PowerLecture: Chapter 2

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PowerLectureChapter 2

• Molecules of Life

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Learning Objectives

• Understand how protons, electrons, and neutrons
  are arranged into atoms and ions.
• Explain how the distribution of electrons in an
  atom or ion determines the number and kinds of
  chemical bonds that can be formed.
• Know the various types of chemical bonds, the
  circumstances under which each forms, and the
  relative strengths of each type.

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Learning Objectives (contd)

• Understand the essential chemistry of water and
  of some common substances dissolved in it.
• Understand how small organic molecules can be
  assembled into large macromolecules by
  condensation. Understand how large macromolecules
  can be broken apart into their basic subunits by
  hydrolysis.

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Learning Objectives (contd)

• Memorize the functional groups presented and know
  the properties they confer when attached to other
  molecules.
• Know the general structure of a monosaccharide
  with six carbon atoms, glycerol, a fatty acid, an
  amino acid, and a nucleotide.
• Know the macromolecules into which these
  essential building blocks can be assembled by
  condensation.

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Learning Objectives (contd)

• Know where these carbon compounds tend to be
  located in cells or organelles and the activities
  in which they participate.

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Impacts/Issues

• Its Elemental

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Its Elemental

• Life depends on chemical reactions.
• An element is a fundamental form of matter that
  has mass and takes up space.
• Organisms consist mostly of carbon, oxygen,
  hydrogen, and nitrogen.
• Trace elements are needed only in small
  quantities.

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Elements in the Human Body vs. Earths Crust
Human Body
Earths Crust
Oxygen 65 Carbon 18 Hydrogen 10 Nitrogen
3 Calcium 2 Phosphorus 1.1 Potassium 0.35 Sulfu
r 0.25 Sodium 0.15 Chlorine 0.15 Magnesium
0.05 Iron 0.004
Oxygen 46.6 Silicon 27.7 Aluminum 8.1 Iron 5.
0 Calcium 3.6 Sodium 2.8 Potassium
2.1 Magnesium 1.5
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How Would You Vote?

• To conduct an instant in-class survey using a
  classroom response system, access JoinIn Clicker
  Content from the PowerLecture main menu.
• Many communities add fluoride to drinking water
  supplies. Do you want it in yours?
• a. Yes, screening lets people make informed
  reproductive decisions about the risk to their
  children.
• b. No, therapies and medications
• for CF continue to improve a
• person with CF can live a full life.

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Section 1

• Atoms, the Starting Point

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Atoms, the Starting Point

• Atoms are composed of smaller particles.
• An atom is the smallest unit of matter that is
  unique to a particular element.
• Atoms are composed of three particles
• Protons (p) are part of the atomic nucleus and
  have a positive charge. Their quantity is called
  the atomic number (unique for each element).
• Electrons (e-) have a negative charge. Their
  quantity is equal to that of the protons. They
  move around the nucleus.
• Neutrons are also a part of the nucleus they are
  neutral. Protons plus neutrons atomic mass
  number.

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Fig. 2.1, p. 16
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Atoms, the Starting Point

• Electron activity is the basis for organization
  of materials and the flow of energy in living
  things.
• Isotopes are varying forms of atoms.
• Atoms with the same number of protons (e.g.,
  carbon has six) but a different number of
  neutrons (carbon can have six, seven, or eight)
  are called isotopes (12C, 13C, 14C).
• Some radioactive isotopes are unstable and tend
  to decay into more stable atoms.
• They can be used to date rocks and fossils.
• Some can be used as tracers to follow the path of
  an atom in a series of reactions or to diagnose
  disease.

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Section 2

• Medical Uses for Radioisotopes

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Medical Uses for Radioisotopes

• Radioisotopes have many important uses in
  medicine.
• Tracers are substances containing radioisotopes
  that can be injected into patients to study
  tissues or tissue function.
• Radiation therapy uses the radiation from
  isotopes to destroy or impair the activity of
  cells that do not work properly, such as cancer
  cells.
• For safety, clinicians usually use isotopes with
  short half-lives (the time it takes the isotope
  to decay to a more stable isotope).

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Example of Radioactive Iodine
Figure 2.2
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Section 3

• What Is a Chemical Bond?

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What Is a Chemical Bond?

• Interacting atoms Electrons rule!
• In chemical reactions, an atom can share
  electrons with another atom, accept extra
  electrons, or donate electrons.
• Electrons are attracted to protons, but are
  repelled by other electrons.
• Orbitals can be thought of as occupying shells
  around the nucleus, representing different energy
  levels.

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Electron Arrangements
Figure 2.4
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What Is a Chemical Bond?

• Chemical bonds join atoms.
• A chemical bond is a union between the electron
  structures of atoms.
• Having a filled outer shell is the most stable
  state for atoms.
• The shell closest to the nucleus has one orbital
  holding a maximum of two electrons.
• The next shell can have four orbitals with two
  electrons each for a total of eight electrons.
• Atoms with unfilled orbitals in their outermost
  shell tend to be reactive with other atomsthey
  want to fill their outer shell with the maximal
  eight electrons allowed.

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Shell Model
Figure 2.5
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What Is a Chemical Bond?

• Atoms can combine into molecules.
• Molecules may contain more than one atom of the
  same element N2 for example.
• Compounds consist of two or more elements in
  strict proportions.
• A mixture is an intermingling of molecules in
  varying proportions.

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Section 4

• Important Bonds in Biological Molecules

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Important Bonds in Biological Molecules

• An ionic bond joins atoms that have opposite
  charges.
• When an atom loses or gains one or more
  electrons, it becomes positively or negatively
  chargedan ion.
• In an ionic bond, () and () ions are linked by
  mutual attraction of opposite charges, for
  example, NaCl.

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Example of an Ionic Bond
Figure 2.7a
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Important Bonds in Biological Molecules

• Electrons are shared in a covalent bond.
• A covalent bond holds together two atoms that
  share one or more pairs of electrons.
• In a nonpolar covalent bond, atoms share
  electrons equally H2 is an example.
• In a polar covalent bond, because atoms share the
  electron unequally, there is a slight difference
  in charge (electronegativity) between the two
  atoms participating in the bond water is an
  example.

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Examples of Covalent Bonds
Figure 2.7b
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Important Bonds in Biological Molecules

• A hydrogen bond is a weak bond between polar
  molecules.
• In a hydrogen bond, a slightly negative atom of a
  polar molecule interacts weakly with a hydrogen
  atom already taking part in a polar covalent
  bond.
• These bonds impart structure to liquid water and
  stabilize nucleic acids and other large
  molecules.

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Example of a Hydrogen Bond
Figure 2.7c
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Section 5

• Antioxidants

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Antioxidants

• Free radicals are formed by the process of
  oxidation.
• Oxidation is the process whereby an atom or
  molecule loses one or more electrons.
• Oxidation can produce free radicals that may
  steal electrons from other molecules.
• In large numbers, free radicals can damage other
  molecules in a cell, such as DNA.

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Antioxidants

• Antioxidants are chemicals that can give up an
  electron to a free radical before it does damage
  to a DNA molecule.

Figure 2.8
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Section 6

• Life Depends on Water

Figure 2.9c
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Life Depends on Water

• Hydrogen bonding makes water liquid.
• Water is a polar molecule
• because of a slightly negative
• charge at the oxygen end and
• a slightly positive charge at
• the hydrogen end.
• Water molecules can form
• hydrogen bonds with each
• other.

Figure 2.9a-b
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Life Depends on Water

• Polar substances are
• hydrophilic (water loving)
• nonpolar ones are
• hydrophobic (water
• dreading) and are repelled
• by water.

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Life Depends on Water

• Water can absorb and hold heat.
• Water tends to stabilize temperature because it
  has a high heat capacitythe ability to absorb
  considerable heat before its temperature changes.
  
• This is an important property in evaporative and
  freezing processes.

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Life Depends on Water

• Water is a biological solvent.
• The solvent properties of water
• are greatest with respect to
• polar molecules because
• spheres of hydration are
• formed around the solute
• (dissolved) molecules.
• For example, the Na of salt
• attracts the negative end of water molecules,
  while the Cl- attracts the positive end.

Figure 2.10
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Section 7

• Acids, Bases, and Buffers Body Fluids
• in Flux

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Acids, Bases, and Buffers

• The pH scale indicates the concentration of
  hydrogen ions.
• pH is a measure of the H concentration in a
  solution the greater the H the lower the value
  on the pH scale.
• The scale extends from 0 (acidic) to 7 (neutral)
  to 14 (basic).

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The pH Scale
Figure 2.11
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Acids, Bases, and Buffers

• Acids give up H and bases accept H.
• A substance that releases hydrogen ions (H) in
  solution is an acidfor example, HCl.
• Substances that release ions such as (OH-) that
  can combine with hydrogen ions are called bases
  (example baking soda).
• High concentrations of
• strong acids or bases
• can disrupt living
• systems both internal
• and external to the body.

Figure 2.12
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Acids, Bases, and Buffers

• Buffers protect against shifts in pH.
• Buffer molecules combine with, or release, H to
  prevent drastic changes in pH.
• Bicarbonate is one of the bodys major buffers.

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Acids, Bases, and Buffers

• A salt releases other kinds of ions.
• A salt is an ionic compound formed when an acid
  reacts with a base example HCl NaOH ? NaCl
  H2O.
• Many salts dissolve into ions that have key
  functions in the body for example, Na, K, and Ca
  in nerve and muscles.

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Section 8

• Molecules of Life

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Molecules of Life

• Biological molecules contain carbon.
• Only living cells synthesize the molecules
  characteristic of lifecarbohydrates, lipids,
  proteins, and nucleic acids.
• These molecules are organic compounds, meaning
  they consist of atoms of carbon and one or more
  other elements, held together by covalent bonds.

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Molecules of Life

• Carbons key feature versatile bonding.
• Living organisms are mostly oxygen, hydrogen, and
  carbon.
• Much of the hydrogen and oxygen are linked as
  water.
• Carbon can form four covalent bonds with other
  atoms to form organic molecules of several
  configurations.

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Molecules of Life

• Functional groups affect the chemical behavior of
  organic compounds.
• By definition a hydrocarbon has only hydrogen
  atoms attached to a carbon backbone.
• Functional groupsatoms or groups of atoms
  covalently bonded to a carbon backboneconvey
  distinct properties, such as solubility, to the
  complete molecule.

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Examples of Functional Groups
Figure 2.13
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Molecules of Life

• Cells have chemical tools to assemble and break
  apart biological molecules.
• Enzymes speed up specific metabolic reactions.
• In condensation reactions, one molecule is
  stripped of its H another is stripped of its
  OH-.
• The two molecule fragments join to form a new
  compound the H and OH- form water (dehydration
  synthesis).
• Cells use series of condensation reactions to
  build polymers out of smaller monomers.

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Examples of Condensation Reactions
Figure 2.14a
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Molecules of Life

• In hydrolysis reactions, the reverse happens one
  molecule is split by the addition of H and OH-
  (from water) to yield the individual components.

Figure 2.14b
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Section 9

• Carbohydrates Plentiful and Varied

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Carbohydrates Plentiful and Varied

• A carbohydrate can be a simple sugar or a larger
  molecule composed of sugar units.
• Carbohydrates are the most abundant biological
  molecules.
• Carbohydrates serve as energy sources or have
  structural roles.

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Carbohydrates Plentiful and Varied

• Simple sugarsthe simplest carbohydrates.
• A monosaccharideone sugar unitis the simplest
  carbohydrate.
• Sugars are soluble in water and may be
  sweet-tasting.
• Ribose and deoxyribose (five-carbon backbones)
  are building blocks for nucleic acids.
• Glucose (six-carbon backbone) is a primary energy
  source and precursor of many organic molecules.

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Carbohydrates Plentiful and Varied

• Oligosaccharides are short chains of sugar units.
• An oligosaccharide is a short chain resulting
  from the covalent bonding of two or three
  monosaccharides.
• Lactose (milk sugar) is glucose plus galactose
  sucrose (table sugar) is glucose plus fructose.
• Oligosaccharides are used to modify protein
  structure and have a role in the bodys defense
  against disease.

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Formation of a Sucrose Molecule
Figure 2.15
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Carbohydrates Plentiful and Varied

• Polysaccharides are sugar chains that store
  energy.
• A polysaccharide consists of many sugar units
  (same or different) covalently linked.
• Glycogen is a storage form of glucose found in
  animal tissues.
• Starch (energy storage in plants) and cellulose
  (structure of plant cell walls) are made of
  glucose units but in different bonding
  arrangements.

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Examples of Polysaccharides
Figure 2.16
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Section 10

• Lipids Fats and Their Chemical Kin

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Lipids Fats and Their Chemical Kin

• Lipids are composed mostly of nonpolar
  hydrocarbon and are hydrophobic.
• Fats are energy-storing lipids.
• Fats are lipids that have one, two, or three
  fatty acids attached to glycerol.
• A fatty acid is a long, unbranched hydrocarbon
  with a carboxyl group (COOH) at one end.
• Saturated fatty acids have only single CC bonds
  in their tails, are solids at room temperature,
  and are
• derived from animal sources.

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Lipids Fats and Their Chemical Kin

• Unsaturated fatty acids have one or more double
• bonds between the carbons that form kinks in
  the tails they tend to come from plants and are
  liquid at room temperature.

Figure 2.17
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Lipids Fats and Their Chemical Kin

• Triglycerides have three fatty acids attached to
  one glycerol.
• They are the bodys most abundant lipids.
• On a per-weight basis, these molecules yield
  twice as much energy as carbohydrates.
• Trans fatty acids are partially saturated
  (hydrogenated) lipids implicated in some types of
  heart disease.

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Formation of a Triglyceride
Figure 2.18
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Lipids Fats and Their Chemical Kin

• Phospholipids are key building blocks of cell
  membranes.
• A phospholipid has a
• glycerol backbone, two
• fatty acids, a phosphate
• group, and a small
• hydrophilic group.
• They are important
• components of cell
• membranes.

Figure 2.19a-c
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Lipids Fats and Their Chemical Kin

• Sterols are building blocks of cholesterol and
  steroids.
• Steroids have a backbone of four carbon rings,
  but no fatty acids.
• Cholesterol is an
• essential component
• of cell membranes in
• animals and can be
• modified to form sex
• hormones.

Figure 2.19d-e
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Section 11

• Proteins Biological Molecules with
• Many Roles

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Proteins

• Because they are the most diverse of the large
  biological molecules, proteins function as
  enzymes, in cell movements, as storage and
  transport agents, as hormones, as antidisease
  agents, and as structural material throughout the
  body.

Figure 2.20
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Proteins

• Proteins are built from amino acids.
• Amino acids are small organic molecules with an
  amino group, an acid group, a hydrogen atom, and
  one of 20 varying R groups.
• They form large polymers called proteins.

Figures 2.20 and 2.21
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Proteins

• The sequence of amino acids is a proteins
  primary structure.
• Primary structure is defined as the chain
  (polypeptide) of amino acids.
• The amino acids are linked together in a definite
  sequence by peptide bonds between an amino group
  of one and an acid group of another.
• The final shape and function of any given protein
  is determined by its primary structure.

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Formation of Peptide Bonds in Proteins
Figure 2.22
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Section 12

• A Proteins Function Depends on Its Shape

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A Proteins Function Depends on Its Shape

• Primary structure determines the shape and
  function of proteins by positioning different
  amino acids so that hydrogen bonds can form
  between them and by putting R groups in positions
  that force them to interact.

Figure 2.23a
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A Proteins Function Depends on Its Shape

• Many proteins fold two or three times.
• Secondary structure is the helical coil or
  sheetlike array that will result from hydrogen
  bonding of side groups on the amino acid chains.
• Tertiary structure is caused by interactions
  among R groups, resulting in a complex
  three-dimensional shape.

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Figure 2.23b-c
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Fig. 2.23, p. 34
Stepped Art
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A Proteins Function Depends on Its Shape

• Proteins can have more than one polypeptide
  chain.
• Hemoglobin, the oxygen-carrying protein in the
  blood, is an example of a protein with quaternary
  structurethe complexing of two or more
  polypeptide chains to form globular or fibrous
  proteins.
• Hemoglobin has four polypeptide chains (globins),
  each coiled and folded with a heme group at the
  center.

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Figure 2.24
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A Proteins Function Depends on Its Shape

• Glycoproteins have sugars attached lipoproteins
  have lipids.
• Certain proteins combine with triglycerides,
  cholesterol, and phospholipids to form
  lipoproteins for transport in the body.
• Glycoproteins form when oligosaccharides are
  added to proteins.

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A Proteins Function Depends on Its Shape

• Disrupting a proteins shape denatures it.
• High temperatures or chemicals can cause the
  three-dimensional shape to be disrupted.
• Normal functioning is lost upon denaturation,
  which is often irreversible.

Figure 2.25
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Section 13

• Nucleotides and
• Nucleic Acids

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Nucleotides and Nucleic Acids

• Nucleotides energy carriers and other roles.
• Each nucleotide has a five-carbon sugar (ribose
  or deoxyribose), a nitrogen-containing base, and
  a phosphate group.
• ATP molecules link cellular reactions that
  transfer energy.
• Other nucleotides include the coenzymes, which
  accept and transfer hydrogen atoms and electrons
  during cellular reactions, and chemical
  messengers

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Figure 2.26
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Nucleotides and Nucleic Acids

• Nucleic acids include DNA and RNA.
• In nucleic acids, nucleotides are bonded together
  to form large single- or double-stranded
  molecules.
• DNA (deoxyribonucleic acid) is double-stranded
  genetic messages are encoded in its base
  sequences.
• RNA (ribonucleic acid) is single-stranded it
  functions in the assembly of proteins.

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Figure 2.27
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Section 14

• Food Production and a Chemical Arms Race

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Food Production and a Chemical Arms Race

• Nearly half of the food grown each year around
  the world is lost to disease or insects.
• Natural plant defenses have been augmented by the
  development of synthetic toxins designed to kill
  pests and increase crop yields.
• Herbicides kill unwanted plants (weeds).
• Insecticides kill insects.
• Fungicides kill or inhibit the growth of harmful
  mold or fungi.

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Food Production and a Chemical Arms Race

• Synthetic chemicals are not without dangers some
  kill good insects and plants while others harm
  humans through exposure.