Chapter 2Chapter 2The Chemical The Chemical

Context of LifeContext of Life

A. Elements and Compounds

1. Matter consists of chemical elements in 1. Matter consists of chemical elements in pure form and in combinations called pure form and in combinations called compoundscompounds..

Organisms are composed of Organisms are composed of mattermatter..

An An elementelement is a substance that cannot be is a substance that cannot be broken down into other substances by chemical broken down into other substances by chemical reactions.reactions.

There are There are 9292 naturally occurring elements. naturally occurring elements.

A A compoundcompound is a substance consisting of two or is a substance consisting of two or more elements in a fixed ratio, example Table salt more elements in a fixed ratio, example Table salt (sodium chloride or NaCl).(sodium chloride or NaCl).

While pure sodium is a metal and chlorine is a While pure sodium is a metal and chlorine is a gas, they combine to form an edible compound. This gas, they combine to form an edible compound. This change in characteristics when elements combine to change in characteristics when elements combine to form a compound is an example of an form a compound is an example of an emergent emergent propertyproperty..

2. 25 chemical elements are essential to life.

About About 25 25 of the 92 natural elements of the 92 natural elements are known to be essential for life.are known to be essential for life. Four elements—carbon (Four elements—carbon (CC), oxygen ), oxygen

((OO), hydrogen (), hydrogen (HH), and nitrogen (), and nitrogen (NN)—)—make up 96% of living matter.make up 96% of living matter.

Most of the remaining 4% of an Most of the remaining 4% of an organism’s weight consists of organism’s weight consists of phosphorusphosphorus (P), (P), sulfur sulfur (S), (S), calciumcalcium (Ca), and (Ca), and potassiumpotassium (K). (K).

TraceTrace elements are required by an elements are required by an organism but only in minute quantities.organism but only in minute quantities.

B. Atoms and Molecules1. Atomic structure determines the 1. Atomic structure determines the

behavior of an element.behavior of an element.

An An atomatom is the smallest unit of matter that still is the smallest unit of matter that still retains the properties of an element.retains the properties of an element.

Atoms are composed of even smaller parts, called Atoms are composed of even smaller parts, called subatomicsubatomic particles. particles.Two of these, Two of these, neutronsneutrons and and protonsprotons, are packed , are packed together to form a dense core, the atomic nucleus, together to form a dense core, the atomic nucleus, at the center of an atom.at the center of an atom.ElectronsElectrons can be visualized as forming a cloud of can be visualized as forming a cloud of negative charge around the nucleus.negative charge around the nucleus.

Each electron has one unit of Each electron has one unit of negativenegative charge. charge.

Each proton has one unit of Each proton has one unit of positivepositive charge. charge.

Neutrons are electrically Neutrons are electrically neutralneutral..

The number of protons is the element’s unique The number of protons is the element’s unique atomic numberatomic number..The atomic number tells us the number of The atomic number tells us the number of protonsprotons and the number of and the number of electronselectrons that are found in a that are found in a neutral atom of a specific element.neutral atom of a specific element.

The The mass numbermass number is the sum of the number of protons is the sum of the number of protons and neutrons in the nucleus of an atom.and neutrons in the nucleus of an atom.

Two atoms of the same element that differ in the Two atoms of the same element that differ in the number of neutrons are called number of neutrons are called isotopes.isotopes.

In nature, an element occurs as a mixture of isotopes.In nature, an element occurs as a mixture of isotopes.For example, 99% of carbon atoms have 6 neutrons For example, 99% of carbon atoms have 6 neutrons (12C).(12C).Most of the remaining 1% of carbon atoms have 7 Most of the remaining 1% of carbon atoms have 7 neutrons (13C) while the rarest carbon isotope, neutrons (13C) while the rarest carbon isotope, with 8 neutrons, is 14C.with 8 neutrons, is 14C.

The nuclei of some isotopes are unstable The nuclei of some isotopes are unstable and decay spontaneously, emitting particles and decay spontaneously, emitting particles and energy.and energy.

14C is one of these unstable isotopes, or 14C is one of these unstable isotopes, or radioactiveradioactive isotopes. isotopes.When 14C decays, one of its neutrons is When 14C decays, one of its neutrons is converted to a proton and an electron.converted to a proton and an electron.This converts 14C to 14N, transforming This converts 14C to 14N, transforming the atom to a different element.the atom to a different element.

2. Electron configuration influences the chemical behavior

of an atom.Atoms are mostly empty space.Atoms are mostly empty space.

When two elements interact during a chemical When two elements interact during a chemical reaction, it is actually their reaction, it is actually their electronselectrons that are that are involved.involved.

The nuclei do not come close enough to interact.The nuclei do not come close enough to interact.

The electrons of an atom vary in the amount of The electrons of an atom vary in the amount of energyenergy they possess. they possess.

EnergyEnergy is the ability to do work. is the ability to do work.

Potential energyPotential energy is the energy that matter stores is the energy that matter stores because of its position or location.because of its position or location.

Because potential energy has been expended, the Because potential energy has been expended, the water stores less energy at the bottom of the dam water stores less energy at the bottom of the dam than it did in the reservoir.than it did in the reservoir.

Electrons have potential energy because of their Electrons have potential energy because of their position relative to the nucleus.position relative to the nucleus.

The different states of potential energy that the The different states of potential energy that the electrons of an atom can have are called energy levels electrons of an atom can have are called energy levels or or electron shellselectron shells..

The first shell, closest to the nucleus, has the The first shell, closest to the nucleus, has the lowest lowest potential energypotential energy..Electrons in outer shells have more Electrons in outer shells have more potential potential energy.energy.

The chemical behavior of an atom is determined by its The chemical behavior of an atom is determined by its electron configuration—the distribution of electrons in electron configuration—the distribution of electrons in its electron shells.its electron shells.

The first electron shell can hold only The first electron shell can hold only 22 electrons. electrons.

The second shell can hold up to The second shell can hold up to 88 electrons. electrons.

The chemical behavior of an atom depends mostly on The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell, the the number of electrons in its outermost shell, the valence shellvalence shell..

Electrons in the valence shell are known Electrons in the valence shell are known as as valence valence electrons.electrons.

Atoms with the same number of Atoms with the same number of valence valence electronselectrons have similar chemical behaviors. have similar chemical behaviors.An atom with a completed valence shell, An atom with a completed valence shell, like neon, is like neon, is nonreactivenonreactive..All other atoms are chemically reactive All other atoms are chemically reactive because they have because they have incompleteincomplete valence valence shells.shells.The reactivity of atoms arises from the The reactivity of atoms arises from the presence of unpaired electrons in one or presence of unpaired electrons in one or more more orbitalsorbitals of their valence shells. of their valence shells.

3. Atoms combine by chemical bonding to form

molecules.Atoms with incomplete valence shells can interact with Atoms with incomplete valence shells can interact with each other by each other by sharingsharing or or transferringtransferring valence valence electrons.electrons.

These interactions typically result in the atoms These interactions typically result in the atoms remaining close together, held by attractions called remaining close together, held by attractions called chemical bondschemical bonds..

The strongest chemical bonds are The strongest chemical bonds are covalentcovalent bonds bonds and and ionicionic bonds. bonds.

A covalent bond is formed by the sharing of a pair of A covalent bond is formed by the sharing of a pair of valence electrons by two atoms.valence electrons by two atoms.

Two or more atoms held together by covalent bonds Two or more atoms held together by covalent bonds constitute a constitute a moleculemolecule..

We can abbreviate the structure of the molecule by We can abbreviate the structure of the molecule by substituting a line for each pair of shared electrons, substituting a line for each pair of shared electrons, drawing the drawing the structuralstructural formula. formula.

H—H is the structural formula for the covalent bond H—H is the structural formula for the covalent bond between two hydrogen atoms.between two hydrogen atoms.

The The molecularmolecular formula indicates the number and formula indicates the number and types of atoms present in a single molecule.types of atoms present in a single molecule.

HH22 is the molecular formula for hydrogen gas. is the molecular formula for hydrogen gas.

Oxygen needs to add 2 electrons to the Oxygen needs to add 2 electrons to the 66 already already present to complete its valence shell.present to complete its valence shell.

Two oxygen atoms can form a molecule by sharing Two oxygen atoms can form a molecule by sharing twotwo pairs of valence electrons. pairs of valence electrons.These atoms have formed a These atoms have formed a doubledouble covalent bond. covalent bond.

Every atom has a characteristic total number of Every atom has a characteristic total number of covalent bonds that it can form, equal to the number covalent bonds that it can form, equal to the number of unpaired electrons in the outermost shell. This of unpaired electrons in the outermost shell. This bonding capacity is called the atom’s bonding capacity is called the atom’s valencevalence..

The valence of hydrogen is The valence of hydrogen is 11..Oxygen is Oxygen is 22..Nitrogen is Nitrogen is 33..Carbon is Carbon is 44..Phosphorus should have a valence of Phosphorus should have a valence of 33, , based on its three unpaired electrons, based on its three unpaired electrons, but in biological molecules it generally but in biological molecules it generally has a valence of has a valence of 55, forming three single , forming three single covalent bonds and one double bond.covalent bonds and one double bond.

CovalentCovalent bonds can form between atoms of the bonds can form between atoms of the same element or atoms of different elements.same element or atoms of different elements.The attraction of an atom for the shared electrons The attraction of an atom for the shared electrons of a covalent bond is called its of a covalent bond is called its electronegativityelectronegativity..

Strongly electronegative atoms attempt to pull Strongly electronegative atoms attempt to pull the the sharedshared electrons toward themselves. electrons toward themselves.

If electrons in a covalent bond are shared equally, If electrons in a covalent bond are shared equally, then this is a then this is a nonpolarnonpolar covalent bond. covalent bond.When two atoms that differ in electronegativity When two atoms that differ in electronegativity bond, they do not share the electron pair equally bond, they do not share the electron pair equally and form a and form a polarpolar covalent bond. covalent bond.

The bonds between oxygen and hydrogen in water are polar covalent because oxygen has a much higher electronegativity than does hydrogen.

An An ionicionic bond can form if two atoms are so bond can form if two atoms are so unequal in their attraction for valence electrons that unequal in their attraction for valence electrons that one atom strips an electron completely from the other.one atom strips an electron completely from the other. For example, sodium, with one valence For example, sodium, with one valence

electron in its third shell, transfers this electron to electron in its third shell, transfers this electron to chlorine, with 7 valence electrons in its third shell.chlorine, with 7 valence electrons in its third shell.

After the transfer, both atoms are no longer After the transfer, both atoms are no longer neutral, but have charges and are called neutral, but have charges and are called ionsions..

Sodium has one more proton than electrons and Sodium has one more proton than electrons and has a net positive charge.has a net positive charge. Atoms with positive charges are Atoms with positive charges are cationscations..

Chlorine has one more electron than protons and Chlorine has one more electron than protons and has a net negative charge.has a net negative charge. Atoms with negative charges are Atoms with negative charges are anionsanions..

Because of differences in charge, cations and Because of differences in charge, cations and anions are attracted to each other to form an anions are attracted to each other to form an ionicionic bond.bond.

4. Weak chemical bonds play 4. Weak chemical bonds play important roles in the chemistry important roles in the chemistry

of life.of life. HydrogenHydrogen bonds form when a hydrogen atom bonds form when a hydrogen atom

already covalently bonded to a strongly already covalently bonded to a strongly electronegative atom is attracted to another strongly electronegative atom is attracted to another strongly electronegative atom.electronegative atom. These strongly electronegative atoms are These strongly electronegative atoms are

typically nitrogen or oxygen.typically nitrogen or oxygen. The partially positive–charged The partially positive–charged hydrogenhydrogen atom atom

is attracted to regions of full or partial negative is attracted to regions of full or partial negative charge on molecules, atoms, or even regions of the charge on molecules, atoms, or even regions of the same large molecule.same large molecule.

For example, ammonia molecules and water For example, ammonia molecules and water molecules interact with weak hydrogen bonds.molecules interact with weak hydrogen bonds.

Molecules or atoms in close proximity can be Molecules or atoms in close proximity can be attracted by fleeting charge differences, creating attracted by fleeting charge differences, creating van van der Waalsder Waals interactions. interactions.

While individual bonds (ionic, hydrogen, van der While individual bonds (ionic, hydrogen, van der Waals) are weak and temporary, collectively they are Waals) are weak and temporary, collectively they are strong and play important biological roles.strong and play important biological roles.

5. A molecule’s biological function is related to its

shape.Molecules with similar shapes can have Molecules with similar shapes can have similar biological effects.similar biological effects.

For example, morphine, heroin, and other For example, morphine, heroin, and other opiate drugs are similar enough in shape opiate drugs are similar enough in shape that they can bind to the same receptors that they can bind to the same receptors as natural signal molecules called as natural signal molecules called endorphins.endorphins.Binding of endorphins to receptors on Binding of endorphins to receptors on brain cells produces euphoria and brain cells produces euphoria and relieves pain. Opiates mimic these relieves pain. Opiates mimic these natural endorphin effects.natural endorphin effects.

6. Chemical reactions form and break chemical bonds.In In chemical reactionschemical reactions, chemical bonds are broken , chemical bonds are broken and reformed, leading to new arrangements of and reformed, leading to new arrangements of atoms.atoms.

The starting molecules in the process are called The starting molecules in the process are called reactantsreactants, and the final molecules are called , and the final molecules are called productsproducts..

In a chemical reaction, all of the atoms in the In a chemical reaction, all of the atoms in the reactants must be present in the products.reactants must be present in the products.

The reactions must be “balanced.”The reactions must be “balanced.”Matter is conserved in a chemical reaction.Matter is conserved in a chemical reaction.Chemical reactions rearrange matter; they do not Chemical reactions rearrange matter; they do not create or destroy matter.create or destroy matter.

For example, we can recombine the covalent bonds of For example, we can recombine the covalent bonds of HH22 and O and O22 to form the new bonds of H to form the new bonds of H22O.O.

In this reaction, In this reaction, twotwo molecules of H molecules of H22 combine with combine with oneone molecule of O molecule of O22 to form to form twotwo molecules of H molecules of H22O.O.

Photosynthesis is an important chemical reaction.Photosynthesis is an important chemical reaction.Green plants combine carbon dioxide (COGreen plants combine carbon dioxide (CO22) from ) from the air and water (Hthe air and water (H22O) from the soil to create O) from the soil to create sugarsugar molecules and release molecular molecules and release molecular oxygenoxygen (O(O22) as a by-product.) as a by-product.This chemical reaction is powered by This chemical reaction is powered by sunlightsunlight..The overall process of photosynthesis is 6COThe overall process of photosynthesis is 6CO22 + + 6H6H22O -> CO -> C66HH1212OO66 + 6O + 6O22..