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Chapter 2Chapter 2

The Chemistry of LifeThe Chemistry of Life

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Section 1Section 1

The Nature of MatterThe Nature of Matter

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AtomsAtoms

Atoms:Atoms: Basic unit of matter.Basic unit of matter. Greek word Greek word atomosatomos..

““unable to be cutunable to be cut””

Factoid:Factoid: Atoms are so small that if you lined up 100 Atoms are so small that if you lined up 100

million of them, they would barely be the million of them, they would barely be the width of your pinky.width of your pinky.

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Though atoms are small, they are Though atoms are small, they are made of even smaller particles.made of even smaller particles.

P. 35, fig. 2-1P. 35, fig. 2-1 Protons-Protons-+ charged+ charged Neutrons-Neutrons-no chargeno charge Electrons- Electrons- (-) charged(-) charged

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Protons & neutrons are bound Protons & neutrons are bound together in the together in the nucleus nucleus of an atom.of an atom.

Electrons are in constant motion Electrons are in constant motion around the nucleusaround the nucleus of an atom. of an atom.

Atoms have Atoms have equalequal numbers of numbers of protons & electrons.protons & electrons.

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Electrons travel around the nucleus in Electrons travel around the nucleus in an an electron cloudelectron cloud..

They travel in what are called They travel in what are called orbitalsorbitals.. Each orbital contains a certain # of Each orbital contains a certain # of

electrons.electrons. 11stst orbital has orbital has 2e2e--

22ndnd orbital has orbital has 8e8e--

33rdrd orbital has orbital has 8e8e--

44thth orbital has orbital has 8e8e--

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What Element is This?What Element is This?

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Elements & IsotopesElements & Isotopes ElementsElements –substances that consist of entirely of –substances that consist of entirely of 11

type of atom.type of atom. Over Over 100100 elements exist, but only about elements exist, but only about 2525 are vital to living are vital to living

things.things. The The 44 most important elements are: most important elements are:

HydrogenHydrogen CarbonCarbon NitrogenNitrogen OxygenOxygen

Elements are abbreviated by symbols.Elements are abbreviated by symbols. HH CC N N OO

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Atomic number:Atomic number: # above the symbol of the element.# above the symbol of the element. This number represents the # of This number represents the # of

electrons & protonselectrons & protons in that element. in that element.

Example:Example: Look at Carbon (C)Look at Carbon (C) What is it atomic #?What is it atomic #?

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What does this mean?What does this mean? 6e & 6p6e & 6p

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IsotopesIsotopes Isotopes:Isotopes:

Atom of an element that have a different Atom of an element that have a different # of neutrons then that of other atoms of # of neutrons then that of other atoms of the same element.the same element.

The sum of protons & neutrons in an The sum of protons & neutrons in an atom is called the atom is called the atomic massatomic mass or or atomic atomic weightweight..

Some examples:Some examples: Carbon-12Carbon-12 Carbon-13Carbon-13 Carbon-14Carbon-14

P. 36, fig. 2-2P. 36, fig. 2-2

Isotopes are identified by their mass Isotopes are identified by their mass #.#.

Since isotopes have the same # of Since isotopes have the same # of electrons, they have the same electrons, they have the same chemical properties.chemical properties.

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Radioactive IsotopesRadioactive Isotopes

Some isotopes are radioactive.Some isotopes are radioactive. This means that their nuclei are This means that their nuclei are

unstable & they breakdown over time.unstable & they breakdown over time. This radiation can be dangerous.This radiation can be dangerous. But, scientists have a number of uses But, scientists have a number of uses

for them:for them: Can be used to treat cancers.Can be used to treat cancers. Can be used to age rocks & other items.Can be used to age rocks & other items. Can be used as a tracer in human organs.Can be used as a tracer in human organs.

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Chemical CompoundsChemical Compounds

In nature most elements are found in In nature most elements are found in compounds.compounds.

CompoundsCompounds –a substance formed by –a substance formed by 2 or more elements.2 or more elements.

These compounds are usually These compounds are usually written as formulas such as:written as formulas such as: NaClNaCl HH2200 COCO22

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Chemical BondsChemical Bonds

Compounds are held together by Compounds are held together by chemical bonds.chemical bonds.

Bond formation involves the electrons Bond formation involves the electrons that surround an atom.that surround an atom. AKA AKA Valence ElectronsValence Electrons

The main types of chemical bonds The main types of chemical bonds are:are: IonicIonic CovalentCovalent

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Ionic BondsIonic Bonds Ionic bondIonic bond –when one or more electrons are –when one or more electrons are

transferred from one atom to another.transferred from one atom to another. Atoms that Atoms that loselose an electron have a pos. an electron have a pos.

charge.charge. NaNa++

Atoms that Atoms that gaingain an electron have a neg. an electron have a neg. charge.charge. ClCl--

Pos. & neg. charged atoms are called Pos. & neg. charged atoms are called ionsions.. Pos. atoms are Pos. atoms are cationscations.. Neg. atoms are Neg. atoms are anionsanions..

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P. 38, fig. 2-3P. 38, fig. 2-3 shows a ionic bond b/t shows a ionic bond b/t NaNa & & ClCl.. NaNa will easily lose an electron b/c it is a will easily lose an electron b/c it is a

+ + NaNa ion. ion. Likewise, Likewise, ClCl will easily gain an electron will easily gain an electron

b/c it is a - b/c it is a - ClCl ion. ion.

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Ionic BondIonic Bond

http://www.youtube.com/watch?v=xTx_DWboEVs&feature=player_detailpage

http://www.youtube.com/watch?v=G49gxlIlSIc

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Covalent BondsCovalent Bonds

Covalent BondsCovalent Bonds –a bond formed when –a bond formed when electrons are electrons are sharedshared b/t atoms. b/t atoms. You can have single, double, or triple covalent You can have single, double, or triple covalent

bonds. bonds. Read bottom paragraph on p. 38Read bottom paragraph on p. 38

MoleculesMolecules are formed when atoms are are formed when atoms are joined via a covalent bond.joined via a covalent bond. A molecule is the smallest unit of most A molecule is the smallest unit of most

compounds.compounds. P. 38, fig. 2-4P. 38, fig. 2-4

Covalent BondingCovalent Bonding

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http://www.youtube.com/watch?v=lGEA5PVWQiQ&feature=related

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Van der Waals ForcesVan der Waals Forces

Van der Waals ForcesVan der Waals Forces –a slight –a slight attraction that develops b/t the attraction that develops b/t the opposite charged regions of nearby opposite charged regions of nearby molecules.molecules.

Example:Example: A gecko’s toes.A gecko’s toes. Fig. 2-5Fig. 2-5

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Chapter 2Chapter 2

Section 2Section 2

Properties of WaterProperties of Water

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75%75% of of the Earth the Earth is covered is covered by water.by water.

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The Water MoleculeThe Water Molecule

Water = HWater = H22OO Water exists in 3 states:Water exists in 3 states:

LiquidLiquid GasGas SolidSolid

Water as a molecule has a neutral charge.Water as a molecule has a neutral charge. Figure it out….Figure it out….

10e10e-- & 10p & 10p++

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Characteristics of WaterCharacteristics of Water Polarity:Polarity:

Water molecules are polar b/c there is Water molecules are polar b/c there is an uneven distribution of e- b/t the O & an uneven distribution of e- b/t the O & H atoms.H atoms.

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Hydrogen Bonds:Hydrogen Bonds: B/c water is polar, it can attract other B/c water is polar, it can attract other

water molecules.water molecules. Fig. 2-7Fig. 2-7

The (+) & (-) charges are weaker than The (+) & (-) charges are weaker than the charges of + & - ions.the charges of + & - ions.

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When 2 or more water molecules When 2 or more water molecules join up, they are held there by a join up, they are held there by a hydrogen bond.hydrogen bond. Hydroge

n Bond

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Hydrogen bonds are Hydrogen bonds are weakerweaker than than ionic or covalent bonds.ionic or covalent bonds.

Also, a water molecule can bond to 4 Also, a water molecule can bond to 4 other water molecules at a time.other water molecules at a time. This enables water to have some This enables water to have some

interesting properties.interesting properties.

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http://www.youtube.com/watch?v=KiZJOTt3Dl0&feature=related

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CohesionCohesion –attraction b/t molecules of –attraction b/t molecules of the same substance.the same substance. Example:Example:

Water forms beads on a smooth surface.Water forms beads on a smooth surface. The reason why some insects can walk on The reason why some insects can walk on

water.water.

AKA AKA surface tensionsurface tension or or water tensionwater tension.. Fig. 2-8Fig. 2-8

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AdhesionAdhesion –an attraction b/t –an attraction b/t molecules of different substances.molecules of different substances. Example:Example:

Capillary actionCapillary action

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Solution & SuspensionsSolution & Suspensions

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The The 22 types of mixtures that can be types of mixtures that can be made w/ water are:made w/ water are: SolutionsSolutions SuspensionsSuspensions

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SolutionsSolutions SolutionSolution –a homogeneous mixture of 2 or –a homogeneous mixture of 2 or

more substances in which the molecules more substances in which the molecules are evenly distributed.are evenly distributed. SoluteSolute –substance which is dissolved. –substance which is dissolved. SolventSolvent –substance that dissolves the solute. –substance that dissolves the solute.

Examples:Examples: Salt waterSalt water Sugar waterSugar water

Fig. 2-9Fig. 2-9

Water is the greatest solvent on Earth!Water is the greatest solvent on Earth!

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SuspensionsSuspensions

Suspension Suspension – mixture of water & – mixture of water & nondissolved substances.nondissolved substances. bloodblood Oil & Water Oil & Water Sand & waterSand & water

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Acids, Bases, & pHAcids, Bases, & pH

The pH ScaleThe pH Scale Fig. 2-10Fig. 2-10 Pure water = 7Pure water = 7

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AcidsAcids AcidAcid –any compound that forms –any compound that forms HH++ ions ions

in a solution.in a solution. Ex:Ex:

Hydrochloric acidHydrochloric acid Sulfuric acidSulfuric acid Nitric acidNitric acid

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BasesBases BaseBase –a compound that produces –a compound that produces OHOH--

ions in a solution.ions in a solution. Examples:Examples:

LyeLye AmmoniaAmmonia Oven cleanerOven cleaner

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BuffersBuffers The pH of fluids w/in cells in the human The pH of fluids w/in cells in the human

body are generally between body are generally between 6.5-7.56.5-7.5.. If higher or lower it may interfere w/ chem. If higher or lower it may interfere w/ chem.

reactions.reactions. Buffers have a lot to do w/ maintaining ph in Buffers have a lot to do w/ maintaining ph in

our bodies & therefore our homeostasis.our bodies & therefore our homeostasis.

BuffersBuffers –weak acids or bases that can –weak acids or bases that can react w/ strong acids or bases to react w/ strong acids or bases to prevent sudden changes in pH.prevent sudden changes in pH.

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Section 2-3Section 2-3

Carbon Carbon CompoundsCompounds

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Read the 1Read the 1stst paragraph…. paragraph….

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The Chemistry of CarbonThe Chemistry of Carbon

Carbon is heavily studied in Carbon is heavily studied in chemistry for a few reasons:chemistry for a few reasons: CC atoms have atoms have 44 valence e valence e--..

This means that This means that CC can join w/ many other can join w/ many other atoms via strong covalent bonds.atoms via strong covalent bonds.

CC can bond such elements as: can bond such elements as: H, O, P, S, & NH, O, P, S, & N

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Also, Also, CC can bond to other can bond to other CC atoms. atoms. This gives This gives CC the ability to form chains. the ability to form chains.

These chains can be unlimited in length.These chains can be unlimited in length.

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Carbon-carbon bonds Carbon-carbon bonds can be:can be: SingleSingle 2e2e DoubleDouble 4e4e TripleTriple 6e6e

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Carbon can form:Carbon can form: ChainsChains RingsRings BranchesBranches

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MacromoleculesMacromolecules

MacromoleculesMacromolecules –extremely large –extremely large molecules found in living orgs.molecules found in living orgs. ““Giant molecules”Giant molecules”

Macromolecules are made of Macromolecules are made of thousands or even hundreds of thousands or even hundreds of thousands of molecules.thousands of molecules.

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Macromolecules are made by Macromolecules are made by polymerizationpolymerization.. In this process, large compounds are In this process, large compounds are

formed by joining smaller ones together.formed by joining smaller ones together.

The smaller units, called The smaller units, called monomersmonomers join to form join to form polymerspolymers. . Monomers can be identical or they can Monomers can be identical or they can

be like beads multicolored necklace.be like beads multicolored necklace.

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There are There are 44 groups of organic carbon groups of organic carbon compounds found in living things:compounds found in living things:

Carbohydrates (Carbs)Carbohydrates (Carbs) LipidsLipids ProteinsProteins Nucleic acidsNucleic acids

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CarbohydratesCarbohydrates

CarbohydratesCarbohydrates –compounds made up –compounds made up of C, H, & O atoms.of C, H, & O atoms. Usually in the ratio of Usually in the ratio of 1:2:11:2:1 Ex:Ex:

CC66HH1212OO66

Orgs. use carbohydrates as a main Orgs. use carbohydrates as a main source of energy (E).source of energy (E).

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Examples of CarbsExamples of Carbs:: Starch Starch SugarsSugars CelluloseCellulose

We break down sugars for energy.We break down sugars for energy. Plants store energy in starches.Plants store energy in starches.

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Single sugar molecules = Single sugar molecules = monosaccharidesmonosaccharides Ex:Ex:

GalactoseGalactose FructoseFructose GlucoseGlucose

NOTE: NOTE: Items them end in “ose” are Items them end in “ose” are sugars.sugars.

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2 sugar molecules = 2 sugar molecules = disaccharidesdisaccharides Ex:Ex:

Glucose + Fructose = SucroseGlucose + Fructose = Sucrose

A large macromolecule formed from many A large macromolecule formed from many monosaccharides is a monosaccharides is a polysaccharidepolysaccharide.. Ex:Ex:

GlycogenGlycogen Also known as animal starch.Also known as animal starch.

Plants have cellulose & starch as their Plants have cellulose & starch as their polysaccharides.polysaccharides.

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LipidsLipids

Lipids Lipids –a carbon compound made –a carbon compound made from mostly C & H.from mostly C & H. Usually Usually insolubleinsoluble in water. in water.

Examples:Examples: FatsFats OilsOils WaxesWaxes SteroidsSteroids

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Lipids are used for:Lipids are used for: Storing energyStoring energy Parts of cell membranesParts of cell membranes Waterproof coatingsWaterproof coatings

Fig. 2-14Fig. 2-14 Glycerol & a fatty acidGlycerol & a fatty acid

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3 types of fatty acids:3 types of fatty acids:

Saturated fatty acidSaturated fatty acid Has the maximum # hydrogen atoms.Has the maximum # hydrogen atoms.

Unsaturated fatty acidUnsaturated fatty acid Has at least 1 double carbon-carbon Has at least 1 double carbon-carbon

bond.bond. Polyunsaturated fatty acidPolyunsaturated fatty acid

Contain more than 1 carbon-carbon Contain more than 1 carbon-carbon double bond.double bond.

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Nucleic AcidsNucleic Acids

Nucleic acidsNucleic acids –macromolecules –macromolecules containing H, O, N, C, & containing H, O, N, C, & PP..

Nucleic acids are polymers made up Nucleic acids are polymers made up of of nucleotidesnucleotides..

NucleotidesNucleotides –consist of –consist of 33 parts: parts: A sugarA sugar A phosphate groupA phosphate group A nitrogen baseA nitrogen base Fig. 2-15Fig. 2-15

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Nucleic acids store Nucleic acids store transmit genetic info.transmit genetic info. There are There are 22 types: types:

DNADNA RNARNA

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ProteinsProteins

Macromolecules that contain Macromolecules that contain NN as as well as C, H, & O.well as C, H, & O.

Proteins are polymers of molecules Proteins are polymers of molecules called called amino acidsamino acids..

Amino acids are the building blocks Amino acids are the building blocks of proteins.of proteins. So, AA’s are monomers of proteins.So, AA’s are monomers of proteins.

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Proteins are some of the most diverse Proteins are some of the most diverse macromolecules.macromolecules.

There are more than 20 AA in nature.There are more than 20 AA in nature. AA are held together by AA are held together by peptide peptide

bondsbonds.. Peptide bonds are covalent bonds.Peptide bonds are covalent bonds.

The instructions for how AA are put The instructions for how AA are put together is stored in our DNA.together is stored in our DNA.

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Proteins do quite a few things for us.Proteins do quite a few things for us. They:They:

Control the rate of reactionsControl the rate of reactions Regulate cell processesRegulate cell processes Used to form bones & muscleUsed to form bones & muscle Used for transport of substances Used for transport of substances Immune responsesImmune responses

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CarbonCompounds

include

that consist of

which contain

that consist of that consist of that consist of

which contain which contain which contain

Carbohydrates Lipids Nucleic acids Proteins

Sugars and starches

Fats and oils Nucleotides Amino Acids

Carbon,hydrogen,

oxygen

Carbon,hydrogen,

oxygen

Carbon,hydrogen,oxygen, nitrogen,

phosphorus

Carbon,hydrogen,oxygen,

nitrogen,

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Section 2-4Section 2-4

Chemical Reactions & Chemical Reactions & EnzymesEnzymes

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Chemical ReactionsChemical Reactions

Chemical ReactionChemical Reaction – process that – process that changes, or transforms, one set of changes, or transforms, one set of chemicals into another.chemicals into another. Chemical reactions can happen very Chemical reactions can happen very

slowly or very quickly.slowly or very quickly. Ex:Ex:

Rust formation on iron. (slow)Rust formation on iron. (slow) P. 49, fig. 2-18P. 49, fig. 2-18

Chemical reactions Chemical reactions alwaysalways involve involve the breaking of chemical bonds.the breaking of chemical bonds.

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Look at this Reaction:Look at this Reaction:P. 49P. 49

Carbon DioxideCarbon Dioxide

WaterWater

Carbonic AcidCarbonic Acid

COCO22 + H + H22O O H H22COCO33

Reactants Reactants ProductsProducts

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Energy in ReactionsEnergy in Reactions

Chemical reactions can Chemical reactions can releaserelease E. E. Called an Called an exothermic reactionsexothermic reactions.. This release can be in the form of:This release can be in the form of:

Heat Heat LightLight SoundSound

Chemical reactions can also Chemical reactions can also absorbabsorb E. E. Called an Called an endothermic reactionsendothermic reactions..

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Every org. must have a source of E Every org. must have a source of E to carry out chemical reactions.to carry out chemical reactions.

Where do they get this Where do they get this EE?? Plants get E through photosynthesis.Plants get E through photosynthesis. Animals get their E by consuming Animals get their E by consuming

plants or animalsplants or animals If you want to breathe, grow, think, If you want to breathe, grow, think,

or dream you need a chemical or dream you need a chemical reaction.reaction. Chemical reactions occur when you Chemical reactions occur when you

metabolize, or break down, digested metabolize, or break down, digested food.food.

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Activation EnergyActivation Energy

Activation energyActivation energy –E that is needed –E that is needed to get a reaction started.to get a reaction started.

P. 50, fig. 2-19P. 50, fig. 2-19

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Energy Absorbing

ActivationEnergy

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Energy Releasing

ActivationEnergy

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EnzymesEnzymes

Some chemical reactions are Some chemical reactions are too too slowslow or have or have too hightoo high of a activation of a activation E to make them practical.E to make them practical.

To make these reactions a possibility To make these reactions a possibility you need a you need a catalystcatalyst.. CatalystCatalyst –substance that speeds up a –substance that speeds up a

chemical reaction.chemical reaction. Catalysts lower the activation E required by Catalysts lower the activation E required by

a reaction.a reaction.

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EnzymesEnzymes –proteins that act as a –proteins that act as a biological catalyst.biological catalyst. Enzymes speed up chemical reactions Enzymes speed up chemical reactions

that take place in cells.that take place in cells. P. 51, fig. 2-20P. 51, fig. 2-20

Enzymes are very specific.Enzymes are very specific. They usually only catalyze one chemical They usually only catalyze one chemical

reaction.reaction. Enzymes are often named after the Enzymes are often named after the

reaction they catalyze.reaction they catalyze.

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Enzyme ActionEnzyme Action

How enzymes do their job:How enzymes do their job: P. 52-53P. 52-53

You have You have 33 parts: parts: The EnzymeThe Enzyme The SubstratesThe Substrates The Enzyme-Substrate ComplexThe Enzyme-Substrate Complex

P. 53, fig. 2-22 bottomP. 53, fig. 2-22 bottom

SubstratesSubstrates –the reactants of enzyme- –the reactants of enzyme-catalyzed reactions.catalyzed reactions.

Enzyme Substrate Enzyme Substrate ComplexComplex

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Regulation of Enzyme Regulation of Enzyme ActivityActivity

Enzyme activity can be affected by:Enzyme activity can be affected by: TempTemp

Most enzymes work well at 37ºC.Most enzymes work well at 37ºC. pHpH

Cells can also control enzyme activity.Cells can also control enzyme activity. They have proteins that act as keys to enzyme They have proteins that act as keys to enzyme

activity.activity. On/offOn/off

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Enzymes are essential for:Enzymes are essential for: Regulating chemical pathways.Regulating chemical pathways. Making materials that cells need.Making materials that cells need. Releasing energyReleasing energy Transferring informationTransferring information

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