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Carbon and the Molecular Diversity of Life

Lecture Presentation by Nicole Tunbridge andKathleen FitzpatrickSlide2

Carbon: The Backbone of LifeLiving organisms consist mostly of carbon-based compoundsCarbon is unparalleled in its ability to form large, complex, and varied moleculesProteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compoundsSlide3

Figure 4.1Slide4

Figure 4.1a

Carbon can bond to four other atoms orgroups of atoms, making a large variety ofmolecules possible.Slide5

Concept 4.1: Organic chemistry is the study of carbon compoundsOrganic chemistry is the study of compounds that contain carbonOrganic compounds range from simple molecules to colossal ones

Most organic compounds contain hydrogen atoms in addition to carbon atomsSlide6

Vitalism was the belief in a life force outside the jurisdiction of physical and chemical lawsIt was thought that organic compounds could only be produced in living organismsVitalism was disproved when chemists were able to synthesize organic compoundsSlide7

Organic Molecules and the Origin of Life on EarthStanley Miller’s classic experiment demonstrated the abiotic synthesis of organic compoundsExperiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of lifeSlide8

Figure 4.2

Water vaporCooled “rain”containingorganicmoleculesSample forchemical analysis

Coldwater

CondenserElectrode“Atmosphere”

CH

4

NH

3

H

2

H

2

O

“sea”Slide9

Pioneers of organic chemistry helped shift the mainstream of biological thought from vitalismto mechanismMechanism is the view that physical and chemical laws govern all natural phenomenaSlide10

Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atomsElectron configuration is the key to an atom’s characteristicsElectron configuration determines the kinds and number of bonds an atom will form with other atomsSlide11

The Formation of Bonds with CarbonWith four valence electrons, carbon can form four covalent bonds with a variety of atomsThis ability makes large, complex molecules possibleIn molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape

However, when two carbon atoms are joined by a double bond, the atoms joined to the carbons arein the same plane as the carbonsSlide12

Figure 4.3

Molecule(a) Methane(b) Ethane(c) Ethene (ethylene)

MolecularFormula

StructuralFormulaBall-and-Stick Model

Space-Filling

Model

CH

4

C

2

H

6

C

2

H

4Slide13

The electron configuration of carbon gives it covalent compatibility with many different elementsThe valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen)are the

building code for the architecture ofliving moleculesSlide14

Figure 4.4

Hydrogen(valence = 1)Oxygen(valence = 2)Nitrogen(valence = 3)Carbon

(valence = 4)Slide15

Carbon atoms can partner with atoms other than hydrogen; for example:Carbon dioxide: CO2

Urea: CO(NH2)2Slide16

Figure 4.UN02

UreaSlide17

Molecular Diversity Arising from Variation in Carbon SkeletonsCarbon chains form the skeletons of most organic moleculesCarbon chains vary in length and shapeSlide18

Figure 4.5

(a) Length(b) Branching(d) Presence of rings(c) Double bond positionEthane

Propane1-Butene

2-ButeneButane

2-Methylpropane

(

isobutane

)

Cyclohexane

BenzeneSlide19

Animation: Carbon SkeletonsSlide20

Figure 4.5a

(a) LengthEthanePropaneSlide21

Figure 4.5b

(b) BranchingButane2-Methylpropane(isobutane)Slide22

Figure 4.5c

(c) Double bond position1-Butene2-ButeneSlide23

Figure 4.5d

(d) Presence of ringsCyclohexaneBenzeneSlide24

HydrocarbonsHydrocarbons are organic molecules consisting of only carbon and hydrogenMany organic molecules, such as fats, have hydrocarbon components

Hydrocarbons can undergo reactions that release a large amount of energySlide25

Figure 4.6

Nucleus Fat droplets (b) A fat molecule(a) Part of a human adipose cell10 μ

mSlide26

Figure 4.6a

Nucleus Fat droplets (a) Part of a human adipose cell10 μmSlide27

IsomersIsomers are compounds with the same molecular formula but different structures and propertiesStructural isomers have different covalent arrangements of their atoms

Cis-trans isomers have the same covalent bonds but differ in spatial arrangementsEnantiomers are isomers that are mirror imagesof each otherSlide28

Figure 4.7

(a) Structural isomers(b) Cis-trans isomersPentanecis

isomer: The two Xs areon the same side.

2-methyl butanetrans isomer: The two Xs are

on opposite sides.

(c) Enantiomers

L isomer

D isomer

CO

2

H

CO

2

H

H

CH

3

CH

3

H

NH

2

NH

2

C

CSlide29

Animation: IsomersSlide30

Figure 4.7a

(a) Structural isomersPentane2-methyl butaneSlide31

Figure 4.7b

(b) Cis-trans isomerscis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.Slide32

Figure 4.7c

(c) EnantiomersL isomerD isomerCO2H

HCH3

HNH2

CO

2

H

NH

2

CH

3

C

CSlide33

Enantiomers are important in the pharmaceutical industryTwo enantiomers of a drug may have different effectsUsually only one isomer is biologically activeDiffering effects of enantiomers demonstrate that organisms are sensitive to even subtle variations

in molecules Slide34

Figure 4.8

DrugEffectsEffectiveEnantiomerIneffectiveEnantiomer

IbuprofenAlbuterol

Reducesinflammationand pain

Relaxes bronchial

(airway) muscles,

improving airflow

in asthma

patients

S

-Ibuprofen

R

-

AIbuterol

S

-

AIbuterol

R

-IbuprofenSlide35

Animation: L-DopaSlide36

Concept 4.3: A few chemical groups are key to molecular functionDistinctive properties of organic molecules depend on the carbon skeleton and on the chemical groups attached to itA number of characteristic groups can replacethe hydrogens attached to skeletons of organic moleculesSlide37

The Chemical Groups Most Important in the Processes of LifeEstradiol and testosterone are both steroids witha common carbon skeleton, in the form of four fused ringsThese sex hormones differ only in the chemical groups attached to the rings of the carbon skeletonSlide38

Figure 4.UN03

EstradiolTestosteroneSlide39

Functional groups are the components of organic molecules that are most commonly involved in chemical reactionsThe number and arrangement of functional groups give each molecule its unique properties Slide40

The seven functional groups that are most important in the chemistry of lifeHydroxyl groupCarbonyl group

Carboxyl groupAmino groupSulfhydryl groupPhosphate groupMethyl groupSlide41

Figure 4.9

Chemical GroupCompound NameExamplesEthanolPropanal

AcetoneAcetic acid

GlycineCysteine

Glycerol phosphate

Organic

phosphate

Thiol

Amine

Carboxylic acid, or

organic acid

Ketone

Aldehyde

Alcohol

Hydroxyl group (—OH)

Carboxyl group (—COOH)

Amino group (—NH

2

)

Sulfhydryl group (—SH)

Phosphate group (—OPO

3

2−

)

Methyl group (—CH

3

)

Methylated

compound

5-Methyl cytosine

Carbonyl group

( C＝O)

—

—Slide42

Figure 4.9a

Chemical GroupCompound NameExamplesEthanolPropanal

AcetoneAcetic acid

GlycineAmine

Carboxylic acid, or

organic acid

Ketone

Aldehyde

Alcohol

Hydroxyl group (—OH)

Carboxyl group (—COOH)

Amino group (—NH

2

)

Carbonyl group

( C＝

O

)

—

—Slide43

Figure 4.9aa

Ethanol, the alcoholpresentin alcoholicbeveragesPolar due to electronegative oxygen. Forms hydrogen bonds with water.Compound name: AlcoholHydroxyl group (—OH)

(may be written HO—)Slide44

Figure 4.9ab

Propanal,an aldehydeAcetone,the simplest ketoneSugars with ketone groups are called ketoses; those with aldehydesare called aldoses.Compound name: Ketone or aldehyde

Carbonyl group

( C＝O)—

—Slide45

Figure 4.9ac

Acetic acid, whichgives vinegar itssour tasteActs as an acid.Compound name: Carboxylic acid, or organic acidCarboxyl group (—COOH)Ionized form of —COOH

(carboxylate ion),found in cellsSlide46

Figure 4.9ad

Glycine, an amino acid(note its carboxyl group)Acts as a base.Compound name: AmineAmino group (—NH2)Ionized form

of —NH2,found in cellsSlide47

Figure 4.9b

CysteineGlycerol phosphateOrganicphosphateThiolSulfhydryl group (—SH)

Phosphate group (—OPO32−

)Methyl group (—CH3)

Methylated

compound

5-Methyl cytosine

Chemical Group

Compound Name

ExamplesSlide48

Figure 4.9ba

Cysteine, a sulfur-containing amino acidTwo —SH groups can react, forming a “cross-link” that helps stabilizeprotein structure.Compound name: ThiolSulfhydryl group (—SH)

(may be written HS—)Slide49

Figure 4.9bb

Glycerol phosphate,which takes part inmany importantchemical reactions incellsContributes negative charge. When attached, confers on a molecule the abilityto react with water, releasing energy.Compound name: Organic phosphatePhosphate group (—OPO

32−)Slide50

Figure 4.9bc

Methyl group (—CH3)Affects the expression of genes. Affects the shape and function ofsex hormones.Compound name: Methylated compound5-Methyl cytosine, acomponent of DNAthat has been modified

by addition of a methylgroupSlide51

ATP: An Important Source of Energy for Cellular ProcessesAn important organic phosphate is adenosine triphosphate (ATP

)ATP consists of an organic molecule called adenosine attached to a string of three phosphate groupsATP stores the potential to react with water,a reaction that releases energy to be used bythe cellSlide52

Figure 4.UN04

AdenosineSlide53

Figure 4.UN05

Reactswith H2OInorganicphosphateADPEnergy

Adenosine

AdenosineATPP

P

P

P

P

P

iSlide54

The Chemical Elements of Life: A ReviewThe versatility of carbon makes possible the great diversity of organic moleculesVariation at the molecular level lies at the foundation of all biological diversitySlide55

Figure 4.UN01aSlide56

Figure 4.UN01b

Some of Stanley Miller’s notes from his1958 hydrogen sulfide (H2S) experimentSlide57

Figure 4.UN01c

Some of Stanley Miller’s original vials from his1958 hydrogen sulfide (H2S) experimentSlide58

Figure 4.UN06Slide59

Figure 4.UN07Slide60

Figure 4.UN08

a

b

c

d

eSlide61

Figure 4.UN09

L-dopaD-dopaSlide62

Figure 4.UN10