to the allosteric site can induce allosteric
inhibition, which changes the active site shape and
prevents substrate binding. Inhibitors sharing a similar
shape to the substrate are considered competitive
inhibitors, which bind and block the active site. 33
Figure 3.2. Feedback inhibition. (a) A biochemical pathway is a
multistep series of enzyme-catalyzed reactions that
produces many intermediates. (b) Biochemical pathways
can be regulated via feedback inhibition. A product or
intermediate can serve as an allosteric regulator for an
enzyme at an earlier point in the pathway. 34
Figure 3.3. Photosynthesis. Photosynthesis uses radiant energy and
carbon dioxide to produce sugar and oxygen. In the
process chemical energy is also produced. 34
Figure 3.4. The Z-scheme. The Z-scheme is a comprehensive
diagram illustrating the energetic transfers that occur
during the light-dependent reactions of photosynthesis.
Absorption of a photon excites P680, which sends the
 List of Figures  •   xv

excited electron to a more actively reducing species.

The electron is transferred through an electron transport
chain (ETC) until it reaches P700. This electron, along
with others, is transferred to NADP+, forming NADPH,
which is needed to facilitate light-independent reactions
(e− = electrons, H+ = hydrogen ions). 36
Figure 3.5. The Calvin cycle. The Calvin cycle describes the
process by which CO2 is converted into sugars. The
process requires three steps: carbon fixation, reduction,
and regeneration. Open circles represent carbon atoms
and gray circles labeled “P” represent phosphate
groups (Pi).37
Figure 3.6. Aerobic cellular respiration. Glucose is completely
oxidized to produce ATP in the presence of oxygen,
with water and carbon dioxide as by products. 39
Figure 3.7. Glycolysis. An initial investment of two ATP initiates
the conversion of glucose into two molecules of pyruvate
and two net molecules of ATP. Two NAD+ are reduced to
NADH, serving as high-energy electron carriers that will
facilitate later events during aerobic cellular respiration.
Open circles represent carbon atoms and gray circles
labeled “P” represent phosphate groups (Pi).40
Figure 3.8. Pyruvate oxidation and the TCA cycle. Each molecule
of pyruvate is oxidized by the enzyme pyruvate
dehydrogenase to produce one molecule of CO2
and promote reduction of NAD+ to form NADH.
The remaining two carbon molecule associates
with Coenzyme A (CoA) before diffusing into the
mitochondria for entry into the TCA cycle. The acetyl
group combines with a 4-carbon molecule (oxaloacetate)
and undergoes a series of enzyme-catalyzed redox
reactions that produces 3 NADH, 1 FADH2, 1 ATP (or
GTP), and 2 CO2 per molecule of acetyl. The 4-carbon
molecule is regenerated at the end of each TCA cycle.
Open circles represent carbon atoms. 42
Figure 3.9. The electron transport chain. Proteins labeled I, II, III,
IV, represent each complex of the ETC chain embedded
in the inner mitochondrial membrane. The ETC uses
NADH and FADH2 to make ATP via chemiosmosis.
The electron flow begins with oxidation of NADH at
complex I or at complex II with oxidation of FADH2.
xvi  •   List of Figures

Transfer of electrons down their energetic gradient is

coupled with active transport of hydrogen ions (H+)
across the mitochondrial membrane. This establishes an
electrochemical gradient that will drive ATP production
via proton motive force through the ATP synthase
enzyme. If these pathways m ­ alfunction, ATP production
is reduced, placing stress on the cell. 43
Figure 3.10. Aerobic respiration. (a) Ethanol fermentation.
Following ­glycolysis, pyruvate is further processed
to form the intermediate acetaldehyde, releasing two
molecules of CO2 in the process. Acetaldehyde is then
reduced to form ethanol by NADH. (b) Lactic acid
fermentation. Pyruvate is reduced by NADH to form
lactate, releasing two molecules of CO2 in the process. 45
Figure 4.1. The cell cycle. Cells exist in two distinct phases,
Interphase and M Phase. Interphase is further
subdivided into the Gap phases (G1 and G2) and
S phase. The Gap phases are characterized by growth
and cellular maintenance; whereas, S phase is when
the cell copies its genome in preparation for M Phase.
M Phase is when the cell divides and is broken down
into five sub-phases, each with distinct organization of
chromosomes to ensure daughter cells are identical to
that of the original cell. 48
Figure 4.2. Maintenance of ploidy. (a) Mitosis is asexual division;
daughter cells are identical and have the same number
of chromosomes (n) as the o­ riginal cell. In humans
this is represented as a diploid (2n) cell p­ roducing
two identical diploid cells. (b) Meiosis reduces the
diploid number of c­ hromosomes (2n) by half (n) to
form gametes. 48
Figure 4.3. Homologous chromosomes. Maternal and paternal
chromosomes containing the similar genomic sequences
are called homologous chromosomes. After S phase of
the cell cycle, each homolog is replicated to produce a
­second copy, called a sister chromatid. Sister chromatids
are held together at the c­ entromere of the chromosome
by the protein cohesin (gray oval). 50
Figure 4.4. Organization of chromatin. Chromatin is comprised
of DNA and histone proteins. DNA wraps around
histone proteins organized into nucleosomes. Each
 List of Figures  •   xvii

nucleosome consists of a little less than two turns of

DNA wrapped around a set of eight histones. Tightly
packed nucleosomes with extensively looped DNA
form chromosomes. 51
Figure 5.1. Meiosis. Meiosis is characterized by two rounds of
cell division. This schematic illustrates chromosome
movement during meiosis I and meiosis II. Note the
spindle complex has been omitted. During meiosis I all
homologous chromosomes pair up to form bivalents and
physically exchange genetic material during crossing
over. Meiosis I is complete when recombined homologs
are separated to form two unique haploid cells. Meiosis II
can be thought of as mitosis without DNA replication. At
this point non-identical sister chromatids are separated to
form four unique haploid cells. 56
Figure 5.2. Crossing over. (a) Homologous pairs align during
synapsis to form bivalents. (b) The synaptonemal
complex forms between each homolog and promotes
physical exchange of genetic material during crossing
over/genetic recombination. 57
Figure 6.1. The Central Dogma. The Central Dogma is a theory,
which aims to characterize the transfer of information
from DNA to functional product. In this theory it is
hypothesized that DNA is converted into mRNA during
transcription, which is followed by conversion of the
code into amino acids during translation. Amino acids
will fold to form final functional protein based on the
chemical properties of the amino acid sequence. 62
Figure 6.2. Eukaryotic gene structure. Eukaryotic genes are flanked
by regulatory sequences. The promoter sequence
represents the beginning of the gene, and is found
upstream of the transcription start site. The terminator
is downstream of the coding sequence, representing the
end of the gene span. When genes are transcribed, the
template strand is used to make a molecular copy of
the coding strand in the form of mRNA. Transcription
machinery binds to the promoter and proceeds
downstream until reaching the terminator. 62
Figure 6.3. RNA processing in eukaryotic organisms. Transcription
of eukaryotic genes results in the production of a
primary transcript containing both coding (exons)
xviii  •   List of Figures

and noncoding sequence (introns). Introns are spliced

out prior to nuclear export to align coding sequence
for translation. The mRNA is also modified by the
addition of a 5′ ­methyl-guanosine cap and the addition
of a 3′ poly A tail. 69
Figure 6.4. The genetic code. mRNA is read in triplet at the ribosome.
Each triplet is referred to as a codon, which codes for a
specific amino acid. 71
Figure 6.5. tRNA decodes mRNA. Each molecule of tRNA carries
an amino acid at the 3′ end of the folded RNA molecule.
The anticodon of the tRNA ­corresponds to specific
codons in the mRNA. The tRNA will complimentary
base pair with the codon in the A site of the ribosome
to ensure the correct amino acid is delivered to the
growing polypeptide. 72
Figure 6.6. Recombinant DNA technology. Plasmids are
extrachromosomal genetic material that can be easily
transferred between prokaryotic organisms. Each
plasmid has specific recognition sites for restriction
enzymes, which cut the plasmid, leaving extra unpaired
nucleotides. In a separate process, DNA from a different
organism can be cut using the same restriction enzymes
to produce a gene of interest with corresponding
nucleotides to the overhang in the plasmid. In the
presence of enzymes and regulatory proteins, the gene
of interest can be ligated into the plasmid during
transformation. Transformation promotes incorporation
of foreign DNA into an organism capable of producing
the gene product. 77
 List of Tables

Table 6.1.  tRNA binding sites in the ribosome 73

Table 6.2.  Mutation classification and consequences 75
Table 7.1.  Characteristics of prezygotic isolation 82
Table 7.2.  Characteristics of postzygotic isolation 82
Table 7.3.  Speciation concepts83
 Acknowledgments

Training and contributions from Derek Cascio are gratefully acknowl-

edged, as he provided tremendous assistance with figure construction.
Without his insight, graphical representation of cellular structures would
not be possible.
Professor Francis Hopcroft and Professor Henderson Pritchard fueled
the inception of this project. Their early input and guidance helped frame
the scope of the manual.
 Introduction

Engineering is largely concerned with designing and improving structures

or systems through the application of interdisciplinary methods. In addi-
tion to training in mathematics and physics, an understanding of biology
is essential for any engineer working with living organisms or engaging
the ecosystems in which they live. The application of cellular properties
will shed light on how variation in molecular composition allows for
­functional diversity and survival among living organisms.
As the relationship between cells and their environment is character-
ized with more detail, new roles are discovered for old favorites and new
techniques are being employed to characterize roles for organic material
that was once considered “junk.” Interdisciplinary conversations have
given rise to many new theories related to the significance of a changing
environment in the context of organismal evolution at the molecular level.
Furthermore, the way in which such changes have simultaneously played
a key role in shaping the environment may assist in conservation efforts.
The scope of biology is vast; thus, it would be impossible for any
human to claim mastery of more than one subdiscipline. There is a com-
mon misconception that understanding biology merely requires memori-
zation and regurgitation of terms—this could not be farther from the truth.
As with any scientific discipline, biology is founded in reason, driven by
hypotheses, and tested regularly in effort to support past paradigms while
promoting progress. In that likeness, the field of biology is by no means
stagnant, in fact, the scientific understanding of cell and molecular ­biology
is regularly outdated as a result of new technology, increased interest,
and diversification of methods from symbiotic fields. This text aims to
­communicate the core of molecular and cellular biology. In that regard
each chapter has been significantly consolidated to provide foundation
and context for those wishing to respect biological life.
 CHAPTER 1

Classification of
Macromolecules

1.1  COMPOSITION OF BIOMOLECULES

Macromolecules are the basic building blocks of living organisms. At a

biochemical level, they can be defined as large organic molecules, or poly-
mers, comprised of smaller molecules, known as monomers. ­Biological
monomers have a carbon (C) backbone with varying degrees of oxygen
(O), nitrogen (N), and hydrogen (H). Other elements are also present
in organic biomolecules; however, the abundance and diversity varies
throughout the cell and throughout species. Macromolecular polymers are
formed as a result of dehydration synthesis reactions (Figure 1.1a), which
form covalent bonds between monomers. Polymers can be broken down
into monomers in the presence of water during hydrolysis reactions so that
biosynthesis of new cellular molecules can proceed (Figure 1.1b).
All biological macromolecules are carbon-based polymers, known
as hydrocarbons. Each macromolecule differs based on the presence of
varied side chains, or functional groups. The molecular composition of
the functional group directly relates to the chemical properties of the mol-
ecule, and thus, the specific function of each macromolecule. Based on
the complexity of the molecule and presence of functional groups, four
distinct biological macromolecules have been categorized: carbohydrates,
nucleic acids, proteins, and lipids. In this section, each macromolecule
is described with respect to its molecular structure and cellular function.

1.2 NUCLEOTIDE STRUCTURE

Nucleic acids are made of small monomers known as nucleotides

­(Figure 1.2a). Each nucleotide is comprised of a five-carbon sugar, known
as a pentose. Each carbon of the pentose is numbered clockwise from
2  •   CELL AND MOLECULAR BIOLOGY

(a)
O
OH HO O H H

(b)
O
O H H OH HO

Figure 1.1.  Synthesis and hydrolysis of biological molecules. (a) Dehydra-

tion synthesis reactions result in the formation of covalent bonds between
monomers to build larger macromolecules. (b) Hydrolysis reactions introduce
a water ­molecule to break covalent bonds between polymers.

(a) (b) NH2 O O

O
N NH NH
NH N O N O N O
O
H H H
Pentose Cytostine Uracil Thymine
P 5′ sugar N O
O O pyrimidines
4′ O 1′ Nitrogenous O NH2
O base
N N
Phosphate NH N
group 3′ 2′
N N NH2 N N
OH H Guanine H Adenine
Purines

Figure 1.2.  The structure of nucleotides. (a) Nucleotides are carbon-based

­macromolecules that comprise nucleic acids. Each nucleotide is comprised
of a pentose sugar attached to a nitrogenous base on the 1′ carbon and a
­phosphate group on the 5′ carbon. (c) There are five common nitrogenous
bases found attached to the 1′ carbon of nucleotides. Pyrimidines ­(cytosine,
thymine, and u­ racil) are single ringed; whereas, purines (adenine and
­guanine) are ­double-ringed.

oxygen with the corresponding number plus the (′) prime symbol. The
numbering of carbons establishes molecular polarity and orientation of the
other nucleotide subunits.
The 1′ carbon is covalently bound to one of five nonpolar nitroge-
nous bases. Nitrogenous bases are also referred to as nitrogen-containing
bases because they include a nitrogen atom that shares chemical properties
with that of a base. Nitrogenous bases come in two flavors: double-ringed
purines or single-ring pyrimidines (Figure 1.2b). Guanine (G) and a­ denine
(A) are purines; whereas, cytosine (C), thymine (T), and uracil (U) are the
most abundant pyrimidines found in nucleic acids.
 Classification of Macromolecules  •  3

Moving clockwise around the molecule, the 2′ and 3′ carbons are

attached to either a hydrogen atom or a hydroxyl group (OH). The 5′ ­carbon
is covalently bound to a phosphate group, which consists of a phospho-
rus bound to four oxygen atoms. The phosphate group attached to the 5′
­carbon of the sugar on one nucleotide forms a covalent ester bond with the
free hydroxyl on the 3′ carbon of the next nucleotide (Figure 1.2). These
bonds are called phosphodiester bonds, and the positioning of nucleotides
in this manner induces formation of a sugar-phosphate backbone.

1.2.1  MOLECULAR COMPOSITION OF DNA

Deoxyribonucleic acid (DNA) encodes the genetic instructions for the cell
in just four letters—A,T,C, and G. These letters represent the nitrogenous
bases found attached to nucleotides. Nucleotides that comprise DNA con-
tain deoxyribose, a pentose sugar distinguished by a free hydroxyl at the
3′ position. DNA is double stranded, consisting of two linear sugar-phos-
phate backbones that run opposite each other and twist together into a
helix. The two strands are antiparallel due to the opposing positions of
the 5′ and 3′ carbons; therefore, the strands are designated as either 5′–3′
or 3′–5′ to distinguish one from the other. This gives the molecule polarity
and plays a large factor in the replication process.
The sugar-phosphate backbone in DNA is negatively charged and
hydrophilic, which promotes bonding with water. The helix is held
together as a result of hydrogen bonding between the nitrogenous bases
on opposing strands. In nearly every circumstance, adenine (A) will form
two hydrogen bonds with thymine (T); whereas, guanine (G) will form
three hydrogen bonds with cytosine (C). The relative amount of each
nitrogenous base varies between different species; however, the bonding
relationship is conserved from unicellular prokaryotic organisms up to
complex multicellular organisms. The order and position of the nitroge-
nous bases corresponds to a molecular code, which serves as instructions
for ­synthesizing all of the proteins and functional Ribonucleic acid (RNA)
within a cell.

1.2.2  MOLECULAR COMPOSITION OF RNA

RNA is the single-stranded biochemical relative of DNA. Ribose is pres-

ent in RNA, which can be distinguished from deoxyribose by the ­presence
of hydroxyl groups on both the 2′ and the 3′ carbon (Figure 1.3a). Addi-
tional variation between DNA and RNA is found in the nitrogenous
bases, as DNA possesses thymine (T), whereas RNA contains Uracil (U)
4  •   CELL AND MOLECULAR BIOLOGY

(a) O

O NH

O P O 5′ Ribose N O
4′ O 1′ Uracil
O
Phosphate group 2′
3′
OH OH

(b) O

O NH
Deoxyribose
O
− P O 5′ N O
4′ O 1′ Thymine
O
Phosphate group 2′
3′
OH
Figure 1.3.  The structural variations between RNA and DNA. (a) RNA is
comprised of ribonucleotides, each c­ onsisting of ribose sugar, a nitroge-
nous base (adenine, guanine, cytosine, or uracil) and a phosphate group.
(b) DNA is comprised of deoxyribonucleotides, each of which contains
deoxyribose, a nitrogenous base (adenine, guanine, cytosine, or thymine),
and a phosphate group. Structurally both form phosphodiester bonds
between the 3′ hydroxyl of one nucleotide and the 5′ carbon of another.

(­ Figure 1.3b). The information stored in DNA is decoded by RNA, which

is chemically similar, yet more diverse, in functionality. During gene
expression, DNA is temporarily opened up by an enzyme known as RNA
polymerase, which uses DNA sequences as a template for synthesizing a
molecular copy in the form of RNA. RNA holds many roles and can be
processed to relay different messages within the cell (more in Chapter 6).
Recent research has highlighted certain RNAs as noncoding, meaning that
they are never translated into protein and serve specific functions on their
own such as catalysis and regulation of gene expression.

1.2.3  OTHER NUCLEIC ACIDS

There are other nucleic acids that are essential to cell function and s­ urvival.
These nucleic acids function primarily in energy storage and transfer, and
 Classification of Macromolecules  •  5

NH2
Phosphate groups
N
O O O N

P P 5′ N N
O P O O O
4′ O 1′ Adenine
O O O Ribose

3′ 2′
OH OH
Figure 1.4.  The structure of adenosine triphosphate (ATP). ATP is a
nucleoside triphosphate.

serve as key players during cellular respiration. Perhaps the most note-
worthy is adenosine triphosphate (ATP), which exists as a nucleotide
monomer of ribose, adenine, and three phosphate groups (Figure 1.4). The
instability of bonds between the phosphate groups allows rapid hydroly-
sis of the terminal phosphate to release energy and facilitate endergonic
reactions.
Nicotinamide adenine dinucleotide is another noteworthy nucleic
acid. The substructure of this coenzyme is characterized as a dinucleotide
due to the presence of only two nucleotides linked together via phospho-
diester bonds. Nicotinamide adenine dinucleotide exists as either oxidized
(NAD+) or reduced (NADH) and is essential for cellular respiration.

1.3  PROTEIN STRUCTURE AND FUNCTION

Proteins are the most diverse macromolecule with respect to shape,

structure, and function. Comprised of amino acids, the varied nature of
proteins is dictated by variation in functional group (R). There are 20 dif-
ferent amino acids; therefore, each is distinguished from one another by
a distinct chemical side chain that dictates the bonding affinity and, thus,
chemical behavior. In addition to the variable R group, all amino acids
have a carboxyl group, an amino group, and a hydrogen atom attached to
a central α carbon (Figure 1.5).
Dehydration synthesis reactions between the carboxyl and amino
group of singular amino acids results in the formation of peptide bonds.
Peptide bonds are incredibly strong and covalent in nature due to the
sharing of valence electrons between C–N (Figure 1.6). Once peptide
bonds are formed between amino acids, the sequences are characterized
as ­residues. The sequence of amino acids determines the function of the
6  •   CELL AND MOLECULAR BIOLOGY

Functional
group
R
H OH
Amino Carboxyl
group N C C group

H O
H

Figure 1.5.  The structure of amino acids. Amino acids are

­carbon-based monomers of proteins. Each amino acid contains a
central carbon bound to a hydrogen atom, a carboxyl group, an
amino group, and a distinct functional (R) group. There are 20
­different amino acids, each differentiated by the variable R group.

R O R
H OH
N C C N C C
H O
H H H

Figure 1.6.  Peptide bonds. Peptide bonds (arrow) form as a result

of dehydration synthesis reactions between the amino groups and
carboxyl groups of different amino acids.

final folded protein, as the interactions between the R groups contort the
molecule into a distinct conformation.

1.3.1  PROTEIN FOLDING

The unique sequence of amino acid residues represents the primary struc-
ture of protein folding (Figure 1.7). Given the 20 potential amino acids
and unlimited possibilities for length and sequence, this structure is of
particular importance because the organization of R groups drives bond
formation during the remainder of protein folding. For example, the prox-
imity of polar and nonpolar amino acids in the primary structure predicts
how this protein will fold in later stages to protect hydrophobic residues
from water and promote the interaction of hydrophilic residues with water.
The secondary structure of protein folding results from hydrogen
bonding between the oxygen on the carboxyl group of one amino acid and
the hydrogen on the amino group of another. These bonds stabilize three
dimensional motifs, or conserved structures, that arise due to hydrogen
bonding along the peptide backbone. The proximity of hydrogen bonds
will result in two distinct shapes: alpha helices or beta pleated sheets.
Alpha helices form when the residues are approximately four linear points
 Classification of Macromolecules  •  7

away from one another, where the first carbonyl bonds with the hydro-
gen on the fourth amino group to establish a pattern of proximity. This
bonding pattern results in a coiled or spiral peptide structure (Figure 1.7).
Beta pleated sheets can result from hydrogen bonding of residues located
further away from one another; however, the result is a kink or fold in the
peptide, which brings the sequences closer together in space.
Secondary structures stabilize the molecule and prime the R groups
for further interactions. In the tertiary structure, R groups bond either with
other R groups or they bond with the backbone itself. The type of bond is

Primary protein structure

Secondary protein structure

β-pleated sheet α-helix

Tertiary protein structure

Quarternary protein structure

Figure 1.7.  Protein folding. The process of protein folding can

be characterized by four distinct structures. The primary protein
structure is characterized by the formation of peptide bonds between
amino acids to form a polypeptide chain. The secondary structure
is driven by hydrogen bonding between carboxyl and amino groups
giving rise to the formation of either alpha-helices or beta pleated
sheets. The tertiary structure forms as a result of bonding between
R-groups g­ iving rise to a 3-dimensional shape. The quaternary
structure forms when two or more polypeptides bond to form a final
functional protein.
8  •   CELL AND MOLECULAR BIOLOGY

dictated by the chemical composition of the R group; however, hydrogen

bonding, hydrophobic interactions, van der Waals interactions, covalent
bonding, and ionic bonding are the most common. It is the diversity of
bonds that allows for the innumerable shapes of proteins. Some proteins
may be completely finished folding at this stage; however, many proteins
are complex and combine multiple subunits to carry out a function.
Proteins that have multiple peptide chains, or subunits, complete fold-
ing as a quaternary structure (Figure 1.7). In this stage, multiple polypep-
tides come together, guided by the same subsets of bonds found in the
tertiary structure. In some proteins, these subunits are completely differ-
ent and represent domains, which are conserved residues associated with
a particular function. In other cases, subunits are identical residues that
complex to serve a distinct function as a whole.

1.3.2  DIVERSITY OF PROTEIN FUNCTION

Once the folding is complete, proteins can be subdivided into two main
classes: fibrous or globular. Fibrous proteins are primarily associated
with structural support or motility; whereas, globular proteins can serve a
diverse array of functions within the cell. Furthermore, proteins can com-
plex together with completely distinct proteins or nucleic acids to form
molecular machines. Molecular machines facilitate many biological pro-
cesses and are often conserved among species, such as ribosomes.
Proteins occupy the majority of jobs in the cell, which range from
structural support to catalysis (Figure 1.8). Given that the shape of a pro-
tein is essential for its function, the folding process is heavily regulated
and guided by accessory proteins to ensure that a specific final structure

Storage

Structure Transport

Regulation Defense

Locomotion Catalysis
Signaling

Figure 1.8.  The many roles of proteins. The diversity of shapes

exhibited by proteins leads to a vast array of functions. In each
case the function of the protein is directly related to its function.
 Classification of Macromolecules  •  9

is achieved. Moreover, any disruption to the structure severely hinders the

protein’s a­ bility to serve the cell. If a protein loses its quaternary, tertiary,
or ­secondary structure, in other words becomes unfolded, it is considered to
be denatured, and thus, no longer functional. Denaturation can occur due to
changes in temperature, pH, chemical composition, or concentration of ions.
­Fortunately, the cell produces specialized chaperone proteins in response to
stress, which act to refold the peptide into the final functional structure.

1.4  LIPID STRUCTURE AND FUNCTION

Lipids are nonpolar, hydrocarbon-based, molecules that are unable to

­dissolve in water. Lipids are one of the largest classes of macromolecules;
however, the relationship between different lipids is fairly loose. The pri-
mary link between lipids is that they all share a high percentage of C–C
and C–H bonds, and thus, they cannot dissolve in water. These bonds can
exist in multiple conformations ranging from linear hydrocarbon tails to
connected ring structures (Figure 1.9).

(a)
Gycerol Fatty acid
H O H H H H H H H
H C O C C C C C C C C H
HH H H H H H

O H H H H H H H
H C O C C C C C C C C H

HH H H H H H

O H H H H H H H

H C O C C C C C C C C H
H HH H H H H H

(b)

Figure 1.9.  The structure of Lipids. Lipids are carbon-based hydro-

phobic ­macromolecules. They exist either as (a) hydro­carbon chains
attached to a g­ lycerol molecule or (b) as c­ onnected ring structures.
10  •   CELL AND MOLECULAR BIOLOGY

1.4.1 ISOPRENOIDS

Isoprene is an excellent example of a water-insoluble lipid. Isoprene is a

five-carbon compound that is completely saturated, or bound by hydro-
gen atoms such that no additional bonds can be formed; thus, it is a true
hydrocarbon. Isoprenes can be linked to other hydrocarbons to form iso-
prenoids, which are also known as terpenes. These naturally occurring
chemicals are primarily produced by plants; however, other living organ-
isms have been shown to produce terpenes in various roles. The diversity
of terpenes comes not only in the hydrocarbon backbone conformation
but also assembly and modifications. Although isoprenoids serve a myriad
of functions within the cell, they also serve as precursors for other lipids.

1.4.2  FATTY ACIDS AND SATURATION

Fatty acids are approximately 14 to 30 carbons attached to a carboxyl

group which can be held together by either single or double bonds. Fatty
acid bond configuration has a large impact on the stereochemistry, or the
orientation of the molecule in space. Fatty acids, which only contain single
bonds, are considered saturated because all carbons are bound to hydrogen,
and thus, the maximum number of bonds are fulfilled (Figure 1.10). Satu-
rated fatty acids tend to have higher melting points and are solid at room
temperature. Alternatively, fatty acids with one or more double bonds are
considered unsaturated because they have fewer than the maximum poten-
tial number of hydrogens attached (Figure 1.10). U ­ nsaturated fatty acids
come in two forms: monounsaturated, having one double bond, and poly-
unsaturated, having multiple double bonds t­hroughout the ­hydrocarbon

(a) (b)
O HH H HH H H H O HH H HH
H

HO C C C C C C C C C H HO C C C C C C
H
C

H H H H H H H H H H H H
C

H
C

H
H

C
H

C
H

H
H

Figure 1.10.  Saturated and unsaturated fatty acids. (a) Saturated fatty acids
contain only single bonds. (b) Unsaturated fatty acids contain at least one
­double bond. Unsaturated fatty acids with one double bond are characterized
as ­monounsaturated; whereas, fatty acids containing more than one double
bond are characterized as polyunsaturated.
 Classification of Macromolecules  •  11

tail. ­Polyunsaturated fatty acids are liquid at room t­emperature but can be
converted back to solid by breaking the double bonds and adding hydro-
gens through a process known as hydrogenation.

1.4.3 TRIGLYCERIDES

Fatty acids can exist as free fatty acids in the cell; however, they are also
present in triglycerides. Triglycerides are formed via dehydration synthe-
sis reactions between free fatty acids and 3-carbon glycerol molecules. The
reaction results in a largely nonpolar molecule with three branched fatty
acid tails covalently bound via an ester linkage to glycerol ­(Figure 1.9a).
Triglycerides are also commonly referred to as fats and function as energy
reserves in the cell.

1.4.4  PHOSPHOLIPIDS AND CELL MEMBRANES

Phospholipids consist of a glycerol that is linked to a phosphate

group bound by a small charged molecule and two hydrocarbon tails
­(Figure 1.11). Phospholipids comprise the majority of the cell membrane,
and the saturation of hydrocarbon tails promotes fluidity and stability. The
hydrocarbon tails are usually comprised of fatty acids; however, in some
ancient unicellular organisms, known as archaea, these tails are comprised
of isoprene (Villanueva 2017). The presence of isoprene in these organ-
isms enhances stability of the phospholipids and allows them to ­survive in
extreme environments.
Phospholipids are considered amphipathic molecules due to the pres-
ence of opposing chemical groups within the substructure. As previously
discussed, molecules containing C–C and C–H bonds are hydrophobic and
repel water; however, the negatively charged phosphate group attached
to a polar group (often choline) in the “head” region of phospholipids
yields the opposite property—a hydrophilic region (Figure 1.11a, b). It is
this property that makes phospholipids ideal for membrane composition.
When placed in solution, phospholipids will spontaneously orient them-
selves to form bilayers, or two rows of phospholipids with a distinct orien-
tation. The charged hydrophilic region will be attracted to water molecules
forming hydrogen bonds; whereas, the hydrophobic tails cannot form such
interactions, and thus, will be positioned away from the water.
The amphipathic nature of phospholipids is the key to their function
in membranes. All cells contain a phospholipid membrane, often referred
12  •   CELL AND MOLECULAR BIOLOGY

(a) CH N+ (CH ) (b)

2 3 3 Choline
Polar
CH hydrophilic
2
Phosphate
group head
O
Glycerol
O = P O

Fatty acid chain

Fatty acid chain

O Nonpolar
hydrophobic
CH2 CH2 CH2 tails

O O
(c)
C=O C=O
Head
CH CH
2 2

Tail
CH CH
2 2

CH CH (d)
2 =
CH
CH –
2 CH
2 –
CH
CH
2 2 –
CH
CH 3
3

Figure 1.11.  The structure and function of phospholipids. (a, b)

Phospholipids consist of two hydrophobic fatty acid tails attached to a
glycerol and a hydrophilic phosphate group with an associated choline.
(c) Icon representation of a phospholipid with the circle r­ epresenting the
hydrophilic region and the lines representing the hydrophobic regions.
(d) Organization of phospholipid bilayer. In this conformation, hydro-
phobic fatty acid tails extend toward each other and the hydrophilic head
regions extend toward water.

to as the phospholipid bilayer, which functions as a semipermeable barrier

between intracellular contents and external environment (Figure 1.11d).
The fluidity of the membrane is determined by the ratio of unsaturated to
saturated fatty acids in the hydrophobic tails. When membranes have a
high percentage of unsaturated fatty acids, fluidity and permeability are
increased. Membranes with a high percentage of saturated fatty acids in
the bilayer tend to be more rigid with decreased permeability as a result of
the tightly packed tails. Most cells have a combination of both saturated
and unsaturated fatty acids in the phospholipid bilayer, which results in an
intermediate permeability.
 Classification of Macromolecules  •  13

1.4.5 STEROIDS

Steroids are a large subclass of lipids characterized by their distinct hydro-

phobic four ring structure. The role of steroids in cells varies based upon
the functional groups, which can be found attached to the ring structure.
For example, estrogen and testosterone, and lipid-insoluble steroids, func-
tion largely in cell–cell communication (Figure 1.9). Since these molecules
are comprised primarily of C–C and C–H bonds, they, too, are insoluble in
water, making them ideal for traveling through the cytoplasm, bloodstream,
and extracellular fluid to initiate pathway cascades and ­cellular responses.
Cholesterol is a common structural steroid found throughout cells.
While cholesterol exhibits the classic four ring structure, it is further dis-
tinguished by the presence of a hydrophobic isoprene tail attached to the
bottom ring as well as a hydrophilic hydroxyl group attached to the top
ring. This results in an amphipathic molecule, capable of incorporating
into cellular membranes. For this reason, cholesterol is often found as
a reinforcing structure within the membrane to enhance durability and
reduce permeability.

1.5 CARBOHYDRATE STRUCTURE AND

FUNCTION

Carbohydrates are organic molecules comprised of carbon, hydrogen, and

oxygen, which serve multiple roles within a cell. Often referred to as sug-
ars, carbohydrates provide structural support, indicate cellular identity by
serving as molecular identification tags, and, perhaps most importantly,
store chemical energy. While carbohydrates do exist independently, they
can be found as subunits of other macromolecules, such as ribose in RNA
or as a hydrocarbon scaffold to produce amino acids.

1.5.1 MONOSACCHARIDES

All carbohydrates are comprised of monomers, known as monosaccha-

rides. Monosaccharides have a 1:2:1 molar ratio of carbon: hydrogen:
oxygen that are characterized as hydrophilic polar molecules. Often
monosaccharides are shown as linear chains; however, sugars containing
five or more carbons will exist as rings in aqueous solution. They can be
distinguished from one another by the number of carbons, as well as by the
position and spatial organization of carbonyl groups.
14  •   CELL AND MOLECULAR BIOLOGY

The most reliable method for characterizing monosaccharides relies

upon the number of carbons, which are numbered consecutively at the
end closest to the carbonyl (similar to numbering in nucleotides). A more
sophisticated method to characterize monosaccharides is based upon the
position of the carbonyl along the hydrocarbon backbone. If the carbonyl
is found at the end of the molecule, the monosaccharide can be classi-
fied as an aldehyde, or aldose sugar. Conversely, if the carbonyl group
is within the hydrocarbon backbone, this simple sugar is classified as a
ketone or a ketose sugar (Figure 1.12a).
While these methods are effective in characterizing monosaccharides,
an added challenge comes when looking only at the molecular formula, as
some monosaccharides have the same number of atoms comprising the
molecule. A classic example of this circumstance is the molecular formula

(a) H O

H C OH H C

C O H C OH

H C OH H C OH

H H

Ketose Aldose

(b) CH2OH CH2OH

OH O H
H
OH H H HO CH2OH
HO OH HO
H OH OH H
Glucose Fructose

(c)
CH2OH CH2OH CH2OH
H O O O OH
OH H O OH H O OH H
HO H
H OH H OH H OH

Figure 1.12.  Carbohydrate structure and properties. (a) Monosaccharides

are monomers of carbohydrates. They are characterized based upon the
position of the carbonyl along the hydrocarbon backbone. The monosac-
charide can be classified as an aldehyde, or aldose sugar if the carbonyl
group is found at the end of the molecule. If the carbonyl group is within
the hydrocarbon backbone, it is classified as a ketone or a ketose sugar.
(b) Glucose and fructose are isomers because they have the same chemical
formula but differ in properties. (c) ­Polysaccharides are comprised of mono-
saccharides linked together by g­ lycosidic linkages as a result of dehydration
synthesis reactions.
 Classification of Macromolecules  •  15

C6H12O6, which is the same for glucose, galactose, and fructose. These
monosaccharides are referred to as isomers (Figure 1.12b). Glucose and
fructose are considered structural isomers because they differ in the posi-
tion of the carbonyl, as glucose is an aldehyde and fructose is a ketone.
Glucose and galactose are considered stereoisomers because they have the
same molecular formula, the same carbonyl; however, the position of the
carbonyl differs in spatial arrangement.

1.5.2 POLYSACCHARIDES

Monosaccharides can covalently bond to form branched and unbranched

chains. When two monosaccharides bond, they are referred to as disac-
charides and when more than two link together they are characterized as
polysaccharides. The process of linking monosaccharides is achieved via
dehydration synthesis between hydroxyl groups and results in a glyco-
sidic linkage (Figure 1.12c). Since monosaccharides have more than one
hydroxyl group, the position and geometry of these bonds varies between
polysaccharides. Linkages are designated α or β to reflect the geometry
of the bond and assigned numbers to represent the carbons being linked
together.
Linkage behaviors can be observed in the context of polysaccharide
function. Highly branched polypeptides, such as glycogen and amylopec-
tin, are associated with energy storage and often exhibit an α 1,6 linkage,
making cleavage easier during energy extraction. Conversely, chitin and
cellulose are unbranched structural carbohydrates that exhibit a β 1,4 link-
age to increase rigidity and support.
 Index

A CAM. See Crassulacean acid

Aerobic cellular respiration metabolism
ATP synthase, 43–44 Carbohydrates
description of, 39–40 definition of, 13
electron transport chain, 43–44 monosaccharides, 13–15
glycolysis, 40–41 polysaccharides, 15
pyruvate oxidation, 41–42 Catabolic reactions, 31
tricarboxylic acid cycle, 42–43 Cell cycle, 48
Alcohol fermentation, 45 Cell membranes, 11–12
Alleles, 58 Cell stages, 47
Allosteric inhibition, 32 Cell theory, 17–18
Alternative splicing, 70 Central Dogma, 62
Anabolic reactions, 31 Chemiosmosis, 35, 44
Anaerobic respiration, 45–46 Chromatin, 65
Anaphase, 52 Cilia, 21
Anaphase I, 57 Cisternae, 25
Anticodon, 72 Citric acid cycle. See Tricarboxylic
Archaea, 11, 18–19 acid (TCA) cycle
Cloning vector, 77
B Coenocytic hyphae, 29
Bacteria, 19–20 Conservation of species, 83–84
Bacterial phospholipids, 20 Constitutive genes, 61
Binary fission, 53 Crassulacean acid metabolism
Biochemical reactions (CAM), 38–39
ATP as cellular chemical energy, Cyclic light-dependent reactions,
31–32 36
classification, 31 Cytokinesis, 53, 58
Biological monomers, 1 Cytoskeleton, 21, 23
Biomolecules, composition of, 1 Cytosol, 23
Budding, 53–54
D
C Deoxyribonucleic acid (DNA), 3
Calvin cycle, 37–38 Descent with modification, 79
104  •  Index

Diploid organisms, 47–48 G

Disaccharides, 15 Gametogenesis, 55
Gene locus, 62
E Genes
Electron transport chain, 43–44 description of, 61–62
Elongation eukaryotic, 62
eukaryotic transcription, 66–67 structure, 62–63
prokaryotic transcription, 64 Genetically modified organism
translation at ribosome, 74 (GMO), 76
Endergonic reactions, 31 Genetic engineering, 76–78
Endoplasmic reticulum, 24–25 Glycolysis, 40–41
Enzymes GMO. See Genetically modified
definition of, 32 organism
regulation of activity, 32–34 Golgi apparatus, 25
Euchromatin, 65
Eukaryotic cells H
animal cells, 22, 26–27 Heterochromatin, 65
description of, 22–23 Histones, 24
fungi cells, 28–29 Homologous chromosomes, 50
organelles, 23–26 Horizontal gene transfer, 20
plant cells, 27–28 Hydrocarbons, 1
Eukaryotic genes, 62 Hyphae, 28
Eukaryotic transcription
elongation, 66–67 I
genes organization, 65 Initiation
initiation, 65–66 eukaryotic transcription, 65–66
RNA processing, 68–70 prokaryotic transcription, 63–64
termination, 67–68 translation at ribosome, 73–74
Evolution Introns, 69
factors in, 80–81 Isomers, 15
as result of natural selection, 80 Isoprenoids, 10
speciation, 81–83
Exergonic reactions, 31 K
Exons, 69 Krebs cycle. See Tricarboxylic
acid (TCA) cycle
F
Fatty acids, 10–11 L
Feedback inhibition, 33–34 Lactic acid fermentation, 45–46
Fimbriae, 19 Light-dependent reactions, 35–36
Flagella, 21 Light-independent reactions,
Frameshift mutations, 76 37–38
Functional groups, 1 Light, source of energy, 34–35
Fungal hyphae, 29 Lipids
Fungi cells, 28–29 cell membranes, 11–12

definition of, 9
fatty acids and saturation,
10–11
isoprenoids, 10
phospholipids, 11–12
steroids, 13
triglycerides, 11
Lysosomes, 25
M definition of, 1
Macromolecular polymers, 1
Macromolecules, 1
Meiosis
genetic diversity as, 58–59
M phase, 47
process, 55
Meiosis I
anaphase I, 57
cytokinesis, 58
metaphase I, 57
prophase I, 55–57
telophase I, 58
Meiosis II, 59
Messenger RNA (mRNA), 62
Metaphase, 52
Metaphase I, 57
Missense mutations, 76
Mitophagy, 26
Mitosis
anaphase, 52
cytokinesis, 53
description of, 50–51
metaphase, 52
prometaphase, 52
prophase, 51–52
telophase, 53
Molecular composition
of DNA, 3
of RNA, 3–4
Monomers, 1
Monosaccharides, 13–15
mRNA. See Messenger RNA
Mutations, 75–76
Mycelium, 28
Index  •   105
N
NAD. See Nicotinamide adenine
dinucleotide
Nicotinamide adenine dinucleotide
(NAD), 5, 39
Nitrogenous bases, 2
Nonsense mutations, 76
Nuclear envelope, 24
Nucleotides
structure of, 2
O
Organelles, 23–26
Oxidative phosphorylation,
43–44
P
Paternal chromosomes, 49
PEP. See Phosphoenolpyruvate
Phosphodiester bonds, 3
Phosphoenolpyruvate (PEP), 38
Phospholipids, 11–12
Photophosphorylation, 35
Photosynthesis
C4 molecule, 38–39
crassulacean acid metabolism,
38–39
cyclic light-dependent reactions,
36
definition of, 34
light as source of energy,
34–35
light-dependent reactions,
35–36
light independent reactions,
37–38
Photosystems, 35
Phylogeny, 81–83
Plant cells, 27–28
Plasma membrane, 20
Plasmids, 21
Plasmodesmata, 28
Ploidy, maintenance of, 47–49
106  •  Index
Point mutations, 75–76
Polyadenylation, 68
Polysaccharides, 15
Post translational modification
(PTM), 74–75
Postzygotic isolation, 82
Prezygotic isolation, 82
Prokaryotic cells
archaea, 18–19
bacteria, 19–20
definition of, 18
structures in archaea and
bacteria, 20–21
Prokaryotic organisms, 63
Prokaryotic transcription
elongation, 64
initiation, 63–64
termination, 64
Prometaphase, 52
Prophase, 51–52
Prophase I, 55–57
Protein
diversity of, 8–9
folding, 6–8
PTM. See Post translational
modification
Pyruvate oxidation, 41–42
R initiation, 73–74
Reaction centers, 35
Recombinant DNA technology,
76–78
Reproductive isolation, 81–82
Restriction enzymes, 76
Ribonucleic acid (RNA), 3–4
polymerases, 4, 63
processing, 68–70
Ribosomes, 21
Rough endoplasmic reticulum, 24
S
Septate hyphae, 28–29
Silent mutations, 76
Sister chromatid, 49
Smooth endoplasmic reticulum,
25
S (synthesis) phase, 49
Spitzenkörper, 28
Spliceosome, 69
Splicing, 69
Substrate level phosphorylation,
41
Synapomorphies, 83
Synaptonemal complex, 56
T
Telophase, 53
Telophase I, 58
Termination
eukaryotic transcription, 67–68
prokaryotic transcription, 64
translation at ribosome, 74
Transcription, 62
eukaryotic, 65–68
prokaryotic, 63–64
Transfer RNA (tRNA), 70–73
Translation at ribosome
elongation, 74
post translational modifications,
74–75
termination, 74
Tricarboxylic acid (TCA) cycle,
42–43
Triglycerides, 11
tRNA. See Transfer RNA
Z
Z-scheme, 36