Chapter 4Chapter 4Chemistry of Chemistry of

CarbonCarbonBuilding Blocks of LifeBuilding Blocks of Life

Why study Carbon?Why study Carbon? All of life is built on carbon All of life is built on carbon CellsCells

~72% H~72% H22O O ~25% carbon compounds~25% carbon compounds

carbohydratescarbohydrates lipidslipids proteins proteins nucleic acidsnucleic acids

~3% salts ~3% salts Na, Cl, K…Na, Cl, K…

Concept 4.1: Organic chemistry is the study of Concept 4.1: Organic chemistry is the study of carbon compoundscarbon compounds

• Organic compounds range from simple molecules to Organic compounds range from simple molecules to colossal onescolossal ones

• Most organic compounds contain hydrogen atoms Most organic compounds contain hydrogen atoms in addition to carbon atomsin addition to carbon atoms

Vitalism, the idea that organic compounds arise Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists only in organisms, was disproved when chemists synthesized the compoundssynthesized the compounds

Mechanism is the view that all natural phenomena Mechanism is the view that all natural phenomena are governed by physical and chemical lawsare governed by physical and chemical laws

Chemistry of LifeChemistry of Life Organic chemistryOrganic chemistry is the study of is the study of carboncarbon

compoundscompounds C atoms are versatile building blocksC atoms are versatile building blocks

bonding propertiesbonding properties 4 stable covalent bonds4 stable covalent bonds

HHC

H

H

Concept 4.2: Carbon atoms can form diverse Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atomsmolecules by bonding to four other atoms

Electron configuration is the key to an atom’s Electron configuration is the key to an atom’s characteristicscharacteristics

Electron configuration determines the kinds and Electron configuration determines the kinds and number of bonds an atom will form with other number of bonds an atom will form with other atomsatoms

The Formation of Bonds with CarbonThe Formation of Bonds with Carbon

With four valence electrons, carbon can form four covalent With four valence electrons, carbon can form four covalent bonds with a variety of atomsbonds with a variety of atoms

This tetravalence makes large, complex molecules possibleThis tetravalence makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to four In molecules with multiple carbons, each carbon bonded to four

other atoms has a tetrahedral shapeother atoms has a tetrahedral shape However, when two carbon atoms are joined by a double bond, However, when two carbon atoms are joined by a double bond,

the molecule has a flat shapethe molecule has a flat shape The electron configuration of carbon gives it covalent The electron configuration of carbon gives it covalent

compatibility with many different elementscompatibility with many different elements The valences of carbon and its most frequent partners (hydrogen, The valences of carbon and its most frequent partners (hydrogen,

oxygen, and nitrogen) are the “building code” that governs the oxygen, and nitrogen) are the “building code” that governs the architecture of living moleculesarchitecture of living molecules

Complex molecules assembled like Tinker Toys

HydrocarbonsHydrocarbons Combinations of C & HCombinations of C & H

non-polarnon-polar not soluble in Hnot soluble in H22OO hydrophobichydrophobic

stablestable very little attraction very little attraction

between moleculesbetween molecules a gas at room temperaturea gas at room temperature

methane(simplest HC)

Hydrocarbons can growHydrocarbons can grow

IsomersIsomers

Molecules with same molecular formula but Molecules with same molecular formula but different structures (shapes) different structures (shapes) different chemical propertiesdifferent chemical properties different biological functionsdifferent biological functions

6 carbons

6 carbons

6 carbons

Enantiomers are important in the pharmaceutical Enantiomers are important in the pharmaceutical industryindustry

Two enantiomers of a drug may have different Two enantiomers of a drug may have different effectseffects

Differing effects of enantiomers demonstrate that Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations organisms are sensitive to even subtle variations in moleculesin molecules

L-Dopa(effective againstParkinson’s disease)

D-Dopa(biologicallyInactive)

Concept 4.3: Functional groups are the parts Concept 4.3: Functional groups are the parts of molecules involved in chemical reactionsof molecules involved in chemical reactions

Distinctive properties of organic molecules depend Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the not only on the carbon skeleton but also on the molecular components attached to itmolecular components attached to it

Certain groups of atoms are often attached to Certain groups of atoms are often attached to skeletons of organic moleculesskeletons of organic molecules

Form affects functionForm affects function Structural differences create important Structural differences create important

functional significancefunctional significance amino acid amino acid alaninealanine

L-alanine used in proteinsL-alanine used in proteins but not D-alaninebut not D-alanine

medicinesmedicines L-version activeL-version active but not D-versionbut not D-version

sometimes withsometimes withtragic results…tragic results…

stereoisomersstereoisomers

Form affects functionForm affects function Thalidomide Thalidomide

prescribed to pregnant women in 50s & 60s prescribed to pregnant women in 50s & 60s reduced morning sickness, but…reduced morning sickness, but… stereoisomer caused severe birth defectsstereoisomer caused severe birth defects

Diversity of moleculesDiversity of molecules Substitute other atoms or groups around the Substitute other atoms or groups around the

carboncarbon ethane vs. ethanolethane vs. ethanol

H replaced by an H replaced by an hydroxyl grouphydroxyl group (–OH) (–OH) nonpolar vs. polarnonpolar vs. polar gas vs. liquidgas vs. liquid biological effects!biological effects!

ethane (C2H6) ethanol (C2H5OH)

Functional groupsFunctional groups Parts of organic molecules that are involved Parts of organic molecules that are involved

in chemical reactionsin chemical reactions give organic molecules distinctive propertiesgive organic molecules distinctive properties

hydroxylhydroxyl aminoamino

carbonylcarbonyl sulfhydrylsulfhydryl

carboxylcarboxyl phosphatephosphate Affect reactivityAffect reactivity

makes hydrocarbonsmakes hydrocarbons hydrophilichydrophilic increase solubility in waterincrease solubility in water

Viva la difference!Viva la difference!

Basic structure of male & female hormones is Basic structure of male & female hormones is identicalidentical identical identical carbon skeletoncarbon skeleton attachment of different functional groupsattachment of different functional groups interact with different targets in the bodyinteract with different targets in the body

different effectsdifferent effects

HydroxylHydroxyl

––OHOH organic compounds with OH = organic compounds with OH = alcoholsalcohols names typically end in names typically end in -ol-ol

ethanolethanol

CarbonylCarbonyl

C=O C=O O double bonded to CO double bonded to C

if C=O at end molecule = if C=O at end molecule = aldehydealdehyde if C=O in middle of molecule = if C=O in middle of molecule = ketoneketone

Carboxyl Carboxyl

––COOH COOH C double bonded to O & single bonded to OH C double bonded to O & single bonded to OH

groupgroup compounds with COOH = compounds with COOH = acidsacids

fatty acidsfatty acids amino acidsamino acids

AminoAmino

-NH-NH22 N attached to 2 HN attached to 2 H

compounds with NHcompounds with NH22 = = aminesamines amino acidsamino acids

NHNH22 acts as base acts as base

ammonia picks up Hammonia picks up H++ from solution from solution

Sulfhydryl Sulfhydryl ––SHSH

S bonded to HS bonded to H compounds with SH = compounds with SH = thiolsthiols SH groups stabilize the structure of proteinsSH groups stabilize the structure of proteins

Phosphate Phosphate ––POPO44

P bound to 4 OP bound to 4 O

connects to C through an Oconnects to C through an O lots of O = lots of negative chargelots of O = lots of negative charge

highly reactivehighly reactive

transfers energy between organic molecules transfers energy between organic molecules ATP, GTP, etc.ATP, GTP, etc.

ATP: An Important Source of Energy for ATP: An Important Source of Energy for Cellular ProcessesCellular Processes

One phosphate molecule, adenosine triphosphate One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule (ATP), is the primary energy-transferring molecule in the cell in the cell

ATP consists of an organic molecule called ATP consists of an organic molecule called adenosine attached to a string of three phosphate adenosine attached to a string of three phosphate groupsgroups