Sinh học - Chapter 4: Carbon and the molecular diversity of life

Chapter 4Carbon and the Molecular Diversity of LifeOverview: Carbon: The Backbone of LifeAlthough cells are 70–95% water, the rest consists mostly of carbon-based compounds.Carbon is unparalleled in its ability to form large, complex, and diverse molecules because each carbon atom makes 4 bonds. Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsWhat properties of carbon underlie its role as the molecular basis of life?Organic chemistry is the study of carbon compoundsOrganic chemistry is the study of compounds that contain carbon.Organic compounds range from simple molecules to colossal ones.Most organic compounds contain hydrogen atoms in addition to carbon atoms.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsStanley Miller ExperimentWater vaporH2NH3“Atmosphere”ElectrodeCondenserColdwaterCooled watercontainingorganicmoleculesSample forchemical analysisH2O“sea”CH4Primative Earth EnvironmentSimple Organic CompoundsSynthesizedCarbon atoms can form diverse molecules by bonding to four other atomsElectron configuration is the key to an atom’s characteristics.Electron configuration determines chemical bonding: the kinds and number of bonds an atom will form with other atoms.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe Formation of Bonds with CarbonWith four valence electrons (outer shell), carbon can form four covalent bonds with a variety of atoms.This tetravalence makes large, complex molecules possible.In 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 molecule has a flat shape.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe Shapes of Tree Dimensional Organic MoleculesNameMolecular FormulaStructural FormulaBall-and-StickModelSpace-FillingModel(a) Methane(b) Ethane(c) Ethene (ethylene)Valences of the major elements of organic moleculesHydrogen(valence = 1)Oxygen(valence = 2)Nitrogen(valence = 3)Carbon(valence = 4)HONCCarbon is versatile and most frequently bonds with: H, O, N, and other C atoms.Carbon atoms partner with other atoms to form compounds such as:Carbon dioxide: CO2Urea: CO(NH2)2Glucose: C6H12O6O = C = OCopyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsUreaMolecular Diversity Arising from Carbon Skeleton VariationCarbon chains form the skeletons of most organic molecules.Carbon chains vary in length and shape.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsVariation in carbon skeletonsEthanePropane1-Butene2-Butene(c) Double bonds(d) RingsCyclohexaneBenzeneButane2-Methylpropane(commonly called isobutane)(b) Branching(a) LengthHydrocarbonsHydrocarbons are organic molecules consisting of only carbon and hydrogen.Many organic molecules, such as fats, have hydrocarbon components in long hydrocarbon chains.Hydrocarbons can undergo reactions that release a large amount of energy.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe role of hydrocarbons in fats - fatty acids (H-C chains)(a) Mammalian adipose cells(b) A fat moleculeFat droplets (stained red)100 µmIsomersIsomers are compounds with the same molecular formula but different structures and properties:Structural isomers have different covalent arrangements of their atoms.Geometric isomers have the same covalent arrangements but differ in spatial arrangements.Enantiomers are isomers that are mirror images of each other.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThree types ofIsomersPentane(a) Structural isomers(b) Geometric isomers2-methyl butanecis isomer: The two Xs areon the same side.trans isomer: The two Xs areon opposite sides.(c) EnantiomersL isomerD isomerEnantiomers, mirror image isomers, are important in the pharmaceutical industry.Two enantiomers of a drug may have different effects.Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe pharmacological importance of enantiomersDrugIbuprofenAlbuterolConditionPain;inflammationAsthmaEffectiveEnantiomerS-IbuprofenR-AlbuterolR-IbuprofenS-AlbuterolIneffectiveEnantiomerA small number of chemical groups are key to the functioning of biological moleculesDistinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it.A number of characteristic groups are often attached to skeletons of organic molecules. These are called functional groups.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsThe Chemical Groups Most Important in the Processes of LifeFunctional groups are the components of organic molecules that are most commonly involved in chemical reactions.The number and arrangement of functional groups give each molecule its unique properties.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsA comparison of chemical groups of female (estradiol) and male (testosterone) sex hormonesEstradiolTestosteroneThe seven functional groups that are most important in the chemistry of life:Hydroxyl group -OHCarbonyl group -C=OCarboxyl group -COOH Amino group -NH2Sulfhydryl group -SHPhosphate group -OPO32-Methyl group -CH3Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsKEY Functional GroupsImportant Chemical GroupsHydroxylCHEMICALGROUPSTRUCTURENAME OF COMPOUNDEXAMPLEFUNCTIONALPROPERTIESCarbonylCarboxyl(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–.)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).Carboxylic acids, or organicacidsKetones if the carbonyl group iswithin a carbon skeletonAldehydes if the carbonyl groupis at the end of the carbonskeletonAlcohols (their specific namesusually end in -ol)Ethanol, the alcohol present inalcoholic beveragesAcetone, the simplest ketoneAcetic acid, which gives vinegarits sour tastePropanal, an aldehydeHas acidic propertiesbecause the covalent bondbetween oxygen and hydrogenis so polar; for example,Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion (here,specifically, the acetate ion).Acetic acidAcetate ionA ketone and an aldehyde maybe structural isomers withdifferent properties, as is thecase for acetone and propanal.These two groups are alsofound in sugars, giving rise totwo major groups of sugars:aldoses (containing analdehyde) and ketoses(containing a ketone).Is polar as a result of theelectrons spending more timenear the electronegative oxygen atom.Can form hydrogen bonds withwater molecules, helpingdissolve organic compoundssuch as sugars.The carbonyl group ( CO)consists of a carbon atomjoined to an oxygen atom by adouble bond.Important Chemical GroupsCHEMICALGROUPSTRUCTURENAME OFCOMPOUNDEXAMPLEFUNCTIONALPROPERTIESAminoSulfhydrylPhosphateMethylA methyl group consists of acarbon bonded to threehydrogen atoms. The methylgroup may be attached to acarbon or to a different atom.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).PThe sulfhydryl groupconsists of a sulfur atombonded to an atom ofhydrogen; resembles ahydroxyl group in shape.(may bewritten HS—)The amino group(—NH2) consists of anitrogen atom bondedto two hydrogen atomsand to the carbon skeleton.AminesThiolsOrganic phosphatesMethylated compounds5-Methyl cytidine5-Methyl cytidine is acomponent of DNA that hasbeen modified by addition ofthe methyl group.In addition to taking part inmany important chemicalreactions in cells, glycerolphosphate provides thebackbone for phospholipids,the most prevalent molecules incell membranes.Glycerol phosphateCysteineCysteine is an importantsulfur-containing aminoacid.GlycineBecause it also has acarboxyl group, glycineis both an amine anda carboxylic acid;compounds with bothgroups are called amino acids.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.Contributes negative chargeto the molecule of which it isa part (2– when at the end ofa molecule; 1– when locatedinternally in a chain ofphosphates).Has the potential to reactwith water, releasing energy.Two sulfhydryl groupscan react, forming acovalent bond. This“cross-linking” helpsstabilize proteinstructure.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.Acts as a base; canpick up an H+ fromthe surroundingsolution (water, in living organisms).Ionized, with acharge of 1+, undercellular conditions.(nonionized)(ionized)Some biologically important chemical groups—carboxyl groupSTRUCTUREEXAMPLENAME OFCOMPOUNDFUNCTIONALPROPERTIESCarboxylAcetic acid, which gives vinegar its sour tasteCarboxylic acids, or organic acidsHas acidic propertiesbecause the covalent bond between oxygen and hydrogen is so polar; for example,Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).Acetic acidAcetate ionCarboxyl group at the end of each moleculeSome biologically important chemical groups—amino groupSTRUCTUREEXAMPLENAME OFCOMPOUNDFUNCTIONALPROPERTIESAminoBecause it also has a carboxyl group, glycine is both an amine anda carboxylic acid; compounds with both groups are called amino acids.AminesActs as a base; can pick up an H+ from the surrounding solution (water, in living organisms).Ionized, with a charge of 1+, under cellular conditions.(ionized)(nonionized)GlycineSome biologically important chemical groups—sulfhydryl groupSTRUCTUREEXAMPLENAME OFCOMPOUNDFUNCTIONALPROPERTIESSulfhydryl(may be written HS—)CysteineCysteine is an important sulfur-containing amino acid.ThiolsTwo 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.Some biologically important chemical groups—phosphate groupSTRUCTUREEXAMPLENAME OFCOMPOUNDFUNCTIONALPROPERTIESPhosphateIn 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.Glycerol phosphateOrganic phosphatesContributes 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).Has the potential to react with water, releasing energy.Some biologically important chemical groups—methyl groupSTRUCTUREEXAMPLENAME OFCOMPOUNDFUNCTIONALPROPERTIESMethyl5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.5-Methyl cytidineMethylated compoundsAddition 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.ATP: An Important Source of Energy for Cellular ProcessesOne phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell. ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsATPAdenosinePPPP iPPAdenosineAdenosineADPATPInorganic phosphateReacts with H2O EnergyThe Chemical Elements of Life: A ReviewThe versatility of carbon makes possible the great diversity of organic molecules.Variation at the molecular level lies at the foundation of all biological diversity.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsWhat is the molecular formula for this organic compound? Can you build it with a model?You should now be able to:Explain how carbon’s electron configuration explains its ability to form large, complex, diverse organic molecules.Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules.Distinguish among the three types of isomers: structural, geometric, and enantiomer.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin CummingsName the major functional groups found in organic molecules; describe the basic structure of each functional group and outline the chemical properties of the organic molecules in which they occur.Explain how ATP functions as the primary energy transfer molecule in living cells.Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings