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Lectures by Stephanie Scher Pandolfi
BIOLOGICAL SCIENCE
FOURTH EDITION
SCOTT FREEMAN
2Water and Carbon: The
Chemical Basis of Life
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Key Concepts
Molecules form when atoms bond to each other. Chemical bonds
are based on electron sharing. The degree of electron sharing
varies depending on the type of bond formed.
Of all small molecules, water is the most important for life. Water
is highly polar and readily forms hydrogen bonds, making it an
extremely efficient solvent.
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Key Concepts
Energy is the capacity to do work or supply heat, and can be (1) a
stored potential or (2) an active motion. Chemical energy is a
form of potential energy, stored in chemical bonds.
Chemical reactions tend to be spontaneous if they lead to lower
potential energy and higher entropy, and nonspontaneous if they
require an input of energy.
Most of the important compounds in organisms contain carbon.
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Basic Atomic Structure
Atoms are composed of:
Protonspositively charged particles Neutronsneutral particles
Electronsnegatively charged particles
Protons and neutrons are located in the nucleus.
Electrons are found in orbitals surrounding the nucleus.
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ElementsThe Building Blocks of Chemical Evolution
Every different atom has a characteristic number of protons inthe nucleus, called the atomic number.
Atoms with the same atomic number have the same chemicalproperties and belong to the same element.
Forms of an element with different numbers of neutrons areisotopes.
The mass number is the number of protons + neutrons of the most
common isotope.
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Electron Arrangement around the Nucleus
Electrons move around atomic nuclei in specific regions called
orbitals.
Each orbital can hold up to two electrons.
Orbitals are grouped into levels called electron shells.
Electron shells are numbered, with smaller numbers closer tothe nucleus.
The electrons in the outermost shell are called valence
electrons.
Elements commonly found in organisms have at least one unpaired
valence electron. The number of unpaired electrons in an atom is its
valence.
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Chemical Bonding
Unfilled electron orbitals allow formation ofchemical bonds, and
atoms are most stable when each electron orbital is filled.
Covalent bond: Each atoms unpaired valence electrons are
shared by both nuclei to fill their orbitals.
Substances held together by covalent bonds are calledmolecules.
Ionic bond: Electrons are transferred from one atom to
another.
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Covalent Bonds
Electrons are not always shared equally. An atom in a molecule
with a high electronegativity will hold the electrons more tightly
and have a partial negative charge (), whereas the other atom will
have a partial positive charge (+).
Differences in electronegativity dictate how electrons are
distributed in covalent bonds.
Nonpolar covalent bond: Electrons are evenly shared between
two atoms and the bond is symmetrical.
Polar covalent bond: Electrons are asymmetrically shared.
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Covalent Bonds
BLAST Animation: Covalent Bonds
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Ions and Ionic Bonds
An atom or molecule that carries a charge is called an ion.
Cation
: An atom that loses an electron and becomes positively
charged.
Anion: An atom that gains an electron and becomes negatively
charged.
The resulting attraction between oppositely charged ions is an ionic
bond.
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The Electron-Sharing Continuum
The degree to which electrons are shared in chemical bonds forms
a continuum, from equal sharing in nonpolar covalent bonds, to
unequal sharing in polar covalent bonds, to the transfer of
electrons in ionic bonds.
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C A ?
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How Many Bonds Can an Atom Have?
The number of unpaired electrons determines the number of bonds
an atom can make.
Atoms with more than one unpaired electron can form multiple
single bonds or double or triple bonds.
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R ti M l l
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Representing Molecules
The shape of a simple molecule is governed by the geometry of its
bonds.
Molecular formulas indicate the numbers and types of atoms in a
molecule (e.g., H2O, CH4).
Structural formulas indicate which atoms are bonded together and
whether the bonds are single, double, or triple bonds.
Ball-and-stick models and space-filling models show 3Dgeometry.
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Chemical Reactions
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Chemical Reactions
Chemical reactions occur when:
1. One substance is combined with another.
Atoms are rearranged in molecules, or small molecules
combine to form larger molecules.
2. One substance is broken down into another substance.
Molecules are split into atoms or smaller molecules.
In most cases, chemical bonds are broken and new bonds form.
Quantifying Molecules
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Quantifying Molecules
The molecular weight of a molecule is the sum of the mass
numbers of all the atoms in the molecule.
One mole, or 6.022 1023 molecules, has a mass equal to the
molecular weight expressed in grams.
The concentration of a substance in a solution is typically
expressed as molarity (M), which is the number of moles per liter.
Why Is Water Such an Efficient Solvent?
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Why Is Water Such an Efficient Solvent?
Life is based on water because water is a great solvent.
The covalent bonds in water are polar because oxygen has a greater
electronegativity than hydrogen.
Oxygen has a partial negative charge.
Hydrogen has a partial positive charge.
Hydrogen bonds are the weak electrical attractions between the
partially negative oxygen of one water molecule and the partially
positive hydrogen of a different water molecule. Can also form between a water molecule and another polar
molecule.
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Water and Hydrogen Bonds
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Water and Hydrogen Bonds
Ions and polar molecules stay in solution because of their
interactions with waters partial charges. These atoms and
molecules are said to be hydrophilic.
Uncharged and nonpolar compounds do not dissolve in water and
are said to be hydrophobic.
Hydrogen bonding makes it possible for almost any charged or
polar molecule to dissolve in water.
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Hydrogen Bonds and Water
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Hydrogen Bonds and Water
BLAST Animation: Hydrogen Bonds in Water
Correlation of Waters Structure and Properties
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Correlation of Water s Structure and Properties
Water is unique due to its small size, bent shape, highly polar
covalent bonds, and overall polarity.
Water also has several remarkable properties, largely due to its
ability to form hydrogen bonds. Water is:
1. Cohesive
2. Adhesive
3. Denser as a solid than a liquid
4. Able to absorb large amounts of energy
A Closer Look at the Properties of Water
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A Closer Look at the Properties of Water
Cohesionbinding between like molecules
Results in high surface tension
Adhesionbinding between unlike molecules
Water expands as it changes from a liquid to a solid. This is why ice floats!
Water has an extraordinarily large capacity for absorbing heat.
High specific heat
High heat of vaporization
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The Properties of Water
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p
Web Activity: Properties of Water
AcidBase Reactions and pH
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p
Proton [hydrogen ion (H+)] concentration is the basis of the pH
scale.
pH expresses proton concentration in a solution.
The pH of pure water is 7.
Acids have a pH of less than 7.
Bases have a pH of greater than 7.
In acidbase reactions, a proton donor (acid) transfers a proton to
a proton acceptor (base).
The pH Scale and Buffers
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The pH scale is logarithmic:
pH = log [H+]
Greater H+ concentrationlower pHmore acidic
Lower H+ concentrationhigher pHmore basic/alkaline
Buffers are compounds that minimize changes in pH.
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How Do Chemical Reactions Happen?
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pp
Chemical reactions have reactants and products. For example:
CO2(g) + H2O(l) H2CO3(aq)
Chemical equilibrium occurs when the forward and reverse
reactions proceed at the same rate and the quantities of reactants
and products remain constant.
Endothermic reactions must absorb heat to proceed, but
exothermic reactions release heat.
What Is Energy?
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gy
Energy is the capacity to do work or supply heat. This capacity
exists in one of two waysas a stored potential or as an active
motion.
Potential Energy and Kinetic Energy
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gy gy
Stored energy is called potentialenergy. An objects position
determines its ability to store energy. For example:
Electrons in an outer shell (farther from the positively
charged nucleus) have more potential energy than do
electrons in an inner shell.
The energy of movement is called kineticenergy orthermal
energy, which is measured as temperature.
Low-temperature objects have slower molecules than high-
temperature objects.
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Heat and the First Law of Thermodynamics
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Heat is the thermal energy transferred between objects of different
temperatures.
The first law of thermodynamics states that energy is conserved
it cannot be created or destroyed, but it can be transferred or
transformed.
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What Makes a Chemical Reaction Spontaneous?
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Chemical reactions are spontaneous if they proceed on their own,
without any continuous external influence such as added energy.
The spontaneity of a reaction is determined by two factors:
1. The amount of potential energy
Products of spontaneous reactions have less potential energy
than the reactants.
2. The degree of order
Products of spontaneous reactions are less ordered than the
reactants.
The Second Law of Thermodynamics
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Entropy (S) is the amount of disorder in a group of molecules.
The second law of thermodynamics states that entropy always
increases.
In other words, chemical reactions result in products with less
ordered (usable) energy.
In general, physical and chemical processes proceed in the direction
that results in lower potential energy and increased disorder.
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Gibbs Free-Energy Change
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The Gibbs free-energy change (G) determines whether a
reaction is spontaneous or requires energy.
G < 0 is an exergonic spontaneous reaction.
G > 0 is an endergonic reaction that requires energy input.
G = 0 is a reaction that is at equilibrium.
Temperature and Concentration Affect Reactions
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Breaking and forming bonds depends on collisions between
substances.
This allows electrons to interact.
The rate of a reaction depends upon the number of collisions.
The number of collisions is dependent on the temperature and
concentration of the reactants:
Higher temperature more collisions faster reaction
Higher concentration
more collisions
faster reaction
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Energy Inputs and the Start of Chemical Evolution
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Formation of formaldehyde (H2CO) and hydrogen cyanide (HCN)
is the first step in chemical evolution and requires energy input.
Photons are packets of light energy emitted by the Sun.
High-energy photons can break molecules apart by knocking
electrons away from valence shells. The resulting free radicals
have unpaired electrons and are extremely unstable and highly
reactive.
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Chemical Energy Is a Form of Potential Energy
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Significant amounts of H2CO and HCN could form under the
temperature and concentration conditions that were likely on
ancient Earth. These products have more potential energy than the reactants.
Potential energy stored in chemical bonds is called chemical
energy.
Thus: solar energy (energy of the Sun) was converted into chemical
energy (in H2CO and HCN).
The Importance of Carbon
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Carbon is the most versatile atom on Earth. Because of its four
valence electrons, carbon can form many covalent bonds.
Carbon-containing molecules can form an almost limitless arrayof molecular shapes with different combinations of single and
double bonds.
The formation of carboncarbon bonds was an important event inchemical evolution.
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Functional Groups: Determinants of Chemical Behavior
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The carbon atoms in an organic molecule furnish the skeleton that
gives the molecule its overall shape.
Amino and carboxyl groups: Attract or drop a proton,
respectively
Carbonyl groups: Sites of reactions that link molecules intolarger, more-complex compounds
Hydroxyl groups: Act as weak acids
Phosphate groups: Have two negative charges
Sulfhydryl groups: Link together via disulfide bonds
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