chapter 2 the chemical context of life. fig. 2-3a sodium the emergent properties of a compound

Chapter 2

• The Chemical Context of Life

Fig. 2-3a

Sodium

The emergent properties of a compound

Fig. 2-3b

Chlorine

The emergent properties of a compound

Fig. 2-3c

Sodium chloride

The emergent properties of a compound

Essential Elements of Life

• Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter

• Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur

– Trace elements are those required by an organism in minute quantities

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Table 2-1

Concept 2.2: An element’s propertiesdepend on the structure of its atoms

• Each element consists of unique atoms

– the smallest unit of matter that still retains the properties of an element

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Subatomic Particles

• Atoms are composed of subatomic particles

– Neutrons (no electrical charge)

– Protons (positive charge)

– Electrons (negative charge)

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• Neutrons and protons form the atomic nucleus

• Electrons form a cloud around the nucleus

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Cloud of negativecharge (2 electrons)

Fig. 2-5

Nucleus

Electrons

(b)(a)

Simplified models of a helium (He) atom

Atomic Number and Atomic Mass

• atomic number

– number of protons in the nucleus

• mass number

– sum of protons plus neutrons in the nucleus

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Isotopes

• Isotopes

– two atoms of the same element that differ in number of neutrons

• Radioactive isotopes

– decay spontaneously, giving off particles and energy

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• Applications of radioactive isotopes:

– Dating fossils

– Tracing atoms through metabolic processes

– Diagnosing medical disorders

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Fig. 2-6a

Compounds includingradioactive tracer(bright blue)

Human cells

Incubators1 2 3

4 5 6

7 8 950ºC45ºC40ºC

25ºC 30ºC 35ºC

15ºC 20ºC10ºC

Humancells areincubatedwith compounds used tomake DNA. One compound islabeled with 3H.

1

2 The cells areplaced in testtubes; their DNA isisolated; andunused labeledcompounds areremoved.

DNA (old and new)

TECHNIQUE

Fig. 2-6b

TECHNIQUE

The test tubes are placed in a scintillation counter.3

Fig. 2-6c

RESULTSC

ou

nts

per

min

ute

( 1

,000

)

010 20 30 40 50

10

20

30

Temperature (ºC)

Optimumtemperaturefor DNAsynthesis

Fig. 2-7

Cancerousthroattissue

The Energy Levels of Electrons

• Energy is the capacity to cause change

• Potential energy

• the energy that matter has stored because of its location or structure

• The electrons of an atom differ in their amounts of potential energy

• An electron’s state of potential energy is called its energy level, or electron shell

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Fig. 2-8

(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons

Third shell (highest energylevel)

Second shell (higherenergy level)

Energyabsorbed

First shell (lowest energylevel)

Atomicnucleus

(b)

Energylost

Electron Distribution and Chemical Properties

• The chemical behavior of an atom

– determined by the distribution of electrons in electron shells

• The periodic table of the elements shows the electron distribution for each element

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Fig. 2-9

Hydrogen

1H

Lithium

3LiBeryllium

4BeBoron

5BCarbon

6CNitrogen

7NOxygen

8O

Fluorine

9FNeon

10Ne

Helium

2HeAtomic number

Element symbol

Electron-distributiondiagram

Atomic mass

2He

4.00Firstshell

Secondshell

Thirdshell

Sodium

11NaMagnesium

12Mg

Aluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16S

Chlorine

17ClArgon

18Ar

• Valence electrons

– those in the outermost shell, or valence shell

– The chemical behavior of an atom is mostly determined by the valence electrons

– Elements with a full valence shell are chemically inert

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http://www.thecatalyst.org/electabl.html

Electron Orbitals

• An orbital is

– the three-dimensional space where an electron is found 90% of the time

• Each electron shell consists of a specific number of orbitals

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Fig. 2-10-1

Electron-distributiondiagram

(a)Neon, with two filled shells (10 electrons)

First shell Second shell

Electron-distributiondiagram

(a)

(b) Separate electronorbitals

Neon, with two filled shells (10 electrons)

First shell Second shell

1s orbital

Fig. 2-10-2

Electron-distributiondiagram

(a)

(b) Separate electronorbitals

Neon, with two filled shells (10 electrons)

First shell Second shell

1s orbital 2s orbital Three 2p orbitals

x y

z

Fig. 2-10-3

Electron-distributiondiagram

(a)

(b) Separate electronorbitals

Neon, with two filled shells (10 electrons)

First shell Second shell

1s orbital 2s orbital Three 2p orbitals

(c) Superimposed electronorbitals

1s, 2s, and 2p orbitals

x y

z

Fig. 2-10-4

The formation and function of molecules depend on chemical bonding between atoms

• Atoms with incomplete valence shells share electrons with other atoms

• This results in a force of attractions called a covalent bond

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Covalent Bonds

• A covalent bond

– the sharing of a pair of valence electrons by two atoms

• the shared electrons count as part of each atom’s valence shell

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Fig. 2-11Hydrogen

atoms (2 H)

Hydrogenmolecule (H2)

• A molecule

– two or more atoms held together by covalent bonds

• A single bond, is the sharing of one pair of electrons

• A double bond, is the sharing of two pairs of electrons

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• structural formula

– H–H

• molecular formula

– H2

Animation: Covalent BondsAnimation: Covalent Bonds

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Fig. 2-12a

(a) Hydrogen (H2)

Name andMolecularFormula

Electron-distribution

Diagram

Lewis DotStructure and

StructuralFormula

Space-fillingModel

Fig. 2-12b

(b) Oxygen (O2)

Name andMolecularFormula

Electron-distribution

Diagram

Lewis DotStructure and

StructuralFormula

Space-fillingModel

Fig. 2-12c

(c) Water (H2O)

Name andMolecularFormula

Electron-distribution

Diagram

Lewis DotStructure and

StructuralFormula

Space-fillingModel

Fig. 2-12d

(d) Methane (CH4)

Name andMolecularFormula

Electron-distribution

Diagram

Lewis DotStructure and

StructuralFormula

Space-fillingModel

• Covalent bonds

– form between atoms of the same element or of different elements

• A compound

– a combination of two or more different elements

• Bonding capacity is called the atom’s valence

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• Electronegativity

– an atom’s attraction for the electrons in a covalent bond

– The more electronegative an atom, the more strongly it pulls shared electrons toward itself

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• nonpolar covalent bond

– Electrons are shared equally

• polar covalent bond

– one atom is more electronegative

– Electrons are not shared equally

• Unequal sharing of electrons

– causes a partial positive or negative charge on the ends of a molecule

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Fig. 2-13

–

+ +H H

O

H2O

Ionic Bonds

• Atoms sometimes strip electrons from their bonding partners

– Example: the transfer of an electron from sodium to chlorine

– After the transfer of an electron, both atoms have charges

• A charged atom (or molecule) is called an ion

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Fig. 2-14-1

Na Cl

NaSodium atom Chlorine atom

Cl

Fig. 2-14-2

Na Cl Na Cl

NaSodium atom Chlorine atom

Cl Na+

Sodium ion(a cation)

Cl–Chloride ion

(an anion)

Sodium chloride (NaCl)

• A cation is a positively charged ion

• An anion is a negatively charged ion

• An ionic bond is an attraction between an anion and a cation

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• Compounds formed by ionic bonds are called ionic compounds, or salts

• Salts, such as sodium chloride (table salt), are often found in nature as crystals

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Fig. 2-15

Na+

Cl–

Weak Chemical Bonds

• Strongest bonds in organisms

– covalent bonds

• Weak chemical bonds are also important

– ionic bonds

– hydrogen bonds,

• Weak chemical bonds

– reinforce shapes of large molecules

– help molecules adhere to each other

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Hydrogen Bonds

• A hydrogen bond

– forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

– In living cells, the electronegative partners are usually oxygen or nitrogen atoms

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Fig. 2-16

+

+

+

+

+

Water (H2O)

Ammonia (NH3)

Hydrogen bond

Van der Waals Interactions

• If electrons are distributed asymmetrically in molecules or atoms

– result in “hot spots” of positive or negative charge

• Van der Waals interactions

– attractions between molecules that are close together as a result of these charges

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• Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface

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Molecular Shape and Function

• A molecule’s shape is very important to its function

– determined by the positions of its atoms’ valence orbitals

– the s and p orbitals may hybridize, creating specific molecular shapes

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Fig. 2-17

s orbital Three porbitals

(a) Hybridization of orbitals

Tetrahedron

Four hybrid orbitals

Space-fillingModel

Ball-and-stickModel

Hybrid-orbital Model(with ball-and-stick

model superimposed)

Unbondedelectronpair

104.5º

Water (H2O)

Methane (CH4)

(b) Molecular-shape models

z

x

y

Fig. 2-17a

s orbitalz

x

y

Three porbitals

Hybridization of orbitals

Four hybrid orbitals

Tetrahedron(a)

Fig. 2-17b

Space-fillingModel

Ball-and-stickModel

Hybrid-orbital Model(with ball-and-stick

model superimposed)

Unbondedelectronpair

104.5º

Water (H2O)

Methane (CH4)

Molecular-shape models(b)

• Biological molecules

– Recognize and interact with each other with a specificity based on molecular shape

– Molecules with similar shapes can have similar biological effects

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Fig. 2-18a

Natural endorphin

Morphine

KeyCarbonHydrogen

NitrogenSulfurOxygen

Structures of endorphin and morphine(a)

Fig. 2-18b

Naturalendorphin

EndorphinreceptorsBrain cell

Binding to endorphin receptors

Morphine

(b)

Chemical reactions make and break chemical bonds

• Chemical reactions

– the making and breaking of chemical bonds

• Reactants

– the starting molecules of a chemical reaction

• Products

– the final molecules of a chemical reaction

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Fig. 2-UN2

Reactants Reaction Products

2 H2 O2 2 H2O

• Photosynthesis is an important chemical reaction

• Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen

6 CO2 + 6 H20 → C6H12O6 + 6 O2

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Fig. 2-19

• All chemical reactions are reversible:

– products of the forward reaction become reactants for the reverse reaction

• Some chemical reactions go to completion: all reactants are converted to products

• Chemical equilibrium

– reached when the forward and reverse reaction rates are equal

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Fig. 2-UN3

Nucleus

Protons (+ charge)determine element

Neutrons (no charge)determine isotope Atom

Electrons (– charge) form negative cloudand determinechemical behavior

Fig. 2-UN4

Fig. 2-UN5

Singlecovalent bond

Doublecovalent bond

Fig. 2-UN6

Ionic bond

Electrontransferforms ions

NaSodium atom

ClChlorine atom

Na+

Sodium ion(a cation)

Cl–

Chloride ion(an anion)

Fig. 2-UN7

Fig. 2-UN8

Fig. 2-UN9

Fig. 2-UN10

Fig. 2-UN11

You should now be able to:

1. Identify the four major elements

2. Distinguish between the following pairs of terms: neutron and proton, atomic number and mass number, atomic weight and mass number

3. Distinguish between and discuss the biological importance of the following: nonpolar covalent bonds, polar covalent bonds, ionic bonds, hydrogen bonds, and van der Waals interactions

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