The Chemistry of LifeThe Chemistry of Life

Chapters 2 and 3Chapters 2 and 3

AtomsAtoms

Smallest unit of matter that retains Smallest unit of matter that retains physical propertiesphysical properties

3 Basic Parts3 Basic PartsProtonProtonNeutronNeutronElectronElectron

Nucleus gives an atom its massNucleus gives an atom its massElectrons give an atom is behaviorElectrons give an atom is behavior

ElementsElements

Made up of only 1 type of atomMade up of only 1 type of atom Isotopes have same number of pIsotopes have same number of p++, but , but

different numbers of ndifferent numbers of n00, so atomic mass varies, so atomic mass variesForm compounds Form compounds

Chemical BondsChemical BondsFormula tells the ratio of atoms in a Formula tells the ratio of atoms in a

compoundcompound98% of living things are made of CHNOPS98% of living things are made of CHNOPS

Chemical BondsChemical Bonds

The valence electrons are involved in the The valence electrons are involved in the bondbondAtoms are stable when their valence shell is Atoms are stable when their valence shell is

filledfilled

Covalent Bonds- atoms share valence Covalent Bonds- atoms share valence electrons and are held togetherelectrons and are held togetherNon-metal to non-metalNon-metal to non-metalMolecule is the smallest part of a compound Molecule is the smallest part of a compound

that retains the properties that retains the properties

PolarityPolarityCovalent bonds share electrons between Covalent bonds share electrons between

atomsatomsElectrons shared equally result in a non-Electrons shared equally result in a non-

polar bondpolar bondElectrons shared unequally between the Electrons shared unequally between the

atoms create regions of positive charge atoms create regions of positive charge and negative charge, though the molecule and negative charge, though the molecule is neutral, results in a polar bondis neutral, results in a polar bondPolar molecules can interact with each other Polar molecules can interact with each other

and with ionsand with ionsWhole molecules can be polar or select bonds Whole molecules can be polar or select bonds

in a molecule can be polarin a molecule can be polar

Ionic Bonds are a result of the transfer of Ionic Bonds are a result of the transfer of valence electronsvalence electronsAtoms that lose electrons have more p+ than Atoms that lose electrons have more p+ than

e- and are called positive ions (cations)e- and are called positive ions (cations)Atoms that gain electrons have more e- than Atoms that gain electrons have more e- than

p+ and are called negative ions (anions)p+ and are called negative ions (anions)Metals form cations and non-metals form Metals form cations and non-metals form

anionsanionsThe positive ion is attracted to the negative The positive ion is attracted to the negative

ion and they stick togetherion and they stick together

EnergyEnergy

Comes in many formsComes in many formsKinetic, Potential, Chemical, Thermal, RadiantKinetic, Potential, Chemical, Thermal, Radiant

The ability to do workThe ability to do workCan be converted from one form to Can be converted from one form to

anotheranotherWhen atoms for chemical bonds energy When atoms for chemical bonds energy

can either be absorbed or releasedcan either be absorbed or released

Living Things and EnergyLiving Things and Energy

All living things require energyAll living things require energy 1000s of chemical reactions occur in living 1000s of chemical reactions occur in living

organisms a dayorganisms a day Energy is either stored in bonds formed during a Energy is either stored in bonds formed during a

reaction or it is released by the reactionreaction or it is released by the reaction Living organisms use this energy to carry out life Living organisms use this energy to carry out life

processesprocesses Metabolism is all of the chemical reactions that occur Metabolism is all of the chemical reactions that occur

in an organismin an organism

Activation EnergyActivation Energy

Energy required for a chemical reaction to Energy required for a chemical reaction to occuroccurCan be a large amountCan be a large amount

Catalysts lower the activation energy for a Catalysts lower the activation energy for a reactionreactionThey are not used up and can be used They are not used up and can be used

repeatedlyrepeatedlyEnzymes are proteins or RNA that act as Enzymes are proteins or RNA that act as

catalysts in living organisms- there are 1000scatalysts in living organisms- there are 1000s

Enzyme has a specific shape that will interact Enzyme has a specific shape that will interact with a specific substratewith a specific substrateSubstrate is reactant being catalyzed fits in active Substrate is reactant being catalyzed fits in active

site on enzymesite on enzyme

Enzyme’s shape is changed when substrate Enzyme’s shape is changed when substrate bonds at active sitebonds at active siteChange in shape causes bonds in substrate to Change in shape causes bonds in substrate to

weaken and breakweaken and breakProducts are released by enzyme Products are released by enzyme Enzyme is unchanged and reacts anew with another Enzyme is unchanged and reacts anew with another

substratesubstrate

Enzymes require very specific temperature and Enzymes require very specific temperature and pH rangespH rangesChanges can cause the enzyme to denatureChanges can cause the enzyme to denature

Enzyme Catalyzed ReactionEnzyme Catalyzed Reaction

Oxidation Reduction ReactionsOxidation Reduction Reactions

AKA- Redox reactionsAKA- Redox reactionsReactions that involve the transfer of Reactions that involve the transfer of

electronselectronsLEO says GERLEO says GER

Lose electrons oxidizeLose electrons oxidizeGain electrons reduceGain electrons reduce

Oxidation and Reduction are coupled Oxidation and Reduction are coupled together- something is oxidized because together- something is oxidized because something else is reducedsomething else is reduced

Water and SolutionsWater and Solutions

Cells are mainly water and the water is an Cells are mainly water and the water is an arena for the chemical reactions of life to arena for the chemical reactions of life to occuroccur

Water is polarWater is polarH is slightly +, O is slightly –H is slightly +, O is slightly –Allows water molecules to interact with each Allows water molecules to interact with each

other, ions, and other polar moleculesother, ions, and other polar moleculesWater is universal solvent because of its Water is universal solvent because of its

polarity- it dissolves a lot of stuffpolarity- it dissolves a lot of stuff

Hydrogen bonds form between water Hydrogen bonds form between water molecules allowing them to stick togethermolecules allowing them to stick togetherHydrogen bonds form between H with a slight + Hydrogen bonds form between H with a slight +

charge and areas of – charge or with anionscharge and areas of – charge or with anionsCan be formed or broken easily and repeatedly- Can be formed or broken easily and repeatedly-

weak independently, strong in great numbersweak independently, strong in great numbersMany occur at one time in waterMany occur at one time in waterH bonds allow water to experienceH bonds allow water to experience

Cohesion- water molecules stick togetherCohesion- water molecules stick togetherAdhesion- water molecules stick to other thingsAdhesion- water molecules stick to other things

When ionic compounds are dissolved in water When ionic compounds are dissolved in water they ionize- break apart into cations and they ionize- break apart into cations and anionsanions

Water is less dense as a solid than as a Water is less dense as a solid than as a liquidliquid Ice floats- pond ecosystems are conserved Ice floats- pond ecosystems are conserved

even in wintereven in winterWater has a high specific heat capacityWater has a high specific heat capacity

Water absorbs large amounts of heat with Water absorbs large amounts of heat with little temperature changelittle temperature change

SolutionsSolutions

Solutions are homogeneous mixturesSolutions are homogeneous mixturesAll substances are evenly distributed All substances are evenly distributed

throughoutthroughoutComposed of solute and solventComposed of solute and solvent

Solute is what is dissolved (less of this)Solute is what is dissolved (less of this)Solvent does the dissolving (more of this)Solvent does the dissolving (more of this)

Can have different concentrationsCan have different concentrationsHow much solute is dissolved in the solventHow much solute is dissolved in the solventSaturated- the max amount of solute is Saturated- the max amount of solute is

dissolveddissolved

Aqueous solutions have water as the Aqueous solutions have water as the solventsolventEssential for lifeEssential for life

Aqueous solutions are essential for cellsAqueous solutions are essential for cellsBlood is an aqueous solutionBlood is an aqueous solutionMany organisms live in aqueous solutions- The Many organisms live in aqueous solutions- The

ocean! Ponds! Lakes! Rivers! Your gut!ocean! Ponds! Lakes! Rivers! Your gut!

Acids and BasesAcids and Bases

Water can ionize (split into ions)Water can ionize (split into ions)HH22O HO H++ + OH + OH --

OH OH -- is the hydroxide ion is the hydroxide ion HH++ is a proton is a proton Water can also accept a proton (HWater can also accept a proton (H++), ),

forming hydronium ion (Hforming hydronium ion (H3300++))

HH++ + H + H22O HO H3300++

This occurs all of the time in waterThis occurs all of the time in water

Acids and bases are determined by the Acids and bases are determined by the ratio of hydronium ions to hydroxide ionsratio of hydronium ions to hydroxide ions

Acids HAcids H3300++ > OH- > OH-

Bases HBases H3300++ < OH- < OH-Compounds that are acids donate a H+ Compounds that are acids donate a H+

and it will react with Hand it will react with H220 to form H0 to form H33OO++

Bases produce OH- which will increase Bases produce OH- which will increase their concentrationtheir concentration

pH scale is a way to measure the pH scale is a way to measure the concentration of Hconcentration of H33OO+ +

It is a logarithmic scale- so each number is a It is a logarithmic scale- so each number is a ten-fold difference in concentration of Hten-fold difference in concentration of H33OO+ +

Buffers are chemical substances that can Buffers are chemical substances that can absorb excess acids or bases to maintain absorb excess acids or bases to maintain pHpHVery important jobVery important job

Enzymes (biological catalysts) can only Enzymes (biological catalysts) can only function in specific pH rangesfunction in specific pH rangesCells must regulate their pHCells must regulate their pH

BiochemistryBiochemistry

The study of the chemistry that allows life The study of the chemistry that allows life to exist and flourishto exist and flourish

Biochemistry is centered around the Biochemistry is centered around the element Carbonelement CarbonOrganic compounds are those that contain Organic compounds are those that contain

carboncarbon Inorganic compounds do not generally contain Inorganic compounds do not generally contain

carboncarbon

CarbonCarbon

Carbon has 4 valence electrons and Carbon has 4 valence electrons and needs 8needs 8Forms covalent bonds to complete its valence Forms covalent bonds to complete its valence

shellshellCarbon is special because is will bond with Carbon is special because is will bond with

up to 4 other carbon atomsup to 4 other carbon atomsCan form rings, straight chains, and branched Can form rings, straight chains, and branched

chainschains

A covalent bond is formed when two A covalent bond is formed when two atoms share 2 electronsatoms share 2 electronsRepresented with a straight line Represented with a straight line

Carbon can form single, double, and triple Carbon can form single, double, and triple bondsbonds

Carbon can form almost endless Carbon can form almost endless compounds as a resultcompounds as a result

Functional GroupsFunctional Groups

Organic molecules all contain Carbon- so Organic molecules all contain Carbon- so what makes one compound different from what makes one compound different from another- Functional Groupsanother- Functional Groups

Functional Groups are specific clusters of Functional Groups are specific clusters of atoms attached to a carbon compoundatoms attached to a carbon compound

Each functional group has specific Each functional group has specific properties that it gives the compoundproperties that it gives the compound

Large Carbon MoleculesLarge Carbon Molecules

Monomers are small, simple molecules Monomers are small, simple molecules that can be bonded together to form that can be bonded together to form polymerspolymers

Macromolecules are made from polymersMacromolecules are made from polymers

Condensation and Hydrolysis Condensation and Hydrolysis ReactionsReactions

Monomers are bonded together through Monomers are bonded together through condensation reactionscondensation reactionsWith the addition of each monomer a water With the addition of each monomer a water

molecule is lostmolecule is lost

Polymers can be broken down into Polymers can be broken down into polymers through hydrolysis reactionspolymers through hydrolysis reactionsA water molecule must be added in order to A water molecule must be added in order to

split one monomer away from the polymersplit one monomer away from the polymer

Energy CurrencyEnergy Currency

Remember chemical bonds contain Remember chemical bonds contain energyenergyBreaking or making a bond can either absorb Breaking or making a bond can either absorb

or release energyor release energySome compounds have a lot of energy Some compounds have a lot of energy

stored in their bondsstored in their bondsThis energy can be used to power cell This energy can be used to power cell

functionsfunctions

Adenosine Triphosphate (ATP) is a high Adenosine Triphosphate (ATP) is a high energy compoundenergy compoundBond between the second and third Bond between the second and third

phosphate is hydrolyzed to release energy for phosphate is hydrolyzed to release energy for cellular functions, leaving ADP and Pcellular functions, leaving ADP and P

ATP + HATP + H22O O ADP + P + Energy ADP + P + Energy

ADP + P + energy ADP + P + energy ATP + H ATP + H22OO

Molecules of LifeMolecules of Life

Carbohydrates, Lipids, Proteins, Nucleic Carbohydrates, Lipids, Proteins, Nucleic AcidsAcidsEach type has different properties and Each type has different properties and

responsibilitiesresponsibilitiesAll have C, H, O; some also have N, P, SAll have C, H, O; some also have N, P, S

Put together in different ratiosPut together in different ratios

CarbohydratesCarbohydratesRoles include energy source and structural Roles include energy source and structural

componentscomponentsMade of C, H, O in a 1:2:1 ratio (CHMade of C, H, O in a 1:2:1 ratio (CH22O)O)nn

Monomer- monosaccharideMonomer- monosaccharideGlucose (simple sugar), galactose (milk), Glucose (simple sugar), galactose (milk),

fructose (fruits)fructose (fruits)Disaccharides are made by a Disaccharides are made by a

condensation rxn joining 2 condensation rxn joining 2 monosaccharidemonosaccharideGlucose + Fructose Glucose + Fructose Sucrose Sucrose

Polymers are polysaccharides- large Polymers are polysaccharides- large molecules made by joining many molecules made by joining many monosaccharidesmonosaccharidesAnimals store excess sugar as GlycogenAnimals store excess sugar as GlycogenPlants store excess sugar as StarchPlants store excess sugar as Starch

Cellulose is a polysaccharide made by Cellulose is a polysaccharide made by plants that gives cell walls strength and plants that gives cell walls strength and rigidityrigidityCan be broken down by hydrolysis reactionsCan be broken down by hydrolysis reactions

ProteinsProteins

Have a diversity of structures, resulting in Have a diversity of structures, resulting in a wide range of functionsa wide range of functionsAccount for ~50% dry mass of cellsAccount for ~50% dry mass of cellsAct as enzymes, play roles in defense, Act as enzymes, play roles in defense,

storage, transport, cell communication, storage, transport, cell communication, movement, structural supportmovement, structural support

Each protein has a unique 3-D shapeEach protein has a unique 3-D shapeComposed of mainly C, H, O, NComposed of mainly C, H, O, N

Monomer is amino acidMonomer is amino acidThere are 20 amino acids used to build There are 20 amino acids used to build

thousands of proteinsthousands of proteinsAmino Acids have same basic structureAmino Acids have same basic structure

Amino group, central C, Carboxyl group, and Amino group, central C, Carboxyl group, and R group (variable- distinguishes 1 aa from R group (variable- distinguishes 1 aa from another)another)

Polymer is polypeptidePolymer is polypeptideLong chain of amino acidsLong chain of amino acidsHeld together by peptide bondsHeld together by peptide bonds

Covalent bonds formed via condensation rxnCovalent bonds formed via condensation rxn

1 or more polypeptide chain(s) fold into 1 or more polypeptide chain(s) fold into complex shapescomplex shapesShape is essential to functionShape is essential to functionChains held together via interactions like Chains held together via interactions like

hydrogen bondshydrogen bondsEnzymes are important group of proteinsEnzymes are important group of proteins

Act as biological catalystsAct as biological catalystsEnzyme has a specific shape that will interact Enzyme has a specific shape that will interact

with a specific substratewith a specific substrateSubstrate is reactant being catalyzed fits in active Substrate is reactant being catalyzed fits in active

site on enzymesite on enzyme

LipidsLipids

Function as long term energy storage, in Function as long term energy storage, in membranes, water proof coverings, membranes, water proof coverings, steroids (hormones) as chemical steroids (hormones) as chemical messengersmessengers

Have C, H, O- higher ratio of C and H to OHave C, H, O- higher ratio of C and H to OLong chains of C and H store more energyLong chains of C and H store more energy

Fatty AcidsFatty AcidsCarboxyl Group connected to a long carbon Carboxyl Group connected to a long carbon

chainchainCarboxyl group is polar and therefore hydrophilicCarboxyl group is polar and therefore hydrophilicHydrocarbon chain is non-polar and hydrophobicHydrocarbon chain is non-polar and hydrophobic

Fatty acids that have each C bonded to 4 Fatty acids that have each C bonded to 4 things are called saturatedthings are called saturated

Fatty acids that have double bonds between Fatty acids that have double bonds between some C atoms are called unsaturatedsome C atoms are called unsaturated

Triglycerides have 3 fatty acids joined to a Triglycerides have 3 fatty acids joined to a glycerol headglycerol headSaturated triglycerides have a high melting Saturated triglycerides have a high melting

point and are solid at room temp- butter, fats, point and are solid at room temp- butter, fats, red meatred meat

Unsaturated triglycerides are usually liquid at Unsaturated triglycerides are usually liquid at room temp- Plant oils (olive, sunflower, etc)room temp- Plant oils (olive, sunflower, etc)

Phospholipids- 2 fatty acids Phospholipids- 2 fatty acids bonded to a glycerol head bonded to a glycerol head and a phosphate groupand a phosphate groupForm water-tight barriers, such Form water-tight barriers, such

as cell membrane (lipid bi-as cell membrane (lipid bi-layer)layer)

Waxes are long chains of Waxes are long chains of fatty acids bonded to large fatty acids bonded to large alcohol groupsalcohol groupsHelp plants retain water and Help plants retain water and

earwax protects ear from earwax protects ear from invadersinvaders

Steroids are made of 4 carbon rings and Steroids are made of 4 carbon rings and functional groups attachedfunctional groups attachedHormones are steroids that have important Hormones are steroids that have important

roles transmitting chemical messages and roles transmitting chemical messages and roles in the cell membrane (cholesterol)roles in the cell membrane (cholesterol)

Nucleic AcidsNucleic Acids

Function to store and transfer information Function to store and transfer information in cells, including hereditary materialin cells, including hereditary material

Composed of C, H, O, N, PComposed of C, H, O, N, PMonomer- NucleotideMonomer- Nucleotide

Three parts: 5-C sugar, Nitrogenous base, Three parts: 5-C sugar, Nitrogenous base, Phosphate groupPhosphate groupATPATP

Polymer- Nucleic AcidPolymer- Nucleic AcidDNA, RNADNA, RNA