INTRO TO CHEMISTRYINTRO TO CHEMISTRY

COOMESCOOMES

PRE-AP BIOLOGYPRE-AP BIOLOGY

WHAT ARE ELEMENTS?WHAT ARE ELEMENTS?

Cannot be broken downCannot be broken down 92 naturally occurring92 naturally occurring 25 required by living organisms25 required by living organisms CHON CHON

(Carbon,Hydrogen,Oxygen,Nitrogen) (Carbon,Hydrogen,Oxygen,Nitrogen) make up 96.3% of human bodymake up 96.3% of human body

Atom: smallest unit of an elementAtom: smallest unit of an element

COMPOUNDSCOMPOUNDS

Composed of 2 or more elementsComposed of 2 or more elements Examples: Sodium Chloride, Water, Examples: Sodium Chloride, Water,

Carbon DioxideCarbon Dioxide

SUBATOMIC PARTICLESSUBATOMIC PARTICLES

Atoms are made of 3 types of Atoms are made of 3 types of particles:particles:• Protons: positive charge, in nucleusProtons: positive charge, in nucleus• Neutrons: neutral charge, in nucleusNeutrons: neutral charge, in nucleus• Electrons: negative charge, outside of Electrons: negative charge, outside of

nucleus in electron cloud (orbitals)nucleus in electron cloud (orbitals)

PERIODIC TABLEPERIODIC TABLE

Contains all of the elements, Contains all of the elements, arranged by class (metals, non-arranged by class (metals, non-metals, noble gases, rare earths) and metals, noble gases, rare earths) and atomic numberatomic number

Atomic number: Number of protonsAtomic number: Number of protons Isotope: Elements with same atomic Isotope: Elements with same atomic

number but different atomic mass number but different atomic mass (different number of neutrons)(different number of neutrons)

IONIC BONDIONIC BOND

Ion: charged atom Ion: charged atom that has lost or that has lost or gained electronsgained electrons

Ionic bond: eletron Ionic bond: eletron is transferrredis transferrred

Example: Sodium Example: Sodium chloride (table saltchloride (table salt

Table SaltTable SaltIonic bondIonic bond

Crystal lattice Crystal lattice structure: very structure: very stable & strongstable & strong

COVALENT BONDSCOVALENT BONDS

Electrons are shared between atomsElectrons are shared between atoms Single bond: C-CSingle bond: C-C Double bond: C=CDouble bond: C=C Triple bond:CTriple bond:C==CC

COVALENT BONDSCOVALENT BONDS

When eletrons are unequally When eletrons are unequally shared, the molecule is POLARshared, the molecule is POLAR

Polar molecules are Polar molecules are charged moleculescharged molecules

HydrophilicHydrophilic

When electrons are When electrons are shared equally, the shared equally, the molecule is NONPOLARmolecule is NONPOLAR Nonpolar molecules Nonpolar molecules

are neutralare neutral HydrophobicHydrophobic

HYDROGEN BONDINGHYDROGEN BONDING

• Contribute to unique properties of waterContribute to unique properties of water• Relatively weak bondsRelatively weak bonds

COHESIONCOHESION

Linking of like moleculesLinking of like molecules• Water Strider (Surface Tension)Water Strider (Surface Tension)• AdhesionAdhesion

Water on windshieldWater on windshield

• TranspirationTranspiration Water moves up the xylem (thin tubes) and Water moves up the xylem (thin tubes) and

evaporates from stomataevaporates from stomata Cling together by cohesion, “adhere” to Cling together by cohesion, “adhere” to

xylem wallsxylem walls

HIGH SPECIFIC HEATHIGH SPECIFIC HEAT

Amount of heat required to raise or Amount of heat required to raise or lower temperature by 1lower temperature by 1 ̊ C̊ C

Moderation of temperatureModeration of temperature• Makes ocean temp relatively stable and able to Makes ocean temp relatively stable and able to

support more animal & plant lifesupport more animal & plant life

INSULATION OF WATER BY INSULATION OF WATER BY FLOATING ICEFLOATING ICE

Water is less dense as a solidWater is less dense as a solid

UNIVERSAL SOLVENTUNIVERSAL SOLVENT

Able to dissolve both acids & basesAble to dissolve both acids & bases

PROPERTIES OF WATER LABPROPERTIES OF WATER LAB

CohesionCohesion• AdhesionAdhesion• Surface TensionSurface Tension

Hydrophobic/Hydrophilic InteractionsHydrophobic/Hydrophilic Interactions• Polar vs. NonpolarPolar vs. Nonpolar

pH ScalepH Scale

Acids: excess Hydrogen Ions (HAcids: excess Hydrogen Ions (H++)) Bases: excess Hydroxide OHBases: excess Hydroxide OH--

Buffers minimize change in pH Buffers minimize change in pH • Accept excess Hydrogen ions or donate Accept excess Hydrogen ions or donate

depleted Hydrogen ionsdepleted Hydrogen ions

• Ex: Carbonic Acid (HEx: Carbonic Acid (H22COCO33): buffer in ): buffer in living systems living systems

Blood plasma, oceanBlood plasma, ocean

pH LabpH Lab

What did we do?What did we do? Control?Control? Hypotheses?Hypotheses? How would you determine pH without How would you determine pH without

the color card? the color card?

BIOMOLECULESBIOMOLECULES

PRE-AP BIOLOGYPRE-AP BIOLOGY

BIOCHEMISTRYBIOCHEMISTRY

Chemistry of living Chemistry of living things organized things organized around CARBON around CARBON (organic chemistry)(organic chemistry)

Methane: simplest Methane: simplest carbon compoundcarbon compound• Major component of Major component of

natural gasnatural gas

HYDROCARBONSHYDROCARBONS

Molecules made of only hydrogen Molecules made of only hydrogen &carbon&carbon

2 ways to represent structures:2 ways to represent structures: ModelModel

FormulaFormula

COVALENT BONDSCOVALENT BONDS

Share electronsShare electrons Single, double, triple bondSingle, double, triple bond Hydrogen: 1Hydrogen: 1 Oxygen: 2Oxygen: 2 Nitrogen: 3Nitrogen: 3 Carbon: 4Carbon: 4

FUNCTIONAL GROUPSFUNCTIONAL GROUPS

R=hydrocarbon groupR=hydrocarbon group

1.1. AlcoholAlcohol

2.2. CarboxylCarboxyl

3.3. AminesAmines

ALCOHOLALCOHOL

Functional group: Functional group: (R-OH)(R-OH)

Hydroxide: baseHydroxide: base R-OH: makes R-OH: makes

alcohols more alcohols more soluble in water soluble in water than similar than similar moleculesmolecules

Methanol: wood Methanol: wood alcohol (antiseptic)alcohol (antiseptic)

Ethanol: beverageEthanol: beverage

Methanol

Ethanol

CARBOXYLCARBOXYL

R-COOH (acid)R-COOH (acid) Releases hydrogen Releases hydrogen

ions in waterions in water ““Organic acids”Organic acids”

AMINESAMINES

R-NHR-NH22

Organic bases Organic bases because they because they accept hydrogen accept hydrogen ions from acidsions from acids

CARBOHYDRATESCARBOHYDRATES

Provide energy for cells when broken Provide energy for cells when broken downdown

Organic compounds made of Carbon, Organic compounds made of Carbon, Hydrogen, & OxygenHydrogen, & Oxygen

Most have 2 atoms of hydrogen for Most have 2 atoms of hydrogen for every oxygenevery oxygen

Classified by # sugar unitsClassified by # sugar units Example: pastaExample: pasta

MONOSACCHARIDESMONOSACCHARIDES

Carbohydrate made of one sugar unitCarbohydrate made of one sugar unit Most common simple sugar: glucoseMost common simple sugar: glucose Primary cellular fuel of most Primary cellular fuel of most

organismsorganisms The building blocks of larger CHOThe building blocks of larger CHO Combined through biosynthesisCombined through biosynthesis

GLUCOSEGLUCOSE

GALACTOSEGALACTOSE

FRUCTOSE (fruit sugar)FRUCTOSE (fruit sugar)

2 Monosaccharides=1 2 Monosaccharides=1 DisaccharideDisaccharide

Sucrose (table sugar): glucose + fructose

Malt Sugar=Glucose + Glucose

Milk Sugar=Glucose + Galactose

POLYSACCHARIDEPOLYSACCHARIDE

>2 monosaccharides>2 monosaccharides Broken down through hydrolysisBroken down through hydrolysis Cellulose Cellulose StarchStarch GlycogenGlycogen

CELLULOSECELLULOSE Major part of leafy vegetables, whole wheat, carrots, & Major part of leafy vegetables, whole wheat, carrots, &

other plant material in your dietother plant material in your diet Often called ‘fiber’ or ‘roughage’Often called ‘fiber’ or ‘roughage’ Body cannot break it down into any glucose moleculesBody cannot break it down into any glucose molecules No energy received from fiberNo energy received from fiber More fiber seems to decrease the risk of cancer in the More fiber seems to decrease the risk of cancer in the

digestive tractdigestive tract Only digested by microorganisms & a few wood-eating Only digested by microorganisms & a few wood-eating

beetlesbeetles Animals that eat grass & leaves depend on these Animals that eat grass & leaves depend on these

microorganisms in their digestive tracts to digest cellulose microorganisms in their digestive tracts to digest cellulose for themfor them

Important to dietImportant to diet

STARCHSTARCH

100’s-1000’s of glucose molecules100’s-1000’s of glucose molecules Examples: potatoes, pastaExamples: potatoes, pasta

GLYCOGENGLYCOGEN

Like starch but for animalsLike starch but for animals Animals store energy as glycogenAnimals store energy as glycogen Stored in liver & musclesStored in liver & muscles

LIPIDSLIPIDS

Non-polar organic moleculesNon-polar organic molecules Do not dissolve in waterDo not dissolve in water Examples: vegetable oil, butter, Examples: vegetable oil, butter,

furniture waxfurniture wax Functions:Functions:

• Barrier b/t cell & environmentBarrier b/t cell & environment Ex: lipid bilayer, blubber in whalesEx: lipid bilayer, blubber in whales

• Store energyStore energy Fatty acids: building blocks of lipidsFatty acids: building blocks of lipids

SATURATED FATSATURATED FAT

Maximum # hydrogen atoms Maximum # hydrogen atoms attached to it (SOLID)attached to it (SOLID)

Non-polarNon-polar Insoluble in waterInsoluble in water No C=C bondsNo C=C bonds

UNSATURATED FATUNSATURATED FAT

Molecules with double bondsMolecules with double bonds C=CC=C LIQUIDLIQUID

POLYUNSATURATED: >2 C=CPOLYUNSATURATED: >2 C=C

TRIGLYCERIDESTRIGLYCERIDES

Majority of fat in an organismMajority of fat in an organism Composed of 3 fatty acids & a 3-C alcohol Composed of 3 fatty acids & a 3-C alcohol

(glycerol)(glycerol) Examples:Examples:

• Butter & LardButter & Lard Made from saturated fatty acidsMade from saturated fatty acids Solid at room temp (fat) Solid at room temp (fat)

• Corn oil & peanut oilCorn oil & peanut oil Made from unsaturated fatty acidsMade from unsaturated fatty acids Liquid at room temp (oil)Liquid at room temp (oil) More common in plants than animalsMore common in plants than animals

FACTSFACTS

Body can store 3-month supply of Body can store 3-month supply of triglycerides & less than a day’s triglycerides & less than a day’s supply of CHOsupply of CHO

Saturated fat=linked to heart diseaseSaturated fat=linked to heart disease

AMINO ACIDSAMINO ACIDS

ALL organisms are composed of ALL organisms are composed of combinations of the same 20 amino acidscombinations of the same 20 amino acids

Amino acid are joined by peptide bondsAmino acid are joined by peptide bonds Building blocks of proteinsBuilding blocks of proteins 4 parts4 parts

• HydrogenHydrogen• Amino groupAmino group• CarboxylCarboxyl• R-group (hydrocarbon that determines identity R-group (hydrocarbon that determines identity

of amino acid)of amino acid)

20 AMINO ACIDS20 AMINO ACIDS

AlanineAlanine LysineLysine AsparagineAsparagine ProlineProline ThreonineThreonine GlycineGlycine ValineValine IsoleucineIsoleucine ArginineArginine PhenylalaninePhenylalanine

SerineSerine Glutamic acidGlutamic acid TyrosineTyrosine HistidineHistidine LeucineLeucine MethionineMethionine Aspartic acidAspartic acid CysteineCysteine TryptophanTryptophan GlutamineGlutamine

STRUCTURE OF AN AMINO ACID

PROTEINSPROTEINS

Amino acids are the building blocks of Amino acids are the building blocks of proteinsproteins

Variety of structure & functionVariety of structure & function MAIN FUNCTION: source of raw materialsMAIN FUNCTION: source of raw materials

• Supplying cells with materials to make new Supplying cells with materials to make new body partsbody parts

Animals are primary sources in dietAnimals are primary sources in diet• Meat, fish, dairyMeat, fish, dairy

Plant: soybeans, beans, legumesPlant: soybeans, beans, legumes Examples: hair, feathers, spider websExamples: hair, feathers, spider webs

MAKING LARGE MOLECULES MAKING LARGE MOLECULES FROM SMALLER ONESFROM SMALLER ONES

Monomer: fundamental molecular Monomer: fundamental molecular unitunit

Polymers & macromolecules result Polymers & macromolecules result when the same type of units are when the same type of units are linkedlinked

TYPES OF REACTIONSTYPES OF REACTIONS

DehydrationDehydration• Most common way to synthesize organic Most common way to synthesize organic

polymerspolymers• Loss of water=reaction between Loss of water=reaction between

monomers=formation of polymersmonomers=formation of polymers HydrolysisHydrolysis

• Breaking apart with waterBreaking apart with water• Most common way polymers are Most common way polymers are

degradeddegraded

ANABOLIC STEROIDSANABOLIC STEROIDS

Synthetic & natural variations of Synthetic & natural variations of testoteronetestoterone• Testoterone: increases bone mass & muscle Testoterone: increases bone mass & muscle

during puberty (in males)during puberty (in males) Used to treat anemia & diseases that Used to treat anemia & diseases that

destroy muscle tissuedestroy muscle tissue If abused, these drugs can cause If abused, these drugs can cause

depression & mood swingsdepression & mood swings Can cause liver damage, high blood Can cause liver damage, high blood

pressure & high cholesterol levelspressure & high cholesterol levels

ANABOLIC STEROIDS (cont.)ANABOLIC STEROIDS (cont.)

Use of steroids can cause the body to Use of steroids can cause the body to decrease its production of decrease its production of testoterone, causing:testoterone, causing:• Shrunken testicles, infertility, reduced Shrunken testicles, infertility, reduced

sex drive, & breast enlargement in sex drive, & breast enlargement in malesmales

• Use by women: menstrual cycle Use by women: menstrual cycle disruption, development of masculine disruption, development of masculine characteristicscharacteristics

• Use by teens: bones may stop growingUse by teens: bones may stop growing

THG (Tetrahydrogestrinone)THG (Tetrahydrogestrinone)

Modified to avoid detection in Modified to avoid detection in ordinary drug testingordinary drug testing

Declared illegal by FDA, first penalty Declared illegal by FDA, first penalty given in 2004 to British sprintergiven in 2004 to British sprinter

Blood doping???Blood doping???

PROTEIN SHAPEPROTEIN SHAPE

Determines functionDetermines function Denaturation (caused by change in Denaturation (caused by change in

salinity/temp/ionic charge) can cause salinity/temp/ionic charge) can cause loss of functionalityloss of functionality

PROTEIN STRUCTUREPROTEIN STRUCTURE

Primary: determined by genetic Primary: determined by genetic inheritanceinheritance• Amino acid sequenceAmino acid sequence• Single amino acid change: sickle cell Single amino acid change: sickle cell

anemiaanemia Secondary: alpha helix or beta-Secondary: alpha helix or beta-

pleated sheetpleated sheet• Pleated sheet: hydrogen bonds work Pleated sheet: hydrogen bonds work

together to make protein strong (spider together to make protein strong (spider web)web)

PROTEIN STRUCTUREPROTEIN STRUCTURE

Tertiary:globular or fibrousTertiary:globular or fibrous• Interacting R-groupsInteracting R-groups• Hydrophobic groups: clump/clusterHydrophobic groups: clump/cluster

Quaternary: 2 or more polypeptide Quaternary: 2 or more polypeptide chains (subunits)chains (subunits)• Subunit interactions associated with Subunit interactions associated with

quaternary structurequaternary structure

TRANSTHYRETINTRANSTHYRETIN

Transports vitamin A & thyroid Transports vitamin A & thyroid hormone in bloodhormone in blood

127 amino acids (primary)127 amino acids (primary) One alpha helix, many pleated One alpha helix, many pleated

sheets (secondary)sheets (secondary) Globular (tertiary)Globular (tertiary) 4 identical globular subunits 4 identical globular subunits

(quaternary)(quaternary)

LINUS PAULINGLINUS PAULING Begin work in chemistry (with chemical Begin work in chemistry (with chemical

bonding) won Nobel Prizebonding) won Nobel Prize Known for his strong opinion against nuclear Known for his strong opinion against nuclear

weapons testing..won Nobel Peace Prizeweapons testing..won Nobel Peace Prize Studied Vitamin C and its benefits (but Studied Vitamin C and its benefits (but

believed it could cure the cold and cancerbelieved it could cure the cold and cancer Hemoglobin’s relationship to sickle cell Hemoglobin’s relationship to sickle cell

anemiaanemia Believed in beginning small & increasing Believed in beginning small & increasing

studies studies Died in 1994Died in 1994