Chapter Chemistry

8/2/2019 Chapter Chemistry

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Chapter 2 LectureChemistry


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Abo ut 25 of the 92 natural elements arekn ow n t o b e essential fo r lif e. Fo ur elements - car bo n (C), ox ygen (O),

hydr o gen (H), and nitr o gen (N) - make up96% of living matter.

Mo st of the remaining 4% of an o rganismsw eight c o nsists of ph o sph o rus (P), sul f ur (S),calcium (Ca), and p o tassium (K).

2. Life requires about 25 chemicalelements

Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings


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E ach element c o nsists of unique at o ms.A n atom is the smallest unit of matter thatstill retains the pr o perties of an element. A to ms are c o mp o sed of even smaller parts,

called su b at o mic particles.

Two

of

these, neutrons and protons, arepacked t o gether t o fo rm a dense c o re, theat o mic nucleus, at the center of an at o m.

Electrons fo rm a cl o ud ar o und the nucleus.

1. Atomic structure determinesthe behavior of an element



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E ach electr o n has o ne unit of negativecharge.E ach pr o to n has o ne unit of po sitivecharge.Neutr o ns are electrically neutral.The attracti o ns b et w een the p o sitivecharges in the nucleus and the negativecharges of the electr o ns keep the

electr o ns in the vicinity of the nucleus.

Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 2.5


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A neutr o n and a pr o to n are alm o stidentical in mass, a bo ut 1.7 x 10 -24 gramper particle.Fo r c o nvenience, an alternative unit of measure, the dalton , is used t o measurethe mass su b at o mic particles, at o ms o r mo lecules. The mass of a neutr o n o r a pr o to n is cl o se t o

1 dalt o n.

The mass of an electr o n is a bo ut 1/2000ththat of a neutr o n o r pr o to n. There fo re, w e typically ign o re the c o ntrib utio n

of electr o ns w hen determining the t o tal mass

of an at o m.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings


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A ll at o ms of a particular element have thesame num b er of pr o to ns in their nuclei. E ach element has a unique num b er of

pr o to ns, its unique atomic number . The at o mic num b er is w ritten as a su b script

b e fo re the sym bo l fo r the element ( fo r e x ample, 2He).

U nless o ther w ise indicated, at o ms haveequal num b ers of pr o to ns and electr o ns -no net charge. There fo re, the at o mic num b er tells us the

num b er of pr o to ns and the num b er of electr o ns that are fo und in a neutral at o m of aspeci f ic element.



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The mass number is the sum of the num b er of pr o to ns and neutr o ns in the nucleus of an at o m. There fo re, w e can determine the num b er of neutr o ns

in an at o m b y su b tracting the num b er of pr o to ns (theat o mic num b er) f r o m the mass num b er.

The mass num b er is w ritten as a superscript b e fo re

an elements sym bo l (fo r e x ample,4

He).The atomic weight of an at o m, a measure of itsmass, can b e appr ox imated b y the massnum b er.

Fo r e x ample, 4He has a mass num b er of 4 and anestimated at o mic w eight of 4 dalt o ns.

Mo re precisely, its at o mic w eight is 4.003 dalt o ns.



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W hile all at o ms of a given element havethe same num b er of pr o to ns, they maydiff er in the num b er of neutr o ns.Two at o ms of the same element thatdiff er in the num b er of neutr o ns arecalled isotopes .In nature, an element o ccurs as amix ture of iso to pes.

Fo r e x ample, 99% of car bo n at o ms have 6neutr o ns ( 12 C).

Mo st of the remaining 1% of car bo n at o mshave 7 neutr o ns ( 13 C) w hile the rarestiso to pe, w ith 8 neutr o ns is 14 C.


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Mo st is o to pes are sta b le; they d o no t tendto loo se particles. Bo th 12 C and 13 C are sta b le is o to pes.

The nuclei of s o me is o to pes are unsta b leand decay sp o ntane o usly, emittingparticles and energy. 14 C is a o ne of these unsta b le o r radioactive

isotopes .

In its decay, an neutr

on is c

onverted t

oapr o to n and electr o n.

This c o nverts 14 C t o 14 N, changing the identityof that at o m.



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To gain an accurate perspective of therelative pr o po rtio ns of an at o m, i f thenucleus w as the size of a g o lf b all, theelectr o ns wo uld b e m o ving a bo ut 1kilo meter f r o m the nucleus.

A to ms are m o stly empty space.W hen t wo elements interact during achemical reacti o n, it is actually their

electr o

ns that are actually invo

lved. The nuclei d o no t c o me cl o se en o ugh t o interact.



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The electr o ns of an at o m may vary in theam o unt of energy that they p o ssess.Energy is the a b ility to do wo rk.Potential energy is the energy that matter st o res b ecause of its p o sitio n o r lo cati o n. W ater st o red b ehind a dam has p o tential

energy that can b e used t o do wo rk turningelectric generat o rs.

Because po

tential energy hasb

een ex

pended,the w ater st o res less energy at the bo tto m of the dam than it did in the reserv o ir.



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E lectr o ns have p o tential energy b ecause of their p o sitio n relative t o the nucleus. The negatively charged electr o ns are attracted

to the p o sitively charged nucleus. The f arther electr o ns are f r o m the nucleus, the

m o re p o tential energy they have.How ever, electr o ns cann o t o ccupy just anylo cati o n a w ay f r o m the nucleus.

Changes in po

tential energy cano

nlyo

ccur in steps of a f ix ed am o unt, m o ving theelectr o n t o a f ix ed l o cati o n. A n electr o n cann o t e x ist b et w een these f ix ed

lo cati o ns.


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The di ff erent states of po tential energy thatthe electr o ns of an at o ms can have arecalled energy levels o r electron shells . The f irst shell, cl o sest t o the nucleus, has the

low est p o tential energy.

E lectr o ns in o uter shells have m o re p o tentialenergy.

E lectr o ns can o nly change their p o sitio n i f theya b s o r b o r release a quantity of energy thatmatches the di ff erence in p o tential energyb et w een the t wo levels.



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Fig. 2.9


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The chemical b ehavi o r of an at o m isdetermined b y its electr o n c o n f igurati o n -the distri b utio n of electr o ns in its electr o nshells. The f irst 18 elements, including th o se m o st

imp o rtant in b io lo gical pr o cesses, can b earranged in 8 c o lumns and 3 r ow s.E lements in the same r ow use the same shells.Mo ving f r o m le f t to right, each element has a

sequential additi o n of electr o ns (and pr o to ns).



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Fig. 2.10


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The f irst electr o n shell can h o ld o nly 2electr o ns. The t wo electr o ns of Helium f ill the f irst shell.A to ms w ith m o re than t wo electr o ns mustplace the e x tra electr o ns in higher shells. Fo r e x ample, Lithium w ith three electr o ns has

two in the f irst shell and o ne in the sec o ndshell.

The seco

nd shell can ho

ld up to

8electr o ns. Ne o n, w ith 10 t o tal electr o ns, has t wo in the

f irst shell and eight in the sec o nd, f illing bo th

shells.


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The chemical b ehavi o r of an at o m dependsmo stly o n the num b er of electr o ns in itso uterm o st shell, the valence shell . E lectr o ns in the valence shell are kn ow n as

valence electrons .

A to ms w ith the same num b er of valenceelectr o ns have similar chemical b ehavi o r.A n at o m w ith a c o mpleted valence shell is

unreactive.A ll o ther at o ms are chemically reactiveb ecause they have inc o mplete valenceshells.



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W hile the paths of electr o ns are of tenvisualized as c o ncentric paths, like planetso r b iting the sun.In reality, an electr o n o ccupies a m o reco mple x three-dimensi o nal space, an

orbital . The f irst shell has r oo m fo r a single spherical

o r b ital fo r its pair of electr o ns.

The seco

nd shell can pack pairsof

electr o

nsinto a spherical o r b ital and three p o r b itals(dum bb ell-shaped).



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Fig. 2.11


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The reactivity of at o ms arises f r o m thepresence of unpaired electr o ns in o ne o r mo re o r b itals of their valence shells. E lectr o ns pre f erentially o ccupy separate

o r b itals w ithin the valence shell until fo rced t o

shareo

r b

itals.The fo ur valence electr o ns of car bo n each o ccupyseparate o r b itals, b ut the f ive valence electr o ns of nitr o gen are distri b uted int o three unshared o r b italsand o ne shared o r b ital.

W hen at o ms interact t o co mplete their valenceshells, it is the unpaired electr o ns that areinvo lved.



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A to ms w ith inc o mplete valence shellsinteract b y either sharing o r trans f erring

valence electr o ns.These interacti o ns typically result in theat o ms remaining cl o se t o gether, held b yan attracti o ns called chemical bonds . The str o ngest chemical bo nds are c o valent

bo nds and i o nic bo nds.

2. Atoms combine by chemicalbonding to form molecules



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A covalent bond is the sharing of a pair of valence electr o ns b y two at o ms. If two at o ms c o me cl o se en o ugh that their

unshared o r b itals o verlap, each at o m canco unt bo th electr o ns t ow ard its g o al of f illingthe valence shell.

Fo r e x ample, i f two hydr o gen at o ms c o meclo se en o ugh that their 1s o r b itals o verlap,then they can share the single electr o ns that

each c o ntrib utes.


Fig. 2.12a


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Two o r m o re at o ms held t o gether b yco valent bo nds c o nstitute a molecule .W e can a bb reviate the structure of thismo lecule b y su b stituting a line fo r each pair of shared electr o ns, dra w ing the structural

formula . H-H is the structural fo rmula fo r the c o valent

bo nd b et w een t wo hydr o gen at o ms.

The molecular formula indicates thenum b er and types of at o ms present in asingle m o lecule. H2 is the m o lecular fo rmula fo r hydr o gen gas.



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Ox ygen needs t o add 2 electr o ns t o the 6already present t o co mplete its valenceshell. Two ox ygen at o ms can fo rm a m o lecule b y

sharing two pairs of valence electr o ns.

These at o ms have fo rmed a double covalentbond .


Fig. 2.12b


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E very at o m has a characteristic t o talnum b er of co valent bo nds that it can fo rm -an at o ms valence . The valence of hydr o gen is 1. Ox ygen is 2.

Nitr o gen is 3. Car bo n is 4. Ph o sph o rus sh o uld have a valence of 3, b ased

o n its three unpaired electr o ns, b ut in b io lo gicalm o lecules it generally has a valence of 5,fo rming three single c o valent bo nds and o nedo ub le bo nd.



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Co valent bo nds can fo rm b et w een at o ms of the same element o r at o ms of diff erent

elements. W hile bo th types are m o lecules, the latter areals o co mp o unds.

W ater, H 2O, is a c o mp o und in w hich t wo hydr o gen at o ms fo rm single c o valent bo ndsw ith an ox ygen at o m.

This satis f ies the valences of bo th elements.

Copyright 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 2.12c


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Fig. 2.12d

Methane, CH 4, satis f ies the valences of bo th Cand H.


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The attracti o n of an at o m fo r the electr o ns of a c o valent bo nd is called its

electronegativity. Str o ngly electr o negative at o ms attempt t o pull

the shared electr o ns t ow ard themselves.If electr o ns in a c o valent bo nd are sharedequally, then this is a nonpolar covalentbond . A co valent bo nd b et w een t wo at o ms of the

same element is al w ays n o np o lar. A co valent bo nd b et w een at o ms that have

similar electr o negativities is als o no np o lar.Because car bo n and hydr o gen d o no t di ff er greatly inelectr o negativities, the bo nds of CH 4 are n o np o lar.



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If the electr o ns in a c o valent bo nd are n o tshared equally b y the t wo at o ms, then this

is a polar covalent bond. The bo nds b et w een ox ygen and hydr o gen in

w ater are p o lar c o valent b ecause ox ygen hasa much higher electr o negativity than d o es

hydr o gen. Co mp o unds w ith a p o lar

co valent bo nd have regi o nsthat have a partial negative

charge near the str o nglyelectr o negative at o m and apartial p o sitive charge near the w eakly electr o negativeat o m.


Fig. 2.13


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A n ionic bond can fo rm i f two at o ms ares o unequal in their attracti o n fo r valence

electr o

ns thato

ne ato

m strips an electr o

nco mpletely f r o m the o ther. Fo r e x ample, s o dium w ith o ne valence electr o n

in its third shell trans f ers this electr o n t o

chl o rine w ith 7 valence electr o ns in its thirdshell. Now , s o dium has a f ull valence shell (the

sec o nd) and chl o rine has a f ull valence shell

(the third).

Fig. 2.14


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Af ter the trans f er, bo th at o ms are n o lo nger neutral, b ut have charges and are called

ions .S o dium has o ne m o re pr o to n thanelectr o ns and has a net p o sitive charge. A to ms w ith p o sitive charges are cations .

Chl o rine has o ne m o re electr o n thanpr o to ns and has a net negative charge. A to ms w ith negative charges are anions .


Fig. 2.14


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Because of diff erences in charge, cati o nsand ani o ns are attracted t o each o ther t o fo rm an ionic bond . A to ms in an i o nic bo nds need n o t have

acquired their charge b y electr o ns trans f erredw

ith eacho

ther.



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Co mp o unds fo rmed b y io nic bo nds areionic compounds o r salts, like NaCl o r ta b le salt.The fo rmula fo r an i o nic c o mp o undindicates the rati o of elements in a crystalof that salt. A to ms in a crystal d o no t fo rm m o lecules w ith a

de f initive size and num b er of at o ms as inco valent bo nds.



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Io nic c o mp o unds can have rati o s of elements di ff erent f r o m 1:1. Fo r e x ample, the i o nic c o mp o und magnesium

chl o ride (MgCl 2) has 2 chl o ride at o ms per magnesium at o m.

Magnesium needs t o loo se 2 electr o ns t o dr o p t o af ull o uter shell, each chl o rine needs t o gain 1.

E ntire m o lecules that have f ull electricalcharges are als o called i o ns.

In the salt amm o nium chl o ride (NH 4Cl), theani o n is Cl - and the cati o n is NH 4 +.

The strength of io nic bo nds depends o n

envir o

nmental co

nditio

ns.Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings


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W ithin a cell, w eak, b rie f bo nds b et w eenmo lecules are imp o rtant t o a variety of pr o cesses. Fo r e x ample, signal m o lecules f r o m o ne neur o n

use w eak bo nds t o b ind b rie f ly to recept o r m o lecules o n the sur f ace of a receiving neur o n.

This triggers a m o mentary resp o nse b y therecipient.

W eak interacti o ns include i o nic bo nds(w eak in w ater), hydr o gen bo nds, and van

der W aals interacti o ns.

3 . Weak chemical bonds play important roles inthe chemistry of life



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H ydrogen bonds fo rm w hen a hydr o genat o m that is already c o valently bo nded t o astr o ngly electr o negative at o m is attracted t o an o ther str o ngly electr o negative at o m. These str o ngly electr o negative at o ms are

typically nitr o gen o r ox ygen. Typically, these bo nds result b ecause the p o lar

co valent bo nd w ith hydr o gen leaves thehydr o gen at o m w ith a partial p o sitive chargeand the o ther at o m w ith a partial negativecharge.

The partially p o sitive charged hydr o gen at o m isattracted t o negatively charged (partial o r f ull)m o lecules, at o ms, o r even regi o ns of the samelarge m o lecule.


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Fo r e x ample, amm o nia m o lecules and w ater mo lecules link t o gether w ith w eak hydr o genbo nds. In the amm o nia m o lecule, the hydr o gen at o ms

have partial p o sitive charges and the m o reelectr o negative nitr o gen at o m has a partial

po sitive charge. In the w ater m o lecule,

the hydr o gen at o msals o have partial

po

sitive charges andthe ox ygen at o mpartial negative charges.

A reas w ith o pp o sitecharges are attracted.


Fig. 2.16


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E ven m o lecules w ith n o np o lar c o valent bo ndscan have partially negative and p o sitive regi o ns.

Because electr o ns are c o nstantly in m o tio n, there canb e peri o ds w hen they accumulate b y chance in o nearea of a m o lecule.

This created ever-changing regi o ns of negative and

po

sitive chargew

ithin a mo

lecule.Mo lecules o r at o ms in cl o se pr ox imity can b eattracted b y these f leeting charge di ff erences,creating van der Waals interactions .

W hile individual bo nds (i o nic, hydr o gen, van der W aals) are w eak, c o llectively they have strength.



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The three-dimensi o nal shape of a m o leculeis an imp o rtant determinant of its f uncti o n ina cell.The shape of a m o lecule is determined b ythe arrangement of electr o n o r b itals that areshared b y the at o ms inv o lved in the bo nd. W hen c o valent bo nds fo rm, the o r b itals in the

valence shell rearrange. A m o lecule w ith t wo at o ms is al w ays linear. How ever, a m o lecule w ith m o re than t wo at o ms

has a mo

re co

mplex

shape.

4 . A molecules biologicalfunction is related to its shape



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Fo r at o ms w ith electr o ns in bo th s and po r b itals, the fo rmati o n of a c o valent bo ndleads t o hyb ridizati o n of the o r b itals t o fo rmfo ur ne w o r b itals in a tetrahedr o n shape.


Fig. 2.17a


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In a w ater m o lecule the hy b rid o r b itals thatox ygen shares w ith hydr o gen at o ms are

spread in a V shape, at an angle of 104.5 o .


Fig. 2.17b


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A methane m o lecule (CH 4) has all fo ur hy b rido r b itals shared and has hydr o gen nuclei atthe c o rners of the tetrahedr o n.In larger m o lecules the tetrahedral shape of car bo n bo nded t o fo ur o ther at o ms is of ten a

repeating m o tif .


Fig. 2.17c


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Bio lo gical m o lecules rec o gnize and interact t o o ne an o ther b ased o n m o lecular shape. Fo r e x ample, signal m o lecules f r o m a

transmitting b rain cell have speci f ic shapes thatf it to gether w ith the shapes of recept o r m o leculeso n the sur f ace of the receiving cell.

The temp o raryattachment of the recept o r and

signal mo

leculestimulatesactivity in therecept o r cell.


Fig. 2.18


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Mo lecules w ith similar shapes can interact insimilar w ays. Fo r e x ample, m o rphine, her o in, and o ther o piate

drugs are similar en o ugh in shape that they canb ind t o the same recept o rs as natural signalm o lecules, called end o rphins.

Binding t o the recept o rspr o duces

eupho

riaand relievespain.


Fig. 2.19


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In chemical reactions chemical bo ndsare b r o ken and re fo rmed, leading t o ne w arrangements of at o ms.

The starting m o lecules in the pr o cess arecalled reactants and the end m o leculesare called products.

In a chemical reacti o n, all of the at o ms inthe reactants must b e acc o unted fo r in thepr o ducts.

The reactio

ns mustb

e b

alanced.

5. Chemical reactions makeand break chemical bonds



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Fo r e x ample, w e can rec o mb ine the c o valentbo nds of H2 and O 2 to fo rm the ne w bo nds of H2O.In this reacti o n, t wo mo lecules of H2 co mb inew ith o ne m o lecule of O 2 to fo rm t wo

mo lecules of H2O.The rati o s of mo lecules are indicated b yco e ff icients.


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Ph o to synthesis is an imp o rtant chemical reacti o n.G reen plants c o m b ine car bo n di ox ide (CO 2) f r o m

the air and w ater (H 2O) f r o m the s o il to create sugar m o lecules and m o lecular ox ygen (O 2), a b ypr o duct.This chemical reacti o n is p ow ered b y sunlight.Humans and o ther animals depend o nph o to synthesis fo r foo d and ox ygen.The o verall pr o cess of ph o to synthesis is 6CO 2 + 6H 2O -> C 6H12 O 6 + 6H 2O

This pr o cess o ccurs in a sequence of individualchemical reacti o ns.



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S o me chemical reacti o ns g o to co mpleti o n; that is,all the reactants are c o nverted t o pr o ducts.

Mo st chemical reacti o ns are reversi b le, thepr o ducts in the fo r w ard reacti o n b ec o ming thereactants fo r the reverse reacti o n.Fo r e x ample in this reacti o n: 3H 2 + N 2 2NH 3hydr o gen and nitr o gen m o lecules c o m b ine t o fo rmamm o nia, b ut amm o nia can dec o mp o se t o hydr o gen and nitr o gen m o lecules. Initially, w hen reactant c o ncentrati o ns are high, they

f requently c o llide t o create pr o ducts. A s pr o ducts accumulate, they c o llide t o re fo rm reactants.



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E ventually, the rate of fo rmati o n of pr o ductsis the same as the rate of b reakd ow n of pr o ducts ( fo rmati o n of reactants) and thesystem is at chemical equilibrium . A t equili b rium, pr o ducts and reactants are

co

ntinuallyb

eingfo

rmed,b

ut there is no

netchange in the c o ncentrati o ns of reactants andpr o ducts.

A t equili b rium, the c o ncentrati o ns of reactants

and pr o ducts are typically n o t equal, b ut their co ncentrati o ns have sta b ilized.



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THE E ND


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R adi o active is o to pes have manyapplicati o ns in b io lo gical research. R adi o active decay rates can b e used t o date

fo ssils. R adi o active is o to pes can b e used t o trace

at o ms in meta bo lism.



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Fig. 2.6


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R adi o active is o to pes are als o used t o diagn o se medical dis o rders.

Fo r e x ample, the rate of e x creti o n in the urinecan b e measured a f ter injecti o n int o the b loo dof kn ow n quantity of radi o active is o to pe.

A lso , radi o active tracers can b e used w ithimaging instruments t o m o nito r chemicalpr o cesses in the bo dy.


Fig. 2.7


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W hile use f ul in research and medicine, theenergy emitted in radi o active decay ishazard o us t o lif e. This energy can destr o y cellular m o lecules. The severity of damage depends o n the type

and amo

untof

energy that ano

rganisma b s o r b s.

Fig. 2.8

Chapter Chemistry

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