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BIO1207 – Cell Biology

Lecture 01
Prokaryotic Cells

Cells, Model Organisms, ! Separated from the eukaryotes due to structural integrity
! Taxonomic groups:
and Viruses • Archaea and Bacteria
J. Iwasa, W. Marshall. (2016). Karp’s Cell and Molecular Biology:
Concepts and Experiments – 8th ed. John Wiley and Sons, Inc. Danvers, ! Figure 1.14a
MA. • Salmonella sp. with surrounding flagella. Inset shows
TEM of single flagellum containing the protein flagellin

Bismark Oliver C. Lemana, M.Sc.

Biology Department, Institute of Arts and Sciences
Far Eastern University, Manila

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Domain Archaea

! More closely related group to Domain Eukarya

! “extremophiles”
• Methanogens, thermophiles (incl. hyperthermophiles), halophiles,
acidophiles
! They may thrive on “normal” environmental conditions

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Domain Bacteria

! The rest of the prokaryotic cells

! Includes the smallest cells recorded
• Mycoplasma (0.2um in diameter)
• Lacks cell wall and with only 500 genes
! Includes the cyanobacteria (formerly blue-green algae)
• Photosynthetic bacteria
! Includes nitrogen fixing bacteria
! Includes important pathogenic bacteria
! Ubiquitous

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Domain Eukarya Cell Differentiation in Eukaryotes

! Includes complex cells from unicellular protists

to fungi, plants, and animals
! Distinct due to the following features:
• Membrane-bound organelles
• Double-membraned nucleus
• Reproduction through
• Mitosis – somatic cells/asexual
• Meiosis – gametes/sexual

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Model Organisms Model Organisms

! Escherichia coli ! Saccharomyces cerevisiae
! Model organism for bacteria ! Baker’s/brewer’s yeast
! Used in the study of the Central ! Model organism for eukaryotic
Dogma cell function
! Can be grown in a haploid state
! Ideal for the identification of
genes through mutants

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Model Organisms Model Organisms

! Arabidopsis thaliana ! Caenorhabditis elegans
! Thale cress ! Nematode with roughly 1000
! Plant model organisms cells
! Unusually small genome (~120m ! Precise cell division patterns
bp) ! Easily cultured, transparent
! Rapid generation time body, and can be kept alive
frozen
! Large seed production
! Compact size

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Model Organisms Model Organisms

! Drosophila melanogaster ! Mus musculus
! fruit fly ! House mouse
! Highly used in genetic studies ! Animal model organism
! Used in gene expression studies ! Easily kept and bred in labs
due to rapid reproduction rates ! Several genetic modifications
with strains for different
applications

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Viruses Viruses
! 19th century ! 1935
• Louis Pasteur • Wendell Stanley
• Infections of plants and animals were due to bacteria • Crystallization of the TMV
• Tobacco Mosaic Disease • Crystallized TMV show high levels of order and structure yet simpler than a cell
• Transmitted from one plant to another through sap, but no bacteria detected • TMV was a mistaken for a protein
• Dmitri Ivanovsky
• Filtered the sap of an infected plant to transmit infection
• Concluded that pathogens smaller than bacteria exist

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Viruses and its pathogenicity Viral Structure

! Human infections ! Viruses bear no resemblance to cells and lack any of the protein-
• HIV, polio, influenza, Ebola, measles, HPV, etc. synthesizing machinery found in cells
• Occurs in different forms
! Viral structure is composed of regular, repeating subunits that give
• Viruses are obligate intracellular parasites rise to their crystalline appearance
• Reproduction dependent on host cell infection
! Virion ! The structure contains only those parts needed to invade and control
a host cell:
• A virus outside the host cell
• Contains genetic material • External coating
• Inanimate and cannot function on its own without a host • Core containing one or more nucleic acid strains of DNA or RNA
• Sometimes one or two enzymes

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Viral Structure Viral Structure

! Capsid: protein shell that surrounds the nucleic acid:
• Nucleocapsid: the capsid together with the nucleic acid
• Naked viruses consist only of a nucleocapsid.
! Envelope: external covering of a capsid, usually a modified piece of
the host’s cell membrane
! Spikes can be found on naked or enveloped viruses:
• Project from the nucleocapsid or the envelope
• Allow viruses to dock with host cells

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Viral Structure
! DNA viruses: Single-stranded (ss) or double-stranded (ds; linear or
circular)
! RNA viruses: can be double-stranded, but more often single-stranded:
• Positive-sense RNA: ready for immediate translation
• Negative-sense RNA: must be converted before translation can occur
• Segmented: individual genes exist on separate pieces of RNA
• Retroviruses: carry their own enzymes to create DNA out of their RNA

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Double-stranded DNA Variola virus Smallpox

Viral Penetration
Herpes simplex II Genital herpes

Single-stranded DNA Parvovirus Erythema infectiosum

(skin condition)

RNA Viruses–Examples

Single-stranded (+) sense Poliovirus Poliomyelitis

Single-stranded (−) sense Influenza virus Influenza

Double-stranded RNA Rotavirus Gastroenteritis

Single-stranded RNA + reverse HIV AIDS

transcriptase

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Viral Specificity Oncoviruses

! Infection depends on viral capsid
structure, relative to the host
• E.g., HIV particle (gp120) targets the
specific proteins (CD4) in T-
Lymphocytes
! Experts estimate that 13% of cancers are caused by viruses
! Transformation: the effect of oncogenic, or cancer-causing viruses:
• Some viruses carry genes that directly cause cancer
• Other viruses produce proteins that induce a loss of growth regulation,
leading to cancer
! Oncoviruses: mammalian viruses capable of initiating tumors:
• Papillomaviruses
• Herpesviruses
• Hepatitis B virus

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Oncoviruses Viroids
! Virus-like agents that parasitize plants
! About one-tenth the size of an average virus
! Composed of naked strands of RNA, lacking a capsid or any other
type of coating
! Significant pathogens in economically important plants: tomatoes,
potatoes, cucumbers, citrus trees, chrysanthemums
! Discovered by T.O. Diener (1971)

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Cadang-Cadang Viroid

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Outline
Because learning changes everything. ®

3.1 Organic Molecules

Biology 3.2 Carbohydrates
Sylvia S. Mader
Michael Windelspecht 3.3 Lipids
Chapter 3 3.4 Proteins
The Chemistry of
Organic Molecules 3.5 Nucleic Acids
Lecture Outline
See separate FlexArt PowerPoint slides for
all figures and tables pre-inserted into
PowerPoint without notes.

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3.1 Organic Molecules Functional Groups 1

Table 3.1 Functional Groups

Organic molecules contain both carbon and
Group Structure Compound Significance
hydrogen atoms.
Hydroxyl Alcohol as in Polar, forms
Four classes of organic molecules ethanol hydrogen bond
Present in sugars,
(biomolecules) exist in living organisms: some amino acids
Carbonyl Aldehyde as in Polar
• Carbohydrates. formaldehyde
Present in sugars
• Lipids.
Ketone as in Polar
• Proteins. acetone
Present in sugars
• Nucleic acids. Carboxyl Carboxylic acid Polar, acidic
(acidic) as in acetic acid
Functions of the four biomolecules in the cell are Present in fatty
diverse. acids, amino acids

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Functional Groups 2 Carbon and Life

Table 3.1 Functional Groups
Group Structure Compound Significance
Amino Amine as in Polar, basic, forms
tryptophan hydrogen bonds
Present in amino
acids
Sulfhydryl Thiol as in Forms disulfide
ethanethiol bonds
Present in some
amino acids
Phosphate Organic Polar, acidic
Phosphate as in
phosphorylated
molecules
Present in
nucleotides, Figure 3.1
phospholipids
R = remainder of molecule
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The Carbon Atom The Carbon Skeleton and

The carbon atom is small, with only six electrons:
two in the first shell and four in the outer shell.
Carbon can form four covalent bonds.
• Bonds with carbon, nitrogen, hydrogen, oxygen,
phosphorus, and sulfur.
• The C—C bond is very stable.
• Long carbon chains, hydrocarbons, can be formed.
• Besides single bonds, double bonds, triple bonds,
and ring structures are also possible.
• Branches may also form at any carbon atom, making
complex carbon chains.
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Functional Groups
The carbon chain of an organic molecule is
called its skeleton, or backbone.
Functional groups are clusters of specific
atoms bonded to the carbon skeleton with
characteristic structures and functions.
• Functional groups determine the chemical
reactivity and polarity of organic molecules.
• Example: Replacement of an H by -OH in the
2-carbon hydrocarbon ethane turns it into
ethanol, and from hydrophobic to hydrophilic.
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Isomers The Biomolecules of Cells

Isomers are organic molecules that have Carbohydrates, lipids, proteins, and nucleic acids
are called biomolecules.
identical molecular formulas but different
arrangements of atoms. Usually consist of many repeating units.
• Each repeating unit is called a monomer.
• A molecule composed of monomers is called a
polymer (many parts).
• Example: amino acids (monomer) are joined
together to form a protein (polymer).
Figure 3.2 • Lipids are not polymers because they contain
two different types of subunits.

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Biomolecules Synthesis and Degradation

Table 3.2 Biomolecules A dehydration reaction is a chemical reaction in

which subunits are joined together by the formation
Category Subunits (monomers) Polymer of a covalent bond and water is produced during the
Carbohydrates* Monosaccharide Polysaccharide reaction.
Lipids Glycerol and fatty acids Does not form
polymers • Used to connect monomers together to make polymers.
Proteins* Amino acids Polypeptide
• Example: formation of starch (polymer) from glucose
Nucleic acids* Nucleotide DNA, RNA subunits (monomer).
*form polymers
A hydrolysis reaction is a chemical reaction in
which a water molecule is added to break a covalent
bond.
• Used to break down polymers into monomers.
• Example: digestion of starch into glucose monomers.
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Synthesis and Degradation of Synthesis and Degradation of

Biomolecules 1 Biomolecules 2

Figure 3.3

Figure 3.3

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Synthesis and Degradation of Synthesis and Degradation of

Biomolecules 3 Biomolecules 4

Figure 3.3

a.Synthesis of a biomolecule
Figure 3.3

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Synthesis and Degradation of Synthesis and Degradation of

Biomolecules 5
Biomolecules 6

a. Synthesis of a biomolecule

Figure 3.3

b.Degradation of a biomolecule

Figure 3.3
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Synthesis and Degradation of Synthesis and Degradation of

Biomolecules 7
Biomolecules 8

a. Synthesis of a biomolecule

b.Degradation of a biomolecule b. Degradation of a biomolecule

Figure 3.3 Figure 3.3
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3.2 Carbohydrates Carbohydrates as Structural

Materials
Functions:
b. Shell contains chitin.

• Energy source.

• Provide building material (structural role).

Contain carbon, hydrogen, and oxygen

atoms in a 1:2:1 ratio
Varieties: monosaccharides,
disaccharides, and polysaccharides a. Cell walls contain cellulose. c. Cell walls contain peptidoglycan.

Figure 3.4

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Monosaccharides Glucose
A monosaccharide is a single sugar molecule.
It is also called a simple sugar.
It has a backbone of 3 to 7 carbon atoms.
Examples:
Glucose (blood sugar), fructose (fruit sugar), and
galactose.
• Hexoses – six carbon atoms.
Figure 3.5
Ribose and deoxyribose (sugars contained in
nucleotides, the monomer of DNA).
• Pentoses – five carbon atoms. Access the text alternative for slide images.

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Disaccharides Synthesis and Degradation of Maltose 1

A disaccharide contains two
monosaccharides joined together during a
dehydration reaction.
Examples:
• Lactose (milk sugar) is composed of galactose
and glucose.
• Sucrose (table sugar) is composed of glucose
and fructose.
• Maltose is composed of two glucose molecules. Figure 3.6

• Lactose-intolerant individuals lack the enzyme

lactase which breaks down lactose into galactose Access the text alternative for slide images.
and glucose.
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Synthesis and Degradation of Maltose 2 Synthesis and Degradation of Maltose 3

Figure 3.6

Figure 3.6

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Synthesis and Degradation of Maltose 4 Synthesis and Degradation of Maltose 5

Figure 3.6

Figure 3.6

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Synthesis and Degradation of Maltose 6 Synthesis and Degradation of Maltose 7

Figure 3.6

Figure 3.6

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Synthesis and Degradation of Maltose 8 Polysaccharides: Energy-Storage

and Structural Molecules
A polysaccharide is a polymer of
monosaccharides.
Examples:
Starch provides energy storage in plants.
Glycogen provides energy storage in animals.
Cellulose is found in the cell walls of plants.
• Most abundant organic molecule on Earth.
• Animals are unable to digest cellulose.
Figure 3.6
Chitin is found in the cell walls of fungi and in the
exoskeleton of some animals.
Peptidoglycan is found in the cell walls of bacteria.
Access the text alternative for slide images.
• Monomers contain an amino acid chain.
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Starch and Glycogen Structure and Cellulose Fibrils

Function

Figure 3.7 Figure 3.8

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3.3 Lipids Types of Lipids

Varied in structure Table 3.3 Lipids

Type Functions Human Uses
Large, nonpolar molecules that are insoluble in
Fats Long-term energy storage and Butter, lard
water insulation in animals
Oils Long-term energy storage Cooking oils
Functions: in plants and their seeds
• Long-term energy storage. Phospholipids Component of plasma membrane Food additive
Steroids Component of plasma membrane Medicines
• Structural components. (cholesterol),
• Heat retention. sex hormones
Waxes Protection, prevention of water Candles, polishes
• Cell communication and regulation. loss (cuticle of plant surfaces),
beeswax, earwax
• Protection.
Varieties: fats, oils, phospholipids, steroids, waxes

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Triglycerides: Long-Term Energy Triglycerides: Long-Term Energy

Storage 1 Storage 2

Also called fats and oils Fatty acids may be either unsaturated or saturated.
Unsaturated – one or more double bonds between
Functions: long-term energy storage and carbons.
insulation • Tend to be liquid at room temperature.
• Example: plant oils.
Consist of one glycerol molecule linked to • Can have chemical groups on the same (cis) or opposite (trans) side of the
double bond.
three fatty acids by dehydration synthesis
Saturated – no double bonds between carbons.
• Tend to be solid at room temperature.
• Examples: butter, lard.

Trans – a triglyceride with at least one bond in a trans

configuration.
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Saturated and Unsaturated Fatty Synthesis and Degradation of a

Acids Triglyceride 1

Figure 3.9

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Figure 3.10
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Synthesis and Degradation of a Synthesis and Degradation of a

Triglyceride 2 Triglyceride 3

Figure 3.10
Figure 3.10
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Synthesis and Degradation of a Phospholipids: Membrane Components

Triglyceride 4

The structure is similar to triglycerides.

It consists of one glycerol molecule linked to two fatty
acids and a modified phosphate group.
• The fatty acids (tails) are nonpolar and hydrophobic.
• The modified phosphate group (head) is polar and hydrophilic.
Function: form plasma membranes of cells.
In water, phospholipids aggregate to form a
phospholipid bilayer (double layer).
Polar phosphate heads are oriented towards the water.
Figure 3.10
Nonpolar fatty acid tails are oriented away from water.
• Nonpolar fatty acid tails form a hydrophobic core.
Access the text alternative for slide images. • Kinks in the tails keep the plasma membrane fluid across a
range of temperatures.
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Phospholipids Form Membranes Steroids: Four Fused Carbon Rings

They are composed of four fused carbon rings.
• Various functional groups attached to the carbon skeleton
Functions: component of animal cell membrane,
regulation
Examples: cholesterol, testosterone, estrogen
• Testosterone and estrogen are sex hormones differing
only in the functional groups attached to the same carbon
skeleton.
Cholesterol is the precursor molecule for several
other steroids.
Cholesterol can also contribute to cardiovascular
Figure 3.11
disorders.
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Steroid Diversity Waxes

Long-chain fatty acids connected to carbon

chains containing alcohol functional groups
Solid at room temperature
Waterproof
Resistant to degradation
Function: protection
Examples: earwax (contains cerumen), plant
Figure 3.12
Access the text alternative for slide images. cuticle, beeswax
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Types of Waxes 3.4 Proteins

Proteins are polymers of amino acids linked together
by peptide bonds.
• A peptide bond is a covalent bond between amino acids.
• As much as 50% of the dry weight of most cells consists of
proteins.
• Several hundred thousand have been identified.
Two or more amino acids joined together are called
peptides.
• Long chains of amino acids joined together are called
polypeptides.
Figure 3.13
A protein is a polypeptide that has folded into a
particular shape, which is essential for its proper
functioning.
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Functions of Proteins Enzymes

Metabolism
• Most enzymes are proteins that act as catalysts to accelerate chemical
Special proteins called enzymes are
reactions within cells.
required for cells to carry out dehydration
Support
synthesis and hydrolysis reactions.
• Some proteins have a structural function, for example, keratin and
collagen.
An enzyme is a molecule that speeds up a
Transport
chemical reaction.
• Membrane channel and carrier proteins regulate what substances enter and
exit cells. Hemoglobin protein transports oxygen to tissues and cells.
Defense
• Enzymes are not consumed in the reaction.
• Antibodies are proteins of our immune system that bind to antigens and
prevent them from destroying cells. • Enzymes are not changed by the reaction.
Regulation
• Enzymes are catalysts.
• Hormones are regulatory proteins that influence the metabolism of cells.
Motion
• Microtubules move cell components to different locations. Actin and myosin
contractile proteins allow muscles to contract.
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Amino Acids: Protein Monomers Types of Amino Acids

There are 20 different common amino acids.
Amino acids differ by their R, or variable groups,
which range in complexity.

Figure 3.14
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Synthesis and Degradation of a Peptide 1 Synthesis and Degradation of a Peptide 2

Figure 3.15

Figure 3.15

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Synthesis and Degradation of a Peptide 3 Synthesis and Degradation of a Peptide 4

Figure 3.15 Figure 3.15

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Shape of Proteins and Levels of Four Structures of Proteins

Protein Structure Primary structure
• Primary structure is the linear sequence of amino acids.
Proteins cannot function properly unless they fold • Hundreds of thousands of different polypeptides can be built
into their proper shape. from just 20 amino acids.
When a protein loses it proper shape, it said to be • Changing the sequence of amino acids can produce different
denatured. proteins.
• Exposure of proteins to certain chemicals, a change in pH, or high
Secondary structure
temperature can disrupt protein structure. • Secondary structure is characterized by the presence of
alpha helices and beta (pleated) sheets held in place with
Proteins can have up to four levels of structure: hydrogen bonds.
• Primary Tertiary structure
• Secondary • Tertiary structure is the overall three-dimensional shape of a
polypeptide.
• Tertiary • It is stabilized by the presence of hydrophobic interactions,
• Quaternary hydrogen, ionic, and covalent bonding.
Quaternary structure
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• Quaternary structure consists of more than one polypeptide.
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Levels of Protein Organization Examples of Fibrous Proteins

Primary structure
This level of structure is
determined by the linear
sequence of amino acids,
coded for in the genes of
the DNA.

Secondary Structure
Hydrogen bonding
between amino acids
causes the polypeptide
to form an alpha helix
or a pleated sheet.

Tertiary Structure
Interactions of amino acid side
chains with water, covalent
bonding between R groups,
and other chemical
interactions determine the
folded three-dimensional
shape of a protein.

Quaternary Structure
Figure 3.17
This level of structure occurs
when two or more folded
polypeptides interact to
perform a biological function.

Figure 3.16
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The Importance of Protein Folding 3.5 Nucleic Acids

and Protein-Folding Diseases
Chaperone proteins help proteins fold into their Nucleic acids are polymers of nucleotides.
normal shapes and may also correct misfolding of
new proteins. Two varieties of nucleic acids:
• Defects in chaperone proteins may play a role in several DNA (deoxyribonucleic acid)
human diseases, such as Alzheimer disease and cystic
fibrosis. • Genetic material that stores information for its own replication
Prions are misfolded proteins that have been and for the sequence of amino acids in proteins.
implicated in a group of fatal brain diseases known
as TSEs. RNA (ribonucleic acid)

• Mad cow disease is one example of a TSE. • Performs a wide range of functions within cells which include
protein synthesis and regulation of gene expression.
• Prions are believed to cause other proteins to fold the
wrong way.
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Structure of a Nucleotide Nucleotides 1

Each nucleotide is composed of three parts:

• A phosphate
• A pentose sugar
• A nitrogen-containing (nitrogenous) base
There are five types of nucleotides found in nucleic
acids.
• DNA contains adenine, guanine, cytosine, and thymine.
• RNA contains adenine, guanine, cytosine, and uracil.
Nucleotides are joined together by a series of a. Nucleotide structure
dehydration synthesis reactions to form a linear Figure 3.18

molecule called a strand, which is a sequence of

nucleotides.
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Nucleotides 2 Nucleotides 3

a. Nucleotide structure b. Deoxyribose versus ribose c. Pyrimidines versus purines

Figure 3.18
Figure 3.18

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Nucleotides 4 Structure of DNA and RNA

The backbone of the nucleic acid strand is composed of
alternating sugar-phosphate molecules.
RNA is predominately a single-stranded molecule, whereas
DNA is a double-stranded molecule.
DNA is composed of two strands held together by hydrogen
bonds between the nitrogen-containing bases. The two strands
twist around each other, forming a double helix.
The nucleotides may be in any order within a strand but between
strands:
• Adenine (purine) makes hydrogen bonds with thymine (pyrimidine).
• Cytosine (pyrimidine) makes hydrogen bonds with guanine (purine).

The bonding between the nitrogen-containing bases in DNA is

referred to as complementary base pairing.
Figure 3.18
• The number of A + G (purines) always equals the number of T + C
(pyrimidines).
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Comparing DNA and RNA RNA Structure

Structure
Table 3.4 Comparing DNA and RNA Structure
DNA RNA
Sugar Deoxyribose Ribose
Bases Adenine, guanine, Adenine, guanine, uracil,
thymine, cytosine cytosine
Strands Double-stranded with Usually single-stranded
base pairing
Helix Yes No

Figure 3.19

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DNA Structure ATP (Adenosine Triphosphate)

ATP is a nucleotide composed of adenine and ribose
(adenosine) and three phosphates.
ATP is a high-energy molecule due to the presence of the
last two unstable phosphate bonds, which are easily
broken.
Hydrolysis of the terminal phosphate bond yields:
The molecule ADP (adenosine diphosphate).
An inorganic phosphate, P.
Energy to do cellular work.
• The hydrolysis of the ATP molecule can be coupled with chemically
unfavorable reactions in the cell to allow the reactions to proceed.
• Example: key steps in the synthesis of carbohydrates and proteins, and
muscle contraction and nerve impulse conduction.
Figure 3.20
ATP is therefore called the energy currency of the cell.
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ATP

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Figure 3.21 www.mheducation.com

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