7Sample for chemical analysis Fig. 4-2EXPERIMENT“Atmosphere”CH4Water vaporElectrodeNH3H2CondenserCooled watercontainingorganicmoleculesColdwaterFigure 4.2 Can organic molecules form under conditions believed to simulate those on the early Earth?H2O“sea”Sample forchemical analysis
10Molecular Formula Structural Formula Ball-and-Stick Model Fig. 4-3Molecular FormulaStructural FormulaBall-and-StickModelSpace-FillingModelName(a) Methane(b) EthaneFigure 4.3 The shapes of three simple organic molecules(c) Ethene(ethylene)
21Based on carbon’s valence (4), how many different molecular shapes can be made from 6 carbons? 1246more than 6Answer: eThis question is aimed at Concept 4.2. It ties the concept of valence and number of bonds with the idea of molecular structure. It is possible to lead this to a discussion involving bond angles and the constraints they impose on the structures. Adding a few more elements to the question might lead to a discussion of isomers.
25Figure 4.7 Three types of isomers Pentane2-methyl butane(a) Structural isomerscis isomer: The two Xs areon the same side.trans isomer: The two Xs areon opposite sides.(b) Geometric isomersFigure 4.7 Three types of isomersL isomerD isomer(c) Enantiomers
26Pentane 2-methyl butane Fig. 4-7aPentane2-methyl butaneFigure 4.7 Three types of isomers(a) Structural isomers
27cis isomer: The two Xs are on the same side. Fig. 4-7bcis isomer: The two Xs areon the same side.trans isomer: The two Xs areon opposite sides.(b) Geometric isomersFigure 4.7 Three types of isomers
28(c) Enantiomers L isomer D isomer Figure 4.7 Three types of isomers Fig. 4-7cL isomerD isomerFigure 4.7 Three types of isomers(c) Enantiomers
30Effective Enantiomer Ineffective Enantiomer Drug Condition Pain; Fig. 4-8EffectiveEnantiomerIneffectiveEnantiomerDrugConditionPain;inflammationIbuprofenS-IbuprofenR-IbuprofenFigure 4.8 The pharmacological importance of enantiomersAlbuterolAsthmaR-AlbuterolS-Albuterol
35Figure 4.10 Some biologically important chemical groups Fig. 4-10aCHEMICALGROUPHydroxylCarbonylCarboxylSTRUCTURE(may be written HO—)In a hydroxyl group (—OH), ahydrogen atom is bonded to anoxygen atom, which in turn isbonded to the carbon skeleton ofthe organic molecule. (Do notconfuse this functional groupwith the hydroxide ion, OH–.)The carbonyl group ( CO)consists of a carbon atomjoined to an oxygen atom by adouble bond.When an oxygen atom isdouble-bonded to a carbonatom that is also bonded toan —OH group, the entireassembly of atoms is calleda carboxyl group (—COOH).NAME OF COMPOUNDAlcohols (their specific namesusually end in -ol)Ketones if the carbonyl group iswithin a carbon skeletonCarboxylic acids, or organicacidsAldehydes if the carbonyl groupis at the end of the carbonskeletonEXAMPLEEthanol, the alcohol present inalcoholic beveragesAcetone, the simplest ketoneAcetic acid, which gives vinegarits sour tasteFigure 4.10 Some biologically important chemical groupsPropanal, an aldehydeFUNCTIONALPROPERTIESIs polar as a result of theelectrons spending more timenear the electronegativeoxygen atom.A ketone and an aldehyde maybe structural isomers withdifferent properties, as is thecase for acetone and propanal.Has acidic propertiesbecause the covalent bondbetween oxygen and hydrogenis so polar; for example,Can form hydrogen bonds withwater molecules, helpingdissolve organic compoundssuch as sugars.These two groups are alsofound in sugars, giving rise totwo major groups of sugars:aldoses (containing analdehyde) and ketoses(containing a ketone).Acetic acidAcetate ionFound in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion (here,specifically, the acetate ion).
36Figure 4.10 Some biologically important chemical groups Fig. 4-10bCHEMICALGROUPAminoSulfhydrylPhosphateMethyl(may bewritten HS—)STRUCTUREThe amino group(—NH2) consists of anitrogen atom bondedto two hydrogen atomsand to the carbon skeleton.The sulfhydryl groupconsists of a sulfur atombonded to an atom ofhydrogen; resembles ahydroxyl group in shape.In a phosphate group, aphosphorus atom is bonded tofour oxygen atoms; one oxygenis bonded to the carbon skeleton;two oxygens carry negativecharges. The phosphate group(—OPO32–, abbreviated ) is anionized form of a phosphoric acidgroup (—OPO3H2; note the twohydrogens).A methyl group consists of acarbon bonded to threehydrogen atoms. The methylgroup may be attached to acarbon or to a different atom.PNAME OFCOMPOUNDAminesThiolsOrganic phosphatesMethylated compoundsEXAMPLEGlycineGlycerol phosphateBecause it also has acarboxyl group, glycineis both an amine anda carboxylic acid;compounds with bothgroups are calledamino acids.CysteineIn addition to taking part inmany important chemicalreactions in cells, glycerolphosphate provides thebackbone for phospholipids,the most prevalent molecules incell membranes.5-Methyl cytidineCysteine is an importantsulfur-containing aminoacid.5-Methyl cytidine is acomponent of DNA that hasbeen modified by addition ofthe methyl group.Figure 4.10 Some biologically important chemical groupsFUNCTIONALPROPERTIESActs as a base; canpick up an H+ fromthe surroundingsolution (water, inliving organisms).Two sulfhydryl groupscan react, forming acovalent bond. This“cross-linking” helpsstabilize proteinstructure.Contributes negative chargeto the molecule of which it isa part (2– when at the end ofa molecule; 1– when locatedinternally in a chain ofphosphates).Addition of a methyl groupto DNA, or to moleculesbound to DNA, affectsexpression of genes.Arrangement of methylgroups in male and femalesex hormones affectstheir shape and function.Cross-linking ofcysteines in hairproteins maintains thecurliness or straightnessof hair. Straight hair canbe “permanently” curledby shaping it aroundcurlers, then breakingand re-forming thecross-linking bonds.Has the potential to reactwith water, releasing energy.(nonionized)(ionized)Ionized, with acharge of 1+, undercellular conditions.
37Carboxyl STRUCTURE NAME OF COMPOUND Carboxylic acids, or organic acids Fig. 4-10cCarboxylSTRUCTURENAME OFCOMPOUNDCarboxylic acids, or organic acidsEXAMPLEFUNCTIONALPROPERTIESHas acidic propertiesbecause the covalent bond between oxygen and hydrogen is so polar; for example,Acetic acid, which gives vinegar its sour tasteFigure 4.10 Some biologically important chemical groups—carbonyl groupAcetic acidAcetate ionFound in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).
38Amino STRUCTURE NAME OF COMPOUND Amines EXAMPLE FUNCTIONAL PROPERTIES Fig. 4-10dAminoSTRUCTURENAME OFCOMPOUNDAminesEXAMPLEFUNCTIONALPROPERTIESActs as a base; can pick up an H+ from the surrounding solution (water, in living organisms).GlycineFigure 4.10 Some biologically important chemical groups—amino groupBecause it also has a carboxyl group, glycine is both an amine anda carboxylic acid; compounds with both groups are called amino acids.(nonionized)(ionized)Ionized, with a charge of 1+, under cellular conditions.
39Sulfhydryl STRUCTURE NAME OF COMPOUND Thiols (may be written HS—) Fig. 4-10eSulfhydrylSTRUCTURENAME OFCOMPOUNDThiols(may be written HS—)EXAMPLEFUNCTIONALPROPERTIESTwo sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.Cross-linking ofcysteines in hairproteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breakingand re-forming thecross-linking bonds.CysteineFigure 4.10 Some biologically important chemical groups—sulfhydryl groupCysteine is an important sulfur-containing amino acid.
40Phosphate STRUCTURE NAME OF COMPOUND Organic phosphates EXAMPLE Fig. 4-10fPhosphateSTRUCTURENAME OFCOMPOUNDOrganic phosphatesEXAMPLEFUNCTIONALPROPERTIESContributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates).Glycerol phosphateFigure 4.10 Some biologically important chemical groups—phosphate groupHas the potential to react with water, releasing energy.In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes.
41activity Methyl STRUCTURE NAME OF COMPOUND Methylated compounds Fig. 4-10gMethylSTRUCTURENAME OFCOMPOUNDMethylated compoundsEXAMPLEFUNCTIONALPROPERTIESAddition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes.Arrangement of methyl groups in male and female sex hormones affectstheir shape and function.Figure 4.10 Some biologically important chemical groups—methyl group5-Methyl cytidine5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.activity