Chapter 2Chapter 2Chemical PrinciplesChemical Principles

I. Elements: I. Elements: Substances that can not be broken down into Substances that can not be broken down into

simpler substances by chemical reactions.simpler substances by chemical reactions. There are 92 naturally occurring elements: There are 92 naturally occurring elements:

Oxygen, carbon, nitrogen, calcium, sodium, etc.Oxygen, carbon, nitrogen, calcium, sodium, etc. Life requires about 25 of the 92 elementsLife requires about 25 of the 92 elements Chemical Symbols: Chemical Symbols:

Abbreviations for the name of each element.Abbreviations for the name of each element. Usually one or two letters of the English or Usually one or two letters of the English or

Latin name of the elementLatin name of the element First letter upper case, second letter lower case. First letter upper case, second letter lower case.

Example: Helium (He), sodium (Na), potassium Example: Helium (He), sodium (Na), potassium (K), gold (Au).(K), gold (Au).

Main ElementsMain Elements: Over: Over 98% 98% of an organism’s of an organism’s mass is made up ofmass is made up of six elements. six elements. OxygenOxygen (O): 65% body mass (O): 65% body mass

Cellular respiration, component of water, and most Cellular respiration, component of water, and most organic compounds.organic compounds.

CarbonCarbon (C): 18% of body mass. (C): 18% of body mass. Backbone of all organic compounds.Backbone of all organic compounds.

HydrogenHydrogen (H): 10% of body mass. (H): 10% of body mass. Component of water and most organic copounds.Component of water and most organic copounds.

NitrogenNitrogen (N): 3% of body mass. (N): 3% of body mass. Component of proteins and nucleic acids (DNA/RNA)Component of proteins and nucleic acids (DNA/RNA)

CalciumCalcium (Ca): 1.5% of body mass. (Ca): 1.5% of body mass. Bones, teeth, clotting, muscle and nerve function.Bones, teeth, clotting, muscle and nerve function.

PhosphorusPhosphorus ( (PP): 1% of body mass): 1% of body mass Bones, nucleic acids, energy transfer (ATP).Bones, nucleic acids, energy transfer (ATP).

Minor Elements: Minor Elements: Found in low amounts. Found in low amounts. Between 1% and 0.01%. Between 1% and 0.01%. PotassiumPotassium (K): Main positive ion inside cells. (K): Main positive ion inside cells.

Nerve and muscle function.Nerve and muscle function.

SulfurSulfur (S): Component of most proteins. (S): Component of most proteins. SodiumSodium (Na): Main positive ion outside cells. (Na): Main positive ion outside cells.

Fluid balance, nerve function.Fluid balance, nerve function.

ChlorineChlorine (Cl): Main negative ion outside cells. (Cl): Main negative ion outside cells. Fluid balance.Fluid balance.

MagnesiumMagnesium (Mg): Component of many (Mg): Component of many enzymes and chlorophyll.enzymes and chlorophyll.

Trace elements: Trace elements: Less than 0.01% of mass:Less than 0.01% of mass: BoronBoron ((BB)) ChromiumChromium ((CrCr)) CobaltCobalt ((CoCo)) CopperCopper ((CuCu)) IronIron ((FeFe)) FluorineFluorine ( (FF)) IodineIodine ( (II)) ManganeseManganese ( (MnMn)) MolybdenumMolybdenum ( (MoMo)) SeleniumSelenium ( (SeSe)) SiliconSilicon ( (SiSi)) TinTin ( (SnSn)) VanadiumVanadium ( (VV)) ZincZinc ( (ZnZn) )

II. Structure & Properties of AtomsII. Structure & Properties of AtomsAtoms: Atoms: Smallest particle of an element that Smallest particle of an element that retains its chemical properties. Made up of retains its chemical properties. Made up of three main subatomic particles.three main subatomic particles.

ParticleParticle LocationLocation MassMass ChargeChargeProtonProton (p (p++) In nucleus ) In nucleus 1 +1 1 +1

NeutronNeutron (n (noo) In nucleus ) In nucleus 1 0 1 0

ElectronElectron (e (e--) Outside nucleus ) Outside nucleus 0 0** -1 -1

** Mass is negligible for our purposes. Mass is negligible for our purposes.

Atomic Particles: Protons, Neutrons, and Electrons

Helium Atom Carbon Atom

Structure and Properties of AtomsStructure and Properties of Atoms1. Atomic number1. Atomic number = # protons = # protons The number of protons is The number of protons is uniqueunique for each for each elementelement Each element has a fixed number of protons in its Each element has a fixed number of protons in its

nucleus. This number will nucleus. This number will nevernever change for a change for a given element.given element.

Written as a Written as a subscriptsubscript to left of element symbol. to left of element symbol.

Examples: Examples: 66C, C, 88O, O, 1616S, S, 2020CaCa

Because atoms are electrically neutral (no Because atoms are electrically neutral (no charge), the charge), the numbernumber of of electronselectrons andand protonsprotons are are always the same.always the same.

In the periodic table elements are organized by In the periodic table elements are organized by increasingincreasing atomic number. atomic number.

Structure and Structure and Properties of Atoms:Properties of Atoms:2. Mass number2. Mass number = # protons + # neutrons = # protons + # neutrons Gives the mass of a specific atom.Gives the mass of a specific atom. Written as a Written as a superscriptsuperscript to the left of the element to the left of the element

symbol.symbol.

Examples: Examples: 1212C, C, 1616O, O, 3232S, S, 4040Ca. Ca. The number of protons for an element is always The number of protons for an element is always

the same, but the number of neutrons may vary.the same, but the number of neutrons may vary. The number of neutrons can be determined by: The number of neutrons can be determined by:

# neutrons = Mass number - Atomic number# neutrons = Mass number - Atomic number

Structure and Structure and Properties of Atoms:Properties of Atoms:

3. Isotopes3. Isotopes:: Variant forms of the same element. Variant forms of the same element. Isotopes have Isotopes have differentdifferent numbers of numbers of neutronsneutrons and and

therefore different therefore different massesmasses.. Isotopes have the Isotopes have the samesame numbers of numbers of protonsprotons and and

electronselectrons.. Example: In nature there are three forms or Example: In nature there are three forms or

isotopes of carbon (isotopes of carbon (66C):C): 1212C: About 99% of atoms. Have 6 pC: About 99% of atoms. Have 6 p++, , 6 n6 noo, and 6 e, and 6 e--.. 1313C: About 1% of atoms. Have 6 pC: About 1% of atoms. Have 6 p++, , 7 n7 noo, and 6 e, and 6 e--. . 1414C: Found in tiny quantities. Have 6 pC: Found in tiny quantities. Have 6 p++, , 8 n8 noo, and 6 e, and 6 e--. .

Radioactive form (unstable). Used for Radioactive form (unstable). Used for datingdating fossils. fossils.

Electrons determine how an atom can bond Electrons determine how an atom can bond with other atomswith other atoms

A. A. Energy levels Energy levels: Electrons occupy different : Electrons occupy different energy levels around the nucleus. energy levels around the nucleus.

Level (Shell)Level (Shell) Electron CapacityElectron Capacity

11 2 (2 (Closest to nucleus, lowest energy)Closest to nucleus, lowest energy)

22 88

33 8 8 (If valence shell, 18 otherwise)(If valence shell, 18 otherwise)

4, 5, & 64, 5, & 6 18 18

B. B. Electron configuration:Electron configuration: Arrangement of Arrangement of

electrons in orbitals around nucleus of atom.electrons in orbitals around nucleus of atom.

C. C. Valence ElectronsValence Electrons: Number of electrons in : Number of electrons in

outerouter energy shell of an atom. energy shell of an atom.

III. How Atoms Form Molecules: III. How Atoms Form Molecules: Chemical BondsChemical Bonds

MoleculeMolecule: : Two or more atoms combined chemically.Two or more atoms combined chemically.CompoundCompound: A substance with two or more elements : A substance with two or more elements

combined in a fixed ratio.combined in a fixed ratio. Water (HWater (H22O)O) Hydrogen peroxide (HHydrogen peroxide (H22OO22)) Carbon dioxide (COCarbon dioxide (CO22)) Carbon monoxide (CO)Carbon monoxide (CO) Table salt (NaCl)Table salt (NaCl)

Atoms are linked by Atoms are linked by chemical bonds.chemical bonds.Chemical FormulaChemical Formula:: Describes the chemical Describes the chemical

composition of a molecule of a compound. composition of a molecule of a compound. Symbols indicate the type of atomsSymbols indicate the type of atoms Subscripts indicate the number of atomsSubscripts indicate the number of atoms

How Atoms Form Molecules: How Atoms Form Molecules: Chemical BondsChemical Bonds

““Octet Rule”Octet Rule”: When the outer shell of an atom : When the outer shell of an atom is not full, i.e.: contains fewer than 8 (or 2) is not full, i.e.: contains fewer than 8 (or 2) electrons (electrons (valence e-valence e-),), the atom tends to gain, the atom tends to gain, lose, or share electrons to achieve a complete lose, or share electrons to achieve a complete outer shell (8, 2, or 0) electrons.outer shell (8, 2, or 0) electrons.

ExampleExample: : Sodium has 11 electrons, 1 valence electron.Sodium has 11 electrons, 1 valence electron.Sodium Sodium losesloses its electron, becoming an ion: its electron, becoming an ion:NaNa ------->-------> NaNa++ + + 1 e1 e--

1(2), 2(8), 1(2), 2(8), 3(1)3(1) 1(2), 2(8)1(2), 2(8)Outer shell has 1 eOuter shell has 1 e-- Outer shell is fullOuter shell is fullSodium atomSodium atom Sodium ionSodium ion

Number of valence electrons determine the Number of valence electrons determine the chemical behavior of atoms.chemical behavior of atoms.

ElementElement ValenceValence CombiningCombiningTendencyTendency

ElectronsElectrons CapacityCapacity

SodiumSodium 11 11 LoseLose 1 1

CalciumCalcium 22 22 LoseLose 2 2

AluminumAluminum 33 33 LoseLose 3 3

CarbonCarbon 44 44 ShareShare 4 4

NitrogenNitrogen 55 33 GainGain 3 3

OxygenOxygen 66 22 GainGain 2 2

ChlorineChlorine 77 11 GainGain 1 1

NeonNeon** 88 00 StableStable

* Noble gas* Noble gas

Electron Arrangements of Important Elements of Life

1 Valence electron 4 Valence electrons 5 Valence electrons 6 Valence electrons

How Atoms Form Molecules: How Atoms Form Molecules: Chemical BondsChemical Bonds

Atoms can lose, gain, or share electrons to satisfy Atoms can lose, gain, or share electrons to satisfy

octet rule octet rule (fill outermost shell).(fill outermost shell).

Two main types of Chemical BondsTwo main types of Chemical Bonds

A. A. Ionic bondIonic bond: Atoms : Atoms gaingain or or loselose electrons electrons

B. B. Covalent bondCovalent bond: Atoms : Atoms shareshare electrons electrons

A. A. Ionic Bond:Ionic Bond: Atoms gain or lose electrons. Atoms gain or lose electrons. Bonds are attractions between Bonds are attractions between ionsions of opposite of opposite charge.charge.

Ionic compoundIonic compound: One consisting of ionic bonds.: One consisting of ionic bonds.

Na + Cl ----------> Na + Cl ----------> NaNa++ Cl Cl--

sodium chlorine Table saltsodium chlorine Table salt

(Sodium (Sodium chloride)chloride)

Two Types of Ions:Two Types of Ions:

Anions:Anions: Negatively charged particle ( Negatively charged particle (ClCl--))

Cations:Cations: Positively charged particle ( Positively charged particle (NaNa++))

B. B. Covalent BondCovalent Bond - Involve the “sharing” of one - Involve the “sharing” of one or more pairs of electrons between atoms.or more pairs of electrons between atoms.

Covalent compoundCovalent compound: One consisting of : One consisting of covalent bonds.covalent bonds.

ExampleExample: Methane (CH: Methane (CH44): Main component ): Main component

of natural gas.of natural gas.

HH ||

H---C---HH---C---H ||HH

Each line represents on shared pair of electrons.Each line represents on shared pair of electrons.Octet rule is satisfiedOctet rule is satisfied: Carbon has 8 electrons,: Carbon has 8 electrons,Hydrogen has 2 electronsHydrogen has 2 electrons

There may be more than one covalent bond between There may be more than one covalent bond between atoms:atoms:

1. 1. Single bond:Single bond: One electron pair is shared between One electron pair is shared between two atoms.two atoms.Example: Chlorine (ClExample: Chlorine (Cl22), water (H), water (H22O); methane O); methane (CH(CH44))

Cl Cl Cl Cl

2. 2. Double bond:Double bond: Two electron pairs share between Two electron pairs share between atoms.atoms.Example: Oxygen gas (OExample: Oxygen gas (O22); carbon dioxide (CO); carbon dioxide (CO22))

O=OO=O3. 3. Triple bondTriple bond:: Three electron pairs shared between Three electron pairs shared between

two atoms.two atoms.Example: Nitrogen gas (NExample: Nitrogen gas (N22))

N = NN = N

Number of covalent bondsNumber of covalent bonds: :

Carbon (4) Carbon (4)

Nitrogen (3)Nitrogen (3)

Oxygen (2)Oxygen (2)

Sulfur (2)Sulfur (2)

Hydrogen (1)Hydrogen (1)

Two Types of Covalent Bonds: Polar and Two Types of Covalent Bonds: Polar and NonpolarNonpolar

A. A. ElectronegativityElectronegativity: : A measure of an A measure of an atom’s ability to attract and hold onto a atom’s ability to attract and hold onto a shared pair of electrons.shared pair of electrons.Some atoms such as Some atoms such as oxygenoxygen or or nitrogennitrogen have a much higher electronegativity have a much higher electronegativity than others, such as carbon and than others, such as carbon and hydrogen.hydrogen.

ElementElement ElectronegativityElectronegativityOO 3.53.5NN 3.03.0

S & CS & C 2.52.5P & HP & H 2.12.1

Polar and Nonpolar Covalent BondsPolar and Nonpolar Covalent Bonds

B.B. Nonpolar Covalent Bond:Nonpolar Covalent Bond: When the atoms in When the atoms in a bond have equal or similar attraction for the a bond have equal or similar attraction for the electrons (electronegativity), they are shared electrons (electronegativity), they are shared equallyequally. .

Example: OExample: O22, H, H22, N, N22, Cl, Cl22

C. C. Polar Covalent BondPolar Covalent Bond: When the atoms in a : When the atoms in a bond have different electronegativities, the bond have different electronegativities, the electrons are shared electrons are shared unequallyunequally. Electrons are . Electrons are closer to the more electronegative atom closer to the more electronegative atom creating a polarity or partial charge.creating a polarity or partial charge.

Example: HExample: H22OO

Oxygen has a partial negative charge.Oxygen has a partial negative charge.

Hydrogens have partial positive charges.Hydrogens have partial positive charges.

Other Bonds: Weak chemical bonds are Other Bonds: Weak chemical bonds are important in the chemistry of living things.important in the chemistry of living things.

Hydrogen bondsHydrogen bonds: : Attraction between theAttraction between the partially positive H of one molecule partially positive H of one molecule and aand a partially negative atom of anotherpartially negative atom of another

Hydrogen bonds are about 20 X easier to Hydrogen bonds are about 20 X easier to break than a normal covalent bond.break than a normal covalent bond.

Responsible for many properties of water.Responsible for many properties of water. Determine 3 dimensional shape of DNA and Determine 3 dimensional shape of DNA and

proteins.proteins. Chemical signaling (molecule to receptor).Chemical signaling (molecule to receptor).

Water - A Unique Compound for Water - A Unique Compound for LifeLife

Water: The Ideal Compound for LifeWater: The Ideal Compound for Life

Living cells are 70-90% waterLiving cells are 70-90% water

Water covers 3/4 of earth’s surfaceWater covers 3/4 of earth’s surface

Water is the ideal solvent for chemical Water is the ideal solvent for chemical

reactionsreactions

On earth, water exists as gas, liquid, and On earth, water exists as gas, liquid, and

solidsolid

I. Polarity of water causes hydrogen bondingI. Polarity of water causes hydrogen bonding

Water molecules are held together by H-bondingWater molecules are held together by H-bonding

Partially positive H attracted to partially Partially positive H attracted to partially

negative O atom.negative O atom.

Individual H bond are weak, but the cumulative Individual H bond are weak, but the cumulative

effect of many H bonds is very strong.effect of many H bonds is very strong.

Unique properties of water caused by H-bondsUnique properties of water caused by H-bonds

Cohesion:Cohesion: Water molecules stick to each other.Water molecules stick to each other.

Adhesion:Adhesion: Water molecules stick to many Water molecules stick to many

surfaces.surfaces.

StableStable TemperatureTemperature:: Water resists changes in Water resists changes in

temperature.temperature.

High heat of vaporizationHigh heat of vaporization: Water must absorb : Water must absorb

large amounts of energy (heat) to evaporate.large amounts of energy (heat) to evaporate.

ExpandsExpands when it freezes (water when it freezes (water denserdenser than than ice) ice)

SolventSolvent: Dissolves many substances.: Dissolves many substances.

II. Biological Consequences of Water’s PolarityII. Biological Consequences of Water’s PolarityA. Capillary Action:A. Capillary Action: Water tends to rise in narrow Water tends to rise in narrow

tubes. This is caused by two factors:tubes. This is caused by two factors: CohesionCohesion: : Molecules of water “stick together”Molecules of water “stick together” AdhesionAdhesion: : Water molecules stick to walls of tubes.Water molecules stick to walls of tubes.

ExamplesExamples: : Upward movement of water through plant Upward movement of water through plant

vessels and fluid in blood vessels.vessels and fluid in blood vessels.

B. Surface tensionB. Surface tension: : Difficulty in “stretching or Difficulty in “stretching or breaking”breaking”

At water/air interface, difficult to pull water apartAt water/air interface, difficult to pull water apart

Causes water to “bead” into tiny ballsCauses water to “bead” into tiny balls

Used by some insects who live on the surface of waterUsed by some insects who live on the surface of water

C. Temperature RegulationC. Temperature Regulation

Water has a very high Water has a very high specific heatspecific heat Specific HeatSpecific Heat: : Amount of heat energy needed to raise 1 Amount of heat energy needed to raise 1

g of substance 1 degree Celsius g of substance 1 degree Celsius

Specific Heat of Water:Specific Heat of Water: 1 calorie/gram/degree C 1 calorie/gram/degree C

Organisms can absorb a lot of heat without drastic Organisms can absorb a lot of heat without drastic

changes in temperature.changes in temperature.

D. Evaporative CoolingD. Evaporative Cooling VaporizationVaporization: : Transformation from liquid to gas.Transformation from liquid to gas.

Heat of VaporizationHeat of Vaporization: : Energy required to convert 1 Energy required to convert 1

gram of a liquid -> gas is high (540 calories/gram)gram of a liquid -> gas is high (540 calories/gram)

Sweating is a form of evaporative cooling.Sweating is a form of evaporative cooling.

Can regulate temperature w/o great water loss.Can regulate temperature w/o great water loss.

E. Ice floats on Water: Life can exist in bodies of E. Ice floats on Water: Life can exist in bodies of waterwater

Ice floats because liquid water is more dense than Ice floats because liquid water is more dense than ice (solid water).ice (solid water).

Water gets more dense as it cools to 4Water gets more dense as it cools to 4ooC.C.

Water gets less dense (Water gets less dense (expandsexpands) as it cools further to ) as it cools further to

form ice.form ice.

Crystalline lattice forms, molecules farther apartCrystalline lattice forms, molecules farther apart

Because ice floats, life can survive and thrive in Because ice floats, life can survive and thrive in bodies of water, even though the earth has gone bodies of water, even though the earth has gone through many winters and ice agesthrough many winters and ice ages

III. Water is the ideal solvent for chemical III. Water is the ideal solvent for chemical reactionsreactions SolutionSolution: : Homogeneous mixture of 2 or more Homogeneous mixture of 2 or more

substances.substances. Examples: Salt water, air, tap water.Examples: Salt water, air, tap water.

SolventSolvent: : Dissolving substance of a solution.Dissolving substance of a solution.

Example: Water, alcohol, oil.Example: Water, alcohol, oil.

SoluteSolute: : Substance dissolved in the solvent.Substance dissolved in the solvent. Example: NaCl, sugar, carbon dioxide.Example: NaCl, sugar, carbon dioxide.

Aqueous solutionAqueous solution: : Water is the solvent.Water is the solvent.

SolubilitySolubility: : Ability of substance to dissolve in a Ability of substance to dissolve in a

given solvent.given solvent.

Solubility of a Solute Depends on its Solubility of a Solute Depends on its Chemical NatureChemical Nature

Two Types of Solutes:Two Types of Solutes:

A. HydrophilicA. Hydrophilic:: “Water loving” dissolve easily “Water loving” dissolve easily in water.in water. Ionic compounds (e.g. salts)Ionic compounds (e.g. salts) Polar compounds (molecules with polar regions)Polar compounds (molecules with polar regions) Examples: Compounds with -OH groups Examples: Compounds with -OH groups

(alcohols).(alcohols). ““Like dissolves in like”Like dissolves in like”

B. HydrophobicB. Hydrophobic: : “Water fearing” do not “Water fearing” do not dissolve in waterdissolve in water Non-polar compounds (lack polar regions)Non-polar compounds (lack polar regions) ExamplesExamples: Hydrocarbons with only C-H non-polar : Hydrocarbons with only C-H non-polar

bonds, oils, gasoline, waxes, fats, etc.bonds, oils, gasoline, waxes, fats, etc.

ACIDS, BASES, pH AND BUFFERSACIDS, BASES, pH AND BUFFERSA. AcidA. Acid: : A substance that donates protons (HA substance that donates protons (H++). ). Separate into one or more protons and an Separate into one or more protons and an

anion:anion:

HCl (into HCl (into HH22OO ) -------> H ) -------> H++ + Cl + Cl--

HH22SOSO44 (into (into HH22OO ) --------> H ) --------> H++ + HSO + HSO44--

Acids Acids INCREASEINCREASE the relative [H the relative [H++] of a ] of a solution.solution.

Water can also dissociate into ions, at low Water can also dissociate into ions, at low levels:levels:

HH22O <======> HO <======> H++ + OH + OH--

B. BaseB. Base: : A substance that accepts protons (HA substance that accepts protons (H++). ). Many bases separate into one or more positive Many bases separate into one or more positive

ions (cations) and a hydroxyl group (ions (cations) and a hydroxyl group (OHOH-- ).). Bases Bases DECREASEDECREASE the relative [H the relative [H++] of a ] of a

solution solution ( and increases the relative [OH( and increases the relative [OH--] )] )

HH22O <======> HO <======> H++ + OH + OH--

DirectlyDirectly NHNH33 + H + H++ <=------> NH <=------> NH44++

IndirectlyIndirectly NaOH ---------> Na NaOH ---------> Na++ + OH + OH--

( H( H++ + + OHOH-- <=====> H <=====> H22O )O )

Strong acids and basesStrong acids and bases: : Dissociation is almost Dissociation is almost complete (99% or more of molecules).complete (99% or more of molecules).

HCl (aq) -------------> HHCl (aq) -------------> H++ + Cl + Cl- -

NaOH (aq) -----------> NaNaOH (aq) -----------> Na++ + OH + OH--

(L.T. 1% in this form)(L.T. 1% in this form) (G.T. 99% in dissociated form) (G.T. 99% in dissociated form)

A relatively small amount of a strong acid or base A relatively small amount of a strong acid or base will drastically affect the pH of solution.will drastically affect the pH of solution.

Weak acids and basesWeak acids and bases: : A small percentage of A small percentage of molecules dissociate at a give time (1% or less)molecules dissociate at a give time (1% or less)

HH22COCO33 <=====> H <=====> H++ + HCO + HCO33--

carbonic acid Bicarbonate ioncarbonic acid Bicarbonate ion(G.T. 99% in this form)(G.T. 99% in this form) (L.T. 1% in dissociated form) (L.T. 1% in dissociated form)

C. pH scale: C. pH scale: [H[H++] and [OH] and [OH--]] pH scale is used to measure how basic or acidic pH scale is used to measure how basic or acidic

a solution is.a solution is. Range of pH scaleRange of pH scale: 0 through 14.: 0 through 14.

Neutral solutionNeutral solution: pH is 7.: pH is 7. [H[H++ ] = [OH ] = [OH--]]

Acidic solutionAcidic solution: : pH is less than 7. pH is less than 7. [H[H++ ] > [OH ] > [OH--]]

Basic solutionBasic solution: : pH is greater than 7. pH is greater than 7. [H[H++ ] < [OH ] < [OH--]]

As [HAs [H++] increases pH decreases (inversely ] increases pH decreases (inversely

proportional).proportional).

Logarithmic scale:Logarithmic scale: Each unit on the pH scale Each unit on the pH scale

represents a ten-fold change in [H+].represents a ten-fold change in [H+].

pH of Common Solutions

D. Buffers keep pH of solutions relatively D. Buffers keep pH of solutions relatively constantconstant

BufferBuffer:: Substance which prevents sudden Substance which prevents sudden large changes in pH when acids or bases are large changes in pH when acids or bases are added.added.

Buffers are biologically important because Buffers are biologically important because most of the chemical reactions required for life most of the chemical reactions required for life can only take place within narrow pH ranges.can only take place within narrow pH ranges.

Example: Example: Normal blood pH 7.35-7.45. Serious health Normal blood pH 7.35-7.45. Serious health

problems will arise if blood pH is not stable.problems will arise if blood pH is not stable.

CHEMICAL REACTIONSCHEMICAL REACTIONS

A chemical change in which sA chemical change in which substances ubstances ((reactantsreactants) are joined, broken down, or ) are joined, broken down, or rearranged to form new substances (rearranged to form new substances (productsproducts).).

Involve the making and/or breaking of Involve the making and/or breaking of chemical bonds.chemical bonds.

Chemical equations are used to represent Chemical equations are used to represent chemical reactions.chemical reactions.

ExampleExample::

2H2H22 ++ OO22 -----------> 2H -----------> 2H22OO

2Hydrogen Oxygen 2Hydrogen Oxygen 2 Water2 WaterMoleculesMolecules Molecule Molecule MoleculesMolecules

Organic CompoundsOrganic Compounds

I. Organic Chemistry: Carbon Based CompoundsI. Organic Chemistry: Carbon Based Compounds

Organic CompoundsOrganic Compounds: : Compounds that contain Compounds that contain carbon and are synthesized by cells (except CO carbon and are synthesized by cells (except CO and COand CO22).). Diverse groupDiverse group:: Several million Several million organicorganic compounds compounds

are known. More are identified daily.are known. More are identified daily. Common:Common: After water,After water, organicorganic compounds are the compounds are the

most common substances in cells. most common substances in cells. Over 98% of theOver 98% of the dry weightdry weight of living cells is made up ofof living cells is made up of

organicorganic compounds.compounds. Less than 2% of theLess than 2% of the dry weightdry weight of living cells is made up of of living cells is made up of

inorganicinorganic compounds. compounds.

Inorganic CompoundsInorganic Compounds: : Compounds Compounds withoutwithout

carbon.carbon.

Organic Compounds are Carbon Based

Carbon Has 4 Valence Electrons and Can Form 4 Covalent Bonds

Organic compounds are incredibly diverseOrganic compounds are incredibly diverse

Organic molecules can vary dramatically in:Organic molecules can vary dramatically in: Length Length (1-100s of C atoms)(1-100s of C atoms) Shape Shape (Linear chain, branched, ring)(Linear chain, branched, ring) Type of bonds:Type of bonds:

SingleSingle DoubleDouble Triple bondsTriple bonds

Other elements that bond to C:Other elements that bond to C: Nitrogen (N)Nitrogen (N) Oxygen (O)Oxygen (O) Hydrogen (H)Hydrogen (H) Sulfur (S)Sulfur (S) Phosphorus (P)Phosphorus (P)

Carbon Skeletons of Organic CompoundsCarbon Skeletons of Organic Compounds

Diversity of Organic CompoundsDiversity of Organic Compounds Hydrocarbons:Hydrocarbons:

Organic molecules thatOrganic molecules that contain C and H onlycontain C and H only. . Good fuels, but not biologically important.Good fuels, but not biologically important. Undergo combustion (burn in presence of oxygen).Undergo combustion (burn in presence of oxygen). In general they are chemically stable.In general they are chemically stable. NonpolarNonpolar: Do not dissolve in water (Hydrophobic).: Do not dissolve in water (Hydrophobic).

ExamplesExamples:: (1C)(1C) MethMethane: ane: CHCH44 (2C)(2C) Eth Ethane: ane: CHCH33CHCH33 (3C)(3C) Prop Propane: ane: CHCH33CHCH22CHCH33 (4C)(4C) But Butane: ane: CHCH33CHCH22CHCH22CHCH33 (5C)(5C) Pent Pentane: ane: CHCH33CHCH22CHCH22CHCH22CHCH33 (6C)(6C) Hex Hexane: ane: CHCH33CHCH22CHCH22CHCH22CHCH22CHCH33 (7C)(7C) Hept Heptane: ane: CHCH33CHCH22CHCH22CHCH22CHCH22CHCH22CHCH33 (8C)(8C) Oct Octane: ane: CHCH33CHCH22CHCH22CHCH22CHCH22CHCH22CHCH22CHCH33

Hydrocarbons have C and H only

IsomersIsomers: Compounds with same chemical : Compounds with same chemical

formula but formula but different structuresdifferent structures

Structural IsomersStructural Isomers:: Differ inDiffer in atom atom arrangement:arrangement:

Example: Isomers of CExample: Isomers of C44HH1010

ButaneButane (C (C44HH1010)) IsobutaneIsobutane (C (C44HH1010))

CHCH33--CH--CH22--CH--CH22--CH--CH33 CHCH33--CH--CH--CH--CH33

| |

CHCH33

IsomersIsomers have different physical and chemical have different physical and chemical properties.properties.

IIII. . Functional groupsFunctional groups determine chemical & determine chemical & physical properties of organic moleculesphysical properties of organic molecules Compounds that are made up solely of carbon and Compounds that are made up solely of carbon and

hydrogen (hydrocarbons) are not very reactive.hydrogen (hydrocarbons) are not very reactive. In an organic compound, the groups of atoms that In an organic compound, the groups of atoms that

usually participate in chemical reactions are called usually participate in chemical reactions are called functional groupsfunctional groups.. Groups of atoms that have Groups of atoms that have unique chemical and unique chemical and

physical propertiesphysical properties.. Biologically important functional groupsBiologically important functional groups::

• Hydroxyl (-OH) Hydroxyl (-OH)

• Carbonyl (=C=O)Carbonyl (=C=O)

• Carboxyl (-COOH)Carboxyl (-COOH)

• Amino (-NHAmino (-NH22))

Notice that all are Notice that all are polarpolar..

A. A. Hydroxyl GroupHydroxyl Group (-OH) (-OH) Polar groupPolar group: Polar covalent bond between O and H.: Polar covalent bond between O and H.

Can form hydrogen bonds with other polar groups.Can form hydrogen bonds with other polar groups.

Generally makes molecule Generally makes molecule water soluble.water soluble.

Found in:Found in:

Alcohols:Alcohols: Organic molecules with a simple hydroxyl Organic molecules with a simple hydroxyl

group. Examples: group. Examples: Methanol (wood alcohol, toxic)Methanol (wood alcohol, toxic)

Ethanol (drinking alcohol)Ethanol (drinking alcohol)

Propanol (rubbing alcohol)Propanol (rubbing alcohol)

SugarsSugars

Water soluble vitaminsWater soluble vitamins

B. B. Carbonyl GroupCarbonyl Group (=CO) (=CO) Polar groupPolar group

O can be involved in H-bonding.O can be involved in H-bonding.

Generally makes molecule Generally makes molecule water soluble.water soluble.

Found in:Found in:

Aldehydes:Aldehydes: Carbonyl is located atCarbonyl is located at endend of molecule of molecule

KetoneKetone: : Carbonyl is locatedCarbonyl is located in in middlemiddle of molecule of molecule

Examples:Examples: Sugars (Aldehydes or ketones)Sugars (Aldehydes or ketones)

Formaldehyde (Aldehyde)Formaldehyde (Aldehyde)

Acetone (Ketone)Acetone (Ketone)

Sugars Have Both -OH and =CO Functional Groups

C. C. Carboxyl GroupCarboxyl Group (-COOH) (-COOH) Polar groupPolar group

Generally makes molecule Generally makes molecule water solublewater soluble

AcidicAcidic because it can because it can donate Hdonate H++ in solution in solution

Found in:Found in:

Carboxylic acidsCarboxylic acids: : Organic acids,Organic acids, can increase can increase

acidity of a solution. Examples: acidity of a solution. Examples: Acetic acid: Sour taste of vinegar.Acetic acid: Sour taste of vinegar.

Ascorbic acid (Vitamin C): Found in fruits and Ascorbic acid (Vitamin C): Found in fruits and

vegetables.vegetables.

Amino acids: Building blocks of proteins. Amino acids: Building blocks of proteins.

D. D. Amino GroupAmino Group (-NH(-NH22))

Polar groupPolar group

Generally makes molecule Generally makes molecule water solublewater soluble

Weak baseWeak base because N can accept a H because N can accept a H++

AmineAmine: : General term given to compound with General term given to compound with

(-NH(-NH22))

Found in:Found in:

Amino acidsAmino acids: Building blocks of proteins.: Building blocks of proteins.

UreaUrea in urine. From protein breakdown.in urine. From protein breakdown.

Amino acid Structure:Amino acid Structure:

Central carbon with:Central carbon with:• H atomH atom

• Carboxyl groupCarboxyl group

• Amino groupAmino group

• Variable R-groupVariable R-group

Amino Acid Structure:Amino Acid Structure:

HH

||(Amino Group)(Amino Group) NHNH22---C------C---COOH (Carboxyl group)COOH (Carboxyl group)

||

RR

(Varies for each amino acid)(Varies for each amino acid)

Amino Acids Have -NHAmino Acids Have -NH22 and -COOH Groups and -COOH Groups

The Macromolecules of Life:The Macromolecules of Life:Carbohydrates, Proteins, Lipids, and Carbohydrates, Proteins, Lipids, and

Nucleic AcidsNucleic Acids

3. Most Biological Macromolecules are 3. Most Biological Macromolecules are PolymersPolymers PolymerPolymer: : Large molecule consisting of many Large molecule consisting of many

identical or similar “subunits” linked through identical or similar “subunits” linked through covalent bonds.covalent bonds.

MonomerMonomer: : “Subunit” or building block of a “Subunit” or building block of a polymer.polymer.

MacromoleculeMacromolecule: : Large organic polymer. Most Large organic polymer. Most macromolecules are constructed from about 70 macromolecules are constructed from about 70 simple monomers.simple monomers.

Only about 70 monomersOnly about 70 monomers are used by are used by all living things all living things on earthon earth to construct a huge variety of molecules to construct a huge variety of molecules

Structural variation of macromoleculesStructural variation of macromolecules is the basis for is the basis for the enormous diversity of life on earth.the enormous diversity of life on earth.

Relatively few monomersRelatively few monomers are used by cells to are used by cells to

make a huge variety of macromoleculesmake a huge variety of macromolecules

MacromoleculeMacromolecule Monomers or Monomers or SubunitsSubunits

1. Carbohydrates1. Carbohydrates 20-3020-30 monosaccharides monosaccharidesor simple sugarsor simple sugars

2. Proteins2. Proteins 20 20 amino acids amino acids

3. Nucleic acids (DNA/RNA)3. Nucleic acids (DNA/RNA) 4 4 nucleotides nucleotides

(A,G,C,T/(A,G,C,T/UU))

4. Lipids (fats and oils)4. Lipids (fats and oils) ~ ~ 20 20 different fatty different fatty acidsacids

and glycerol.and glycerol.

Making PolymersMaking PolymersA. A. Condensation or Dehydration Synthesis reactions:Condensation or Dehydration Synthesis reactions: Process in which one monomer isProcess in which one monomer is covalentlycovalently linked to linked to

another monomer (or polymer). another monomer (or polymer). The equivalent of aThe equivalent of a waterwater molecule ismolecule is removed.removed. Anabolic ReactionsAnabolic Reactions: : Make large molecules from smaller Make large molecules from smaller

ones.ones. Require energy (endergonic)Require energy (endergonic)

General Reaction:General Reaction: EnzymeEnzyme

X -X - OH OH + + HHOO - Y- Y --------> --------> X - O - YX - O - Y + + HH22OO

Monomer 1 Monomer 2 Dimer WaterMonomer 1 Monomer 2 Dimer Water(Unlinked) (or Polymer) (Unlinked) (or Polymer) (or Polymer) (or Polymer)

Example:Example: EnzymeEnzyme

Glucose + Fructose ---------> Sucrose + Glucose + Fructose ---------> Sucrose + H H22OO (Monomer) (Monomer)(Monomer) (Monomer) (Dimer)(Dimer) WaterWater

Breaking PolymersBreaking PolymersB. B. Hydrolysis ReactionsHydrolysis Reactions: : “Break with water”.“Break with water”. Break down polymers into monomers.Break down polymers into monomers. Bonds between subunits are broken by Bonds between subunits are broken by adding wateradding water.. Catabolic ReactionsCatabolic Reactions: : Break large molecules into smaller Break large molecules into smaller

onesones. . Release energy (exergonic)Release energy (exergonic)

General Reaction:General Reaction:EnzymeEnzyme

X - O - YX - O - Y + + HH22O O ----------> ----------> X -X - OHOH + + HHO - YO - Y

PolymerPolymer WaterWater Monomer 1 Monomer 2Monomer 1 Monomer 2 (or Dimer)(or Dimer)

ExampleExample:: EnzymeEnzyme

SucroseSucrose + + H H22OO ---------> ---------> Glucose + FructoseGlucose + Fructose(Dimer)(Dimer) WaterWater (Monomer) (Monomer)(Monomer) (Monomer)

Synthesis and Hydrolysis of Sucrose

IV. Carbohydrates:IV. Carbohydrates: Molecules that store energy Molecules that store energy and are used as building materialsand are used as building materials

General Formula: General Formula: (CH(CH22O)nO)n

Simple sugars and their polymers.Simple sugars and their polymers. Diverse group includes sugars, starches, cellulose.Diverse group includes sugars, starches, cellulose. Biological FunctionsBiological Functions::

• Fuels, energy storage Fuels, energy storage

• Structural component (cell walls)Structural component (cell walls)

• DNA/RNA componentDNA/RNA component

Three types of carbohydrates:Three types of carbohydrates:A. A. MonosaccharidesMonosaccharidesB. B. Disaccharides Disaccharides C. C. PolysaccharidesPolysaccharides

A. A. MonosaccharidesMonosaccharides: : “Mono”“Mono” single & single & “sacchar”“sacchar” sugar sugar

Preferred source of chemical energy for cells (Preferred source of chemical energy for cells (glucoseglucose)) Can be synthesized by plants from light, HCan be synthesized by plants from light, H22O and COO and CO2.2.

Store energy in chemical bonds.Store energy in chemical bonds. Carbon skeletons used to synthesize other molecules.Carbon skeletons used to synthesize other molecules.

CharacteristicsCharacteristics::1. May have 3-8 carbons. -OH on each carbon; one with C=01. May have 3-8 carbons. -OH on each carbon; one with C=0

2. Names end in 2. Names end in -ose-ose. Based on number of carbons:. Based on number of carbons: 5 carbon sugar: 5 carbon sugar: pentosepentose 6 carbon sugar: 6 carbon sugar: hexose.hexose.

3. Can exist in 3. Can exist in linearlinear or or ringring forms forms

4. 4. Isomers:Isomers: Many molecules with the same molecular Many molecules with the same molecular formula, but different atomic arrangement.formula, but different atomic arrangement. ExampleExample: Glucose and fructose are both C: Glucose and fructose are both C66HH1212OO66..

Fructose is sweeter than glucose.Fructose is sweeter than glucose.

Monosaccharides Can Have 3 to 8 Carbons

Linear and Ring Forms of Glucose

B. B. DisaccharidesDisaccharides: : “Di”“Di” double & double & “sacchar”“sacchar” sugar sugar

Covalent bond formed by condensation reaction Covalent bond formed by condensation reaction between 2 monosaccharides.between 2 monosaccharides.

ExamplesExamples::

1. 1. MaltoseMaltose: Glucose + Glucose. : Glucose + Glucose.

• Energy storage in seeds. Energy storage in seeds.

• Used to make beer.Used to make beer.

2. 2. LactoseLactose: Glucose + Galactose. : Glucose + Galactose.

• Found in milk.Found in milk.

• Lactose intoleranceLactose intolerance is common among adults. is common among adults.• May cause gas, cramping, bloating, diarrhea, etc.May cause gas, cramping, bloating, diarrhea, etc.

3. 3. SucroseSucrose: Glucose + Fructose. : Glucose + Fructose.

• Most common disaccharide (table sugar). Most common disaccharide (table sugar).

• Found in plant sap.Found in plant sap.

Maltose and Sucrose are Disaccharides

C. C. PolysaccharidesPolysaccharides: : “Poly”“Poly” many (8 to 1000) many (8 to 1000)

FunctionsFunctions: Storage of chemical energy and structure.: Storage of chemical energy and structure.

Storage polysaccharidesStorage polysaccharides: : Cells can store simple sugars Cells can store simple sugars in polysacharides and hydrolyze them when needed.in polysacharides and hydrolyze them when needed.

1. 1. StarchStarch: Glucose polymer (Helical): Glucose polymer (Helical)

Form of glucose storage in Form of glucose storage in plantsplants (amylose) (amylose) Stored in plant cell organelles called Stored in plant cell organelles called plastidsplastids

2. 2. GlycogenGlycogen: Glucose polymer (Branched): Glucose polymer (Branched)

Form of glucose storage in Form of glucose storage in animalsanimals ( (muscle and liver muscle and liver

cells)cells)

Structural PolysaccharidesStructural Polysaccharides: : Used as structural Used as structural components of cells and tissues.components of cells and tissues.

1. 1. CelluloseCellulose: Glucose polymer.: Glucose polymer.

The major component of plant cell walls.The major component of plant cell walls. CANNOTCANNOT be digested by animal enzymes. be digested by animal enzymes. Only microbes have enzymes to hydrolyze cellulose, Only microbes have enzymes to hydrolyze cellulose,

found in digestive systems of:found in digestive systems of:• Cows, goats, and rabbitsCows, goats, and rabbits

• TermitesTermites

2. 2. ChitinChitin: Polymer of an amino sugar (with NH: Polymer of an amino sugar (with NH22 group) group)

Forms exoskeleton of arthropods (insects)Forms exoskeleton of arthropods (insects) Found in cell walls of some fungiFound in cell walls of some fungi

Three Different Polysaccharides of Glucose

V. V. ProteinsProteins: Large three-dimensional : Large three-dimensional macromolecules responsible for most macromolecules responsible for most cellular functionscellular functions

Polypeptide chainsPolypeptide chains: : Polymers of amino acids Polymers of amino acids

linked by linked by peptide bondspeptide bonds in a in a specificspecific linearlinear

sequence.sequence.

ProteinProtein: : Macromolecule composed of one or Macromolecule composed of one or

more polypeptide chains folded into a more polypeptide chains folded into a specificspecific

three-dimensionalthree-dimensional conformationconformation..

Proteins have important and varied functions:Proteins have important and varied functions:

1.1. EnzymesEnzymes: : Catalysis of cellular reactionsCatalysis of cellular reactions

2. 2. Structural ProteinsStructural Proteins: : Maintain cell shapeMaintain cell shape

3. 3. TransportTransport: : Transport in cells/bodies (e.g. hemoglobin). Transport in cells/bodies (e.g. hemoglobin).

Channels and carriers across cell membrane.Channels and carriers across cell membrane.

4. 4. CommunicationCommunication: : Chemical messengers, hormones, and Chemical messengers, hormones, and

receptors.receptors.

5. 5. DefensiveDefensive: : Antibodies and other molecules that bind to Antibodies and other molecules that bind to

foreign molecules and help destroy them.foreign molecules and help destroy them.

6. 6. ContractileContractile: : Muscular movement.Muscular movement.

7. 7. StorageStorage: : Store amino acids for later use (e.g. egg white).Store amino acids for later use (e.g. egg white).

Protein functionProtein function is is dependentdependent upon its upon its 3-D shape3-D shape..

PolypeptidePolypeptide: Polymer of amino acids : Polymer of amino acids connected in connected in a specific sequencea specific sequence

A. A. Amino acidAmino acid: : The monomer of polypeptidesThe monomer of polypeptides

Central carbon with:Central carbon with:• H atomH atom

• Carboxyl groupCarboxyl group

• Amino groupAmino group

• Variable R-groupVariable R-group

Amino Acid Structure:Amino Acid Structure:

HH

||

(Amino Group)(Amino Group) NHNH22---C------C---COOH (Carboxyl group)COOH (Carboxyl group) ||

RR

(Varies for each amino acid)(Varies for each amino acid)

A Protein’s Specific Shape (Conformation) A Protein’s Specific Shape (Conformation) Determines its Determines its FunctionFunction

ConformationConformation: : The 3-D structure of a protein. The 3-D structure of a protein.

Determined by the Determined by the amino acid sequence.amino acid sequence.

Four Levels of Protein StructureFour Levels of Protein Structure

1. 1. Primary structurePrimary structure: : Linear amino acid sequence, Linear amino acid sequence,

determined by determined by gene for that protein.gene for that protein.

2. 2. Secondary structureSecondary structure: : Regular coiling/folding of Regular coiling/folding of

polypeptide.polypeptide. Alpha helix or beta sheet. Alpha helix or beta sheet.

Caused by H-bonds between amino acids.Caused by H-bonds between amino acids.

3. 3. Tertiary structureTertiary structure: : Overall 3-dimensional shape Overall 3-dimensional shape

of a polypeptide chain.of a polypeptide chain.

4. 4. Quaternary structureQuaternary structure: : Only found in proteins Only found in proteins

with 2 or more polypeptides. with 2 or more polypeptides.

Overall 3-D shape of all polypeptide chains.Overall 3-D shape of all polypeptide chains.

Example: Hemoglobin (2 alpha and 2 beta Example: Hemoglobin (2 alpha and 2 beta

polypeptides)polypeptides)

What determines a protein’s What determines a protein’s ConformationConformation ? ?

A. A. Primary structurePrimary structure: : Exact location of each Exact location of each

amino acid along the chain determines amino acid along the chain determines

folding patternfolding pattern

ExampleExample: : Sickle Cell Hemoglobin proteinSickle Cell Hemoglobin protein Mutation changes amino acid #6 on the alpha Mutation changes amino acid #6 on the alpha

chain.chain.

Defective hemoglobin causes red blood cells to Defective hemoglobin causes red blood cells to

assume sickle shape, which damages tissue and assume sickle shape, which damages tissue and

capillaries.capillaries.

Sickle cell anemia gene is carried in 10% of Sickle cell anemia gene is carried in 10% of

African Americans.African Americans.

B. B. Chemical & Physical Environment:Chemical & Physical Environment:

Presence of other compounds, pH, Presence of other compounds, pH,

temperature, salts.temperature, salts. DenaturationDenaturation: : Process which alters native Process which alters native

conformation and therefore biological activity conformation and therefore biological activity

of a proteinof a protein

pH and saltspH and salts:: Disrupt hydrogen, ionic bonds.Disrupt hydrogen, ionic bonds.

TemperatureTemperature:: Can disrupt weak interactions.Can disrupt weak interactions.

Example:Example: Function of an enzyme depends on Function of an enzyme depends on

pH, temperature, and salt concentrationpH, temperature, and salt concentration..

VI. VI. Nucleic acidsNucleic acids store and transmit hereditary store and transmit hereditary information for all living thingsinformation for all living things

There are two types of nucleic acids in living things:There are two types of nucleic acids in living things:

A. A. Deoxyribonucleic Acid Deoxyribonucleic Acid (DNA)(DNA)

Has segments called Has segments called genesgenes which provide information to which provide information to make each and every protein in a cellmake each and every protein in a cell

Double-stranded molecule whichDouble-stranded molecule which replicates replicates each time a each time a cell divides.cell divides.

B. B. Ribonucleic Acid Ribonucleic Acid (RNA)(RNA)

Three main types called Three main types called mRNA, tRNA, rRNAmRNA, tRNA, rRNA RNA molecules are copied from DNA and used to make RNA molecules are copied from DNA and used to make

gene products (proteins).gene products (proteins). Usually exists in single-stranded form.Usually exists in single-stranded form.

DNA and RNADNA and RNA are polymers of are polymers of nucleotidesnucleotides Nucleic acidNucleic acid: : A polymer of nucleotidesA polymer of nucleotides NucleotideNucleotide:: Subunits of DNA or RNA. Subunits of DNA or RNA.

Nucleotides have three components: Nucleotides have three components:

1. Pentose sugar1. Pentose sugar ( (riboseribose or or deoxydeoxyriboseribose))

2. Phosphate group to link nucleotides (-PO2. Phosphate group to link nucleotides (-PO44))

3. Nitrogenous base3. Nitrogenous base (A,G,C,T or (A,G,C,T or UU)) Purines:Purines: Have 2 rings. Have 2 rings.

• Adenine (A)Adenine (A)• Guanine (G)Guanine (G)

PyrimidinesPyrimidines: Have one ring.: Have one ring.

• Cytosine (C)Cytosine (C)

• Thymine (T) in DNA or Thymine (T) in DNA or uracil (U) in RNA.uracil (U) in RNA.

James Watson and Francis CrickJames Watson and Francis Crick determined the 3- determined the 3-D shape of DNA in 1953D shape of DNA in 1953

Double helixDouble helix:: The DNA molecule is a double helix.The DNA molecule is a double helix. AntiparallelAntiparallel: The two DNA strands run in opposite : The two DNA strands run in opposite

directions.directions. Strand 1: 5’ to 3’ direction (------------>)Strand 1: 5’ to 3’ direction (------------>) Strand 2: 3’ to 5’ direction (<------------)Strand 2: 3’ to 5’ direction (<------------)

Complementary Base Pairing:Complementary Base Pairing: A & T (U) and G & C. A & T (U) and G & C. A on one strand hydrogen bonds to T (or U in RNA). A on one strand hydrogen bonds to T (or U in RNA). G on one strand hydrogen bonds to C.G on one strand hydrogen bonds to C.

ReplicationReplication: : The double-stranded DNA molecule can The double-stranded DNA molecule can easily replicate based on easily replicate based on A=T and G=C pairing.A=T and G=C pairing.

------

SEQUENCE of nucleotides in a DNA molecule dictate SEQUENCE of nucleotides in a DNA molecule dictate the amino acid SEQUENCE of polypeptidesthe amino acid SEQUENCE of polypeptides

DNA is a Double Helix Held Together by H-Bonds

A GeneA Gene is a specific segment of a DNA molecule with is a specific segment of a DNA molecule with information for cell to make one polypeptideinformation for cell to make one polypeptide

DNA DNA ((transcribedtranscribed into single stranded RNA “copy”)into single stranded RNA “copy”)

!!

! !

mRNAmRNA (single stranded “copy” of the gene)(single stranded “copy” of the gene)

!!

!!

PolypeptidePolypeptide (mRNA message (mRNA message translatedtranslated into polypeptide) into polypeptide)

VII. VII. LipidsLipids: Fats, phospholipids, and steroids: Fats, phospholipids, and steroids

Diverse groups of compounds.Diverse groups of compounds.

Composition of Lipids:Composition of Lipids: C, H, and small amounts of O.C, H, and small amounts of O.

Functions of Lipids:Functions of Lipids: Biological fuelsBiological fuels Energy storageEnergy storage InsulationInsulation Structural components of cell membranesStructural components of cell membranes HormonesHormones

LipidsLipids: Fats, phospholipids, and steroids: Fats, phospholipids, and steroids

1. Simple Lipids1. Simple Lipids: Contain C, H, and O only.: Contain C, H, and O only.

A. A. FatsFats (Triglycerides). (Triglycerides). GlycerolGlycerol : : Three carbon molecule with three hydroxylsThree carbon molecule with three hydroxyls.. Fatty AcidsFatty Acids: : Carboxyl group and long hydrocarbon Carboxyl group and long hydrocarbon

chains.chains. Characteristics of fats:Characteristics of fats:

Most abundant lipids in living organismsMost abundant lipids in living organisms.. HydrophobicHydrophobic (insoluble in water) because nonpolar (insoluble in water) because nonpolar.. Economical form of energy storage (provide 2X the Economical form of energy storage (provide 2X the

energy/weight than carbohydrates).energy/weight than carbohydrates). Greasy or oily appearance.Greasy or oily appearance.

LipidsLipids: Fats, phospholipids, and steroids: Fats, phospholipids, and steroids

Simple LipidsSimple Lipids: Continued: Continued

Types of FatsTypes of Fats Saturated fatsSaturated fats: : Hydrocarbons saturated Hydrocarbons saturated

with H. Lack -C=C- double bonds.with H. Lack -C=C- double bonds. Solid Solid at room temp (butter, animal fat, lard)at room temp (butter, animal fat, lard)

Unsaturated fatsUnsaturated fats: : Contain -C=C- double Contain -C=C- double bonds.bonds. Usually Usually liquidliquid at room temp (corn, peanut, at room temp (corn, peanut,

olive oils)olive oils)

Fats (Triglycerides): Glycerol + 3 Fatty Acids

2. Complex Lipids2. Complex Lipids: In addition to C, H, and O, : In addition to C, H, and O,

also contain other elements, such as phosphorus, also contain other elements, such as phosphorus,

nitrogen, and sulfur.nitrogen, and sulfur.

A.A. PhospholipidsPhospholipids: : Are composed of:Are composed of: GlycerolGlycerol 2 fatty acids, 2 fatty acids, Phosphate groupPhosphate group

AmphipathicAmphipathic Molecule Molecule HydrophobicHydrophobic fatty acid “tails”. fatty acid “tails”. HydrophilicHydrophilic phosphate “head”. phosphate “head”.

Function: Primary component of the plasma membrane of cells

B.B. SteroidsSteroids: : Lipids with four fused carbon ringsLipids with four fused carbon ringsIncludes cholesterol, bile salts, reproductive, and adrenal Includes cholesterol, bile salts, reproductive, and adrenal

hormones.hormones. CholesterolCholesterol: : The basic steroid found in animals The basic steroid found in animals

• Common component of animal cell membranes.Common component of animal cell membranes.

• Precursor to make Precursor to make sex hormones (estrogen, testosterone)sex hormones (estrogen, testosterone)

• Generally only Generally only soluble in other fatssoluble in other fats (not in water) (not in water)

• Too much increases chance of Too much increases chance of atherosclerosis.atherosclerosis.

C. C. WaxesWaxes: : One fatty acid linked to an alcohol.One fatty acid linked to an alcohol. Very hydrophobic. Very hydrophobic. Found in cell walls of certain bacteria, plant and insect Found in cell walls of certain bacteria, plant and insect

coats. Help prevent water loss.coats. Help prevent water loss.

Cholesterol: The Basic Steroid in Animals