Chemical Context

7/26/2019 Chemical Context

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Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

PowerPoint Lectures forBiology, Seventh Edition

Neil Campbell and Jane Reece

Lectures by Chris Romero

Chapter 2

he Chemical Conte!t o" #i"e


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Overview: Chemical Foundations of Biology


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The bombardier beetle uses chemistry todefend itself

Figure 2.1


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Concept !": #atter consists of chemical

elements in pure form and in combinationscalled compounds


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Elements and Compounds

Organisms are composed of matter$ whichis anything that ta%es up space and has

mass


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#atter is made up of elements$ substancesthat cannot be bro%en down to other

substances by chemical reactions


7/63Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings&odium Chloride &odium Chloride

'

( compound

$ )s a substance consisting of two or moreelements combined in a fi*ed ratio

$ +as characteristics different from those of its

elements

Figure 2.2


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Essential Elements o" #i"e

,ssential elements

$ )nclude carbon$ hydrogen$ o*ygen$ andnitrogen

$ #a%e up -./ of living matter



( few other elements

$ #a%e up the remaining 0/ of living matter

Table 2.1



(a) Nitrogen deficiency (b) Iodine deficiency

The effects of essential element deficiencies

Figure 2.3



Trace elements

$ (re re1uired by an organism in only minute1uantities



Concept !: (n element2s properties

depend on the structure of its atoms



,ach element

$ Consists of a certain %ind of atom that isdifferent from those of other elements

(n atom

$ )s the smallest unit of matter that still retains

the properties of an element



Subatomic Particles

(toms of each element

$ (re composed of even smaller parts calledsubatomic particles


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3elevant subatomic particles include

$ 4eutrons$ which have no electrical charge

$ Protons$ which are positively charged

$ ,lectrons$ which are negatively charged


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Protons and neutrons

$ (re found in the atomic nucleus

,lectrons

$ &urround the nucleus in a 5cloud6


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4ucleus

(a) (b) )n this even more simplifiedmodel$ the electrons are

shown as two small blue

spheres on a circle around the

nucleus!

Cloud of negative

charge 7 electrons8,lectrons

This model represents theelectrons as a cloud of

negative charge$ as if we had

ta%en many snapshots of the

electrons over time$ with each

dot representing an electron9s

position at one point in time!

&implified models of an atom

Figure 2.4


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Atomic Number and Atomic Mass

(toms of the various elements

$ iffer in their number of subatomic particles


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The atomic number of an element

$ )s the number of protons

$ )s uni1ue to each element


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The mass number of an element

$ )s the sum of protons plus neutrons in thenucleus of an atom

$ )s an appro*imation of the atomic mass of an

atom


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Isotopes

(toms of a given element

$ #ay occur in different forms


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)sotopes of a given element

$ iffer in the number of neutrons in the atomicnucleus

$ +ave the same number of protons


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3adioactive isotopes

$ &pontaneously give off particles and energy


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$ Can be used in biology

A!ICATI"N &cientists use radioactive isotopes to label certain chemical substances$ creating

tracers that can be used to follow a metabolic process or locate the substance within an organism!

)n this e*ample$ radioactive tracers are being used to determine the effect of temperature on the

rate at which cells ma%e copies of their 4(!

4( 7old and new8

)ngredients including

3adioactive tracer

7bright blue8

+uman cells

)ncubators

" ;

0 < .

-=>

1#$C 1%$C 2#$C

2%$C 3#$C 3%$C

4#$C 4%$C %#$C

T&C'NI&

"

The cells are placed in test

tubes$ their 4( is isolated$

and unused ingredients are

removed! " ; 0 < . > = -

)ngredients for

ma%ing 4( are

added to human cells! One

ingredient is labeled with ;+$ a

radioactive isotope of hydrogen! 4ine dishes of cells

are incubated at different temperatures! The cellsma%e new 4($ incorporating the radioactive tracer

with ;+!


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Temperature 7?C8

The fre1uency of flashes$ which is recorded as counts per minute$ is

proportional to the amount of the radioactive tracer present$ indicating the amount of new

4(! )n this e*periment$ when the counts per minute are plotted against temperature$ it is

clear that temperature affects the rate of 4( synthesis@the most 4( was made at

;


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$ Can be used in biology

Cancerous

throat

tissue

Figure 2.,


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The Energy Levels o Electrons

(n atom2s electrons

$ ary in the amount of energy they possess


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,nergy

$ )s defined as the capacity to cause change

Potential energy

$ )s the energy that matter possesses becauseof its location or structure


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The electrons of an atom

$ iffer in the amounts of potential energy theypossess

( ball bouncing down a flight

of stairs provides an analogy

for energy levels of electrons$

because the ball can only rest

on each step$ not between

steps!

(a)

Figure 2.-A


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,nergy levels

$ (re represented by electron shells

Third energy level 7shell8

&econd energy level 7shell8

First energy level 7shell8

,nergy

absorbed

,nergy

lost

(n electron can move from one level to another only if the energy

it gains or loses is e*actly e1ual to the difference in energy between

the two levels! (rrows indicate some of the stepDwise changes in

potential energy that are possible!

(b)

(tomicnucleus

Figure 2.-


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Electron Coniguration and Chemical Properties

The chemical behavior of an atom

$ )s defined by its electron configuration anddistribution


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The periodic table of the elements

$ &hows the electron distribution for all theelements

+econd

/hell

+elium

+e

Fir/t/hell

Third

/hell

+ydrogen

"+

'e

0!AA(tomic mass

(tomic number

,lement symbol

,lectronDshell

diagram

Lithium

;Li

Beryllium

0BeBoron

;B

Carbon

.C4itrogen

>4

O*ygen

=OFluorine

-F

4eon

"A4e

&odium

""4a

#agnesium

"#g

(luminum

";(l&ilicon

"0&i

Phosphorus

"Cl

(rgon

"=(r

Figure 2.0


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alence electrons

$ (re those in the outermost$ or valence shell

$ etermine the chemical behavior of an atom

El t ! bit l


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Electron !rbitals

(n orbital

$ )s the threeDdimensional space where anelectron is found -A/ of the time


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,ach electron shell

$ Consists of a specific number of orbitals

&lectron orbital/.

,ach orbital holdsup to two electrons!

"sorbital sorbital Three porbitals "s,s$ and porbitals

(a) Fir/t /hell

7ma*imum

electrons8

(b) +econd /hell

7ma*imum

= electrons8

(c) Neon ith to filled /hell/

7"A electrons8

&lectron/hell diagra/.

,ach shell is shown with

its ma*imum number of

electrons$ grouped in pairs!

*

E

Figure 2.5


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Concept !;: The formation and function of

molecules depend on chemical bonding

between atoms

C l t " d


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Covalent "onds

( covalent bond

$ )s the sharing of a pair of valence electrons


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Figure 2.1#

Formation of a covalent bond+ydrogen atoms 7 +8

+ydrogen

molecule 7+8

' '

' '

' '

)n each hydrogen

atom$ the single electron

is held in its orbital by

its attraction to the

proton in the nucleus!

"

Ghen two hydrogen

atoms approach each

other$ the electron of

each atom is also

attracted to the proton

in the other nucleus!

The two electrons

become shared in a

covalent bond$

forming an +molecule!

;


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( molecule

$ Consists of two or more atoms held togetherby covalent bonds

( single bond

$ )s the sharing of one pair of valence electrons

( double bond

$ )s the sharing of two pairs of valence electrons


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(a)

(b)

Nae

(olecularforula)

&lectron

/helldiagra

+tructural

forula

+pace

fillingodel

'ydrogen ('2).

Two hydrogen

atoms can form a

single bond!

"6ygen ("2).

Two o*ygen atoms

share two pairs of

electrons to form

a double bond!

+ +

O O

Figure 2.11 A

&ingle and double covalent bonds


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Nae

(olecularforula)

&lectron

/helldiagra

+tructural

forula

+pace

fillingodel

(c)

7ethane (C'4).

Four hydrogen

atoms can satisfy

the valence of

one carbon

atom$ forming

methane!

8ater ('2").

Two hydrogen

atoms and one

o*ygen atom are

Hoined by covalentbonds to produce a

molecule of water!

(d)

+O

+

+ +

+

+

C

Figure 2.11 C 9

Covalent bonding in compounds


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,lectronegativity

$ )s the attraction of a particular %ind of atom forthe electrons in a covalent bond

The more electronegative an atom

$ The more strongly it pulls shared electrons

toward itself


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)n a nonpolar covalent bond

$ The atoms have similar electronegativities

$ &hare the electron e1ually


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Figure 2.12

This results in a

partial negative

charge on the

o*ygen and a

partial positive

charge on

the hydrogens!

+2O

I

"

' '' '

Because o*ygen 7O8 is more electronegative than hydrogen 7+8$

shared electrons are pulled more toward o*ygen!

)n a polar covalent bond

$ The atoms have differing electronegativities

$ &hare the electrons une1ually

Ionic "onds


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Ionic "onds

)n some cases$ atoms strip electrons away

from their bonding partners


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,lectron transfer between two atoms

creates ions

)ons

$ (re atoms with more or fewer electrons

than usual

$ (re charged atoms


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(n anion

$ )s negatively charged ions

( cation

$ )s positively charged


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Cl:

Chloride ion7an anion8

:

The lone valence electron of a sodium

atom is transferred to Hoin the > valence

electrons of a chlorine atom!

" ,ach resulting ion has a completed

valence shell! (n ionic bond can form

between the oppositely charged ions!

4a 4aCl Cl

;

Na&odium atom

7an uncharged

atom8

ClChlorine atom

7an uncharged

atom8

Na;

&odium on7a cation8

&odium chloride 74aCl8Figure 2.13

(n ionic bond

$ )s an attraction between anions and cations


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4a

'

ClI

Figure 2.14

)onic compounds

$ (re often called salts$ which may form crystals

#ea$ Chemical "onds


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#ea$ Chemical "onds

&everal types of wea% chemical bonds are

important in living systems

%ydrogen "onds


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%ydrogen "onds

I '

'

Gater7+2O8

(mmonia

74+38

O+

+

'

I

4

++ +

( hydrogen

bond results

from the

attraction

between the

partial positive

charge on the

hydrogen atom

of water and

the partial

negative charge

on the nitrogen

atom of

ammonia!' '

Figure 2.1%

( hydrogen bond

$ Forms when a hydrogen atom covalentlybonded to one electronegative atom is also

attracted to another electronegative atom


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Gea% chemical bonds

$ 3einforce the shapes of large molecules

$ +elp molecules adhere to each other

Molecular Shape and 'unction


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Molecular Shape and 'unction

The precise shape of a molecule

$ )s usually very important to its function in theliving cell

$ )s determined by the positions of its atoms2

valence orbitals


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sorbital

ZThree porbitals

X

Y

Four hybrid orbitals

(a) 'ybridi


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+pacefilling

odel

'ybridorbital odel

7with ballDandDstic%

model superimposed8

nbonded,lectron pair

"A0!


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#olecular shape

$ etermines how biological moleculesrecogniJe and respond to one another with

specificity


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7orphine

Carbon

+ydrogen

4itrogen

&ulfur

O*ygenNatural

endorphin

(a) +tructure/ of endorphin and orphine.The bo*ed portion of the endorphin molecule 7left8 binds to

receptor molecules on target cells in the brain! The bo*ed portion of the morphine molecule is a close match!

(b) inding to endorphin receptor/.,ndorphin receptors on the surface of a brain cell

recogniJe and can bind to both endorphin and morphine!

4atural

endorphin

,ndorphin

receptors

#orphine

Brain cell

Figure 2.1-


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Concept !0: Chemical reactions ma%e and brea%

chemical bonds


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( Chemical reaction

$ )s the ma%ing and brea%ing of chemical bonds

$ Leads to changes in the composition of matter


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*eactant/ *eaction roduct

+2 O2 +O

'

'

Chemical reactions

$ Convert reactants to products


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Photosynthesis

$ )s an e*ample of a chemical reaction

Figure 2.10


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Chemical Context