Chemical Foundations Chemical Foundations for Cellsfor Cells

Chapter 2Chapter 2

You are chemical, and You are chemical, and so so

is every living and is every living and nonliving thing in the nonliving thing in the

universe. universe.

ElementsElements

Fundamental forms of Fundamental forms of

mattermatter

• Can’t be broken apart by Can’t be broken apart by

normal meansnormal means 92 occur naturally on Earth92 occur naturally on Earth

Most Common Elements in Most Common Elements in Living OrganismsLiving Organisms

OxygenOxygen

HydrogenHydrogen

CarbonCarbon

NitrogenNitrogen

What Are Atoms?What Are Atoms?

Smallest particles that retain Smallest particles that retain

properties of an elementproperties of an element Made up of subatomic particles:Made up of subatomic particles:

Protons (+)Protons (+) Electrons (-) Electrons (-) Neutrons (no charge) Neutrons (no charge)

Atomic NumberAtomic Number

Number of protonsNumber of protons All atoms of an element have the All atoms of an element have the

same atomic numbersame atomic number Atomic number of hydrogen = 1Atomic number of hydrogen = 1 Atomic number of carbon = 6Atomic number of carbon = 6

Mass NumberMass Number

Number of protonsNumber of protons

++Number of neutronsNumber of neutrons

Isotopes vary in mass numberIsotopes vary in mass number

IsotopesIsotopes

Atoms of an element with different Atoms of an element with different numbers of neutrons (different mass numbers of neutrons (different mass numbers)numbers)

Carbon 12 has 6 protons, 6 neutronsCarbon 12 has 6 protons, 6 neutrons Carbon 14 has 6 protons, 8 neutronsCarbon 14 has 6 protons, 8 neutrons

What Determines What Determines whether Atoms Will whether Atoms Will

Interact?Interact?

The number and arrangement The number and arrangement of their electronsof their electrons

ElectronsElectrons

Carry a negative Carry a negative chargecharge

Repel one another Repel one another Are attracted to Are attracted to

protons in the nucleusprotons in the nucleus Move in orbitals - Move in orbitals -

volumes of space that volumes of space that surround the nucleussurround the nucleus

Z

X

When all p orbitals are full

y

Shell ModelShell Model

First shell First shell Lowest energyLowest energy Holds 1 orbital with up to 2 Holds 1 orbital with up to 2

electronselectrons

Second shellSecond shell 4 orbitals hold up to 8 4 orbitals hold up to 8

electronselectronsCALCIUM20p+ , 20e-

Electron VacanciesElectron Vacancies

Unfilled shells Unfilled shells make atoms make atoms likely to reactlikely to react

Hydrogen, Hydrogen, carbon, oxygen, carbon, oxygen, and nitrogen all and nitrogen all have vacancies in have vacancies in their outer shellstheir outer shells

CARBON6p+ , 6e-

NITROGEN7p+ , 7e-

HYDROGEN1p+ , 1e-

Chemical Bonds, Molecules, Chemical Bonds, Molecules, & Compounds& Compounds

Bond is union between electron Bond is union between electron structures of atomsstructures of atoms

Atoms bond to form moleculesAtoms bond to form molecules Molecules may contain atoms of only Molecules may contain atoms of only

one element - Oone element - O22

Molecules of compounds contain Molecules of compounds contain more than one element - Hmore than one element - H22OO

Chemical BookkeepingChemical Bookkeeping

Use symbols for elements when Use symbols for elements when writing formulaswriting formulas

Formula for glucose is CFormula for glucose is C66HH1212OO66

6 carbons 6 carbons

12 hydrogens12 hydrogens

6 oxygens6 oxygens

Chemical BookkeepingChemical Bookkeeping

Chemical equation shows reactionChemical equation shows reaction

Reactants ---> ProductsReactants ---> Products

Equation for photosynthesis:Equation for photosynthesis:

6CO6CO22 + 6H + 6H22O ---> + CO ---> + C66HH1212OO12 12 + 6H+ 6H22OO

Important Bonds in Important Bonds in Biological MoleculesBiological Molecules

Ionic BondsIonic Bonds

Covalent BondsCovalent Bonds

Hydrogen BondsHydrogen Bonds

Ionic BondingIonic Bonding

One atom loses electrons, One atom loses electrons, becomes positively charged becomes positively charged ionion

Another atom gains these Another atom gains these electrons, becomes electrons, becomes negatively charged ionnegatively charged ion

Charge difference attracts Charge difference attracts the two ions to each otherthe two ions to each other

Formation of NaClFormation of NaCl

Sodium atom (Na) Sodium atom (Na) Outer shell has one electronOuter shell has one electron

Chlorine atom (Cl) Chlorine atom (Cl) Outer shell has seven electronsOuter shell has seven electrons

Na transfers electron to Cl, forming NaNa transfers electron to Cl, forming Na++ and Cland Cl--

Ions remain together as NaClIons remain together as NaCl

Covalent BondingCovalent Bonding

Atoms share a pair or pairs of Atoms share a pair or pairs of electrons to fill outermost shellelectrons to fill outermost shell

•Single covalent bond

•Double covalent bond

•Triple covalent bond

Molecular hydrogen

Polar or Nonpolar BondsPolar or Nonpolar Bonds

Nonpolar if atoms share Nonpolar if atoms share electrons equally electrons equally Hydrogen gas (H - H)Hydrogen gas (H - H)

Polar if electrons spend more Polar if electrons spend more time near nucleus with most time near nucleus with most protonsprotons Water Water Electrons more attracted to O Electrons more attracted to O

nucleus than to H nuclei nucleus than to H nuclei

Hydrogen BondingHydrogen Bonding

Atom in one polar covalent molecule is Atom in one polar covalent molecule is attracted to oppositely charged atom in attracted to oppositely charged atom in another such molecule or in same another such molecule or in same moleculemolecule

Water molecule

Ammonia molecule

Figure 2.11aPage 27

Hydrogen Bonding in DNAHydrogen Bonding in DNA

Figure 2.11dPage 27

Water Is a Polar Water Is a Polar Covalent MoleculeCovalent Molecule

Molecule has no net Molecule has no net chargecharge

Oxygen end has a Oxygen end has a slight negative chargeslight negative charge

Hydrogen end has a Hydrogen end has a slight positive chargeslight positive charge

H H

O

Figure 2.12aPage 28

Properties of WaterProperties of Water

Bonds to hydrophilic substances Bonds to hydrophilic substances Repels hydrophobic onesRepels hydrophobic ones Temperature stabilizingTemperature stabilizing Expands when it freezesExpands when it freezes CohesiveCohesive Capacity to dissolve substancesCapacity to dissolve substances

Liquid water Ice

Figure 2.12b,cPage 28

Hydrogen Ions: HHydrogen Ions: H++

Unbound protonsUnbound protons

Have important biological Have important biological

effectseffects

Form when water ionizesForm when water ionizes

The pH ScaleThe pH Scale

Measures HMeasures H++ concentration of fluid concentration of fluid Change of 1 on scale means 10X Change of 1 on scale means 10X

change in Hchange in H++ concentration concentration

Highest HHighest H++ Lowest H Lowest H++

0---------------------7-------------------140---------------------7-------------------14Acidic Neutral BasicAcidic Neutral Basic

Examples of pHExamples of pH

Pure water is neutral with pH of 7.0 Pure water is neutral with pH of 7.0 AcidicAcidic

Stomach acid: pH 1.0 - 3.0Stomach acid: pH 1.0 - 3.0 Lemon juice: pH 2.3Lemon juice: pH 2.3

BasicBasic Seawater: pH 7.8 - 8.3Seawater: pH 7.8 - 8.3 Baking soda: pH 9.0Baking soda: pH 9.0

Acids & BasesAcids & Bases

AcidsAcids Donate HDonate H++ when dissolved in water when dissolved in water

Acidic solutions have pH < 7Acidic solutions have pH < 7

BasesBases Accept HAccept H++ when dissolved in water when dissolved in water

Acidic solutions have pH > 7Acidic solutions have pH > 7

SaltsSalts

Compounds that release ions other Compounds that release ions other than Hthan H++ and OH and OH-- when dissolved in when dissolved in water water

Example: NaCl releases NaExample: NaCl releases Na++ and Cl and Cl––

Many salts dissolve into ions that Many salts dissolve into ions that play important biological roles play important biological roles