1Organic ChOrganic Chemistryemistry

Ch. 3 - Organic MoleculesCh. 3 - Organic Molecules

InorganicInorganic – Chemistry of elements other than carbon – Chemistry of elements other than carbonOrganicOrganic – Carbon-based chemistry – Carbon-based chemistry

Usually associatedUsually associatedliving systemsliving systems

Often associated with Often associated with nonliving matternonliving matter

Often quite large, withOften quite large, withmany atomsmany atoms

Always withAlways withfew atomsfew atoms

AlwaysAlwayscovalent bondingcovalent bonding

UsuallyUsuallyionic bondingionic bonding

Always containAlways containcarbon and hydrogencarbon and hydrogen

Usually withUsually with+ & - ions+ & - ions

OrganicOrganicInorganicInorganic

p. 36 text

2Carbohydrates as structural materials

3Organic ChOrganic Chemistryemistry

Carbon AtomCarbon Atom

Carbon atoms:Carbon atoms:

Contain a total of 6 electronsContain a total of 6 electrons

Only four electrons in the outer shellOnly four electrons in the outer shell

Very diverse as one atom can bond with up to Very diverse as one atom can bond with up to four other atomsfour other atoms

Often bonds with other carbon atoms to make Often bonds with other carbon atoms to make hydrocarbonshydrocarbons

Can produce long carbon chains like octaneCan produce long carbon chains like octane

Can produce ring forms like cyclohexaneCan produce ring forms like cyclohexane

4Octane & Cyclohexane

5Organic ChOrganic Chemistryemistry

Functional Groups and IsomersFunctional Groups and Isomers

Functional groupsFunctional groups::

Specific combinations of bonded atomsSpecific combinations of bonded atoms

Attached as a group to other moleculesAttached as a group to other molecules

­ Always react in the same manner, regardless of Always react in the same manner, regardless of where attachedwhere attached

­ Determine activity and polarity of large organic Determine activity and polarity of large organic moleculesmolecules

Many functional groups, but only a few are of Many functional groups, but only a few are of major biological importancemajor biological importance

6Organic ChOrganic Chemistryemistry

Polar; some sugarsPolar; some sugarsExample: AcetoneExample: Acetone

Polar, forms H-bonds; some sugarsPolar, forms H-bonds; some sugarsand amino acids Example: Ethanoland amino acids Example: EthanolR OH

RHCO

R RCO

ROHCO

RHN H

R SH

Biologically ImportantBiologically ImportantFunctional Groups (Fig. 3.2)Functional Groups (Fig. 3.2)

ThiolsThiols

PhosphatePhosphate

AminesAminesAminoAmino

CarboxylicCarboxylicAcidsAcidsCarboxylCarboxyl

KetonesKetones

AldehydesAldehydesCarbonylCarbonyl

AlcoholsAlcoholsHydroxylHydroxylCompoundCompoundStructureStructureGroupGroup

SulfhydrylSulfhydryl

R OHPO

OH

OrganicOrganicPhosphatesPhosphates

SignificanceSignificance

Polar; some sugarsPolar; some sugarsExample: FormaldehydeExample: Formaldehyde

Polar, acidic; fats and amino acidsPolar, acidic; fats and amino acidsExample: Acetic acidExample: Acetic acid

Polar, basic; amino acidsPolar, basic; amino acidsExample: TryptophanExample: Tryptophan

Disulfide Bonds; some amino acidsDisulfide Bonds; some amino acidsExample: EthanethiolExample: Ethanethiol

Polar, acidic; some amino acidsPolar, acidic; some amino acidsExample: Adenosine triphosphateExample: Adenosine triphosphate

Polar, forms H-bonds; some sugarsPolar, forms H-bonds; some sugarsand amino acids; Example: Ethanoland amino acids; Example: Ethanol

Polar; some sugarsPolar; some sugarsExample: FormaldehydeExample: Formaldehyde

Polar; some sugarsPolar; some sugarsExample: AcetoneExample: Acetone

Polar, acidic; fats and amino acidsPolar, acidic; fats and amino acidsExample: Acetic acidExample: Acetic acidPolar, acidic; some amino acidsPolar, acidic; some amino acidsExample: Adenosine triphosphateExample: Adenosine triphosphate

Disulfide Bonds; some amino acidsDisulfide Bonds; some amino acidsExample: EthanethiolExample: Ethanethiol

Polar, basic; amino acidsPolar, basic; amino acidsExample: TryptophanExample: Tryptophan

7Organic ChOrganic Chemistryemistry

IsomersIsomers

IsomersIsomers - organic molecules that have: - organic molecules that have: Identical molecular formulas, butIdentical molecular formulas, butDiffering internal arrangement of atomsDiffering internal arrangement of atoms

8Organic ChOrganic Chemistryemistry

MacromoleculesMacromolecules

Some molecules called macromolecules because of Some molecules called macromolecules because of their large sizetheir large size

Usually consist of many repeating unitsUsually consist of many repeating units Resulting molecule is a Resulting molecule is a polymerpolymer (many parts) (many parts) Repeating units are called Repeating units are called monomersmonomers

Some examples:Some examples:

NucleotideNucleotideDNA, RNADNA, RNANucleic AcidsNucleic Acids

Amino acidAmino acidPolypeptidePolypeptideProteinsProteins

MonosaccharideMonosaccharidePolysaccharidePolysaccharideCarbohydratesCarbohydrates

Glycerol & fatty acidsGlycerol & fatty acidsFatFatLipidsLipids

Subunit(s)Subunit(s)ExampleExampleCategoryCategory

9Common Foods

10Organic ChOrganic Chemistryemistry

Dehydration and HydrolysisDehydration and Hydrolysis

Dehydration (condensation)Dehydration (condensation) - Removal of - Removal of water moleculewater moleculeConnects monomers together to make Connects monomers together to make polymerspolymers

Glucose monomers condense to make starchGlucose monomers condense to make starch

HydrolysisHydrolysis - Addition of water molecule - Addition of water moleculeDisassembles polymers into monomer partsDisassembles polymers into monomer partsDigestion of starch into glucose monomersDigestion of starch into glucose monomers

Specific enzymes required for each reactionSpecific enzymes required for each reactionAccelerate reactionAccelerate reactionAre not used in the reactionAre not used in the reaction

11Synthesis and Degradationof Polymers

12Organic ChOrganic ChemistryemistryFour Classes of Organics:Four Classes of Organics:

1 - Carbohydrates1 - Carbohydrates

MonosaccharidesMonosaccharides::Single sugar moleculeSingle sugar moleculeGlucose, ribose, deoxyriboseGlucose, ribose, deoxyribose

DisaccharidesDisaccharides::Contain two monosaccharides Contain two monosaccharides SucroseSucrose

PolysaccharidesPolysaccharides::

Polymers of monosaccharidesPolymers of monosaccharidesStarch, glycogen, cellulose, chitinStarch, glycogen, cellulose, chitin

13Popular Models for Representing

Glucose Molecules

14Synthesis and Degradation

of Maltose, a Disaccharide

15Organic ChOrganic ChemistryemistryCarbohydrates Examples:Carbohydrates Examples:

MonosaccharidesMonosaccharides

Single sugar moleculesSingle sugar molecules

Quite soluble and sweet to tasteQuite soluble and sweet to taste

ExamplesExamples

GlucoseGlucose (blood), fructose (fruit) and galactose (blood), fructose (fruit) and galactose

­ HexosesHexoses - Six carbon atoms - Six carbon atoms

­ Isomers of CIsomers of C66HH1212OO66

RiboseRibose and and deoxyribosedeoxyribose (in nucleotides) (in nucleotides)

­ PentosesPentoses – Five carbon atoms – Five carbon atoms

16Organic ChOrganic ChemistryemistryCarbohydrates Examples:Carbohydrates Examples:

DisaccharidesDisaccharides

Two monosaccharides joined by dehydration Two monosaccharides joined by dehydration Soluble and sweet to tasteSoluble and sweet to taste

ExamplesExamplesSucroseSucrose

­ Table sugar, maple sugarTable sugar, maple sugar

­ One glucose and one fructose joined togetherOne glucose and one fructose joined together

MaltoseMaltose

­Malt sugarMalt sugar

­ Two glucoses joined togetherTwo glucoses joined together

17Organic ChOrganic ChemistryemistryCarbohydrates Examples:Carbohydrates Examples:

Polysaccharides (1)Polysaccharides (1)

Polymers of monosaccharidesPolymers of monosaccharidesLow solubility; not sweet to tasteLow solubility; not sweet to tasteExamplesExamples

StarchStarch­Polymer of glucosePolymer of glucose­Used for short-term energy storageUsed for short-term energy storage

Plant starchPlant starchOften branched chainOften branched chain

AmyloseAmylose, corn starch, corn starchAnimal starchAnimal starch

UnbranchedUnbranchedGlycogenGlycogen in liver and muscles in liver and muscles

18Organic ChOrganic ChemistryemistryCarbohydrates Examples:Carbohydrates Examples:

Polysaccharides (2)Polysaccharides (2)

More polysaccharide examplesMore polysaccharide examplesCelluloseCellulose­ Long, coiled polymer of glucoseLong, coiled polymer of glucose­ Structural element for plantsStructural element for plants­ Indigestible by most animalsIndigestible by most animals

ChitinChitin­ Polymer of glucosePolymer of glucose­ Very resistant to wear and digestionVery resistant to wear and digestion­ Arthropod exoskeletons, cell walls of fungiArthropod exoskeletons, cell walls of fungi

19StarchStructure and

Function

20GlycogenStructure and

Function

21CelluloseStructure and

Function

22Organic ChOrganic ChemistryemistryFour Classes of Organics:Four Classes of Organics:

2 - Lipids2 - Lipids

Insoluble in waterInsoluble in water Long chains of repeating CHLong chains of repeating CH22 units units Renders molecule nonpolarRenders molecule nonpolar

Types of LipidsTypes of Lipids

MedicinesMedicinesComponent of plasma Component of plasma membrane; hormonesmembrane; hormonesSteroidsSteroids

No-stick pan sprayNo-stick pan sprayComponent of plasma Component of plasma membranemembranePhospholipidsPhospholipids

Cooking oilsCooking oilsLong-term energy storage in Long-term energy storage in plants and their seedsplants and their seedsOilsOils

Butter, lardButter, lardLong-term energy storage & Long-term energy storage & thermal insulation in animalsthermal insulation in animalsFatsFats

Human UsesHuman UsesOrganismal UsesOrganismal UsesTypeType

Candles, polishesCandles, polishesWear resistance; retain waterWear resistance; retain waterWaxesWaxes

23Blubber

24Types of Lipids:Triglycerides

25Organic ChOrganic ChemistryemistryTypes of Lipids:Types of Lipids:

Triglycerides (1)Triglycerides (1)

TriglyceridesTriglycerides (Fats) (Fats)Long-term energy storageLong-term energy storageBackbone of one Backbone of one glycerolglycerol molecule molecule Three fatty acids attached to each glycerol Three fatty acids attached to each glycerol moleculemolecule­ Long hydrocarbon chainLong hydrocarbon chain

SaturatedSaturated - no double bonds between carbons - no double bonds between carbons UnsaturatedUnsaturated - - 1 double bonds between carbons1 double bonds between carbons

­ Carboxylic acid at one endCarboxylic acid at one end

26Dehydration Synthesis of Triglyceridefrom Glycerol and Three Fatty Acids

27Organic ChOrganic ChemistryemistryTypes of Lipids:Types of Lipids:

Phospholipids (2)Phospholipids (2)

PhospholipidsPhospholipidsDerived from triglyceridesDerived from triglycerides

GlycerolGlycerol backbone backboneTwo fatty acids attached instead of threeTwo fatty acids attached instead of threeThird fatty acid replaced by Third fatty acid replaced by phosphate groupphosphate group­ The fatty acids are nonpolar and hydrophobicThe fatty acids are nonpolar and hydrophobic­ The phosphate group is polar and hydrophilicThe phosphate group is polar and hydrophilic

Molecules self arrange when placed in waterMolecules self arrange when placed in waterPolar Polar phosphate phosphate ““headsheads”” next to water next to waterNonpolar Nonpolar fatty acid fatty acid ““tailstails”” overlap and overlap and exclude waterexclude water

Spontaneously form double layer & a sphereSpontaneously form double layer & a sphere

28Phospholipids Form Membranes

29Organic ChOrganic ChemistryemistryTypes of Lipids:Types of Lipids:

Steroids & Waxes (3)Steroids & Waxes (3)

SteroidsSteroids

Cholesterol, testosterone, estrogenCholesterol, testosterone, estrogen

Skeletons of four fused carbon ringsSkeletons of four fused carbon rings

WaxesWaxes

Long-chain fatty acid bonded to a long-chain Long-chain fatty acid bonded to a long-chain alcoholalcohol

­ High melting pointHigh melting point

­WaterproofWaterproof

­ Resistant to degradationResistant to degradation

30Steroid Diversity

31Waxes

32Organic ChOrganic ChemistryemistryFour Classes of Organics:Four Classes of Organics:

3 -Proteins3 -Proteins

FunctionsFunctions

Support – CollagenSupport – Collagen

Enzymes – Almost all enzymes are proteinsEnzymes – Almost all enzymes are proteins

Transport – Hemoglobin; membrane proteinsTransport – Hemoglobin; membrane proteins

Defense – AntibodiesDefense – Antibodies

Hormones – Many hormones; insulinHormones – Many hormones; insulin

Motion – Muscle proteins, microtubulesMotion – Muscle proteins, microtubules

33Organic ChOrganic ChemistryemistryProtein Subunits:Protein Subunits:

The Amino AcidsThe Amino Acids

Proteins are polymers of Proteins are polymers of amino acidsamino acidsEach amino acid has a central carbon atom to Each amino acid has a central carbon atom to

which are attachedwhich are attached a hydrogen atom,a hydrogen atom, an an amino groupamino group –NH –NH22,, A carboxylic acid group –COOH,A carboxylic acid group –COOH, and one of 20 different types of –and one of 20 different types of –RR

(remainder) (remainder) groupsgroupsThere are 20 different amino acids that make There are 20 different amino acids that make

up proteinsup proteinsAll of them have basically the same structure All of them have basically the same structure

except for what occurs at the placeholder except for what occurs at the placeholder RR

34Structural Formulas for the

20 Amino Acids

35Organic ChOrganic ChemistryemistryProteins:Proteins:

The Polypeptide BackboneThe Polypeptide Backbone

Amino acids joined together end-to-endAmino acids joined together end-to-end

COOH of one AA covalently bonds to the NHCOOH of one AA covalently bonds to the NH22 of the next AAof the next AA

Special name for this bond - Special name for this bond - Peptide BondPeptide Bond

­ Two AAs bonded together – Two AAs bonded together – DipeptideDipeptide

­ Three AAs bonded together – Three AAs bonded together – TripeptideTripeptide

­ Many AAs bonded together – Many AAs bonded together – PolypeptidePolypeptide

Characteristics of a protein determined by Characteristics of a protein determined by composition and sequence of AA’scomposition and sequence of AA’s

Virtually unlimited number of proteinsVirtually unlimited number of proteins

36Synthesis and Degradation of a Peptide

37Organic ChOrganic ChemistryemistryProtein Molecules:Protein Molecules:

Levels of StructureLevels of Structure

PrimaryPrimary:: Literally, the sequence of amino acidsLiterally, the sequence of amino acids

SecondarySecondary:: The way the amino acid chain coils or foldsThe way the amino acid chain coils or folds

TertiaryTertiary:: Overall three-dimensional shape of a Overall three-dimensional shape of a

polypeptidepolypeptide

QuaternaryQuaternary:: Consists of more than one polypeptideConsists of more than one polypeptide

38Levels of Protein Organization

39Examples of Fibrous Proteins

40Organic ChOrganic Chemistryemistry

Protein-folding DiseasesProtein-folding Diseases

Assembly of AA’s into protein extremely Assembly of AA’s into protein extremely complexcomplex

Process overseen by “Process overseen by “chaperonechaperone” molecules” molecules

Inhibit incorrect interactions between Inhibit incorrect interactions between RR groups as polypeptide growsgroups as polypeptide grows

Defects in these chaperones can corrupt the Defects in these chaperones can corrupt the tertiary structure of proteinstertiary structure of proteins

Mad cow disease could be due to mis-folded Mad cow disease could be due to mis-folded proteinsproteins

41Organic ChOrganic ChemistryemistryFour Classes of Organics:Four Classes of Organics:

4 -Nucleic Acids4 -Nucleic Acids

Polymers of nucleotidesPolymers of nucleotides

Very specific cell functionsVery specific cell functionsDNADNA ( (deoxyribonucleic aciddeoxyribonucleic acid))­ Double-stranded helical spiral (twisted ladder)Double-stranded helical spiral (twisted ladder)­ Serves as genetic information centerServes as genetic information center­ In chromosomesIn chromosomes

RNARNA ( (ribonucleic acidribonucleic acid))­ Single-strandedSingle-stranded­ Serves primarily in assembly of proteinsServes primarily in assembly of proteins­ In nucleus and cytoplasm of cellIn nucleus and cytoplasm of cell

42Organic ChOrganic ChemistryemistryThe Nucleotides ofThe Nucleotides of

Nucleic AcidsNucleic Acids

Three components:Three components:

­ A phosphate group,A phosphate group,

­ A pentose sugar (ribose or deoxyribose), andA pentose sugar (ribose or deoxyribose), and

­ A A nitrogenous basenitrogenous base (4 kinds in DNA, 4 kinds in (4 kinds in DNA, 4 kinds in RNA, 3 common to both)RNA, 3 common to both)

Nucleotide subunits connected end-to-end to Nucleotide subunits connected end-to-end to make nucleic acidmake nucleic acid

Sugar of one connected to the phosphate of Sugar of one connected to the phosphate of the nextthe next

Sugar-phosphate backboneSugar-phosphate backbone

43Nucleotides

44DNA Structure

45RNA Structure

46Organic ChOrganic Chemistryemistry

NoNoYesYesHelixHelix

Interprets genetic info; Interprets genetic info; protein synthesisprotein synthesis

Heredity; cellular Heredity; cellular control centercontrol centerFunctionFunction

Cell nucleus and Cell nucleus and cytoplasmcytoplasm

Chromosomes of cell Chromosomes of cell nucleusnucleusWhereWhere

Comparison of DNA & RNAComparison of DNA & RNA

Table 3.4Table 3.4

Single strandedSingle strandedDouble-stranded; Double-stranded; Pairing across strandsPairing across strandsStrandsStrands

Cytosine, guanine;Cytosine, guanine;adenine, adenine, uraciluracil

Cytosine, guanine;Cytosine, guanine;adenine, adenine, thyminethymineBasesBases

RiboseRiboseDeoxyriboseDeoxyriboseSugarSugar

RNARNADNADNAFeatureFeature

47Organic ChOrganic Chemistryemistry

Other Nucleic AcidsOther Nucleic Acids

ATP (adenosineATP (adenosine triphosphate) is composed of triphosphate) is composed of adenine, ribose, and three phosphatesadenine, ribose, and three phosphates

In cells, one phosphate bond is hydrolyzed – In cells, one phosphate bond is hydrolyzed – Yields:Yields:

The molecule The molecule ADPADP ( (adenosine diphosphateadenosine diphosphate))

An inorganic phosphate molecule pAn inorganic phosphate molecule pii

EnergyEnergy

Other energy sources used to put ADP and pOther energy sources used to put ADP and p ii back together againback together again

48ATP