Overview: Inquiring About Life

• An organism’s adaptations to its environment are

the result of evolution
– For example, the ghost plant is adapted to
conserving water; this helps it to survive in the
crevices of rock walls

• Evolution is the process of change that has

transformed life on Earth.

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Some
properties of life.

Order

Response to
the environment

Evolutionary adaptation

Reproduction

Regulation

Energy processing

Growth and
development
Levels of Biological Organization
The biosphere
Tissues
Ecosystems
Organs and
organ systems

Communities
Cells
Organelles

Organisms Atoms

Populations Molecules
Emergent Properties
• Emergent properties result from the arrangement
and interaction of parts within a system
• Emergent properties characterize nonbiological
entities as well
– For example, a functioning bicycle emerges only
when all of the necessary parts connect in the
correct way

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Systems Biology
• A system is a combination of components that
function together
• Systems biology constructs models for the
dynamic behavior of whole biological systems
• The systems approach poses questions such as
– How does a drug for blood pressure affect other
organs?
– How does increasing CO2 alter the biosphere?

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Theme: Organisms Interact with Other
Organisms and the Physical Environment
• Every organism interacts with its environment,
including nonliving factors and other organisms
• Both organisms and their environments are
affected by the interactions between them
– For example, a tree takes up water and minerals
from the soil and carbon dioxide from the air; the
tree releases oxygen to the air and roots help
form soil

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 • Humans have modified our environment
– For example, half the human-generated CO2
stays in the atmosphere and contributes to global
warming
• Global warming is a major aspect of global
climate change
• It is important to understand the effects of global
climate change on the Earth and its populations

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Theme: Life Requires Energy Transfer
and Transformation
• A fundamental characteristic of living organisms is
their use of energy to carry out life’s activities
• Work, including moving, growing, and reproducing,
requires a source of energy
• Living organisms transform energy from one form
to another
– For example, light energy is converted to chemical
energy, then kinetic energy
• Energy flows through an ecosystem, usually
entering as light and exiting as heat
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Theme: Structure and Function Are
Correlated at All Levels of Biological
Organization
• Structure and function of living organisms are
closely related
– For example, a leaf is thin and flat, maximizing
the capture of light by chloroplasts
– For example, the structure of a bird’s wing is
adapted to flight

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Theme: The Cell Is an Organism’s Basic
Unit of Structure and Function
• The cell is the lowest level of organization that
can perform all activities required for life
• All cells
– Are enclosed by a membrane
– Use DNA as their genetic information

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 • A eukaryotic cell has membrane-enclosed
organelles, the largest of which is usually the
nucleus
• By comparison, a prokaryotic cell is simpler and
usually smaller, and does not contain a nucleus or
other membrane-enclosed organelles

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Theme: The Continuity of Life Is Based on
Heritable Information in the Form of DNA
• Chromosomes contain most of a cell’s genetic
material in the form of DNA (deoxyribonucleic
acid)
• DNA is the substance of genes
• Genes are the units of inheritance that transmit
information from parents to offspring
• The ability of cells to divide is the basis of all
reproduction, growth, and repair of multicellular
organisms.

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DNA Structure and Function
• Each chromosome has one long DNA molecule
with hundreds or thousands of genes
• Genes encode information for building proteins
• DNA is inherited by offspring from their parents
• DNA controls the development and maintenance
of organisms

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 • Each DNA molecule is made up of two long chains
arranged in a double helix
• Each link of a chain is one of four kinds of
chemical building blocks called nucleotides and
nicknamed A, G, C, and T

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 • Genes control protein production indirectly
• DNA is transcribed into RNA then translated into
a protein
• Gene expression is the process of converting
information from gene to cellular product

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Genomics: Large-Scale Analysis of DNA
Sequences
• An organism’s genome is its entire set of genetic
instructions
• The human genome and those of many other
organisms have been sequenced using DNA-
sequencing machines
• Genomics is the study of sets of genes within
and between species

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 • The genomics approach depends on
– “High-throughput” technology, which yields
enormous amounts of data
– Bioinformatics, which is the use of computational
tools to process a large volume of data
– Interdisciplinary research teams

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PearsonEducation,
Education,Inc.
Inc.
Theme: Feedback Mechanisms Regulate
Biological Systems
• Feedback mechanisms allow biological processes
to self-regulate
• Negative feedback means that as more of a
product accumulates, the process that creates it
slows and less of the product is produced
• Positive feedback means that as more of a product
accumulates, the process that creates it speeds up
and more of the product is produced

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Evolution, the Overarching Theme of
Biology
• Evolution makes sense of everything we
know about biology
• Organisms are modified descendants of
common ancestors

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 • Evolution explains patterns of unity and
diversity in living organisms
• Similar traits among organisms are explained
by descent from common ancestors
• Differences among organisms are explained
by the accumulation of heritable changes

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Classifying the Diversity of Life
• Approximately 1.8 million species have been
identified and named to date, and thousands more
are identified each year
• Estimates of the total number of species that
actually exist range from 10 million to over 100
million

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Grouping Species: The Basic Idea
• Taxonomy is the branch of biology that names
and classifies species into groups of increasing
breadth
• Domains, followed by kingdoms, are the
broadest units of classification

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Figure 1.15

(a) Domain Bacteria (b) Domain Archaea

2 mm
2 mm
(c) Domain Eukarya
Kingdom Animalia

100 mm

Kingdom Plantae

Protists

Kingdom Fungi
The Three Domains of Life
• Organisms are divided into three domains
• Domain Bacteria and domain Archaea compose
the prokaryotes
• Most prokaryotes are single-celled and
microscopic

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 • Domain Eukarya includes all eukaryotic
organisms
• Domain Eukarya includes three multicellular
kingdoms
– Plants, which produce their own food by
photosynthesis
– Fungi, which absorb nutrients
– Animals, which ingest their food

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 • Other eukaryotic organisms were formerly
grouped into the Protist kingdom, though these
are now often grouped into many separate groups

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Unity in the Diversity of Life
• A striking unity underlies the diversity of life; for
example
– DNA is the universal genetic language common
to all organisms
– Unity is evident in many features of cell structure

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Charles Darwin and the Theory of
Natural Selection
• Fossils and other evidence document the
evolution of life on Earth over billions of years

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 • Charles Darwin published On the Origin of
Species by Means of Natural Selection in 1859
• Darwin made two main points
– Species showed evidence of “descent with
modification” from common ancestors
– Natural selection is the mechanism behind
“descent with modification”
• Darwin’s theory explained the duality of unity and
diversity

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 • Darwin observed that
– Individuals in a population vary in their traits,
many of which are heritable
– More offspring are produced than survive, and
competition is inevitable
– Species generally suit their environment

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 • Darwin inferred that
– Individuals that are best suited to their
environment are more likely to survive and
reproduce
– Over time, more individuals in a population will
have the advantageous traits
• Evolution occurs as the unequal reproductive
success of individuals

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 • In other words, the environment “selects” for the
propagation of beneficial traits
• Darwin called this process natural selection

Natural selection results in the adaptation of

organisms to their environment

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The Tree of Life
• “Unity in diversity” arises from “descent with
modification”
– For example, the forelimb of the bat, human, and
horse and the whale flipper all share a common
skeletal architecture
• Fossils provide additional evidence of anatomical
unity from descent with modification

© 2011 Pearson Education, Inc.

 • Darwin proposed that natural selection could
cause an ancestral species to give rise to two or
more descendent species
– For example, the finch species of the Galápagos
Islands are descended from a common ancestor
• Evolutionary relationships are often illustrated with
treelike diagrams that show ancestors and their
descendants

© 2011 Pearson Education, Inc.

SCIENTIFIC INQUIRY:

"the diverse ways in which scientists

study the natural world and propose
explanations based on the evidence
derived from their work. Scientific
inquiry also refers to the activities
through which students develop
knowledge and understanding of
scientific ideas, as well as an
understanding of how scientists study
the natural world." NSTA
Scientific inquiry is a powerful
way of understanding science
content. Students learn how to
ask questions and use evidence
to answer them. In the process
of learning the strategies of
scientific inquiry, students learn
to conduct an investigation and
collect evidence from a variety
of sources, develop an
explanation from the data, and
communicate and defend their
conclusions.
In studying nature, scientists make
observations and then form and test
hypotheses
• The word science is derived from Latin and
means “to know”
• Inquiry is the search for information and
explanation
• The scientific process includes making
observations, forming logical hypotheses, and
testing them

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Making Observations
• Biologists describe natural structures and
processes
• This approach is based on observation and the
analysis of data

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Types of Data
• Data are recorded observations or items of
information; these fall into two categories
– Qualitative data, or descriptions rather than
measurements
• For example, Jane Goodall’s observations of
chimpanzee behavior
– Quantitative data, or recorded measurements,
which are sometimes organized into tables and
graphs

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Inductive Reasoning
• Inductive reasoning draws conclusions through
the logical process of induction
• Repeating specific observations can lead to
important generalizations
– For example, “the sun always rises in the east”

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Forming and Testing Hypotheses
• Observations and inductive reasoning can lead us
to ask questions and propose hypothetical
explanations called hypotheses

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The Role of Hypotheses in Inquiry
• A hypothesis is a tentative answer to a well-
framed question
• A scientific hypothesis leads to predictions that
can be tested by observation or experimentation

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Deductive Reasoning and Hypothesis Testing
• Deductive reasoning uses general premises to
make specific predictions
• For example, if organisms are made of cells
(premise 1), and humans are organisms
(premise 2), then humans are composed of cells
(deductive prediction)

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Questions That Can and Cannot Be
Addressed by Science
• A hypothesis must be testable and falsifiable

• Supernatural and religious explanations are

outside the bounds of science

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The Flexibility of the Scientific Method
• The scientific method is an idealized process of
inquiry
• Hypothesis-based science is based on the
“textbook” scientific method but rarely follows all
the ordered steps

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 • In science, observations and experimental results
must be repeatable

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Theories in Science
• In the context of science, a theory is
– Broader in scope than a hypothesis
– General, and can lead to new testable hypotheses
– Supported by a large body of evidence in
comparison to a hypothesis

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Science benefits from a cooperative
approach and diverse viewpoints

• Most scientists work in teams, which often include

graduate and undergraduate students
• Good communication is important in order to share
results through seminars, publications, and
websites

© 2011 Pearson Education, Inc.

Building on the Work of Others
• Scientists check each others’ claims by performing
similar experiments
• It is not unusual for different scientists to work on
the same research question
• Scientists cooperate by sharing data about model
organisms (e.g., the fruit fly Drosophila
melanogaster)

© 2011 Pearson Education, Inc.

Science, Technology, and Society
• The goal of science is to understand natural
phenomena
• The goal of technology is to apply scientific
knowledge for some specific purpose
• Science and technology are interdependent
• Biology is marked by “discoveries,” while
technology is marked by “inventions”

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 • The combination of science and technology has
dramatic effects on society
– For example, the discovery of DNA by James
Watson and Francis Crick allowed for advances in
DNA technology such as testing for hereditary
diseases
• Ethical issues can arise from new technology, but
have as much to do with politics, economics, and
cultural values as with science and technology

© 2011 Pearson Education, Inc.

The Value of Diverse Viewpoints in Science
• Many important inventions have occurred
where different cultures and ideas mix
– For example, the printing press relied on
innovations from China (paper and ink) and
Europe (mass production in mills)
• Science benefits from diverse views from
different racial and ethnic groups, and from
both women and men

© 2011 Pearson Education, Inc.

Please indicate your answers to the following Questions and
save this document- Review of content and submission of
answers will be discussed the first week of class.
Which of the following is not a theme that unifies
biology?

A. systems biology
B. emergent properties
C. inductive reasoning
D. reductionism
E. genomics

© 2014 Pearson Education, Inc.

What is the correct order (from small to large)?

A. cells, organelles, organ system, community,

ecosystems
B. molecules, organism, population, communities,
biosphere
C. molecules, cells, tissues, ecosystems, communities
D. organelles, cells, population, biosphere, ecosystems
E. cells, organs, population, ecosystems, communities

© 2014 Pearson Education, Inc.

Which of the following scientific studies would represent an
example of a “systems biology” approach?

A. measuring the effect of an invading insect that eats

oak leaves on the numbers of oak trees and on any
subsequent changes in the number and types of
decomposer fungi in the soil
B. discovering the structure of an enzyme that is important in
digestion of protein
C. comparing the microscopic structure of leaves of two
different species of magnolias
D. measuring the reproductive rate of emperor penguins
during exceptionally warm and exceptionally cold years
E. comparing the DNA sequence of two closely related plants
and inferring their evolutionary histories
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Like jackrabbits, elephants have many blood vessels in
their ears that help them cool their bodies by radiating
heat. Which of the following statements about this
radiated energy would be accurate?

A. The original source of the energy was the sun.

B. The energy will be recycled through the ecosystem.
C. The radiated energy will be trapped by predators of
the elephants.
D. More energy is radiated in cold conditions than in
hot conditions.
E. More energy is radiated at night than during the
day.

© 2014 Pearson Education, Inc.

The idea that form and function are related would not
be exemplified by which of the following examples?

A. Cells in the intestinal lining of vertebrates have

many small projections that increase the surface
area for absorption of nutrients.
B. Plants that live in dry areas have large roots for
absorbing water.
C. Seeds that are dispersed by wind are very light.
D. Fish that swim rapidly have bodies that are
streamlined.
E. none of the above

© 2014 Pearson Education, Inc.

Imagine that you have just discovered a new multicellular
but microscopic organism that swims in ponds. You see
that it is propelled by cilia on the outside of the organism.
What can you say about the evolutionary relationships of
this organism?

A. The presence of cilia shows that it is more closely

related to Paramecium than to humans.
B. The presence of cilia shows that it shares a
common ancestor with Paramecium and humans.
C. It is probably closely related to pond algae.
D. It is probably most closely related to prokaryotes.
E. The presence of cilia demonstrates the diversity, but
not the unity, of life.
© 2014 Pearson Education, Inc.
Examine the figure on the next slide and predict which
species pair has the most similar DNA sequence.

A. vegetarian tree finch (Platyspiza crassirostris) and

mangrove finch (Cactospiza heliobates)
B. medium tree finch (Camarhynchus pauper) and
large tree finch (Camarhynchus psittacula)
C. large tree finch (Camarhynchus psittacula) and
small tree finch (Camarhynchus parvulus)
D. sharp-beaked ground finch (Geospiza difficilis) and
large ground finch (Geospiza magnirostris)
E. No such predictions are possible.

© 2014 Pearson Education, Inc.

© 2014 Pearson Education, Inc.
Which of the following is an activity that would not reflect the
practice of science?

A. Science is typically performed alone in the lab.

B. Data are typically collected by teams of students and
experienced researchers.
C. Scientists typically reexamine conclusions or repeat
experiments from other large, famous labs.
D. Scientists who work in forests studying ecology often
collaborate closely with geneticists who work only in the
lab.
E. The practice of science results in a discovery that lends
new insight, and technology involves how this new
insight will be applied to develop a new drug.
© 2014 Pearson Education, Inc.
Overview: A Chemical Connection to Biology

§ Biology is a multidisciplinary science

§ Living organisms are subject to basic laws of physics
and chemistry

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 Matter consists of chemical elements in pure form
and in combinations called compounds

§ Organisms are composed of matter

§ Matter is anything that takes up space and has
mass

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Elements and Compounds

§ Matter is made up of elements

§ An element is a substance that cannot be broken
down to other substances by chemical reactions
§ A compound is a substance consisting of two or
more elements in a fixed ratio
§ A compound has emergent properties,
characteristics different from those of its elements

© 2014 Pearson Education, Inc.

The Elements of Life

§ Of 92 natural elements, about 20–25% are essential

elements, needed by an organism to live a healthy
life and reproduce
§ Trace elements are required in only minute
quantities
§ For example, in vertebrates, iodine (I) is required for
normal activity of the thyroid gland
§ In humans, an iodine deficiency can cause goiter

© 2014 Pearson Education, Inc.

Evolution of Tolerance to Toxic Elements

§ Some naturally occurring elements are toxic to

organisms
§ In humans, arsenic is linked to many diseases and
can be lethal
§ Some species have become adapted to environments
containing elements that are usually toxic
§ For example, sunflower plants can take up lead, zinc,
and other heavy metals in concentrations lethal to
most organisms
§ Sunflower plants were used to detoxify contaminated
soils after Hurricane Katrina
© 2014 Pearson Education, Inc.
 An element s properties depend on the structure
of its atoms
§ Each element consists of a certain type of atom,
different from the atoms of any other element
§ An atom is the smallest unit of matter that still
retains the properties of an element

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Subatomic Particles

§ Atoms are composed of smaller parts called

subatomic particles
§ Relevant subatomic particles include
§ Neutrons (no electrical charge)
§ Protons (positive charge)
§ Electrons (negative charge)

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§ Neutrons and protons form the atomic nucleus
§ Electrons form a cloud around the nucleus
§ Neutron mass and proton mass are almost identical
and are measured in daltons

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 Simplified models of a helium (He) atom

Cloud of negative Electrons

charge (2 electrons)
Nucleus

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Atomic Number and Atomic Mass

§ Atoms of the various elements differ in number of

subatomic particles
§ An element’s atomic number is the number of
protons in its nucleus
§ An element s mass number is the sum of protons
plus neutrons in the nucleus
§ Atomic mass, the atom s total mass, can be
approximated by the mass number

© 2014 Pearson Education, Inc.

 Mass number = number of protons + neutrons
= 23 for sodium

23Na
11

Atomic number = number of protons

= 11 for sodium
Because neutrons and protons each have a mass of approximately
1 dalton, we can estimate the atomic mass (total mass of one atom)
of sodium as 23 daltons
© 2014 Pearson Education, Inc.
Isotopes

§ All atoms of an element have the same number of

protons but may differ in number of neutrons
§ Isotopes are two atoms of an element that differ in
number of neutrons
§ Radioactive isotopes decay spontaneously,
giving off particles and energy

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§ Some applications of radioactive isotopes in
biological research are
§ Dating fossils
§ Tracing atoms through metabolic processes
§ Diagnosing medical disorders

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The Energy Levels of Electrons

§ Energy is the capacity to cause change

§ Potential energy is the energy that matter has
because of its location or structure
§ The electrons of an atom differ in their amounts of
potential energy
§ Changes in potential energy occur in steps of fixed
amounts
§ An electron s state of potential energy is called its
energy level, or electron shell

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§ Electrons are found in different electron shells,
each with a characteristic average distance from the
nucleus
§ The energy level of each shell increases with
distance from the nucleus
§ Electrons can move to higher or lower shells by
absorbing or releasing energy, respectively

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A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons.

Third shell (highest

energy level in this
model)
Second shell (higher Energy
energy level) absorbed

First shell (lowest

energy level)
Energy
lost
Atomic
nucleus
Electron Distribution and Chemical Properties

§ The chemical behavior of an atom is determined by

the distribution of electrons in electron shells
§ The periodic table of the elements shows the
electron distribution for each element

© 2014 Pearson Education, Inc.

 Figure 2.6

Hydrogen 2 Atomic number Helium

1H He 2He
Atomic mass 4.00
First Element symbol
shell
Electron
distribution
diagram

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

3Li 4Be 5B 6C 7N 8O 9F 10Ne

Second
shell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar

Third
shell

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§ Chemical behavior of an atom depends mostly on the
number of electrons in its outermost shell, or valence
shell
§ Valence electrons are those that occupy the
valence shell
§ The reactivity of an atom arises from the presence of
one or more unpaired electrons in the valence shell
§ Atoms with completed valence shells are unreactive,
or inert

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The formation and function of molecules depend
on chemical bonding between atoms

§ Atoms with incomplete valence shells can share or

transfer valence electrons with certain other atoms
§ This usually results in atoms staying close together,
held by attractions called chemical bonds

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Covalent Bonds

§ A covalent bond is the sharing of a pair of valence

electrons by two atoms
§ In a covalent bond, the shared electrons count as
part of each atom s valence shell
§ Two or more atoms held together by valence bonds
constitute a molecule

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 Hydrogen atoms (2 H)

Formation of a covalent bond

Hydrogen
molecule (H2)
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§ The notation used to represent atoms and bonding
is called a structural formula
§ For example, H—H
§ This can be abbreviated further with a molecular
formula
§ For example, H2

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§ In a structural formula, a single bond, the sharing of
one pair of electrons, is indicated by a single line
between the atoms
§ For example, H—H

§ A double bond, the sharing of two pairs of electrons,

is indicated by a double line between atoms
§ For example, O O

© 2014 Pearson Education, Inc.

 Covalent bonding in
four molecules Name and Electron Structural Space-
Molecular Distribution Formula Filling
Formula Diagram Model
(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

(d) Methane (CH4)

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§ Each atom that can share valence electrons has a
bonding capacity, the number of bonds that the
atom can form
§ Bonding capacity, or valence, usually corresponds
to the number of electrons required to complete the
atom

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§ Pure elements are composed of molecules of one
type of atom, such as H2 and O2

§ Molecules composed of a combination of two or

more types of atoms are called compounds, such as
H2O or CH4

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§ Atoms in a molecule attract electrons to varying
degrees
§ Electronegativity is an atom s attraction for the
electrons in a covalent bond
§ The more electronegative an atom, the more
strongly it pulls shared electrons toward itself

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§ In a nonpolar covalent bond, the atoms share the
electron equally
§ In a polar covalent bond, one atom is more
electronegative, and the atoms do not share the
electron equally
§ Unequal sharing of electrons causes a partial positive
or negative charge for each atom or molecule

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 Polar covalent bonds in a water molecule

d−

H H
d+ d+
H2O

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Ionic Bonds

§ Atoms sometimes strip electrons from their bonding

partners
§ An example is the transfer of an electron from
sodium to chlorine
§ After the transfer of an electron, both atoms have
charges
§ Both atoms also have complete valence shells

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 Electron transfer and ionic bonding

+ −

Na Cl Na Cl

Na Cl Na+ Cl−
Sodium atom Chlorine atom Sodium ion Chloride ion
(a cation) (an anion)

Sodium chloride (NaCl)

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§ A cation is a positively charged ion
§ An anion is a negatively charged ion
§ An ionic bond is an attraction between an anion and
a cation

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§ Compounds formed by ionic bonds are called ionic
compounds, or salts
§ Salts, such as sodium chloride (table salt), are
often found in nature as crystals

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 A sodium chloride (NaCl) crystal

Na+
Cl−

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Weak Chemical Bonds

§ Most of the strongest bonds in organisms are

covalent bonds that form a cell s molecules
§ Weak chemical bonds, such as ionic bonds and
hydrogen bonds, are also important
§ Many large biological molecules are held in their
functional form by weak bonds

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Hydrogen Bonds

§ A hydrogen bond forms when a hydrogen atom

covalently bonded to one electronegative atom is
also attracted to another electronegative atom
§ In living cells, the electronegative partners are
usually oxygen or nitrogen atoms

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 d− d+

Water (H2O)

d+
Hydrogen bond
d−

Ammonia (NH3)

d+ d+

d+
© 2014 Pearson Education, Inc.
Van der Waals Interactions

§ If electrons are distributed asymmetrically in

molecules or atoms, they can result in hot spots
of positive or negative charge
§ Van der Waals interactions are attractions
between molecules that are close together as a
result of these charges

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§ Van der Waals interactions are individually weak
and occur only when atoms and molecules are
very close together
§ Collectively, such interactions can be strong, as
between molecules of a gecko s toe hairs and a
wall surface

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Molecular Shape and Function

§ A molecule s shape is usually very important to its

function
§ Molecular shape determines how biological
molecules recognize and respond to one another

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§ Biological molecules recognize and interact with each
other with a specificity based on molecular shape
§ Molecules with similar shapes can have similar
biological effects

© 2014 Pearson Education, Inc.

 Figure 2.14
Key
Carbon Nitrogen
Natural endorphin Hydrogen Sulfur
Oxygen

Morphine

(a) Structures of endorphin and morphine

Natural
endorphin Morphine

Endorphin
Brain cell receptors

(b) Binding to endorphin receptors

© 2014 Pearson Education, Inc.
Chemical reactions make and break chemical
bonds
§ Chemical reactions are the making and breaking
of chemical bonds
§ The starting molecules of a chemical reaction are
called reactants
§ The final molecules of a chemical reaction are
called products

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§ Photosynthesis is an important chemical reaction
§ Sunlight powers the conversion of carbon dioxide
and water to glucose and oxygen
6 CO2 +6 H2O à C6H12O6 + 6 O2

© 2014 Pearson Education, Inc.

§ All chemical reactions are reversible: Products of the
forward reaction become reactants for the reverse
reaction
§ Chemical equilibrium is reached when the forward
and reverse reaction rates are equal

© 2014 Pearson Education, Inc.

Hydrogen bonding gives water properties that
help make life possible on Earth
§ All organisms are made mostly of water and live in
an environment dominated by water
§ Water molecules are polar, with the oxygen region
having a partial negative charge (δ−) and the
hydrogen region a slight positive charge (δ+)
§ Two water molecules are held together by a
hydrogen bond

© 2014 Pearson Education, Inc.

 Hydrogen bonds between water molecules

Hydrogen
bond

Polar covalent
bonds

© 2014 Pearson Education, Inc.

 ****
§ Four emergent properties of water contribute to
Earth s suitability for life:
§ Cohesive behavior
§ Ability to moderate temperature
§ Expansion upon freezing
§ Versatility as a solvent

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Cohesion of Water Molecules

§ Water molecules are linked by multiple hydrogen

bonds
§ The molecules stay close together because of this;
it is called cohesion

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§ Cohesion due to hydrogen bonding contributes to
the transport of water and nutrients against gravity
in plants
§ Adhesion, the clinging of one substance to
another, also plays a role

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 Adhesion

Two types of
water-conducting
cells

Cohesion
Direction
of water
movement 300 mm

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§ Surface tension is a measure of how hard it is to
break the surface of a liquid
§ Surface tension is related to cohesion

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Moderation of Temperature by Water

§ Water absorbs heat from warmer air and releases

stored heat to cooler air
§ Water can absorb or release a large amount of heat
with only a slight change in its own temperature

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Temperature and Heat

§ Kinetic energy is the energy of motion

§ Thermal energy is a measure of the total amount of
kinetic energy due to molecular motion
§ Temperature represents the average kinetic energy
of molecules
§ Thermal energy in transfer from one body of matter
to another is defined as heat

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§ The Celsius scale is a measure of temperature
using Celsius degrees (oC)
§ A calorie (cal) is the amount of heat required to
raise the temperature of 1 g of water by 1oC

§ The Calories on food packages are actually

kilocalories (kcal), where 1 kcal = 1,000 calories
§ The joule (J) is another unit of energy, where
1 J = 0.239 cal, or 1 cal = 4.184 J

© 2014 Pearson Education, Inc.

Water s High Specific Heat

§ The specific heat of a substance is the amount of

heat that must be absorbed or lost for 1 g of that
substance to change its temperature by 1oC
§ The specific heat of water is 1 cal/g/oC
§ Water resists changing its temperature because of
its high specific heat

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§ Water s high specific heat can be traced to
hydrogen bonding
§ Heat is absorbed when hydrogen bonds break
§ Heat is released when hydrogen bonds form
§ The high specific heat of water keeps temperature
fluctuations within limits that permit life

© 2014 Pearson Education, Inc.

 Burbank San Bernardino
Santa Barbara 73° 100°
90°
Los Angeles Riverside 96°
(Airport) 75° Santa Ana
84° Palm Springs
70s (°
F) 106°
80s
Pacific Ocean 68°
90s
100s San Diego 72° 40 miles

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Evaporative Cooling

§ Evaporation is transformation of a substance from

liquid to gas
§ Heat of vaporization is the heat a liquid must absorb
for 1 g to be converted to gas
§ As a liquid evaporates, its remaining surface cools, a
process called evaporative cooling
§ Evaporative cooling of water helps stabilize
temperatures in organisms and bodies of water

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Floating of Ice on Liquid Water

§ Ice floats in liquid water because hydrogen bonds

in ice are more ordered, making ice less dense
§ Water reaches its greatest density at 4oC

§ If ice sank, all bodies of water would eventually

freeze solid, making life impossible on Earth

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 Hydrogen bond Liquid water:
Hydrogen bonds
break and re-form

Ice:
Hydrogen bonds
are stable

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Water: The Solvent of Life

§ A solution is a liquid that is a homogeneous mixture

of substances
§ A solvent is the dissolving agent of a solution
§ The solute is the substance that is dissolved
§ An aqueous solution is one in which water is the
solvent

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§ Water is a versatile solvent due to its polarity, which
allows it to form hydrogen bonds easily
§ When an ionic compound is dissolved in water, each
ion is surrounded by a sphere of water molecules
called a hydration shell

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 Na+

Na+

Cl− Cl−

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§ Water can also dissolve compounds made of
nonionic polar molecules
§ Even large polar molecules such as proteins can
dissolve in water if they have ionic and polar regions

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 A water-soluble protein

d+

d−

d+

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Hydrophilic and Hydrophobic Substances

§ A hydrophilic substance is one that has an affinity

for water
§ A hydrophobic substance is one that does not
have an affinity for water
§ Oil molecules are hydrophobic because they have
relatively nonpolar bonds
§ A colloid is a stable suspension of fine particles in
a liquid

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Solute Concentration in Aqueous Solutions

§ Most biochemical reactions occur in water

§ Chemical reactions depend on collisions of molecules
and therefore on the concentration of solutes in an
aqueous solution

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§ Molecular mass is the sum of all masses of all
atoms in a molecule
§ Numbers of molecules are usually measured in
moles, where 1 mole (mol) = 6.02 X1023 molecules
§ Avogadro s number and the unit dalton were defined
such that 6.02 X1023 daltons = 1 g
§ Molarity (M) is the number of moles of solute per liter
of solution

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Acids and Bases

§ Sometimes a hydrogen ion (H+ ) is transferred from

one water molecule to another, leaving behind a
hydroxide ion (OH−)
§ The proton (H+ ) binds to the other water molecule,
forming a hydronium ion (H3O+)
§ By convention, H+ is used to represent the
hydronium ion

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 + −

2 H2 O Hydronium Hydroxide
ion (H3O+) ion (OH−)

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§ Though water dissociation is rare and reversible, it
is important in the chemistry of life
§ H+ and OH− are very reactive
§ Solutes called acids and bases disrupt the balance
between H+ and OH− in pure water
§ Acids increase the H+ concentration in water, while
bases reduce the concentration of H+

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§ An acid is any substance that increases the H+
concentration of a solution
§ A base is any substance that reduces the H+
concentration of a solution

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§ A strong acid like hydrochloric acid, HCl, dissociates
completely into H+ and Cl− in water:
HCl à H+ + Cl−

§ Sodium hydroxide, NaOH, acts as a strong base

indirectly by dissociating completely to form
hydroxide ions

§ These combine with H+ ions to form water:

NaOH àNa+ + OH−

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§ Ammonia, NH3, acts as a relatively weak base when
it attracts an H+ ion from the solution and forms
ammonium, NH4+
§ This is a reversible reaction, as shown by the double
arrows:
NH3 +H+ NH4+

§ Carbonic acid, H2CO3, acts as a weak acid, which

can reversibly release and accept back H+ions:

H2CO3 HCO3− + H+

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The pH Scale

§ In any aqueous solution at 25oC, the product of H+

and OH− is constant and can be written as

[H+][OH−] = 10−14

§ The pH of a solution is defined by the negative

logarithm of H+ concentration, written as

pH = −log [H+]

§ For a neutral aqueous solution, [H+] is 10−7, so

−log [H+] = −(−7) = 7
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§ Acidic solutions have pH values less than 7
§ Basic solutions have pH values greater than 7
§ Most biological fluids have pH values in the range of
6 to 8

© 2014 Pearson Education, Inc.

 pH Scale

1
Battery acid

Increasingly Acidic
2 Gastric juice, lemon juice

[H+] >[OH−]
3 Vinegar, wine,
cola
4 Tomato juice
Acidic
solution Beer
5 Black coffee
Rainwater
6 Urine
Saliva
Neutral 7 Pure water
[H+] =[OH−] Human blood, tears
8 Seawater
Neutral
Inside of small intestine
solution
Increasingly Basic

9
[H+] <[OH−]

10
Milk of magnesia
11
Household ammonia
12
Basic
solution Household
13 bleach
Oven cleaner
14
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Buffers

§ The internal pH of most living cells must remain close

to pH 7
§ Buffers are substances that minimize changes in
concentrations of H+ and OH− in a solution
§ Most buffers consist of an acid-base pair that
reversibly combines with H+

© 2014 Pearson Education, Inc.

§ Carbonic acid is a buffer that contributes to pH
stability in human blood:

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Acidification: A Threat to Our Oceans

§ Human activities such as burning fossil fuels threaten

water quality
§ CO2 is the main product of fossil fuel combustion
§ About 25% of human-generated CO2 is absorbed by
the oceans
§ CO2 dissolved in seawater forms carbonic acid; this
causes ocean acidification

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§ As seawater acidifies, H+ ions combine with
CO32− ions to form bicarbonate ions (HCO3–)
§ It is predicted that carbonate ion concentrations
will decline by 40% by the year 2100
§ This is a concern because organisms that build
coral reefs or shells require carbonate ions

© 2014 Pearson Education, Inc.

 CO2

CO2 +H2O ® H2CO3

Atmospheric CO2 H2CO3 ® H++HCO3−

from human
activities and its H++CO32− ® HCO3−
fate in the ocean
CO32− +Ca2+ ® CaCO3

© 2014 Pearson Education, Inc.

Please indicate your answers to the following Questions and
save this document- Review of content and submission of
answers will be discussed the first week of class.
Based on the periodic table shown here, which
elements will most likely form an ionic bond?

A. Na and Cl, and Li and F

B. C and O
C. N and O
D. Si and Cl
E. all of the above

© 2014 Pearson Education, Inc.

Based on the periodic table shown here, which
elements will most likely form a covalent bond?

A. Na and Cl
B. C and O
C. N and O
D. Si and Cl
E. H and H

© 2014 Pearson Education, Inc.

What do elements with atomic numbers 6, 14, and
22 have in common?

A. same number of electrons

B. same atomic mass
C. same valence and will form the same number
of covalent bonds
D. all of the above
E. none of the above

© 2014 Pearson Education, Inc.

What type of bond is very prevalent in lipids and
gives lipids their properties?

A. polar covalent
B. nonpolar covalent
C. strong ionic bond
D. weak ionic bond
E. hydrogen bond

© 2014 Pearson Education, Inc.

Water shows high cohesion and surface tension and
can absorb large amounts of heat because of large
numbers of which of the following bonds between
water molecules? Solutions of other molecules have
much less bonding between molecules.

A. strong ionic bonds

B. nonpolar covalent bonds
C. polar covalent bonds
D. hydrogen bonds
E. weak ionic bonds

© 2014 Pearson Education, Inc.

Which of the following observations would distinguish
between the alternative hypotheses that geckos walk
on vertical surfaces via either hydrogen bonding or
van der Waals interactions?

A. Geckos can walk up dry surfaces.

B. Geckos can walk up smooth glass surfaces—
silicon dioxide is a polar, hydrophilic compound.
C. Geckos can walk up smooth plastic surfaces—
plastics are hydrophobic.

© 2014 Pearson Education, Inc.

What are the four emergent properties of water that
are important for life?

A. cohesion, expansion upon freezing, high heat of

evaporation, capillarity
B. cohesion, moderation of temperature,
expansion upon freezing, solvent properties
C. moderation of temperature, solvent properties,
high surface tension, capillarity
D. heat of vaporization, high specific heat, high
surface tension, capillarity
E. polarity, hydrogen bonding, high specific heat,
high surface tension
© 2014 Pearson Education, Inc.
Water has an unusually high specific heat. This is
directly related to which one of the following?

A. At its boiling point, water changes from liquid to

vapor.
B. More heat is required to raise the temperature
of water.
C. Ice floats in liquid water.
D. Salt water freezes at a lower temperature than
pure water.
E. Floating ice can insulate bodies of water.

© 2014 Pearson Education, Inc.

Surfactants reduce surface tension of a liquid.
Which of the following would result if water was
treated with surfactants?

A. Surfactant-treated water droplets will form a thin

film instead of beading on a waxed surface.
B. Surfactant-treated water will form smaller
droplets when dripping from a sink.
C. Water striders will sink.
D. All of the above will occur.
E. Only A and C will occur.

© 2014 Pearson Education, Inc.

Overview: Carbon Compounds and Life

§ Aside from water, living organisms consist mostly

of carbon-based compounds
§ Carbon is unparalleled in its ability to form large,
complex, and diverse molecules
§ A compound containing carbon is said to be an
organic compound

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§ Critically important molecules of all living things fall
into four main classes
§ Carbohydrates
§ Lipids
§ Proteins
§ Nucleic acids
§ The first three of these can form huge molecules
called macromolecules

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Carbon atoms can form diverse molecules by
bonding to four other atoms
§ An atom’s electron configuration determines the
kinds and number of bonds the atom will form with
other atoms
§ This is the source of carbon’s versatility

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The Formation of Bonds with Carbon

§ With four valence electrons, carbon can form four

covalent bonds with a variety of atoms
§ This ability makes large, complex molecules
possible
§ In molecules with multiple carbons, each carbon
bonded to four other atoms has a tetrahedral shape
§ However, when two carbon atoms are joined by a
double bond, the atoms joined to the carbons are in
the same plane as the carbons

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§ When a carbon atom forms four single covalent
bonds, the bonds angle toward the corners of an
imaginary tetrahedron
§ When two carbon atoms are joined by a double bond,
the atoms joined to those carbons are in the same
plane as the carbons

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 Molecular Structural Ball-and-Stick Space-Filling
Name
Formula Formula Model Model

Methane

Ethane

Ethene
(ethylene)

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§ The electron configuration of carbon gives it covalent
compatibility with many different elements
§ The valences of carbon and its most frequent
partners (hydrogen, oxygen, and nitrogen) are the
building code that governs the architecture of living
molecules

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 Valences of the major elements of organic molecules

Hydrogen Oxygen Nitrogen Carbon

(valence =1) (valence =2) (valence =3) (valence =4)

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§ Carbon atoms can partner with atoms other than
hydrogen; for example:
§ Carbon dioxide: CO2

§ Urea: CO(NH2)2

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Molecular Diversity Arising from Variation in
Carbon Skeletons
§ Carbon chains form the skeletons of most organic
molecules
§ Carbon chains vary in length and shape

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 Four ways that carbon skeletons can vary

(a) Length (c) Double bond position

Ethane Propane 1-Butene 2-Butene

(b) Branching (d) Presence of rings

Butane 2-Methylpropane Cyclohexane Benzene

(isobutane)

© 2014 Pearson Education, Inc.

***Some Chemical Group Compound Name Examples
Hydroxyl group ( OH)
biologically Alcohol
Ethanol

important
Carbonyl group ( C O)
chemical Ketone

Aldehyde
groups Acetone Propanal
Carboxyl group ( COOH)

Carboxylic acid,
or organic acid
Acetic acid

Amino group ( NH2)

Amine

Glycine
Sulfhydryl group ( SH)

Thiol Cysteine

Phosphate group ( OPO32–)

Glycerol
Organic
phosphate
phosphate

Methyl group ( CH3)

Methylated 5-Methyl cytosine

compound

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 Hydroxyl group ( OH)
Alcohol
(The specific name
usually ends in -ol.)
(may be written HO )

Ethanol, the alcohol present

in alcoholic beverages

© 2014 Pearson Education, Inc.

 Carbonyl group ( C O)
Ketone if the carbonyl
group is within a carbon
skeleton

Aldehyde if the carbonyl

group is at the end of a
carbon skeleton

Acetone, the simplest ketone Propanal, an aldehyde

© 2014 Pearson Education, Inc.

 Carboxyl group ( COOH)

Carboxylic acid, or
organic acid

Acetic acid, which gives Ionized form of COOH

vinegar its sour taste (carboxylate ion),
found in cells

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 Amino group ( NH2)

Amine

Glycine, an amino acid Ionized form of NH2

(note its carboxyl group) found in cells

© 2014 Pearson Education, Inc.

 Sulfhydryl group ( SH)

Thiol
(may be written HS )

Cysteine, a sulfur-
containing amino acid

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 Phosphate group ( OPO32–)

Organic phosphate

Glycerol phosphate, which

takes part in many important
chemical reactions in cells

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 Methyl group ( CH3)

Methylated compound

5-Methyl cytosine, a
component of DNA that has
been modified by addition of
a methyl group

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ATP: An Important Source of Energy for Cellular
Processes
§ One organic phosphate molecule, adenosine
triphosphate (ATP), is the primary energy-
transferring molecule in the cell
§ ATP consists of an organic molecule called
adenosine attached to a string of three phosphate
groups

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 Reacts
with H2O
Adenosine Adenosine Energy
ATP Inorganic ADP
phosphate

© 2014 Pearson Education, Inc.

Macromolecules are polymers, built from monomers

§ A polymer is a long molecule consisting of many

similar building blocks
§ These small building-block molecules are called
monomers
§ Some molecules that serve as monomers also have
other functions of their own

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The Synthesis and Breakdown of Polymers

§ Cells make and break down polymers by the same

process
§ A dehydration reaction occurs when two monomers
bond together through the loss of a water molecule
§ Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the reverse
of the dehydration reaction
§ These processes are facilitated by enzymes, which
speed up chemical reactions

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 Dehydration reaction: synthesizing a polymer

Short polymer Unlinked monomer

Dehydration removes
a water molecule,
forming a new bond.

Longer polymer

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 Hydrolysis: breaking down a polymer

Hydrolysis adds
a water molecule,
breaking a bond.

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The Diversity of Polymers

§ Each cell has thousands of different macromolecules

HO

§ Macromolecules vary among cells of an organism,

vary more within a species, and vary even more
between species
§ An immense variety of polymers can be built from a
small set of monomers

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 Carbohydrates serve as fuel and building material

§ Carbohydrates include sugars and the polymers of

sugars
§ The simplest carbohydrates are monosaccharides,
or simple sugars
§ Carbohydrate macromolecules are polysaccharides,
polymers composed of many sugar building blocks

© 2014 Pearson Education, Inc.

Sugars

§ Monosaccharides have molecular formulas that

are usually multiples of CH2O
§ Glucose (C6H12O6) is the most common
monosaccharide
§ Monosaccharides are classified by the number of
carbons in the carbon skeleton and the placement
of the carbonyl group

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 Triose: 3-carbon sugar (C3H6O3) Pentose: 5-carbon sugar (C5H10O5)

Glyceraldehyde
An initial breakdown Ribose
product of glucose in cells A component of RNA

Examples of monosaccharides
Hexoses: 6-carbon sugars (C6H12O6)

Glucose Fructose
Energy sources for organisms
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§ Though often drawn as linear skeletons, in aqueous
solutions many sugars form rings
§ Monosaccharides serve as a major fuel for cells and
as raw material for building molecules

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 Linear and ring forms

Abbreviated ring structure

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§ A disaccharide is formed when a dehydration
reaction joins two monosaccharides
§ This covalent bond is called a glycosidic linkage

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 Glucose Fructose

1–2
glycosidic
linkage

Sucrose

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Polysaccharides

§ Polysaccharides, the polymers of sugars, have

storage and structural roles
§ The structure and function of a polysaccharide are
determined by its sugar monomers and the positions
of glycosidic linkages

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Storage Polysaccharides

§ Starch, a storage polysaccharide of plants, consists

entirely of glucose monomers
§ Plants store surplus starch as granules
§ The simplest form of starch is amylose

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§ Glycogen is a storage polysaccharide in animals
§ Humans and other vertebrates store glycogen
mainly in liver and muscle cells

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 Figure 3.10

Starch granules
in a potato tuber cell Starch (amylose)

Glucose
monomer
Glycogen granules
in muscle
tissue Glycogen

Cellulose microfibrils
in a plant cell wall Cellulose

Cellulose
Hydrogen bonds
molecules
between —OH groups
(not shown) attached to
carbons 3 and 6

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Structural Polysaccharides

§ The polysaccharide cellulose is a major component

of the tough wall of plant cells
§ Like starch and glycogen, cellulose is a polymer of
glucose, but the glycosidic linkages in cellulose differ
§ The difference is based on two ring forms for
glucose

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§ In starch, the glucose monomers are arranged in
the alpha (a) conformation
§ Starch (and glycogen) are largely helical
§ In cellulose, the monomers are arranged in the beta
(b) conformation
§ Cellulose molecules are relatively straight

© 2014 Pearson Education, Inc.

 aand bglucose
ring structures

aGlucose bGlucose

Starch: 1–4 linkage of aglucose monomers

Cellulose: 1–4 linkage of bglucose monomers

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§ In straight structures (cellulose), H atoms on one
strand can form hydrogen bonds with OH groups on
other strands
§ Parallel cellulose molecules held together this way
are grouped into microfibrils, which form strong
building materials for plants

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§ Enzymes that digest starch by hydrolyzing alinkages
can’t hydrolyze blinkages in cellulose
§ Cellulose in human food passes through the
digestive tract as insoluble fiber
§ Some microbes use enzymes to digest cellulose
§ Many herbivores, from cows to termites, have
symbiotic relationships with these microbes

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§ Chitin, another structural polysaccharide, is found in
the exoskeleton of arthropods
§ Chitin also provides structural support for the cell
walls of many fungi

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 Lipids are a diverse group of hydrophobic molecules

§ Lipids do not form true polymers

§ The unifying feature of lipids is having little or no
affinity for water
§ Lipids are hydrophobic because they consist mostly
of hydrocarbons, which form nonpolar covalent bonds
§ The most biologically important lipids are fats,
phospholipids, and steroids

© 2014 Pearson Education, Inc.

Fats

§ Fats are constructed from two types of smaller

molecules: glycerol and fatty acids
§ Glycerol is a three-carbon alcohol with a hydroxyl
group attached to each carbon
§ A fatty acid consists of a carboxyl group attached
to a long carbon skeleton

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§ Fats separate from water because water molecules
hydrogen-bond to each other and exclude the fats
§ In a fat, three fatty acids are joined to glycerol by an
ester linkage, creating a triacylglycerol, or
triglyceride

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 Fatty acid
(in this case, palmitic acid)

Glycerol
One of three dehydration reactions in the synthesis of a fat

Ester linkage

(b) Fat molecule (triacylglycerol)

© 2014 Pearson Education, Inc.
§ Fatty acids vary in length (number of carbons) and
in the number and locations of double bonds
§ Saturated fatty acids have the maximum number
of hydrogen atoms possible and no double bonds
§ Unsaturated fatty acids have one or more double
bonds

© 2014 Pearson Education, Inc.

 Saturated fat Unsaturated fat

Structural
formula of a
saturated fat
molecule
Structural
formula
of an
unsaturated
Space-filling fat molecule
model of
stearic acid,
a saturated
fatty acid
Space-filling
model of oleic
acid, an
unsaturated
fatty acid Double bond
causes bending.

© 2014 Pearson Education, Inc.

§ Fats made from saturated fatty acids are called
saturated fats and are solid at room temperature
§ Most animal fats are saturated
§ Fats made from unsaturated fatty acids, called
unsaturated fats or oils, are liquid at room
temperature
§ Plant fats and fish fats are usually unsaturated

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§ The major function of fats is energy storage
§ Fat is a compact way for animals to carry their
energy stores with them

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Phospholipids

§ In a phospholipid, two fatty acids and a phosphate

group are attached to glycerol
§ The two fatty acid tails are hydrophobic, but the
phosphate group and its attachments form a
hydrophilic head
§ Phospholipids are major constituents of cell
membranes

© 2014 Pearson Education, Inc.

 Hydrophilic head
The structure of a phospholipid

Choline

Phosphate

Glycerol
Hydrophobic tails

Fatty acids

Hydrophilic
head

Hydrophobic
tails

Structural formula Space-filling model Phospholipid

symbol bilayer

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§ When phospholipids are added to water, they self-
assemble into a bilayer, with the hydrophobic tails
pointing toward the interior
§ This feature of phospholipids results in the bilayer
arrangement found in cell membranes

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Steroids

§ Steroids are lipids characterized by a carbon

skeleton consisting of four fused rings
§ Cholesterol, an important steroid, is a component in
animal cell membranes
§ Although cholesterol is essential in animals, high
levels in the blood may contribute to cardiovascular
disease

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 Cholesterol, a steroid

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 *** Proteins include a diversity of structures,
resulting in a wide range of functions
§ Proteins account for more than 50% of the dry mass
of most cells
§ Protein functions include defense, storage, transport,
cellular communication, movement, and structural
support

© 2014 Pearson Education, Inc.

 Protein Functions: An Overview

Enzymatic proteins Defensive proteins

Function: Selective acceleration of Function: Protection against disease
chemical reactions Example: Antibodies inactivate and help
Example: Digestive enzymes catalyze the destroy viruses and bacteria.
hydrolysis of bonds in food molecules.
Antibodies

Enzyme Virus Bacterium

Storage proteins Transport proteins

Function: Storage of amino acids Function: Transport of substances
Examples: Casein, the protein of milk, is Examples: Hemoglobin, the iron-containing
the major source of amino acids for baby protein of vertebrate blood, transports
mammals. Plants have storage proteins oxygen from the lungs to other parts of the
in their seeds. Ovalbumin is the protein body. Other proteins transport molecules
of egg white, used as an amino acid across cell membranes.
source for the developing embryo.
Transport
protein

Ovalbumin Amino acids

for embryo Cell membrane
© 2014 Pearson Education, Inc.
 Hormonal proteins Receptor proteins
Function: Coordination of an organism’s Function: Response of cell to chemical
activities stimuli
Example: Insulin, a hormone secreted by Example: Receptors built into the
the pancreas, causes other tissues to membrane of a nerve cell detect signaling
take up glucose, thus regulating blood molecules released by other nerve cells.
sugar concentration.
Receptor
protein
Insulin Signaling molecules
High secreted Normal
blood sugar blood sugar
Structural proteins
Contractile and motor proteins Function: Support
Function: Movement Examples: Keratin is the protein of hair,
Examples: Motor proteins are responsible horns, feathers, and other skin appendages.
for the undulations of cilia and flagella. Insects and spiders use silk fibers to make
Actin and myosin proteins are their cocoons and webs, respectively.
responsible for the contraction of Collagen and elastin proteins provide a
muscles. fibrous framework in animal connective
tissues.
Actin Myosin
Collagen

Muscle tissue 30 mm Connective tissue 60 mm

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§ Life would not be possible without enzymes
§ Enzymatic proteins act as catalysts, to speed up
chemical reactions without being consumed by the
reaction

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§ Polypeptides are unbranched polymers built from
the same set of 20 amino acids
§ A protein is a biologically functional molecule that
consists of one or more polypeptides

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Amino Acids

§ Amino acids are organic molecules with carboxyl

and amino groups
§ Amino acids differ in their properties due to differing
side chains, called R groups

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 Amino acid structure

Side chain (R group)

acarbon

Amino Carboxyl
group group

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 The 20 amino acids of Nonpolar side chains; hydrophobic
proteins: Side chain
(R group)

Glycine Alanine Valine Leucine Isoleucine

(Gly or G) (Ala or A) (Val or V) (Leu or L) (I
le or I
)

Methionine Phenylalanine Tryptophan Proline

(Met or M) (Phe or F) (Trp or W) (Pro or P)

Polar side chains; hydrophilic

Serine Threonine Cysteine Tyrosine Asparagine Glutamine

(Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q)

Electrically charged side chains; hydrophilic

Basic (positively charged)

Acidic (negatively charged)

Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)

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Polypeptides

§ Amino acids are linked by peptide bonds

§ A polypeptide is a polymer of amino acids
§ Polypeptides range in length from a few to more
than a thousand monomers
§ Each polypeptide has a unique linear sequence of
amino acids, with a carboxyl end (C-terminus) and
an amino end (N-terminus)

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 Making a
polypeptide chain

Peptide bond

New peptide
bond forming

Side
chains

Back-
bone

Amino end Peptide Carboxyl end

(N-terminus) bond (C-terminus)
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Protein Structure and Function

§ A functional protein consists of one or more

polypeptides precisely twisted, folded, and coiled
into a unique shape

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§ The sequence of amino acids, determined
genetically, leads to a protein’s three-dimensional
structure
§ A protein’s structure determines its function

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 An antibody binding to a protein from a flu virus

Antibody protein Protein from flu virus

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Four Levels of Protein Structure

§ Proteins are very diverse, but share three

superimposed levels of structure called primary,
secondary, and tertiary structure
§ A fourth level, quaternary structure, arises when a
protein consists of more than one polypeptide chain

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§ The primary structure of a protein is its unique
sequence of amino acids
§ Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide chain
§ Tertiary structure is determined by interactions
among various side chains (R groups)
§ Quaternary structure results from interactions
between multiple polypeptide chains

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 Primary structure

Amino
acids

1 5 10

Amino end

30 25 20 15

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 Secondary structure

ahelix

Hydrogen bond
bpleated sheet
bstrand

Hydrogen
bond

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 Tertiary structure

Hydrogen
bond
Hydrophobic
interactions and
van der Waals
interactions
Disulfide
bridge
Ionic bond

Polypeptide
backbone

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 Quaternary structure

Heme
Iron
bsubunit

asubunit

asubunit

bsubunit
Hemoglobin
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Sickle-Cell Disease: A Change in Primary Structure

§ Primary structure is the sequence of amino acids

on the polypeptide chain
§ A slight change in primary structure can affect a
protein’s structure and ability to function
§ Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in the
protein hemoglobin

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 A single amino acid substitution in a protein causes sickle-cell disease.

Secondary
Primary Quaternary Red Blood Cell
and Tertiary Function
Structure Structure Shape
Structures
Normal Molecules do not
1 hemoglobin associate with one
2 another; each carries
3 oxygen.
Normal

4
a
5 bsubunit b
6
7 a
5 mm
b

Exposed hydro- Sickle-cell Molecules crystallized

1 phobic region hemoglobin into a fiber; capacity to
carry oxygen is reduced.
2
Sickle-cell

3
4
a
5 b
6 bsubunit
7 a
b 5 mm

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What Determines Protein Structure?

§ In addition to primary structure, physical and

chemical conditions can affect structure
§ Alterations in pH, salt concentration, temperature, or
other environmental factors can cause a protein to
unravel
§ This loss of a protein’s native structure is called
denaturation
§ A denatured protein is biologically inactive

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 Normal protein Denatured protein

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Protein Folding in the Cell

§ It is hard to predict a protein’s structure from its

primary structure
§ Most proteins probably go through several
intermediate structures on their way to their final,
stable shape
§ Scientists use X-ray crystallography to determine
3-D protein structure based on diffractions of an
X-ray beam by atoms of the crystalized molecule

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 Nucleic acids store, transmit, and help express
hereditary information

§ The amino acid sequence of a polypeptide is

programmed by a unit of inheritance called a gene
§ Genes are made of DNA, a nucleic acid made of
monomers called nucleotides

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The Roles of Nucleic Acids

§ There are two types of nucleic acids

§ Deoxyribonucleic acid (DNA)
§ Ribonucleic acid (RNA)
§ DNA provides directions for its own replication
§ DNA directs synthesis of messenger RNA (mRNA)
and, through mRNA, controls protein synthesis

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DNA ® RNA ® protein
DNA

1 Synthesis
of mRNA
mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into Ribosome
cytoplasm

3 Synthesis
of protein

Amino
Polypeptide acids
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The Components of Nucleic Acids

§ Nucleic acids are polymers called polynucleotides

§ Each polynucleotide is made of monomers called
nucleotides
§ Each nucleotide consists of a nitrogenous base, a
pentose sugar, and one or more phosphate groups
§ The portion of a nucleotide without the phosphate
group is called a nucleoside

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§ The sugar in DNA is deoxyribose; in RNA it is
ribose
§ A prime (¢) is used to identify the carbon atoms in the
ribose, such as the 2¢carbon or 5¢carbon
§ A nucleoside with at least one phosphate attached is
a nucleotide

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 Sugars

Deoxyribose (in DNA) Ribose (in RNA)

§ Each nitrogenous base has one or two rings that
include nitrogen atoms
§ The nitrogenous bases in nucleic acids are called
cytosine (C), thymine (T), uracil (U), adenine (A),
and guanine (G)
§ Thymine is found only in DNA, and uracil only in
RNA; the rest are found in both DNA and RNA

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 Nitrogenous bases
Pyrimidines

Cytosine (C) Thymine Uracil

(T, in DNA) (U, in RNA)
Purines

Adenine (A) Guanine (G)

Nucleotide Polymers

§ Adjacent nucleotides are joined by covalent bonds

that form between the —OH group on the 3¢carbon
of one nucleotide and the phosphate on the 5¢
carbon of the next
§ These links create a backbone of sugar-phosphate
units with nitrogenous bases as appendages
§ The sequence of bases along a DNA or mRNA
polymer is unique for each gene

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 Sugar-phosphate backbone
5¢end (on blue background)

5¢
C

3¢
C

Nucleoside
Nitrogenous
base

Phosphate
5¢
C group Sugar
(pentose)
3¢
C
Nucleotide

3¢end
(a) Polynucleotide, or nucleic acid
The Structures of DNA and RNA Molecules

§ RNA molecules usually exist as single polypeptide

chains
§ DNA molecules have two polynucleotides spiraling
around an imaginary axis, forming a double helix
§ In the DNA double helix, the two backbones run in
opposite 5¢
→ 3¢directions from each other, an
arrangement referred to as antiparallel
§ One DNA molecule includes many genes

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§ The nitrogenous bases in DNA pair up and form
hydrogen bonds: adenine (A) always with thymine
(T), and guanine (G) always with cytosine (C)
§ This is called complementary base pairing
§ Complementary pairing can also occur between
two RNA molecules or between parts of the same
molecule
§ In RNA, thymine is replaced by uracil (U), so A and
U pair

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 The structures of DNA and tRNA molecules

5¢ 3¢ Sugar-phosphate
backbones
Hydrogen bonds

Base pair joined

by hydrogen
bonding

3¢ 5¢ Base pair joined

by hydrogen bonding
(a) DNA (b) Transfer RNA

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DNA and Proteins as Tape Measures of Evolution

§ The linear sequences of nucleotides in DNA

molecules are passed from parents to offspring
§ Two closely related species are more similar in DNA
than are more distantly related species
§ Molecular biology can be used to assess
evolutionary kinship

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Please indicate your answers to the following Questions and
save this document- Review of content and submission of
answers will be discussed the first week of class.
The type of bonds present in a molecule determine its
properties. Which type of bond is associated with
molecules that are soluble in water (i.e., molecules that
do not precipitate)?

A. strong ionic bond

B. polar covalent bond
C. nonpolar covalent bond
D. hydrophobic interaction (force between hydrophobic
molecules that causes oil to separate from vinegar
solutions)

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The chemical bonds present in a molecule contribute to the
properties of the molecule. Carbon is an unusual atom in that it
can form multiple bonds. Which statement is not true?

A. A carbon-to-carbon cis double bond is the type found in

nature and is associated with cardiovascular health.
B. A carbon-to-carbon trans double bond is made artificially in
food processing and is associated with poor cardiovascular
health.
C. Multiple carbon-to-carbon double bonds located near each
other can absorb light, so they are found in molecules in the
eye or in chloroplasts.
D. Multiple carbon-to-carbon bonds are stronger than single
bonds.
E. Saturated fats are those that have a carbon-to-carbon
double bond and are associated with good health.
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Silicon (atomic number 14, atomic weight 28) is in the
same column as carbon in the periodic table of the
elements (Group IV). Why isn’t life on Earth based on
silicon, instead of carbon?

A. Silicon is far more rare in the Earth’s crust than

carbon.
B. Silicon cannot form polar covalent bonds with
oxygen.
C. Silicon has a different valence than carbon.
D. Silicon compounds often have very different
physico-chemical properties than the analogous
carbon compounds.

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Which polysaccharide has the greatest number
of branches?

A. cellulose
B. chitin
C. amylose
D. amylopectin
E. glycogen

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Given a chemical formula for an organic molecule
(e.g., C6H12O6), what can one usually deduce?

A. structure
B. its molecular weight
C. its solubility in water
D. all of the above
E. its molecular weight and solubility in water

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High-glucose diets result in glucose-binding tendon proteins,
making them yellow and stiff. Treatment of diabetes and high
blood sugar is quantified by measuring the amount of glucose-
bound hemoglobin. The reaction involved is the formation of a
new bond between the carbonyl group of glucose and the amino
group of proteins. Which of the following is true?

A. The linear form of glucose is unhealthy.

B. The ring form of glucose is unhealthy.
C. The —O—H group of proteins is important in this reaction.
D. In blood, the linear form is more common than the ring form.

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All lipids

A. are made from glycerol and fatty acids.

B. contain nitrogen.
C. have low energy content.
D. are acidic when mixed with water.
E. do not dissolve well in water.

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Sickle-cell disease is caused by a mutation in the
beta-hemoglobin gene that changes a charged
amino acid, glutamic acid, to valine, a hydrophobic
amino acid. Where in the protein would you expect
to find glutamic acid?

A. on the exterior surface of the protein

B. in the interior of the protein, away from water
C. at the active site, binding oxygen
D. at the heme-binding site

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Which is not a function of proteins?

A. help make up membranes

B. carry the code for translation from the
nucleus to the ribosome
C. bind to hormones (hormone receptor)
D. can be hormones
E. speed chemical reactions

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How does RNA differ from DNA?

A. DNA encodes hereditary information; RNA

does not.
B. DNA forms duplexes; RNA does not.
C. DNA contains thymine; RNA contains uracil.
D. all of the above

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