The Chemical The Chemical Context of LifeContext of Life

chapter 2chapter 2

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Energy & MatterEnergy & Matter

Universe is composed of 2 things ……Universe is composed of 2 things ……

EnergyEnergy Ability to do workAbility to do work

o Force on an object that causes it to moveForce on an object that causes it to move

MatterMatter Anything that has mass and occupies Anything that has mass and occupies

spacespace Atoms/elementsAtoms/elements

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Elements and Elements and CompoundsCompoundsElement -- cannot be broken down to Element -- cannot be broken down to

other substances by ordinary other substances by ordinary physical or chemical meansphysical or chemical means

Compound -- consists of two or more Compound -- consists of two or more elements in a fixed ratioelements in a fixed ratio

Essential Elements of Essential Elements of LifeLife

Around 25 elements are essential to Around 25 elements are essential to lifelife

C, H, O, and N -- 96% of living C, H, O, and N -- 96% of living mattermatter

Ca, P, K, and S -- most of the restCa, P, K, and S -- most of the restTrace elements -- required by an Trace elements -- required by an

organism in minute quantitiesorganism in minute quantities

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An atom is the smallest An atom is the smallest unit of matter that still unit of matter that still retains the properties of retains the properties of

an elementan element

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Subatomic ParticlesSubatomic ParticlesAtoms -- subatomic particlesAtoms -- subatomic particles

Neutrons (no electrical charge)Neutrons (no electrical charge) Protons (positive charge)Protons (positive charge) Electrons (negative charge)Electrons (negative charge)

Nucleus -- Neutrons and protons Nucleus -- Neutrons and protons Electrons -- cloud around nucleusElectrons -- cloud around nucleus

Mostly empty spaceMostly empty space

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Nucleus

ElectronsCloud of negativecharge (2 electrons)

10Site: colonial.net

Physicist Brian Greene puts it in these Physicist Brian Greene puts it in these terms …..terms …..

11http://io9.com/a-friendly-reminder-that-you-are-mostly-nothing-471778130

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Firstshell

Hydrogen

1H

Lithium

3Li

Secondshell

Thirdshell

Sodium

11Na

Beryllium

4Be

Magnesium

12Mg

Boron

5B

Aluminum

12AlSilicon

14Si

Carbon

6CNitrogen

7N

Phosphorus

15P

Oxygen

8O

Sulfur

16SChlorine

17Cl

Fluorine

9FNeon

10Ne

Argon

18Ar

Helium

2HeAtomic number

Element symbol

Electron-shelldiagram

Atomic mass

2He4.00

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Atomic Number & Atomic Number & Atomic MassAtomic Mass

Atoms -- differ in number of subatomic Atoms -- differ in number of subatomic particlesparticles atomic number -- number of protonsatomic number -- number of protons mass number -- protons + neutrons mass number -- protons + neutrons atomic mass -- approximated by the mass atomic mass -- approximated by the mass

number (mass number + electrons)number (mass number + electrons)o Mass electron … 0.000544Mass electron … 0.000544

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Atoms and IsotopesAtoms and Isotopes

Atoms -- differ in number of subatomic Atoms -- differ in number of subatomic particlesparticles NOTE: NOTE: atoms:atoms: protons == electrons protons == electrons

Isotopes -- two atoms of an element Isotopes -- two atoms of an element that differ in number of neutronsthat differ in number of neutrons Stability/ radioactivityStability/ radioactivity

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Electron Configuration Electron Configuration and Chemical Propertiesand Chemical Properties

Distribution of electrons in electron shells Distribution of electrons in electron shells determines behaviordetermines behavior

The periodic table shows electron The periodic table shows electron distributionsdistributions

Elements in common rows and/or columns Elements in common rows and/or columns similar propertiessimilar properties

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Electron OrbitalsElectron Orbitals

three-dimensional space where three-dimensional space where electrons are (90%)electrons are (90%)

each shell -- specific number and each shell -- specific number and kind kind of orbitalsof orbitals

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Electronorbitals

Electron-shelldiagrams

1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals

First shell(maximum2 electrons)

Second shell(maximum8 electrons)

Neon, with twofilled shells(10 electrons)

x

z

y

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Valence electrons – outermost level or Valence electrons – outermost level or “shell”“shell”

Chemical behavior -- valence electronsChemical behavior -- valence electrons

Interactions – chemical bondsInteractions – chemical bonds

Complete Valence Shell – 8 electronsComplete Valence Shell – 8 electrons

Atoms with incomplete valence shells – Atoms with incomplete valence shells – sharing/transferring valence electronssharing/transferring valence electrons

Valence ElectronsValence Electrons

Water (H2O)

Oxygen (O2)

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Molecule -- two or more Molecule -- two or more atoms held together by atoms held together by

chemical bondschemical bondsSingle bond = sharing of one pair of Single bond = sharing of one pair of valence electronsvalence electrons

Double bond = sharing of two pairs of Double bond = sharing of two pairs of valence electronsvalence electrons

Triple bond = Triple bond =

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Characteristic Bonding Characteristic Bonding PatternsPatterns

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1 2 3 4 5 6 7 8

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Types of BondsTypes of Bonds

Strong Chemical BondsStrong Chemical Bonds Covalent BondsCovalent Bonds Ionic BondsIonic Bonds

Weak BondsWeak Bonds Hydrogen BondsHydrogen Bonds Van der Waals ForcesVan der Waals Forces

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Covalent BondsCovalent Bonds

Sharing valence Sharing valence electronselectrons

Part of each atom’s Part of each atom’s valence shellvalence shell

Hydrogen atoms (2 H)

Hydrogenmolecule (H2)

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Covalent bonds can form Covalent bonds can form between atoms of the same between atoms of the same

element element oror atoms of atoms of different elementsdifferent elements

compound vs moleculecompound vs molecule

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ElectronegativityElectronegativity -- measure an -- measure an atom’s attraction for electrons in a atom’s attraction for electrons in a covalent bond covalent bond more electronegative -- stronger the pullmore electronegative -- stronger the pull

PolarPolar covalent bond – atoms share covalent bond – atoms share the electron unequally -- one atom is the electron unequally -- one atom is more electronegativemore electronegative

NonpolarNonpolar covalent bond -- atoms covalent bond -- atoms share the electron equallyshare the electron equally

Covalent BondsCovalent Bonds

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H

O

H

H2O+ +

–

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Ionic BondsIonic Bonds

Ion – unequal numbers of Ion – unequal numbers of electrons and protonselectrons and protons Anion -- negatively charged ionAnion -- negatively charged ion Cation -- positively charged ionCation -- positively charged ion

Ionic bond -- attraction between Ionic bond -- attraction between an anion and a cationan anion and a cation

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Ionic BondsIonic BondsHighly reactive atoms sometimes Highly reactive atoms sometimes

strip electrons from their bonding strip electrons from their bonding partnerspartners

NaCl -- transfers electronsNaCl -- transfers electrons

NaSodium atom(an uncharged

atom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium ion(a cation)

Cl–

Chlorine ion(an anion)

Sodium chloride (NaCl)

NaSodium atom(an uncharged

atom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium ion(a cation)

Cl–

Chlorine ion(an anion)

Sodium chloride (NaCl)

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

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

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Free RadicalsFree Radicals

MoleculeMolecule whose atoms have one or whose atoms have one or more unpaired electrons in their outer more unpaired electrons in their outer shellsshells

Highly unstable and reactiveHighly unstable and reactive Steal electronsSteal electrons Cause cell deathCause cell death

Potentially involved in causing heart Potentially involved in causing heart disease, Alzheimer’s, cancer, and agingdisease, Alzheimer’s, cancer, and aging

Antioxidants (vitamins C and E) render Antioxidants (vitamins C and E) render free radicals harmlessfree radicals harmless

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H

O

H

H2O+ +

–

NaSodium atom(an uncharged

atom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium ion(a cation)

Cl–

Chlorine ion(an anion)

Sodium chloride (NaCl)

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Weak Chemical BondsWeak Chemical Bonds

covalent bonds are the strongestcovalent bonds are the strongestweak chemical bonds also weak chemical bonds also

importantimportant reinforce shapesreinforce shapes help molecules adhere to each help molecules adhere to each

otherother

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Hydrogen BondsHydrogen Bonds

Happens Happens between between moleculesmoleculesa hydrogen atom covalently a hydrogen atom covalently

bonded to one electronegative bonded to one electronegative atom is also attracted to another atom is also attracted to another electronegative atom electronegative atom in a in a different moleculedifferent molecule

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

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Water(H2O)

Ammonia(NH3)

Hydrogen bond

+

+

–

+

+

+

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Van der Waals Van der Waals InteractionsInteractions

Molecules or atoms that are very Molecules or atoms that are very close together can be attracted by close together can be attracted by fleeting charge differencesfleeting charge differences

These weak attractions are called These weak attractions are called van der Waals interactionsvan der Waals interactions

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

Van der Waals Van der Waals InteractionsInteractions

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Common BondsCommon Bonds

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Chemical reactions make Chemical reactions make and break chemical bondsand break chemical bondsChemical reactions lead to new Chemical reactions lead to new

arrangements of atomsarrangements of atomsThe starting molecules of a The starting molecules of a

chemical reaction are called chemical reaction are called reactantsreactants

The final molecules of a chemical The final molecules of a chemical reaction are called productsreaction are called products

Reactions Reactions must must balancebalance

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Photosynthesis is an important Photosynthesis is an important chemical reactionchemical reaction

Sunlight powers the conversion of Sunlight powers the conversion of COCO22 and H and H22O to glucose (CO to glucose (C66HH1212OO66) ) and Oand O22

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Reactants Reaction Products

2 H2OO22 H2

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Some rxns “go to completion” -- Some rxns “go to completion” -- All reactants converted to All reactants converted to productsproducts

Many rxns reversible: Products of Many rxns reversible: Products of the forward reaction become the forward reaction become reactants for the reverse reactionreactants for the reverse reaction CaCOCaCO3 3 ↔ ↔ CaO + COCaO + CO22

Chemical Equilibrium is reached Chemical Equilibrium is reached when the forward and reverse when the forward and reverse reaction reaction ratesrates are equal are equal

Reactions DifferReactions Differ

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http://www.bbc.co.uk/news/uk-england-leeds-11959381

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