Chapter 2

The Chemical Context of Life

Lecture Outline
Overview: A Chemical Connection to Biology
Living organisms and the world they live in are subject to the basic laws of physics and chemistry. Biology is a multidisciplinary science, drawing on insights from other sciences. Life can be organized into a hierarchy of structural levels. o o Atoms are organized into molecules, and molecules are organized into cells. Somewhere in the transition from molecules to cells, we cross the boundary between nonlife and life.

At each successive level, additional emergent properties appear.

Concept 2.1 Matter consists of chemical elements in p re form an! in com"inations calle! compo n!s.
Organisms are composed of matter. o o atter is anything that ta!es up space and has mass. atter is made up of elements.

An element is a substance that cannot be bro!en down into other substances by chemical reactions. o o There are 92 naturally occurring elements. Each element has a unique symbol, usually the first one or two letters of its name. Some symbols are derived from Latin or German names. #able salt $sodium chloride or %a&l' is a compound with e(ual numbers of atoms of the elements chlorine and sodium. Although pure sodium is a metal and chlorine is a gas, they combine to form an edible compound. #his change in characteristics when elements combine to form a compound is an e"ample of an emergent property.

A compo n! is a substance that consists of two or more elements in a fi"ed ratio. o o o

Twenty-five chemical elements are essential for life. About )* of the +) naturally occurring elements are !nown to be essential for life. o ,our elements-carbon $&', o"ygen $O', hydrogen $.', and nitrogen $%'-ma!e
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Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

up +/0 of living matter. o ost of the remaining 10 of an organism2s weight consists of phosphorus $3', sulfur $S', calcium $&a', and potassium $4'. Some trace elements, li!e iron $,e', are re(uired by all organisms. Other trace elements are re(uired by only some species. ,or e"ample, vertebrates $animals with bac!bones' re(uire the element iodine for normal activity of the thyroid gland. A daily inta!e of only 5.6* milligram $mg' of iodine is ade(uate for normal activity of the human thyroid.

Trace elements are re(uired by an organism but only in minute (uantities. o o

Concept 2.2 An element#s properties !epen! on the str ct re of its atoms.

7ach element consists of uni(ue atoms. An atom is the smallest unit of matter that still retains the properties of an element. Atoms are composed of even smaller parts called subatomic particles. o #wo subatomic particles, ne trons and protons, are pac!ed together to form a dense core, the atomic n cle s, at the center of an atom. o $lectrons can be visualized as forming a cloud of negative charge around the nucleus. 7ach electron has one unit of negative charge, each proton has one unit of positive charge, and neutrons are electrically neutral. #he attractions between the positive charges in the nucleus and the negative charges of the electrons !eep the electrons in the vicinity of the nucleus. A neutron and a proton have almost identical mass8 about 6.9 : 65 ;)1 gram per particle. ,or convenience, a smaller unit, the !alton% is used to measure the masses of subatomic particles, atoms, and molecules. o #he mass of a neutron or a proton is close to 6 dalton. #he mass of an electron is about 6<),555 the mass of a neutron or proton. o =e typically ignore the contribution of electrons when determining the total mass of an atom. All atoms of a particular element have the same number of protons in their nuclei. o #his number of protons is the element2s uni(ue atomic n m"er. o #he atomic number is written as a subscript before the symbol for the element. ,or e"ample, ).e means that an atom of helium has ) protons in its nucleus. >nless otherwise indicated, atoms have e(ual numbers of protons and electrons and, therefore, no net charge. o #herefore, the atomic number tells the number of protons and the number of electrons in a neutral atom of a specific element. The mass number is the sum of the number of protons and the number of neutrons in the nucleus of an atom. o We can determine the number of neutrons in an atom by subtracting the number
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Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

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of protons (the atomic number) from the mass number. The mass number is written as a superscript before an elements symbol (for example, 4He). Because neutrons and protons each have a mass very close to 1 dalton, the mass number is an approximation of the total mass of an atom, called its atomic mass.

#wo atoms of the same element that differ in the number of neutrons are called isotopes. ?n nature, an element occurs as a mi"ture of isotopes. o ,or e"ample, ++0 of carbon atoms have / neutrons $6)&'. o ost of the remaining 60 of carbon atoms have 9 neutrons $ 6@&', while the rarest carbon isotope, with A neutrons, is 61&. ost isotopes are stableB they do not tend to lose particles. o Both 6)& and 6@& are stable isotopes. #he nuclei of some isotopes are unstable and decay spontaneously, emitting particles and energy. o 61& is one of these unstable isotopes, or ra!ioactive isotopes. o =hen 61& decays, one of its neutrons is converted to a proton and an electron. o ?n this process, 61& is converted to 61%, a different element. Cadioactive isotopes have many applications in biological research. o Cadioactive decay rates can be used to date fossils. o Cadioactive isotopes can be used to trace atoms through metabolic processes. Cadioactive isotopes are also used to diagnose medical disorders. o A !nown (uantity of a substance labeled with a radioactive isotope can be injected into the blood, and its rate of e"cretion in the urine can be measured. o Cadioactive tracers can be used with imaging instruments such as 37# scanners to monitor chemical processes in the body. #hough useful in research and medicine, the energy emitted in radioactive decay is hazardous to life. o #his energy can destroy molecules within living cells. o #he severity of damage depends on the type and amount of radiation that the organism absorbs. Simplified models of the atom greatly distort the atom2s relative dimensions. ?n an accurate representation of the relative proportions of an atom, if an atom of helium were the size of Yankee Stadium, the nucleus would be only the size of a pencil eraser in the center of the field. o #he electrons would be li!e two gnats buzzing around the stadium. o Atoms are mostly empty space. =hen two elements interact during a chemical reaction, it is actually their electrons that are involved. o #he nuclei do not come close enough to interact. #he electrons of an atom vary in the amounts of energy they possess.
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Electron configuration influences the chemical behavior of an atom.

Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

$nergy is the ability to do wor!. &otential energy is the energy that matter stores because of its position or location. o =ater stored behind a dam has potential energy that can be used to do wor! turning electric generators. o Because potential energy has been e"pended, the water stores less energy at the bottom of the dam than it did in the reservoir. 7lectrons have potential energy because of their positions relative to the nucleus. o #he negatively charged electrons are attracted to the positively charged nucleus. o #he farther electrons are from the nucleus, the more potential energy they have. &hanges in an electron2s potential energy can occur only in steps of a fi"ed amount, moving the electron to a fi"ed location relative to the nucleus. o An electron cannot e"ist between these fi"ed locations. #he different states of potential energy that the electrons of an atom can have are called electron shells. o #he first shell, closest to the nucleus, has the lowest potential energy. o 7lectrons in outer shells have higher potential energy. o 7lectrons can change their position only if they absorb or release a (uantity of energy that matches the difference in potential energy between the two levels. #he chemical behavior of an atom is determined by its electron configuration-the distribution of electrons in its electron shells. The periodic table of the elements shows the distribution of electrons in the first 18 elements from hydrogen to argon. o #he elements are arranged in three rows or periods, corresponding to the number of electron shells in their atoms. o 7lements in the same row have the same shells filled with electrons. o As we move from left to right in the table, each element has one more electron $and proton' than the element before. #he first electron shell can hold only ) electrons. o #he ) electrons of helium fill the first shell. Atoms with more than 2 electrons must have the extra electrons in higher shells. o Lithium, with @ electrons, has ) electrons in the first shell and 6 in the second shell. #he second shell can hold up to A electrons. o %eon, with 65 total electrons, has ) in the first shell and A in the second, thus filling both shells. #he chemical behavior of an atom depends mostly on the number of electrons in its outermost shell, the valence shell. o 7lectrons in the valence shell are !nown as valence electrons. o Lithium has 6 valence electronB neon has A. Atoms with the same number of valence electrons have similar chemical behaviors. An atom with a completed valence shell, li!e neon, is inert or chemically nonreactive. All other atoms are chemically reactive because they have incomplete valence shells.
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Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

#he paths of electrons are often portrayed as concentric paths, li!e planets orbiting the sun. ?n reality, an electron occupies a more comple" threeDdimensional space, an or"ital. #he orbital is the space in which the electron is found +50 of the time. o 7ach orbital can hold a ma"imum of ) electrons. o #he first shell has room for a single spherical 6 s orbital for its pair of electrons. o #he second shell can pac! pairs of electrons into one spherical ) s orbital and three dumbbellDshaped )p orbitals. #he reactivity of atoms arises from the presence of unpaired electrons in one or more orbitals of their valence shells. o 7lectrons occupy separate orbitals within the valence shell until forced to share orbitals. o #he 1 valence electrons of carbon each occupy separate orbitals, but the * valence electrons of nitrogen are distributed into three unshared orbitals and one shared orbital. =hen atoms interact to complete their valence shells, it is the unpaired electrons that are involved.

Concept 2.' The formation an! f nction of molec les !epen! on chemical "on!ing "etween atoms.
Atoms with incomplete valence shells can interact with each other by sharing or transferring valence electrons. #hese interactions typically result in the atoms remaining close together, held by attractions called chemical "on!s. #he strongest chemical bonds are covalent bonds and ionic bonds. A covalent "on! is formed when two atoms share a pair of valence electrons. o ?f two atoms come close enough that their unshared orbitals overlap, they can share their newly paired electrons. 7ach atom can count both electrons toward its goal of filling the valence shell. o ,or e"ample, if two hydrogen atoms come close enough that their 6 s orbitals overlap, then they can share a pair of electrons, with each atom contributing one. #wo or more atoms held together by covalent bonds constitute a molec le. =e can draw the str ct ral form la of a molecule by using a line for each pair of shared electrons. o .-. is the structural formula for the covalent bond between two hydrogen atoms. #he line represents a single covalent "on!% a pair of shared electrons. #he molec lar form la indicates the numbers and types of atoms in a single molecule. o .) is the molecular formula for hydrogen gas. O"ygen needs to add ) electrons to the / already present to complete its valence shell. o #wo o"ygen atoms can form a molecule by sharing two pairs of valence electrons. o #hese atoms form a !o "le covalent "on!. 7very atom has a characteristic total number of covalent bonds that it can form, e(ual to the number of unpaired electrons in the outermost shell. #his bonding capacity is called
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Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

the atom2s valence. o #he valence of hydrogen is 6B o"ygen is )B nitrogen is @B carbon is 1. o 3hosphorus should have a valence of @, based on its @ unpaired electrons, but in biological molecules it generally has a valence of *, forming three single covalent bonds and one double bond. &ovalent bonds can form between atoms of the same element or atoms of different elements. o Although both types are molecules, the latter are also compounds. o =ater $.)O' is a compound in which two hydrogen atoms form single covalent bonds with an o"ygen atom. #his satisfies the valences of both elements. o ethane $&.1' satisfies the valences of both & and .. #he attraction of an atom for the shared electrons of a covalent bond is called its electronegativity. o Strongly electronegative atoms attempt to pull the shared electrons toward themselves. ?f electrons in a covalent bond are shared e(ually, then this is a nonpolar covalent "on!. o A covalent bond between two atoms of the same element is always nonpolar. o A covalent bond between atoms that have similar electronegativities is also nonpolar. o Because carbon and hydrogen do not differ greatly in electronegativities, the bonds of &.1 are nonpolar. =hen two atoms that differ in electronegativity bond, they do not share the electron pair e(ually and they form a polar covalent "on!. o #he bonds between o"ygen and hydrogen in water are polar covalent because o"ygen has a much higher electronegativity than does hydrogen. o &ompounds with a polar covalent bond have regions of partial negative charge near the strongly electronegative atom and regions of partial positive charge near the wea!ly electronegative atom. An ionic "on! can form if two atoms are so une(ual in their attraction for valence electrons that one atom strips an electron completely from the other. o ,or e"ample, sodium, with 6 valence electron in its third shell, transfers this electron to chlorine, with 9 valence electrons in its third shell. o #hen sodium has a full valence shell $the second' and chlorine has a full valence shell $the third'. After the transfer, both atoms are no longer neutral but have charges and are called ions. Atoms with positive charges are cations. o Sodium has one more proton than electrons and has a net positive charge. Atoms with negative charges are anions. o &hlorine has one more electron than protons and has a net negative charge. Because of differences in charge, cations and anions are attracted to each other to form an ionic "on!. o Atoms in an ionic bond need not have ac(uired their charges by transferring electrons with each other. &ompounds formed by ionic bonds are ionic compo n!s% or salts. An e"ample is %a&l,
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Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

or table salt. o #he formula for an ionic compound indicates the ratio of elements in a crystal of that salt. %a&l is not a molecule but a salt crystal with e(ual numbers of %a E and &l; ions. ?onic compounds can have ratios of elements different from 686. o ,or e"ample, the ionic compound magnesium chloride $ g&l )' has two chloride atoms per magnesium atom. o agnesium needs to lose ) electrons to drop to a full outer shellB each chlorine atom needs to gain 6 electron. 7ntire molecules that have full electrical charges are also called ions. o ?n the salt ammonium chloride $%.1&l', the anion is &l; and the cation is %.1E. #he strength of ionic bonds depends on environmental conditions, such as moisture. =ater can dissolve salts by reducing the attraction between the salt2s anions and cations. =ithin a cell, wea!, brief bonds between molecules are important to a variety of processes. o Large biological molecules are held in their functional form by weak bonds. o =hen two molecules in the cell make contact, they may adhere temporarily by weak bonds. The reversibility of weak bonding can be an advantage: Two molecules can come together, respond to each other in some way, and then separate. =ea! interactions include ionic bonds between ions dissociated in water, hydrogen bonds, and van der =aals interactions. (y!rogen "on!s form when a hydrogen atom that is already covalently bonded to one electronegative atom is attracted to another electronegative atom. o ?n cells, the electronegative partners are typically nitrogen or o"ygen. o .ydrogen bonds form because a polar covalent bond leaves the hydrogen atom with a partial positive charge and the other atom with a partial negative charge. o #he partially positiveFcharged hydrogen atom is attracted to regions of full or partial negative charge on molecules, atoms, or even regions of the same large molecule. ,or e"ample, ammonia molecules and water molecules interact with wea! hydrogen bonds. o ?n the ammonia molecule, the hydrogen atoms have partial positive charges, and the more electronegative nitrogen atom has a partial negative charge. o ?n the water molecule, the hydrogen atoms have partial positive charges, and the o"ygen atom has a partial negative charge. o Areas with opposite charges are attracted to each other. 7ven molecules with nonpolar covalent bonds can have temporary regions of partial negative and positive charge. o Because electrons are constantly in motion, there may be times when they accumulate by chance in one area of a molecule. o #his creates everDchanging regions of partial negative and positive charge within a molecule.
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Weak chemical bonds play important roles in the chemistry of life.

Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

olecules or atoms in close pro"imity can be attracted by fleeting charge differences, creating van !er )aals interactions. Although individual bonds $ionic, hydrogen, van der =aals' are temporary and individually wea!, collectively they are strong and play important biological roles. o The cumulative effect of individual bonds is to reinforce the three-dimensional shape of a large molecule.

A molecules biological function is related to its shape. #he threeDdimensional shape of a molecule is an important determinant of its function in a cell. A molecule with two atoms is always linearB a molecule with more than two atoms has a more comple" shape. #he shape of a molecule is determined by the positions of the electron orbitals that are shared by the atoms involved in the bond. o =hen covalent bonds form, the orbitals in the valence shell of each atom rearrange. ,or atoms with electrons in both s and p orbitals, the formation of a covalent bond leads to hybridization of the orbitals to four new orbitals in a tetrahedral shape. ?n a water molecule, two of o"ygen2s four hybrid orbitals are shared with hydrogen atoms. #he water molecule is shaped li!e a G, with its two covalent bonds spread apart at an angle of 651.*H. ?n a methane molecule $&.1', the carbon atom shares all four of its hybrid orbitals with . atoms. #he carbon nucleus is at the center of the tetrahedron, with hydrogen nuclei at the four corners. Large organic molecules contain many carbon atoms. ?n these molecules, the tetrahedral shape of carbon bonded to four other atoms is often a repeating motif. Biological molecules recognize and interact with one another with a specificity based on molecular shape. Molecules with similar shapes can have similar biological effects. o ,or e"ample, morphine, heroin, and other opiate drugs are similar enough in shape that they can bind to the same receptors as natural signal molecules called endorphins. o #he binding of endorphins to receptors on brain cells produces euphoria and relieves pain. Opiates mimic these natural endorphin effects.

Concept 2.* Chemical reactions ma+e an! "rea+ chemical "on!s.

?n chemical reactions% chemical bonds are bro!en and reformed, leading to new arrangements of atoms. #he starting molecules in the process are called reactants% and the final molecules are called pro! cts. ?n a chemical reaction, all of the atoms in the reactants must be present in the products. o #he reactions must be Ibalanced.J o atter is conserved in a chemical reaction.
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Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

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&hemical reactions rearrange matterB they do not create or destroy matter. ,or e"ample, the covalent bonds of .) and O) can recombine to form the new bonds of .)O. #wo molecules of .) combine with one molecule of O) to form two molecules of .)O.

3hotosynthesis is an important chemical reaction. o .umans and other animals ultimately depend on photosynthesis for food and o"ygen. o Kreen plants combine carbon dio"ide $&O)' from the air and water $.)O' from the soil to create sugar molecules, and they release molecular o"ygen $O )' as a byDproduct. o #his chemical reaction is powered by sunlight. o #he overall process of photosynthesis is / &O) E / .)O &/.6)O/ E / O). o #his process occurs in a se(uence of individual chemical reactions that rearrange the atoms of the reactants to form the products. Some chemical reactions go to completionB that is, all the reactants are converted to products. All chemical reactions are reversible, with the products in the forward reaction becoming the reactants in the reverse reaction. o o o ,or e"ample, in the reaction @ .) E %) L ) %.@, hydrogen and nitrogen molecules combine to form ammonia, but ammonia can decompose to hydrogen and nitrogen molecules. ?nitially, when reactant concentrations are high, the reactants fre(uently collide to create products. As products accumulate, they collide to reform reactants.

7ventually, the rate of formation of products is the same as the rate of brea!down of products $formation of reactants', and the system is at chemical e, ili"ri m. o At e(uilibrium, products and reactants are continually being formed, but there is no net change in the concentrations of reactants and products. o At e(uilibrium, the concentrations of reactants and products are typically not e(ual, but their concentrations have stabilized at a particular ratio.

Lecture Outline for Campbell/Reece Biology, 8th Edition, Pearson Education, Inc.

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