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Zombie Parasites

• The study of life reveals fascinating
characteristics of living species

• Biology also leads to the development of
medicines and research tools that benefit the
lives of people

• Example: Neuroparasitology – the study of
how parasites control the nervous systems of
their hosts.

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distribution without the prior written consent of McGraw-Hill Education.

Examples of Zombie Parasites

Table 1.1 Examples of Zombie Parasites

Host Parasite Description

House cricket
(Acheta domesticus)

Horsehair worm
(Paragordius
varius)

A horsehair worm larva infects a cricket and grows inside it. The cricket is terrestrial, but the adult
stage of the horsehair worm is aquatic. When the larva matures into an adult, it alters the
behavior of the cricket, causing it to jump into the nearest body of water! As the cricket drowns,
an adult horsehair worm emerges.

Spider (Plesiometa
argyra)

Wasp
(Hymenoepimecis
argyraphaga)

A female wasp glues an egg onto a spider’s body. After the egg develops into a larva, the larva
pokes a few holes in the spider’s abdomen, which allows it to suck the spider’s blood and also to
transfer chemicals into the spider, which control its behavior. The spider stops building its normal
orb-shaped web and starts building a web whose geometry is strikingly different: The new web is
designed to suspend the larva’s cocoon in the air, where it will be protected from predators.

Various vertebrates,
including mice and
rats

Protozoan
(Toxoplasma
gondii)

Toxoplasma gondii is a parasite whose life cycle involves more than one vertebrate host. The
definitive host is the cat, which is where T. gondii becomes mature and reproduces sexually. An
intermediate host can be any of a variety of vertebrates, including mice and rats, which can ingest
the parasite from cat feces. In the intermediate host, the parasite develops and reproduces
asexually. To escape an intermediate host, such as a mouse or rat, and move to the definitive
host, T. gondii dramatically alters the host’s behavior. The infected animal becomes attracted to
the smell of cat urine! This makes it more likely to be eaten by a cat and thereby allows T. gondii
to enter its definitive host and mature.

Chapter 1

An Introduction to Biology

Key Concepts:

• Levels of Biology

• Core Concepts of Biology

• Biological Evolution

• Classification of Living Things

• Biology as a Scientific Discipline

• Core Skills of Biology

Levels of
Biological Organization

• Atoms

• Molecules

• Cells

• Tissues

• Organs

• Organism

• Population

• Community

• Ecosystem

• Biosphere

Figure 1.3: Levels of Biological Organization

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Core Concepts of Biology

• Evolution

• Structure and function

• Information flow, exchange, and storage

• Pathways and transformations of energy
and matter

• Systems

Biological Evolution
Unity

• All life displays a common set of
characteristics

• United by a shared evolutionary history

Diversity

• Life has a diversity of form in diverse
environments

Evolutionary History 1

• Life began on Earth as primitive cells between
3.5 to 4 billion years ago (bya)

• Those primitive cells underwent evolutionary
changes to give rise to the species of today

• Evolutionary history helps us understand
the structure and function of an organism

Evolutionary History 2

• Evolutionary change involves modifications
of pre-existing characteristics

• Structures may be modified to serve new
purposes

•

Example:

Walking limbs were modified into a dolphin’s
flipper or a bat’s wing

Figure 1.5: Modification as a Result of Evolution

Two mechanisms of evolutionary
change 1

Vertical descent with mutation

• Progression of changes in a lineage

• New species evolve from pre-existing species by
the accumulation of mutations

• Natural selection takes advantage of beneficial
mutations

Figure 1.6: Vertical Evolution Example

Two mechanisms of evolutionary
change 2

Horizontal gene transfer

• Genetic exchange between different species

• Relatively rare

• Genes that confer antibiotic resistance are
sometimes transferred between different
bacteria species

Figure 1.7: Horizontal Gene Transfer

Bacterial species such as
Escherichia coli

Bacterial species such as
Streptococcus pneumoniae

Tree or web of life?

• Horizontal gene transfer was an important part
of the process that gave rise to modern species

• Tree of life focuses on vertical evolution

• Web of life includes the contribution of
horizontal gene transfer

Figure 1.8: The Web of Life

Genomes and Proteomes 1

Genome

The complete genetic makeup of an organism

Genomics

• Techniques used to analyze DNA sequences
• Comparison of genomes of different species

Proteome

The complete complement of proteins of an organism

Proteomics

• Techniques used to analyze the proteins of a species
• Comparison of proteomes of different species

Genomes and Proteomes 2

The genome carries the information
to make the proteome.

Genomic and proteome analysis
illuminate the evolutionary history
and relatedness of all living organisms.

Classification of Living Things

Taxonomy is the grouping of species based on
common ancestry

Three domains of life

• Bacteria- unicellular prokaryote

• Archaea- unicellular prokaryote

• Eukarya- unicellular and multicellular eukaryotes

• Complex cells with a nucleus

• Four kingdoms:
• Protista, Plantae, Fungi, and Animalia

Domain Bacteria: Mostly unicellular prokaryotes that
inhabit many diverse environments on Earth.

a) Domain Bacteria: Mostly unicellular prokaryotes that inhabit
many diverse environments on Earth.

©BSIP/age fotostock

Domain Archaea: Unicellular prokaryotes that often live
in extreme environments, such as hot springs.

b) Domain Archaea: Unicellular prokaryotes that often live in extreme
environments, such as hot springs.

©Eye of Science/Science Source

Domain Eukarya: Unicellular and multicellular organisms having
cells with internal compartments that serve various functions.

c) Domain Eukarya: Unicellular and multicellular organisms having cells with internal compartments that serve various functions.

Protists: Unicellular and small multicellular organisms
that are now subdivided into seven broad groups based
on their evolutionary relationships.

Plants: Multicellular organisms that can carry out
photosynthesis.

Fungi: Unicellular and multicellular organisms that have a cell
wall but cannot carry out photosynthesis. Fungi usually survive
on decaying organic material.

Animals: Multicellular organisms that usually have a nervous
system and are capable of locomotion. They must eat other
organisms or the products of other organisms to live.

(protists): ©Jan Hinsch/Getty lmages;(plants): ©Kent Foster/Science Source; (fungi): ©Carl Schmidt-Luchs/Science Source; c(animals): ©Ingram Publishing/age fotostock

How Organisms are Classified

A species is placed into progressively
smaller groups that are more closely related

Emphasizes the unity and diversity of
different species

Example:

• Clownfish (Amphiprion ocellaris)

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Figure 1.11: Taxonomic classification of the
ocellaris clownfish

Taxonomic
group

The ocellaris
clownfish is
found in

Approximate time
when the common
ancestor for this
group arose

Approximate
number of
modern species
in this group

Examples

Domain Eukarya 2,000 million
years ago

> 5,000,000

Supergroup Opisthokonta 2,000 million
years ago

> 1,000,000

Kingdom Animalia 600 million
years ago

> 1,000,000

Phylum Chordata 525 million
years ago

50,000

Class Actinopterygii 420 million
years ago

30,000

Order Perciformes 80 million
years ago

7,000

Family Pomacentridae Approximately 40
million years ago

360

Genus Amphiprion Approximately
9 million years ago

Species ocellaris
< 3 million years ago

Classification

Binomial nomenclature

• Each species has a unique scientific name

• Genus name capitalized

• Species descriptor is not capitalized

• Both names are italicized

Amphiprion ocellaris = Ocellaris clownfish

Biology as a Scientific Discipline

Science is the observation, identification,
experimental investigation, and theoretical
explanation of natural phenomena

The Scientific Method is used to test theories

Some scientists also gather information

• “Fact-finding mission”

Biologists investigate life at different levels

Different branches of biology study life at
different levels using a variety of tools.

• Ecology, anatomy, physiology, cell biology,
molecular biology, etc.

As new tools become available, they allow
scientists to ask new questions

Systems biology aims to understand how
emergent properties arise, at any level

Figure 1.13 a and b: Biological Investigation
at Different Levels

a) Ecology—population/
community/ecosystem
levels

b) Anatomy and physiology—
tissue/organ/organism levels

a: ©Diane Nelson; b: ©Purestock/SuperStock;

Figure 1.14 c and d: Biological Investigation
at the Cell and Molecular Levels

c) Cell biology—cellular levels d) Molecular biology—
atomic/molecular levels

c: ©Erik Isakson/Blend Images; d: ©Northwestern, Shu-Ling Z hou/AP Images

Figure 1.13 e: Biological Investigation at the
Systems Level

e) Systems biology—all levels, shown here at the molecular level

Systems biologists may study
groups of molecules. The
microarray shown in the inset
determines the expression of
many genes simultaneously.

©Andrew Brookes/Corbis/Getty Images; (inset): ©Alfred Pasieka/Science Source

Hypothesis or Theory? 1

Hypothesis

• A proposed explanation for a natural phenomenon

• Based on previous observations or experiments

• Hypotheses must make predictions that can be shown
to be correct or incorrect (must be testable)

• Additional observations or experiments can
support or reject a hypothesis, but a hypothesis is
never really proven

Example:

• “Maple trees drop their leaves in autumn because of
shortened hours of sunlight”

Hypothesis or Theory? 2
Theory

• Broad explanation of some aspect of the natural world that is
substantiated by a large body of evidence

• Allows us to make many predictions

• Also can never be proved true, but due to overwhelming
evidence, may be very likely to be true

Two key attributes of a theory:

• Consistent with a vast amount of known data

• Able to make many correct predictions

Example

• “DNA is the genetic material”

• Overwhelming body of evidence supports this theory

Understanding biology

Curiosity is the key

No rigid set of steps

Two general approaches

•

Discovery-based science

• Hypothesis testing

Discovery-based science

Collection and analysis of data without the
need for a preconceived hypothesis

Goal is to gather information

• Test drugs to look for action against disease

• Sequence genomes and proteomes

Often leads to hypothesis testing

Hypothesis Testing

Five stages

• Observations are made regarding natural
phenomena.

• These observations lead to a testable hypothesis
that tries to explain the phenomena.

• Experiments are conducted to determine if the
predictions are correct.

• The data are analyzed.

• The hypothesis is accepted or rejected.

These steps comprise the Scientific Method

Figure 1.14: Steps of the Scientific Method

1. OBSERVATIONS The leaves on maple trees fall in autumn when the days get colder and shorter.

2. HYPOTHESIS The shorter amount of daylight causes the leaves to fall.

3. EXPERIMENTATION
Small maple trees are grown in
2 greenhouses where the only
variable is the length of light.

Control group:
Amount of daily light remains
constant for 180 days.

Experimental group:
Amount of daily light becomes
progressively shorter for 180 days.

4. THE DATA

A statistical analysis
can determine if
the control and the
experimental data
are significantly
different. In this
case, they are.

5. CONCLUSION The hypothesis cannot be rejected.

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Common features
Data are often collected in parallel

• Control and experimental groups

• Differ by only a single variable

Data analysis

• Apply statistical analysis to determine if the control
and experimental groups are different because of
the single variable that is different

• Are differences statistically significant?
• If the two sets are found not to be significantly

different, we must reject our hypothesis.
• If the two sets of data are significantly different, we

accept our hypothesis (though it is not proven)

Example: Cystic Fibrosis 1

• Affects about 1 in every 3,500 Americans

• Persons with CF produce abnormally thick
and sticky mucus that obstructs the lungs
and pancreas

• Average lifespan for people with CF is currently
in their mid- to late 30s

Example: Cystic Fibrosis 2

• In 1945, Dorothy Anderson determined that
cystic fibrosis is a genetic disorder

• In 1989, research groups headed by Lap-Chi Tsui,
Francis Collins, and John Riordan identified
the CF gene

• Discovery-based science, not hypothesis-testing,
found the CF gene

Hypothesis for function of CF gene 1

Hypothesis: The CF gene encodes a protein that
transports chloride ions  Cl across the
membrane of cells

Led to experiments to test normal cells and
cells from CF patients for ability to transport Cl

• CF cells were found defective in chloride transport
• Transferring a normal CF gene into cells in the lab

corrects this defect

Chloride transport hypothesis is accepted

Figure 1.15: CFTR Gene and Hypothesis Testing

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Hypothesis for function of CF gene 2
• Results supported the hypothesis that the CF gene

encodes a protein that transports Cl
 across the plasma

membrane

• A mutation in this gene causes it to encode a defective

transporter protein, leading to a salt imbalance

• This imbalance affects water levels outside the cell,

which explains the thick and sticky mucus in CF patients

• In this example, hypothesis testing has provided a way

to accept or reject an idea regarding how a disease is

caused by a genetic change

Biology is a Social Discipline

• Within a lab, students, postdocs, technicians, and
the PI work together

• Different labs often collaborate

• At meetings, scientists discuss new data – and
debate!

• You can discuss science without having “all the
answers”

• Science is a never-ending series of questions

Figure 1.16: The Social Aspects of Science

©Dita Alangkara/AP Images

Core Skills of Biology

• Ability to apply the process of science

• Ability to use quantitative reasoning

• Ability to use models and simulation

• Ability to tap into the interdisciplinary
nature of science

• Ability to communicate and collaborate
with professionals in other disciplines

• Ability to understand the relationship
between science and society

Features of This Textbook
• Feature Investigations allow you to apply the

process of science.

• BioTIPS help you refine and apply your problem
solving skills.

• Quantitative reasoning is a key component of the
Feature Investigations and many questions.

• Modeling Challenges allow you to interpret a
given model or propose your own model based
on a scenario or data.

• “Connections” and “Science and Society”
highlight the interdisciplinary nature of science

Model-Based Learning

Scientific model

• is a conceptual, mathematical, or physical
depiction of a real-world phenomenon.

• In biology, models are testable ideas that are
usually derived from observations and
experiments.

Model-based learning allows students to
evaluate or generate models to enhance
understanding and improve critical thinking
skills.

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Chapter 2

Lecture Outline

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Chapter 2

The Chemical Basis of Life, I:
Atoms, Molecules, and Water

Key Concepts:

•

Atoms

•

Chemical Bonds and Molecules

•

Properties of Water

•

and Buffers

Atoms

• The smallest functional units of matter that
form all chemical substances

• Cannot be further broken down into other
substances by ordinary means

• Each specific type of atom is a chemical
element

Three subatomic particles

Protons

• positive charge (+)
• found in nucleus

Neutrons

• neutral
• found in nucleus

Electrons

• negative charge (−)
• found in orbitals

Protons and electrons are present in equal numbers,
giving the atom no net charge

The number of neutrons can vary

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Table 2.1

Table 2.1 Characteristics of Major
Subatomic Particles

Particle Location Charge
Mass relative
to electron

Proton Nucleus +1 1,836

Neutron Nucleus 0 1,839

Electron Around the
nucleus

−1 1

Electrons occupy orbitals

Scientists initially visualized an atom as a
miniature solar system

• This is an oversimplified but convenient image

Electrons travel within regions surrounding
the nucleus (orbitals) in which the probability
of finding that electron is high

Can be depicted as a cloud

Figure 2.1

Figure 2.2 panels 1 to 3

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Figure 2.2 panels 4 to 6

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Orbitals
• s orbitals are spherical

• p orbitals are propeller or dumbbell shaped

• Each orbital can hold only 2 electrons

Orbital
name 1s 2s 2p

Number of
electrons
per electron
shell

2 per orbital;
8 total

Orbital
shape

Spherical First orbital:
spherical

Second to
fourth orbital:
dumbbell-
shaped

Electron Shells

Atoms with more electrons have orbitals within
electron shells that are at greater and greater
distances from the center of the nucleus

1st shell

• 1 spherical orbital (1s) – holds one pair of electrons

2nd shell

• 1 spherical orbital (2s) – holds one pair of electrons

• 3 dumbbell-shaped orbitals (2p) – three pairs of
electrons

• Can hold four pairs of electrons = 8 electrons

Example: Nitrogen atom

7 protons and 7 electrons

2 electrons fill 1st shell

• 2 in the 1s orbital

5 electrons in 2nd shell

• 2 fill the 2s orbital
• 1 in each of the three 2p orbitals

Note: the outer 2nd shell is not full

Electrons in the outer shell available to combine with other
atoms are called valence electrons

Figure 2.4 a

a) Simplified depiction of a nitrogen atom

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Figure 2.4 b

b) Nitrogen atom showing electrons in orbitals

Protons

Number of protons is what distinguishes
one element from another

Atomic number

• Equals number of protons

• Also equal to the number of electrons in the
atom so that the net charge is zero

Periodic table

• Organized by atomic number

• Rows correspond to number of electron shells

• Columns, from left to right, indicate the numbers
of electrons in the outer shell (the number of
valence electrons)

• Similar properties of elements within a column
occur because they have the same number of
electrons in their outer shells, and therefore they
have similar chemical bonding properties

Figure 2.5

Atomic mass

Protons and neutrons are nearly equal in mass, and
both are more than 1,800 times the mass of an
electron

Atomic mass scale indicates an atom’s mass relative to
the mass of other atoms

Most common form of carbon has six protons and six
neutrons, is assigned an atomic mass of exactly 12

• Hydrogen atom (atomic mass of 1) has 1/12 the
mass of a carbon atom

• Magnesium atom (atomic mass of 24) has twice the mass
of a carbon atom

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distribution without the prior written consent of McGraw-Hill Education.

Atomic mass in relation to mass of an
electron

Table 2.1 Characteristics of Major
Subatomic Particles
Particle Location Charge
Mass relative
to electron
Proton Nucleus +1 1,836
Neutron Nucleus 0 1,839
Electron Around the
nucleus
−1 1

Mass versus weight

Weight is derived from the gravitational pull
on a given mass

A man weighs 154 pounds on Earth

• On the moon he weighs about 25 pounds

• On a neutron star’s surface he would weigh 21
trillion pounds

His mass is the same in all locations

Units

Dalton

• Unit of measurement for atomic mass

• Also known as atomic mass unit (amu)

• One Dalton (Da) equals 1/12 the mass of a carbon
atom

• Carbon has an atomic mass of 12 Daltons

Mole

• 1 mole of any element contains the same number of
atoms— 236.022 10

• Avogadro’s number

Isotopes

• Multiple forms of an element that
differ in the number of neutrons

• 12 C contains 6 protons and 6 neutrons

•
14

C contains 6 protons and 8 neutrons

• Atomic masses are averages of the weights of
different isotopes of an element

Figure 2.6

©Steven Needell/Science Source

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Hydrogen, oxygen, carbon, & nitrogen

Make up about 95% of the atoms in living
organisms

• Hydrogen and oxygen occur primarily in water

• Nitrogen is found in proteins

• Carbon is the building block of all living matter

Mineral elements – less than 1%

Trace elements – less than 0.01%

• Yet they are essential for normal growth and function

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distribution without the prior written consent of McGraw-Hill Education.

Table 2.2

Table 2.2 Chemical Elements Essential for Life
in Many Organisms*

Most abundant in living organisms (approximately 95% of total mass)

Element Symbol
% Human
body mass

% All atoms in
human body

Oxygen O 65 25.5

Carbon C 18 9.5

Hydrogen H 9 63.0

Nitrogen N 3 1.4

Mineral elements
(less than 1% of
total mass)

Calcium Ca Potassium K

Chlorine Cl Sodium Na

Magnesium Mg Sulfur S

Phosphorus P

Trace elements
(less than 0.01% of
total mass)

Boron B Manganese Mn

Chromium Cr Molybdenum Mo

Cobalt Co Selenium Se

Copper Cu Silicon Si

Fluorine F Tin Sn

Iodine I Vanadium V

Iron Fe Zinc Zn

*Although these are the most common elements in living organisms, many other trace and mineral
elements have reported functions. For example, aluminum is believed to be a cofactor for certain
chemical reactions in animals, but it is generally toxic to plants.

Chemical Bonds and Molecules

Molecule
• Two or more atoms bonded together

Molecular formula

• Contains chemical symbols of the elements in the
molecule (C6H12O6)

• Subscript indicates how many of each atom are
present (H2O has two hydrogens, 1 oxygen)

Compound

• Any molecule composed of two or more elements
• N2 and O2 are examples of molecules that are not

compounds

Three types of bonds

Covalent Bond

• Electrons are shared to fill valence shells
• Can be polar covalent or nonpolar covalent

Hydrogen Bond

• Hydrogen atom from one polar molecule is attracted
to an electronegative atom from another molecule

Ionic Bond

• Electrons are transferred, forming ions that are
attracted to each other

Covalent bonds

Atoms share a pair of electrons

Occurs between atoms with unfilled valence
electron shells

Covalent bonds are strong chemical bonds,
because the shared electrons behave as if
they belong to each atom

Can share …

• 1 pair of electrons – single bond, example H-F
• 2 pairs of electrons – double bond, example O=O
• 3 pairs of electrons – triple bond, example N≡N

Figure 2.7

Octet rule

• Atoms are stable when their outer shell is
full

• For many atoms, the outer shell is filled with
8 electrons (“the octet rule”)

• An exception is hydrogen, which fills its
outer shell with just 2 electrons

Figure 2.8

Figure 2.9

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Polar covalent bonds

• Form between atoms of different
electronegativity (attraction to electrons)

• Shared electrons are more likely to be close to
the more electronegative atom

• The unequal distribution of electrons creates
a polarity (difference in electric charge)
across the molecule

Water has polar covalent bonds

• The classic example of polar covalent bonds

• Electrons tend to be near the more
electronegative oxygen atom rather than the
less electronegative hydrogen atoms

• Water molecule has a partial negative charge

 δ around the oxygen and a partial positive
charge  δ around the hydrogens

Figure 2.10

Nonpolar covalent bonds

• Between atoms with similar
electronegativities (attraction to electrons)

• Equal sharing of electrons

• No charge difference across molecule

Hydrogen bonds
The hydrogen atom from one polar molecule is
attracted to an electronegative atom of another

Represented as dashed or dotted lines

Individually, these are weak bonds that can form
and break easily

Collectively, many H bonds can be strong overall

• Holds DNA strands together

Figure 2.11 a and b

Ionic bonds

An ion is an atom or molecule that has
gained or lost one or more electrons

• Cations – have a net positive charge (+)

• Anions – have a net negative charge (−)

Ionic bond occurs when a cation binds to
an anion by electrostatic attraction

Ionic compounds are called salts

• Example NaCl, KCl, CaCl2

Figure 2.12 a and b

a) Formation of ions and an ionic bond

b) Sodium chloride (NaCl) crystals

Molecules May Change Their Shapes

• Atoms combine to form a molecule with three
dimensional shape

• The shape is determined by the arrangement and
number of bonds between atoms

• Angles that form between atoms give molecules
specific shapes

• Covalent bonds are not rigid and rotation around
single covalent bonds allows molecules to change
shape

Figure 2.13

Figure 2.14

Free radicals

• Highly reactive molecules

• Can form by exposure to radiation and some
toxins

• Can cause cell damage

• Can kill invading bacteria

• Benefits of antioxidants

Chemical Reactions

When one or more substances are changed
into other substances

• Reactants → products

Properties of chemical reactions

• Require a source of energy

• In living organisms, they often require an enzyme
as catalyst

• Tend to proceed in a particular direction but will
eventually reach equilibrium

• Occur in liquid (water)

Properties of Water

Solution = solutes in a solvent

• Solutes are dissolved substances

• Solvent is the liquid

In an aqueous solution, water is the solvent

Ions and molecules with polar covalent bonds
will dissolve in water

These are hydrophilic

Figure 2.16

Solutes
Hydrophilic – “water-loving”

• Readily dissolve in water

• Molecules with ionic and/or polar covalent bonds

Hydrophobic – “water-fearing”

• Do not dissolve in water

• Nonpolar molecules like hydrocarbons, oils

Amphipathic – “both loves”

• Have both polar/ionized and nonpolar regions

• May form micelles in water

• Detergent is an amphipathic molecule

Figure 2.17

• Polar (hydrophilic) regions
at the surface of the
micelle

• Nonpolar (hydrophobic)
ends are oriented toward
the interior of the micelle

(top right): ©Jeremy Burgess/Science Source

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Measuring solutions

Concentration

• Amount of a solute dissolved in a unit volume of solution

• 1 gram of NaCl dissolved in 1 liter of water = 1 gram/Liter

Molarity

• Number of moles of a solute dissolved in 1 Liter of water

• 1 mole of a substance is the amount of the substance in
grams equal to its atomic or molecular mass

H2O in three states of matter

Solid (ice), liquid (water), and gas (water vapor)

Changes in state, such as changes between the solid, liquid,
and gas states of H2O, involve an input or release of energy

• Heat of vaporization – energy to boil

• Heat of fusion – energy to melt

Specific heat is the amount of heat energy to raise

temperature 1 Celsius

Water is extremely stable as a liquid, due to high
heats of vaporization and fusion, and high specific heat

Figure 2.18

Colligative properties of water

Temperature at which a solution freezes or
boils is influenced by amounts of dissolved
solutes

Addition of solutes to water

• lowers the freezing point below 0 Celsius

• raises the boiling point above 100 Celsius

Some animals produce antifreeze molecules,
lowering the freezing point of body fluids to
prevent blood and cells from freezing

Not just a solvent

Water has many important functions in living
organisms:

• Participates in chemical reactions (hydrolysis or
condensation)

• Provides force or support

• Removes toxic waste components

• Evaporative cooling

• Cohesion and adhesion

• Surface tension

• Lubrication

Figure 2.19

b: ©Aaron Haupt/Science Source; d: ©Chris McGrath/Getty Images; e: ©Dana Tezarr/Getty Images; f: ©Gallo Images-Anthony Bannister/DigitalVision/Getty Images; g: ©Matti Suopajarvi/mattisj/Getty Images

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Acids and Bases 1

• Pure water ionizes to a very small extent into

hydrogen ions  H and hydroxide ions  OH

• In pure water
7 7 14

H OH 10 M 10 M 10 M
                   

Acids and Bases 2

Acids are molecules that release hydrogen

ions in solution

• A strong acid releases more H


than a weak acid

Bases lower the H concentration

• Some release OH

• Others bind H

The pH scale

•
10

pH log Η
    

• Acidic solutions are pH 6 or below

• pH 7 is neutral

• Alkaline solutions are pH 8 or above

Figure 2.20

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Effects of pH

The pH of a solution can affect

• The shapes and functions of molecules

• The rates of many chemical reactions

• The ability of two molecules to bind to each other

• The ability of ions or molecules to dissolve in
water

Buffers
• Organisms usually tolerate only small changes

in pH

• Buffers help to maintain a constant pH

• An acid-base buffer system can shift to

remove or release H to adjust for changes in

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Chapter 3

Lecture Outline

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Chapter 3

The Chemical Basis of Life II:
Organic Molecules

Key Concepts:

• The Carbon Atom

• Formation of Organic Molecules and Macromolecules

• Overview of the Four Major Classes of
Organic Molecules Found in Living Cells

•

Carbohydrates

•

Lipids

•

Proteins

• Nucleic Acids

The Carbon Atom

• Organic molecules contain carbon

• Organic molecules are abundant in living
organisms

• Macromolecules are large, complex organic
molecules

Carbon

Carbon has 4 electrons in its outer shell

Needs 4 more electrons to fill the shell

It can make up to four bonds

• Usually single or double bonds

Carbon can form nonpolar or polar bonds

• Molecules with polar bonds are water soluble

• Molecules with nonpolar bonds (like
hydrocarbons) are not very water soluble

Figure 3.1

a) Electron orbitals in carbon

b) Simplified depiction of carbon’s electron shells

Figure 3.2

Propionic acid

C—C and C—H
bonds are
electrically neutral
and nonpolar.

Oxygen is more
electronegative
than carbon; thus,
C—O and C=O
bonds are polar.

Functional Groups

• Groups of atoms with special chemical
features that are functionally important

• Each type of functional group exhibits the
same properties in all molecules in which it
occurs

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distribution without the prior written consent of McGraw-Hill Education.

Table 3.1 top half

Table 3.1 Some Biologically Important Functional Groups That Bond to Carbon

Functional group*
(with shorthand notation) Formula’ Examples of where the group is found Properties

Amino (-NH2) Amino acids (proteins) Weakly basic (can accept
+

H ); polar; forms
part of peptide bonds

Carbonyl (-CO)‡

Ketone
Steroids, waxes, and proteins Polar; highly chemically reactive; forms

hydrogen bonds

Aldehyde (-CHO) Linear forms of sugars and some odor molecules

Carboxyl (-COOH) Amino acids, fatty acids Acidic (gives up +H in water); forms part of
peptide bonds

Hydroxyl (-OH) Steroids, alcohol, carbohydrates, some amino acids Polar; forms hydrogen bonds with water

*This list contains many of the functional groups that are important in biology. However, many more functional groups have been identified by biochemists.
†R and R’ represent the remainder of the molecule.
‡A carbonyl group is C=O. In a ketone, the carbon of this group forms covalent bonds with two other carbon atoms. In an aldehyde, the carbon is bonded to a hydrogen atom.

Copyright © McGraw-Hill Education. All rights reserved. No reproduction or
distribution without the prior written consent of McGraw-Hill Education.

Table 3.1 bottom half

Table 3.1 Some Biologically Important Functional Groups That Bond to Carbon

Functional group*
(with shorthand notation) Formula’ Examples of where the group is found Properties

Methyl (-CH3) May be attached to DNA, proteins, and
carbohydrates

Nonpolar

Phosphate  24PO


 Nucleic acids, ATP, phospholipids Polar; weakly acidic and negatively charged
at typical pH of living organisms

Sulfate  4SΟ


 May be attached to carbohydrates, proteins,
and lipids

Polar; negatively charged at typical pH
of living organisms

Sulfhydryl (-SH) Proteins that contain the amino acid
cysteine

Polar; forms disulfide bridges in many
proteins

Isomers

Two molecules with an identical molecular formula but
different structures and characteristics

Structural isomers – contain the same atoms but in
different bonding relationships

Stereoisomers – identical bonding relationships, but the
spatial positioning of the atoms differs in the two isomers

• Cis-trans isomers – positioning around double bond

• Enantiomers – mirror image molecules

Figure 3.3

Structural isomers

b) Two types of stereoisomers

Formation of Organic Molecules

and Macromolecules 1

Condensation reaction

Links monomers to form polymers

A polymer begins as two
monomers combine in a
dehydration reaction.

Elongation of the polymer continues
with additional dehydration reactions.

The final polymer may
consist of many
monomers.

Formation of Organic Molecules

and Macromolecules 2

Hydrolysis reaction

Polymers broken down into monomers.

Polymer formation by dehydration reactions

A molecule of water is removed each time a new monomer is
added, thus a “dehydration” reaction

The process repeats to form long polymers

A polymer can consist of thousands of monomers

Dehydration is catalyzed by enzymes

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Breakdown of a polymer by hydrolysis reactions

• A molecule of water is added back each time a monomer is
released

• The process repeats to break down long polymer

• Hydrolysis is catalyzed by enzymes

Carbohydrates

• Composed of carbon, hydrogen, and oxygen
atoms

• Cn(H2O)n

• Most of the carbon atoms in a carbohydrate are
linked to a hydrogen atom and a hydroxyl group

Monosaccharides
Simplest sugars

Most common are 5 or 6 carbons

Pentoses
• Ribose C5H10O5
• Deoxyribose (C5H10O4)

Hexose
• Glucose (C6H12O6)

Different ways to depict structures

Ring
Linear

Figure 3.5a

a) Linear and ring structures
of D-glucose

Glucose isomers

Structural isomers

Different arrangement of same elements

Example: Glucose and galactose

Stereoisomers

α andβ glucose‐‐
• Hydroxyl group of carbon 1 is above or below ring

D- and L-glucose
• Enantiomers with mirror image structure

Disaccharides

• Composed of two monosaccharides

• Joined by dehydration or condensation
reaction

Glycosidic bond

• Broken apart by hydrolysis

• Examples: sucrose, maltose, lactose

Figure 3.5b

b) Isomers of glucose

Figure 3.6

Polysaccharides

• Many monosaccharides linked together to
form long polymers

• Examples:

Energy storage – starch, glycogen

Structural – cellulose, chitin, glycosaminoglycans

Figure 3.7

Lipids

• Composed predominantly of hydrogen and
carbon atoms

• Defining feature of lipids is that they are
nonpolar and therefore very insoluble in water

• Include fats, phospholipids, steroids, waxes

• Lipids comprise about 40% of the organic matter
in the average human body

Fats 1

• Also known as triglycerides or triacylglycerols

• Formed by bonding glycerol to 3 fatty acids

• Joined by dehydration; broken apart by hydrolysis

The hydrogens from
each hydroxyl group in
glycerol are removed.

The hydroxyl groups from each
carboxyl group of the 3 fatty acids
are removed.

The new bond created is
called an ester bond.

Fatty acids

• Saturated – all carbons linked by single bonds
Tend to be solid at room temperature

• Unsaturated – contain one or more double bonds
Tend to be liquid at room temperature (known as oils)

Cis forms naturally; trans formed artificially

Trans fats are linked to disease

Access the text alternative for slide images.

Figure 3.10

• Animal fats are usually saturated fats

• Plant fats are usually unsaturated fats

a) Animal fats at high and low
temperatures

b) Vegetable fats at low temperature

High temperature converts
solid, saturated fasts to liquid.

After cooling, saturated fats
return to their solid form.

Unsaturated fats have low
melting points and are liquid at
room temperature.

a (left, right): ©Tom Pantages; b: ©Felicia Martinez Photography/PhotoEdit

Fats 2

• Fats are important for energy storage

1 gram of fat stores more energy than 1 gram of
glycogen or starch

• Fats can also be structural, providing
cushioning and insulation

Phospholipids
• Formed from glycerol, two fatty acids and a

phosphate group

• Phospholipids are amphipathic molecules

Phosphate head – polar / hydrophilic

Fatty acid tail – nonpolar / hydrophobic

Figure 3.11a and b

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Steroids

• Four interconnected rings of carbon atoms

• Usually insoluble in water

• Example: Cholesterol

• Tiny differences in structure can lead to
profoundly different, specific biological
properties
Estrogen versus testosterone

Figure 3.12 1

Figure 3.12 2

(left, right): ©Adam Jones/Science Source

Proteins

• Composed of carbon, hydrogen, oxygen,
nitrogen, and small amounts of other
elements, notably sulfur

• Building blocks of proteins are amino acids

20 different amino acids

Common structure with variable sidechain that
determines structure and function

Amino acid structure

General designation
for an amino acid
side chain

Amino group –
positively charged
at neutral pH

Carboxyl group –
negatively charged at
neutral pH

Figure 3.13

Figure 3.13: Nonpolar Amino Acids
only

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Figure 3.13 Polar Amino Acids –
Uncharged and Charged

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Polypeptide formation

• Amino acids joined by dehydration reaction

Carboxy + amino forms peptide bond

Polymers of amino acids known as polypeptides

Proteins may be formed from one or several
polypeptides

• Polypeptides are broken down by hydrolysis

Figure 3.14a: Reactants only

Formation of a peptide bond

between 2 amino acids

Formation of a peptide bond

Figure 3.14a, b, and c

a) Formation of a peptide bond between 2 amino acids

b) Polypeptide – a linear chain of amino acids

c) Numbering system of amino acids in a polypeptide Access the text alternative for slide images.

Figure 3.15

Access the text alternative for slide images.

Primary structure

• Amino acid sequence

• Encoded directly by
genes

Secondary Structure

• Chemical and physical interactions cause protein
folding

• α helices and β pleated sheets
Key determinants of a protein’s
characteristics

• “Random coiled regions”
Not α helix or β pleated sheet
Shape is specific and
important to function

Tertiary structure

• Folding gives
protein complex 3D
shape

• This is the final level
of structure for a
single polypeptide
chain

Quaternary structure

• Made up of two or more polypeptides

Individual polypeptide chains are protein subunits

Protein can be formed from several copies of the
same polypeptide

Or may be multimeric
– composed from
different polypeptides

Five factors that promote protein
folding and stability

• Hydrogen bonds

• Ionic bonds and other polar interactions

• Hydrophobic effects

• Van der Waals forces

• Disulfide bridges

Figure 3.17

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Protein-protein interactions

Many cellular processes involve steps in which
two or more different proteins interact

Specific binding at surface

Use first four factors to bind

• Hydrogen bonds
• Ionic bonds and other polar interactions
• Hydrophobic effects
• Van der Waals forces

Figure 3.18

Anfinsen Showed That the
Primary Structure of Ribonuclease

Determines Its Three-Dimensional Structure

• Prior to 1960s, the mechanisms by which proteins assume
their 3D structures were not understood.

• Christian Anfinsen postulated that proteins contain all the
information necessary to fold into their proper conformation
without needing organelles or factors

• He hypothesized that proteins spontaneously assume their
most stable conformation based on the laws of chemistry and
physics

Anfinsen’s Ribonuclease experiment 1

• Won him the Nobel Prize in 1972

• Performed in vitro – no other cellular components present

• Chemicals that disrupt bonds caused the enzyme to lose
function; removal of those chemicals restored function

• Conclusion:

Even in the complete absence of any cellular
factors or organelles, an unfolded protein can

refold into its functional structure

• Since then, we have learned that some proteins
do require assistance in folding

Anfinsen’s Ribonuclease experiment 2

HYPOTHESIS Within their amino acid sequence, proteins contain all the information needed to fold into their correct, three-dimensional shapes.

KEY MATERIALS Purified ribonuclease, RNA, denaturing chemicals, size-exclusion chromatography columns.

1. Incubate purified
ribonuclease in test tube with
RNA, and measure its ability
to degrade RNA.

Numerous H bonds and
ionic bonds (not shown)
and 4 S—S bonds.
Protein is properly folded.
(For simplicity, the three-
dimensional shape is not
shown; see Panel 3 for a
computer model of the
true structure.)

2. Denature ribonuclease
by adding β-mercaptoethanol
(breaks S—S bonds) and urea
(breaks H bonds and ionic
bonds). Measure its ability to
degrade RNA.

No more H bonds,
ionic bonds, or S—S
bonds. Protein is
unfolded.

Feature investigation
HYPOTHESIS Within their amino acid sequence, proteins contain all the information needed to fold into their correct, three-dimensional shapes.

KEY MATERIALS Purified ribonuclease, RNA, denaturing chemicals, size-exclusion chromatography columns.

3. Pour mixture from step 2 into a
size-exclusion chromatography
column. Beads in the column trap
β-mercaptoethanol and urea,
whereas ribonuclease flows to the
bottom. Collect ribonuclease in a
test tube. Allow ribonuclease to
sit for up to 20 hours and then
measure its ability to degrade
RNA.

Beads have
microscopic pores
that trap β-mercaptoethanol
and urea, but not
ribonuclease.

Computer model of
properly folded structure
of ribonuclease

4. THE DATA 5. CONCLUSION Certain proteins, like ribonuclease, can
spontaneously fold into their final, functional shapes
without assistance from other cellular structures or
factors. (However, as described in the text, this is
not true of many other proteins.)

6. SOURCE Haber, E., and Anfinsen, C.B. 1961. Regeneration of enzyme
activity by air oxidation of reduced subtilisin-modified
ribonuclease. Journal of Biological Chemistry 236:422 to 424.

Proteins Contain Functional Domains
Within Their Structures

• Modules or domains in proteins have distinct
structures and function

• Example: Signal transducer and activator of
transcription (STAT) protein

• Each domain of this protein is involved in a
distinct biological function

• Proteins that share a particular domain also share
the associated function

Genomes & Proteomes

Nucleic Acids

Responsible for the storage, expression, and
transmission of genetic information

Two classes

Deoxyribonucleic acid (DNA)

• Stores genetic information encoded in the sequence of
nucleotide monomers

Ribonucleic acid (RNA)

• Decodes DNA into instructions for linking together a specific
sequence of amino acids to form a polypeptide chain

Nucleic acid monomer is a nucleotide

Made up of phosphate group, a five-carbon sugar
(either ribose or deoxyribose), and a single or
double ring of carbon and nitrogen atoms known as
a base

Nucleotides are linked into polymer by a
sugar-phosphate backbone

Figure 3.22

DNA versus RNA

DNA RNA

Deoxyribonucleic acid Ribonucleic acid

Deoxyribose Ribose

Thymine (T) Uracil (U)

Adenine (A), guanine
(G), cytosine (C) used in

both

Adenine (A), guanine
(G), cytosine (C) used in
both

2 strands, double helix Single strand

1 form Several forms

Figure 3.23

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Chapter 4

Lecture Outline

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Chapter 4

General Features of Cells

Key Concepts:

• Origin of Living Cells on Earth
•

Microscopy

•

Overview of Cell Structure

•

The

Cytosol

• The Nucleus and Endomembrane System
• Semiautonomous Organelles
• Protein Sorting to Organelles
• Systems Biology of Cells: A Summary

Origin of life – four overlapping stages

• Nucleotides and amino acids produced prior
to the existence of cells

• Nucleotides and amino acids became
polymerized to form DNA, RNA and proteins

• Polymers became enclosed in membranes

• Polymers enclosed in membranes acquired
cellular properties

Stage 1: Origin of organic molecules

• Conditions on primitive Earth may have been
more conducive to spontaneous formation
of organic molecules

• Prebiotic or abiotic synthesis
Little free oxygen gas

Formed prebiotic soup

• Several hypotheses on where and how
organic molecules originated

Origin of organic molecules 1

Reducing atmosphere hypothesis
Based on geological data

Atmosphere rich in water vapor, H2, CH4, NH3
(and little O2)

Stanley Miller used a chamber apparatus to simulate this
atmosphere and bolts of lightning

Formed precursors, amino acids, sugars and nitrogenous bases

First attempt to apply scientific experiments to understand origin
of life

Since 1950s, ideas about early Earth atmosphere changed

• Still, similar results

Figure 4.1

Origin of organic molecules 2

Extraterrestrial hypothesis

Meteorites brought organic carbon to Earth

• Includes amino acids and nucleic acid bases

Opponents argue that most of this would be destroyed in the
intense heating and collision

Deep-sea vent hypothesis

Biologically important molecules may have been formed in the
temperature gradient between extremely hot vent water and cold
ocean water
Supported by experiments
Complex biological communities found here that derive energy
from chemicals in the vent (not the sun)

Figure 4.2a

a) Deep-sea vent hypothesis

Figure 4.2b

b) A deep-sea vent community

Stage 2: Organic polymers

• Experimentally, prebiotic synthesis of
polymers not possible in aqueous solutions

Hydrolysis competes with polymerization

• Experiments have shown formation of nucleic
acid polymers and polypeptides on clay
surface

Stage 3:

Formation of boundaries

Protobiont

• An aggregate of prebiotically produced molecules
and macromolecules

• Have acquired a boundary, such as a lipid bilayer,
that allow it to maintain an internal chemical
environment distinct from that of its surroundings

Formation of boundaries

Four characteristics of a protobiont:

• Boundary separated external environment from
internal contents

• Polymers inside the protobiont contained
information

• Polymers inside the protobiont had catalytic
function

• Protobionts capable of self-replication

Living cells may have evolved from

• Coacervates
Droplets that form spontaneously from the association
of charged polymers

Enzymes trapped inside can perform primitive metabolic
functions

• Liposomes
Vesicles surrounded by a lipid layer

Clay can catalyze formation of liposomes that grow and
divide

Can enclose RNA

Figure 4.3

Stage 4: RNA world

Majority of scientists favor RNA as the first
macromolecule of protobionts

Three key RNA functions:

• Ability to store information

• Capacity for self-replication

• Enzymatic function (ribozymes)

DNA and proteins cannot do all 3 functions

Chemical selection

A chemical within a mixture has special
properties that cause it to increase in number
compared to other chemicals in the mixture

Hypothetical scenario with two steps:

• One of the RNA molecules mutates and has
enzymatic ability to attach nucleotides together
• Advantage of faster replication

• Second mutation produces enzymatic ability to
synthesize nucleotides
• No reliance on prebiotic synthesis

Figure 4.4

1a Mutation: A mutation provides an RNA molecule with the
catalytic ability to synthesize new RNA molecules using
pre-existing RNA molecules as templates.

1b Chemical selection:
The amount of this mutant
RNA with catalytic function
increases because it can
self-replicate faster.

2a Mutation: A second mutation provides an RNA
molecule with the ability to catalyze a step in the
synthesis of ribonucleotides.

2b Chemical selection:
The second mutation is also
favored, so after many
generations, the protobionts
have 2 catalytic functions—
self-replication and
ribonucleotide synthesis.

Advantages of DNA / RNA / protein world

• Information storage
DNA would have relieved RNA of informational role
and allowed RNA to do other functions

DNA is less likely to suffer mutations

• Metabolism and other cellular functions
Proteins have a greater catalytic potential and
efficiency

Proteins can perform other tasks – cytoskeleton,
transport, etc.

Cell theory

• All living organisms are composed of one or
more cells

• Cells are the smallest units of life

• New cells come only from pre-existing cells
by cell division

Microscopy

• Resolution
Ability to observe two adjacent objects as distinct
from one another

• Contrast
How different one structure looks from another

Contrast can be enhanced by special dyes to reveal
cellular structure

• Magnification
Ratio between the size of an image produced by a
microscope and its actual size

Two kinds of microscopes

Type of microscope is based on the source of
illumination

• Light microscope
• Uses light for illumination
• Resolution 0.2 micrometer

• Electron microscope
• Uses a beam of electrons for illumination
• Resolution 2 nanometer (100 times better)

Figure 4.5

Types of Light Microscopy

• Standard (bright field)
Light is focused with glass lenses
Light passes directly through sample

• Phase contrast
Microscope amplifies differences in phase of light
transmitted or reflected by sample
Improved contrast of denser structures

• Differential interference contrast (DIC or
Nomarski microscopy)
Another method using optics to improve contrast
Good for internal cellular structures

Figure 4.6a

a) Three different methods of light microscopy on the same unstained sample

Standard light microscopy
(bright field, unstained sample).
Light is passed directly through a sample,
and the light is focused using glass lenses.
Simple, inexpensive, and easy to use but
offers little contrast with unstained
samples.

Phase contrast microscopy.
As an alternative to staining, this microscope
controls the path of light and amplifies
differences in the phase of light transmitted
or reflected by a sample. The dense structures
appear darker than the background, thereby
improving the contrast in different parts of
the specimen. Can be used to view living,
unstained cells.

Differential interference contrast (Nomarski)
microscopy.
Similar to a phase contrast microscope in
that it uses optical modifications to improve
contrast in unstained specimens. Can be
used to visualize the internal structures of
cells and is commonly used to view whole
cells or large cell structures such as nuclei.

Courtesy of Molecular Expressions

Figure 4.6b

b) Two different methods of fluorescence microscopy on the same sample

Standard (wide-field) fluorescence microscopy.
Fluorescent molecules specifically label a particular
type of cellular protein or organelle. A fluorescent
molecule absorbs light at a particular wavelength
and emits light at a longer wavelength. This
microscope has filters that illuminate the sample
with the wavelength of light that a fluorescent
molecule absorbs, and then only the light that is
emitted by the fluorescent molecules is allowed to
reach the observer. To detect their cellular
location, researchers often label specific cellular
proteins using fluorescent antibodies that bind
specifically to a particular protein.

Confocal fluorescence microscopy.
Uses lasers that illuminate various points in the
sample. These points are processed by a
computer to give a very sharp focal plane. In this
example, this microscope technique is used in
conjunction with fluorescence microscopy to
view fluorescent molecules within a cell.

Courtesy of Molecular Expressions

Electron microscope types

• Transmission electron microscopy (TEM)

Beam of electrons transmitted through sample
Thin slices stained with heavy metals
Some electrons are scattered while others pass
through to form an image

• Scanning electron microscopy (SEM)

Sample coated with heavy metal
Beam scans surface to make 3D image

Figure 4.7

a) Transmission electron
micrograph (TEM)

b) Scanning electron
micrograph (SEM)

Overview of Cell Structure

Two categories of life:

• Prokaryotes
Simple cell structure
No nucleus

• Eukaryotes
More complex cells
DNA enclosed within membrane-bound nucleus
Internal membranes form organelles

Prokaryotic cells

Two categories of prokaryotes:

• Bacteria
Small cells, 1 micrometer to 10 micrometer in diameter
Very abundant in environment and our bodies
Vast majority are not harmful to humans
Some species cause disease

• Archaea
Also small cells, 1 micrometer to 10 micrometer in
diameter
Less common
Often found in extreme environments

Typical bacterial cell

• Inside the plasma membrane:
Cytoplasm – contained within plasma membrane

Nucleoid region – where DNA is located

Ribosomes – synthesize proteins

• Outside the plasma membrane:
Cell wall – provides support and protection

Glycocalyx – traps water, gives protection, help evade
immune system

Appendages – pilli (attachment), flagella (movement)

Figure 4.8

a) Diagram of a typical rod-shaped bacterium b) A colorized TEM of Escherichia coli

Eukaryotic cells

• DNA is housed inside membrane-bound nucleus

• Compartmentalized functions

• Organelles
Membrane-bound compartments
Each has a unique structure and function

• Variety
Shape, size, and organization of cells vary considerably
Differences between species
Differences between specialized cell types

Animal cell

Access the text alternative for slide images.

Cell morphology

• Size and shape of eukaryotic cells show great
variation

• Even cells that share the same genome can
have very different morphologies

Plant cell

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The Proteome Largely Determines the
Characteristics of a Cell 1

• How does a single organism produce different
types of cells?

• The DNA is identical in each cell of an
organism

• However, the cells have different proteomes

The Proteome Largely Determines the
Characteristics of a Cell 2

The DNA in different cells is identical — but they
have different proteomes

Structure determines function

Protein profile varies based on:

• Which proteins are expressed
• Levels of expression
• Which subtypes of proteins are expressed
• post-translational modifications

Relevant to disease: proteomes of healthy cells are
different from those of cancerous cells

Cell surface area and volume

As cells get larger, the surface area-to-volume
ratio gets smaller. This affects cell function

Radius (micrometer): 1 10 100

Surface area  2micrometer
 2A 4πr 

12.6 Approximately 1,260 Approximately 124,600

Volume  3micrometer
 34V πr3 

4.2 Approximately 4,200 Approximately 4,200,000

Surface area/volume ratio: 3.0 : 1 0.3 : 1 0.03 : 1

The Cytosol

• Region of a eukaryotic cell that is outside the
cell organelles but inside the plasma
membrane

• Cytoplasm includes everything inside the
plasma membrane

Cytosol

Endomembrane system

Semiautonomous organelles

Figure 4.13

Molecular synthesis and breakdown

• Sum of all chemical reactions by cells

• Catabolism

Breakdown of a molecule into smaller components

• Anabolism
Synthesis of cellular molecules and macromolecules

• Cytosol is central coordinating region for
metabolic activities of eukaryotic cells

Cytoskeleton

Network of three types of protein filaments

• Microtubules
Long, hollow cylindrical structures
Dynamic instability

• Intermediate filaments
Intermediate in size
Form twisted, ropelike structure

• Actin filaments
Also known as microfilaments
Long, thin fibers

Table 4.1

Table 4.1 Types of Cytoskeletal Filaments Found In Eukaryotic Cells

Characteristic Microtubules Intermediate filaments Actin filaments

Diameter 25 nanometer 10 nanometer 7 nanometer

Structure Hollow tubule Twisted filament Spiral filament

(left): ©Thomas Deerinck, NCMIR/Getty Images; (middle): ©Cultura Science/Alvin Telser, PhD/Getty Images; (right): ©Dr. Gopal Murti/SPL/Science Source

Protein composition Hollow tubule composed of the protein
tubulin

Can be composed of different proteins
including keratin, lamin, and others that
form twisted filaments

Two intertwined strands composed of the
protein actin

Common functions Cell shape; organization of cell organelles;
chromosome sorting in cell division;
intracellular movement of cargo; cell
motility (cilia and flagella)

Cell shape; provide cells with mechanical
strength; anchorage of cell and nuclear
membranes

Cell shape; cell strength; muscle
contraction; intracellular movement of
cargo; cell movement (amoeboid
movement); cytokinesis in animal cells

Motor Proteins

Use ATP as a source of energy for movement

Three domains— the head, hinge, and tail

Walking analogy
• The ground is the cytoskeletal filament, your leg is the

head of the motor protein, and your hip is the hinge

Three kinds of movements
• Motor protein carries cargo along the filament
• Motor protein remains in place, the filament moves
• Motor protein and filament both restrained – action of

the motor protein exerts a force that bends the filament

Figure 4.14

a) Three-domain structure of myosin, a motor protein

b) Movement of a motor protein along a cytoskeletal filament
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Figure 4.15

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Flagella and cilia

• Flagella
Usually longer than cilia
Present singly or in pairs
9 + 2 microtubule array

• Cilia
Often shorter than flagella
Tend to cover all or part of the cell surface
Also a 9 + 2 microtubule array

• Movement involves the propagation of a bend, beginning at the
base and moving toward the tip

Figure 4.16

b: Courtesy of Dr. Barbara Surek, Culture Collection of Algae at the University of Cologne (CCAC); c: ©SPL/Science Source

Figure 4.17

The Nucleus and
Endomembrane System

• Network of membranes enclosing the
nucleus, endoplasmic reticulum, Golgi
apparatus, lysosomes, and vacuoles

• Also includes plasma membrane

• May be directly connected to each other or
pass materials via vesicles

Figure 4.18

Nuclear envelope

• Double-membrane structure enclosing nucleus

• Outer membrane of the nuclear envelope is
continuous with the ER membrane

• Nuclear pores provide passageways

• Materials within the nucleus are not part of the
endomembrane system

Figure 4.19

Nucleus

• Chromosomes
Composed of DNA and proteins = chromatin

• Nuclear matrix
Filamentous network
Organizes chromosomes

• Ribosome assembly occurs in the nucleolus

Figure 4.20

Courtesy of Felix A. Habermann

Endoplasmic reticulum

• Network of membranes that form flattened,
fluid-filled tubules or cisternae

• ER membrane encloses a single compartment
called the ER lumen

• Rough endoplasmic reticulum (rough ER)
Studded with ribosomes
Involved in protein synthesis and sorting

• Smooth endoplasmic reticulum (smooth ER)
Lacks ribosomes
Detoxification, carbohydrate metabolism, calcium
balance, synthesis, and modification of lipids

Figure 4.21

Golgi apparatus

• Also called the Golgi body, Golgi complex, or simply
Golgi

• Stack of flattened, membrane-bounded
compartments

• Vesicles transport materials between stacks

• Three overlapping functions
Secretion, processing, and protein sorting

Figure 4.22

Secreted Proteins Move Sequentially Through Organelles
of the Endomembrane System

• George Palade used pulse-chase experiments to trace path of
radioactive proteins

• Studied pancreatic cells – primary function is protein
secretion

• Dark spots in TEM images revealed radioactive proteins

• First evidence that secreted proteins are synthesized into
rough ER and move through a series of compartments before
secretion

Figure 4.23 through Step 2

HYPOTHESIS Proteins that are to be secreted follow a particular intracellular pathway.

KEY MATERIALS Male guinea pigs.

1. Inject guinea pigs with a radioactive amino
acid, 3 H – leucine   . After 3 minutes, inject them
with nonlabeled leucine, which is
called a chase.

2. At various times after the second injection,
remove samples of pancreatic cells.

Access the text alternative for slide images.

Figure 4.23: Steps 3 to 5

3. Stain the sample with osmium tetroxide,
which is a heavy metal that binds to
membranes.

4. Cut thin sections of the samples, and place a
thin layer of radiation-sensitive emulsion
over the sample. Allow time for radioactive
emission from radiolabeled proteins to
precipitate silver atoms in the emulsion.
Wash away unprecipitated silver atoms.

5. Observe the sample under a transmission
electron microscope.

Figure 4.23 Steps 6 to 8

6. THE DATA

Schematic drawings of transmission
electron micrographs

7. CONCLUSION To be secreted, proteins move from the ER to the Golgi to secretory vesicles and then to the plasma membrane, where they are
released to the outside of the cell.

8. SOURCE Caro, L.G., and Palade, G.E. 1964. Protein synthesis, storage, and discharge in the pancreatic exocrine cell. An autoradiographic study.
Journal of Cell Biology 20: 473 to 495.

Lysosomes

• Contain acid hydrolases that perform hydrolysis

• Many different types of acid hydrolases to break
down proteins, carbohydrates, nucleic acids, and
lipids

• Autophagy

Recycling of worn-out organelles through endocytosis

Vacuoles

• Functions are extremely varied, and they differ
among cell types and environmental conditions

• Central vacuoles in plants for storage and
support

• Contractile vacuoles in protists for expelling
excess water

• Phagocytic vacuoles in protists and white blood
cells for degradation

Figure 4.24

a: ©Biophoto Associates/Science Source; b: Courtesy of Dr. Peter Luykx, Biology, University of Miami; c: ©Dr. David Patterson/Science Source

Peroxisomes

• Catalyze certain reactions that break down
molecules by removing hydrogen or adding
oxygen

• Hydrogen peroxide (H2O2) is a byproduct

• Catalase breaks down dangerous H2O2 into
water and oxygen

Figure 4.25

1. Vesicles bud from the ER and
fuse with each other to form a
premature peroxisome.

2. The import of additional
proteins and lipids results
in a mature peroxisome.

3. Mature peroxisomes
may divide to produce
more peroxisomes.

Plasma membrane

• Boundary between the cell and the
extracellular environment

• Functions

Membrane transport in and out of cell, with
selective permeability

Cell signaling using receptors

Cell adhesion

Figure 4.26

Cell adhesion:
Proteins in the plasma
membranes of adjacent cells
hold the cells together.

Membrane transport:
Proteins in the plasma
membrane allow the
transport of substances
into and out of cells.

Cell signaling:
An extracellular signal
binds to a receptor in
the plasma membrane
that activates a signal
transduction pathway,
leading to a cellular
response.

Semiautonomous organelles

• Mitochondria and chloroplasts

• Grow and divide to reproduce themselves

• They are not completely autonomous because
they depend on the cell for synthesis of
internal components

Figure 4.27

Mitochondria

• Primary role is to make ATP

• Outer and inner membrane

Intermembrane space and mitochondrial matrix

• Also involved in the synthesis, modification,
and breakdown of several types of cellular
molecules

Figure 4.28

Chloroplasts

• Photosynthesis

Capture light energy and use some of that energy to
synthesize organic molecules such as glucose

• Found in nearly all species of plants and algae

• Outer and inner membrane
Intermembrane space
Thylakoid membrane

Figure 4.29

Chloroplasts and mitochondria

Contain their own DNA, divide by binary fission

a) Binary fission of
mitochondria

b) Transmission electron
micrograph of the
process

1. Mitochondrial
genome replicates.

2. Mitochondrion
begins to divide by
binary fission.

3. Binary fission is
completed.

Endosymbiosis of chloroplast and
mitochondrion

• Modern mitochondria
were derived from
purple bacteria, also
called α proteobacteria‐

• Similarly, chloroplasts
were derived from
cyanobacteria (a
photosynthetic blue-
green bacteria)

Protein sorting

Eukaryotic proteins are sorted to the right
destination

• Remain in cytosol

• Cotranslational sorting

• Post-translational sorting

Figure 4.32
Protein synthesis begins on
ribosomes in the cytosol.

Cytosolic proteins complete
their synthesis in the cytosol
and remain there due to the
lack of a sorting signal.

For proteins with an ER sorting signal,
translation is paused, and the protein is
then synthesized into the ER. Some of
these proteins contain ER retention
signals and remain in the ER. The others
are sent to the Golgi via vesicles.

Some of these proteins contain
Golgi retention signals and
remain in the Golgi. The others
are sent, via vesicles, to the
lysosomes, plasma membrane, or
outside the cell via secretory
vesicles.

These proteins are completely
synthesized in the cytosol. They
contain sorting signals that send
them to the nucleus,
mitochondria, chloroplasts, or
peroxisomes.

Cotranslational sorting

For ER, Golgi, lysosomes, vacuoles, plasma
membrane, and secreted proteins

Begins in cytosol during translation

• ER signal sequence binds SRP and associates
with ER channel

Second step in cotranslational sorting

• Vesicle buds from ER membrane and fuses with
the target membrane and protein is delivered

Figure 4.33

Access the text alternative for slide images.

Post-translational sorting

• Most proteins for nucleus, mitochondria,
chloroplasts, and peroxisomes

• Synthesized in cytosol and taken up by target
organelle

• Short amino acid sequence directs the protein
to its target where it is taken up from the
cytosol

Figure 4.34

Access the text alternative for slide images.

Systems biology of cells

• Systems Biology – the study of how new properties
of life arise from complex interactions of its components

• “Emergent properties”

• The cells is viewed in terms of functional connections (not
just individual molecules)

• Eukaryotic cells have dynamic organization
The nucleus, cytosol, endomembrane system and semiautonomous
organelles work together

Table 4.2

Table 4.2 A Comparison of Cell Complexity Among Bacterial, Animal, and Plant Cells

Structures Bacteria Animal cells Plant cells

Extracellular structures

Cell wall* Present Absent Present

Flagella/cilia Flagella sometimes present Cilia or flagella present on certain cell
types

Rarely presentϮ

Plasma membrane Present Present Present

Interior structures

Cytoplasm Usually a single compartment inside
the plasma membrane

Composed of membrane-bound
organelles that are surrounded by the
cytosol

Composed of membrane-bound organelles
that are surrounded by the cytosol

Ribosomes Present Present Present

Chromosomes Typically one circular chromosome
per nucleoid; a nucleoid is not a
membrane-bound compartment.

Multiple linear chromosomes in the
nucleus, which is surrounded by a
double membrane. Mitochondria also
have chromosomes.

Multiple linear chromosomes in the
nucleus, which is surrounded by a double
membrane. Mitochondria and chloroplasts
also have chromosomes.

Endomembrane system Absent Present Present

Mitochondria Absent Present Present

Chloroplasts Absent Absent Present

*Note that the biochemical composition of bacterial cell walls is very different from plant cell walls.
ϮSome plant species produce sperm cells with flagella, but flowering plants produce sperm within pollen grains that lack flagella.

Figure 4.35

Nucleus
• Location of most of the genome
• Gene expression and regulation
• Organization and protection of

chromosomes via the nuclear matrix
• Site for ribosome subunit assembly

Endomembrane system
1. Nuclear envelope

• Double membrane that surrounds the nucleus
2. Endoplasmic reticulum
Protein secretion and sorting

• Glycosylation
• Lipid synthesis
• Metabolic functions and accumulation of 2Ca 

3. Golgi apparatus
• Protein secretion and sorting
• Glycosylation

4. Lysosome/vacuoles
• Degradation of organic molecules
• Storage of organic molecules
• Accumulation of water (plant vacuoles)

5. Peroxisomes
• Breakdown of toxic molecules such as H2O2
• Breakdown and synthesis of organic molecules

6. Plasma membrane
• Uptake and excretion of ions and molecules
• Cell signaling
• Cell adhesion

Semiautonomous organelles
1. Mitochondria

• Synthesis of ATP
• Synthesis and modification of other

organic molecules
• Production of heat

2. Chloroplasts (plants and algae)
• Photosynthesis

Cytosol
• Coordination of responses to the

environment
• Coordination of metabolism
• Synthesis of the proteome
• Organization and movement via

cytoskeleton and motor proteins

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