What is Photosynthesis

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Is it possible to walk on water?
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Chapter 2 Outline

• 2.1 What Are Atoms?
• 2.2 How Do Atoms Interact to Form Molecules?
• 2.3 Why is Water So Important to Life?

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Section 2.1 Outline

• 2.1 What Are Atoms?
• Atoms Are Basic Structural Units Composed of
  Still Smaller Particles
• Electrons Orbit the Nucleus at Fixed Distances

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Atoms Are Composed of Small Particles

• Atoms are the fundamental structural units of
  matter that are composed of three types of
  particles
• In the central nucleus there are positively
  charged protons
• Uncharged neutrons
• In orbit around the nucleus are lighter,
  negatively charged electrons

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Atoms Are Composed of Small Particles

• Atoms are electrically neutral because they have
  an equal number of positive protons as negative
  electrons (see Figure 2-1(a), p. 22)

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electron shell
e-
p
nucleus
Hydrogen (H)
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Atoms Are Composed of Small Particles

• The number of protons in the nucleus of an atom
  is known as the atomic number

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Elements and Isotopes

• An element is a category of atoms that cannot be
  broken down by ordinary chemical reactions
• All atoms belong to one of 96 naturally occurring
  elements

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Elements and Isotopes

• The atomic number (number of protons) is the
  defining value for an element (see Table 2-1, p.
  22)
• All atoms of an element have the same atomic
  number
• e.g. Carbon has 6 protons, nitrogen has 7

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Lyrics to and recordings of The Elements by Tom
Lehrer. In 1959, jack of all trades, Tom Lehrer
wrote and sang this song naming all of the
elements in front of a Harvard audience. You've
got to imagine the guys recording this song
early twenties, with seven-eights inch crewcut
hair, plastic rimed glasses, sharp white shirts
and loosened black ties. They gathered around a
high tech tape recorder and forever preserved
this song. In 2002, Flash animator Mike
Stanfill put the song in motion. http//www.priva
tehand.com/flash/elements.html
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Elements and Isotopes

• Atoms of an element may vary in the number of
  neutrons they have in the nucleus
• Variant atomic forms of an element are called
  isotopes
• Some isotopes are radioactive and are used in
  research
• Elements may occur as solids, liquids, or gases
  at room temperature

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Electrons Orbit the Nucleus at Fixed Distances

• Larger atoms can accommodate more electrons than
  smaller ones can
• Electrons are distributed about the nucleus of an
  atom in electron shells (see Figure 2-2, p. 24)
• The first shell or energy level holds 2 electrons
• The second shell holds up to 8

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2e
8e
5e
4e
6e
8e
8e
2e
2e
2e
2e
6p
8p
15p
20p
6n
8n
16n
20n
Carbon (C)
Oxygen (O)
Phosphorus (P)
Calcium (Ca)
C
Ca
O
P
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Electrons Orbit the Nucleus at Fixed Distances

• Roles of the nucleus and the electrons
• The nucleus provides stability
• The electrons interact with other atoms (e.g.
  forming bonds)

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Section 2.2 Outline

• 2.2 How Do Atoms Interact to Form Molecules?
• Atoms Interact When There Are Outermost Electron
  Shell Vacancies
• Charged Atoms (Ions) Form Ionic Bonds
• Uncharged Atoms Can Stabilize by Forming Covalent
  Bonds
• Most Biological Molecules Feature Covalent Bonds
• Electron Sharing Determines Covalent Bond
  Polarity
• Highly Reactive Free Radicals Can Damage Cells
• Hydrogen Bonds Are Weak Attractions within Some
  Covalently-Bonded Molecules

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Atoms Interact When There Are Outermost Electron
Shell Vacancies

• Molecules are made of two or more atoms bonded
  together through electron shells
• A substance made of atoms of different elements
  is a compound

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Atoms Interact When There Are Outermost Electron
Shell Vacancies

• Reactions between atoms depend upon the
  configuration of electrons in the outermost
  electron shell

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Atoms Interact When There Are Outermost Electron
Shell Vacancies

• Atoms will not react with other atoms if the
  outermost shell is completely empty or full (such
  atoms considered inert)
• Example Neon, with 8 electrons in outermost
  shell (full)

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Atoms Interact When There Are Outermost Electron
Shell Vacancies

• Atoms will react with other atoms if the
  outermost shell is partially full (such atoms
  considered reactive)
• Example Oxygen, with 6 electrons in outermost
  shell (can hold 2 more electrons)

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Chemical Reactions Result From Electron
Interaction

• Reactive atoms gain stability by electron
  interactions (chemical reactions)
• Electrons can be lost to empty the outermost
  shell
• Electrons can be gained to fill the outermost
  shell
• Electrons can be shared with another atom where
  both atoms have full outermost shells

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Chemical Reactions Result From Electron
Interaction

• Attractive forces (chemical bonds) hold atoms
  together in molecules (see Table 2-2, p. 26)

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Charged Atoms Called Ions Interact to Form Ionic
Bonds

• Atoms that have lost electrons become positively
  charged ions (e.g. sodium Na)
• Atoms that have gained electrons become
  negatively charged ions (e.g. chlorine Cl-)

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Charged Atoms Called Ions Interact to Form Ionic
Bonds

• Oppositely charged ions are attracted to each
  other are bond into a molecule by ionic bonds
  (see Figure 2-3 (a b), p. 25)

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Na
Cl
Chlorine atom (neutral)
Sodium atom (neutral)
11p
17p
11n
18n
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Na
Cl
Chloride ion ()
Sodium ion ()
11p
17p
11n

18n
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Charged Atoms Called Ions Interact to Form Ionic
Bonds

• Salt crystals are repeated, orderly arranged
  sodium and chloride ions (see Figure 2-3 (c), p.
  25)

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Na
Cl
An ionic compound NaCl
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Uncharged Atoms Can Become Stable by Sharing
Electrons, Forming Covalent Bonds

• Atoms with partially full outer electron shells
  can share electrons
• Two electrons (one from each atom) are shared in
  a covalent bond

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Uncharged Atoms Can Become Stable by Sharing
Electrons, Forming Covalent Bonds

• Covalent bonds are found in H2 (single bond), O2
  (double bond), N2 (triple bond) and H2O
• Covalent bonds are stronger than ionic bonds but
  vary in their stability

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Uncharged Atoms Can Become Stable by Sharing
Electrons, Forming Covalent Bonds

• Most biological molecules contain covalent bonds
  (see Table 2-3, p. 27)

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Polar Covalent Bonds Result From Unequal Sharing

• Atoms within a molecule may have different
  nuclear charges
• Those atoms with greater positive nuclear charge
  pull more strongly on electrons in a covalent bond

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Polar Covalent Bonds Result From Unequal Sharing

• In diatomic molecules like H2, both atoms exert
  the same pulling force on bond electrons the
  covalent bond is nonpolar

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Polar Covalent Bonds Result From Unequal Sharing

• In molecules where atoms of different elements
  are involved (like H2O), the bond electrons are
  not equally shared the covalent bond is polar

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Polar Covalent Bonds Result From Unequal Sharing

• A molecule with polar bonds may be polar overall
• H2O is a polar molecule
• The (slightly) positively charged pole is around
  each hydrogen
• The (slightly) negatively charged pole is around
  the oxygen

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Polar Covalent Bonds Result From Unequal Sharing

• Polar/nonpolar bonding is illustrated in Figure
  2-4 (a b), p, 26

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Nonpolar covalent bonding
Hydrogen (HH or H2)
8p
8p
8n
8n
Oxygen (OO or O2)
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Polar covalent bonding
(slightly negative)
8p
8n
(slightly positive)
Water (HOH or H2O)
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Free Radicals Are Highly Reactive and Can Damage
Cells

• Some cellular reactions produce free radicals
• Free radical a molecule whose atoms have one or
  more unpaired electrons in their outer shells

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Free Radicals Are Highly Reactive and Can Damage
Cells

• Free radicals are highly unstable and reactive
• Free radicals steal electrons, destroying other
  molecules
• Cell death can occur from free radical attack

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Free Radicals Are Highly Reactive and Can Damage
Cells

• Free radicals are involved in causing heart
  disease, Alzheimers, cancer, and aging
• Antioxidants like vitamins C and E render free
  radicals harmless

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Hydrogen Bonds Are Weaker ElectricalAttractions
Between or Within Moleculeswith Polar Covalent
Bonds

• Polar molecules like water have partially charged
  atoms at their ends
• Hydrogen bonds form when partial opposite charges
  in different molecules attract each other
• The partially positive hydrogens of one water
  molecule are attracted to the partially negative
  oxygen on another (see Figure 2-5, p. 28)

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O ()
H ()
H ()
H ()
O ()
H ()
hydrogren bonds
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Hydrogen Bonds Are Weaker ElectricalAttractions
Between or Within Moleculeswith Polar Covalent
Bonds

• Polar biological molecules can form hydrogen
  bonds with water, each other, or even within the
  same molecule
• Hydrogen bonds are rather weak but can
  collectively be quite strong (see Table 2-2, p.
  26)

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Section 2.3 Outline

• 2.3 Why Is Water So Important to Life?
• Water Interacts with Many Other Molecules
• Water Molecules Tend to Stick Together
• Water-Based Solutions Can Be Acidic, Basic, or
  Neutral
• Buffers Help Maintain Relatively Constant pH
• Water Moderates the Effects of Temperature Change
• Water Forms an Unusual Solid Ice

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Water Interacts with Many Other Molecules

• Water is an excellent solvent
• A wide range of substances dissolve in water to
  form solutions (see Figure 2-6, p. 29)

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Na
H
Cl
O
H
Cl
H
H
Na
O
Na
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Water Interacts with Many Other Molecules

• Water-soluble molecules are hydrophilic
• Water molecules are attracted to and can surround
  ions or polar molecules (dissolving them), such
  as sugars and amino acids (see Figure 2-7, p. 29)

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water
hydrogen bond
glucose
hydroxyl group
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Water Interacts with Many Other Molecules

• Water-insoluble molecules are hydrophobic
• Water molecules repel and drive together
  uncharged and nonpolar molecules like fats and
  oils
• The clumping of nonpolar molecules is called
  hydrophobic interaction

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Water Molecules Tend to Stick Together

• Hydrogen bonding between water molecules produces
  high cohesion
• Water cohesion explains how water molecules can
  form a chain in delivering moisture to the top of
  a tree (see Figure 2-8 (b), p. 30)

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Water Molecules Tend to Stick Together

• Cohesion of water molecules along a surface
  produces surface tension
• Fishing spiders and water striders rely on
  surface tension to move across the surface of
  ponds (see Figure 2-8 (a), p. 30)

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Water Molecules Tend to Stick Together

• Water molecules stick to polar or charged
  surfaces in the property called adhesion
• Adhesion helps water climb up the thin tubes of
  plants to the leaves

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Water-Based Solutions Can Be Acidic, Basic, or
Neutral

• A small fraction of water molecules break apart
  into ions
• H2O ? OH- H

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Water-Based Solutions Can Be Acidic, Basic, or
Neutral

• Solutions where H gt OH- are acidic
• e.g. Hydrochloric acid ionizes HCl ? H Cl-
• Lemon juice and vinegar are naturally produced
  acids

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Water-Based Solutions Can Be Acidic, Basic, or
Neutral

• Solutions where OH- gt H are basic
• e.g. Sodium hydroxide ionizes NaOH ? Na OH-
• Baking soda, chlorine bleach, and ammonia are
  basic

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Water-Based Solutions Can Be Acidic, Basic, or
Neutral

• The degree of acidity of a solution is measured
  using the pH scale (see Figure 2-9, p. 31)
• pHs 0-6 are acidic (H gt OH-)
• pH 7 is neutral (H OH-)
• pH 8-14 is basic (OH- gt H)

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pH
H concentration (moles/liter)
value
1-molar hydrochloric acid (HCI)
0
100
stomach acid lime juice
1
101
102
lemon juice
2
"acid rain" (2.55.5) vinegar, cola, orange
juice, tomatoes
3
103
increasingly acidic (H gt OH)
beer
4
104
black coffee, tea
5
105
normal rain (5.6) urine (5.7)

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6
106
neutral (H OH)

7
107
pure water (7.0) saliva blood, sweat (7.4)
7

8
108
seawater (7.8

8.3)
8

9
baking soda
9
109

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phosphate detergents chlorine bleach milk of
magnesia
10
1010
increasingly basic (H lt OH)

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household ammonia some detergents (without
phosphates)
11
1011

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washing soda
12
1012

13
1013
oven cleaner
13
1-molar sodium hydroxide (NaOH)
14

14
1014
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pH value
H concentration (moles/liter)
1-molar hydrochloric acid (HCI)
0
100
1
stomach acid lime juice
101
102
2
lemon juice
"acid rain" (2.55.5) vinegar, cola, orange
juice, tomatoes
3
103
increasingly acidic (H gt OH)
101
beer
4
black coffee, tea
5
105
normal rain (5.6) urine (5.7)
106
6
65
neutral
107
pure water (7.0) aliva blood, sweat (7.4)
7
(H OH)
108
seawater (7.88.3)
8
baking soda
9
109
phosphate detergents chlorine bleach milk of
magnesia
10
1010
increasingly basic (H lt OH)
household ammonia some detergents (without
phosphates)
11
1011
washing soda
12
1012
1013
oven cleaner
13
1-molar sodium hydroxide (NaOH)
14
1014
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A Buffer Helps Maintain a Solution at a
Relatively Constant pH

• A buffer is a compound that accepts or releases
  H in response to pH change
• The bicarbonate buffer found in our bloodstream
  prevents pH change

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A Buffer Helps Maintain a Solution at a
Relatively Constant pH

• If the blood becomes too acidic, bicarbonate
  accepts (and absorbs) H to make carbonic acid
• HCO3- H ?
  H2CO3
• bicarbonate hydrogen ion
  carbonic acid

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A Buffer Helps Maintain a Solution at a
Relatively Constant pH

• If the blood becomes too basic, carbonic acid
  liberates hydrogen ions to combine with OH- to
  form water
• H2CO3 OH- ? HCO3-
  H2O
• carbonic acid hydroxide ion bicarbonate
  water

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Water Moderates the Effects of Temperature Changes

• Very low or very high temperatures may damage
  enzymes or slow down important chemical reactions

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Water Moderates the Effects of Temperature Changes

• Water moderates the effect of temperature change
• Temperature reflects the speed of molecular
  motion
• It requires 1 calorie of energy to raise the
  temperature of 1g of water 1oC (the specific heat
  of water), so it heats up very slowly

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Water Moderates the Effects of Temperature Changes

• Water requires a lot of energy to turn from
  liquid into a gas (heat of vaporization)
• Evaporating water uses up heat from its
  surroundings cooling the nearby environment (as
  occurs during sweating)

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Water Moderates the Effects of Temperature Changes

• Water requires a lot of energy to be withdrawn in
  order to freeze (heat of fusion)
• Water freezes more slowly than other liquids

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Water Forms an Unusual Solid Ice

• Most substances become denser when they solidify
  from a liquid
• Ice is unusual because it is less dense than
  liquid water

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Water Forms an Unusual Solid Ice

• Water molecules spread apart slightly during the
  freezing process (see unnumbered photo on p. 32)

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Water Forms an Unusual Solid Ice

• Ice floats in liquid water
• Ponds and lakes freeze from the top down and
  never freeze completely to the bottom
• Many plants and fish therefore are not frozen