Chapter 4. Carbon and the Molecular Diversity of Life

Transcription

1 Lecture Outline Chapter 4 Carbn and the Mlecular Diversity f Life Overview: Carbn The Backbne f Bilgical Mlecules Althugh cells are 70 95% water, the rest cnsists f mstly carbn-based cmpunds. Carbn enters the bisphere when phtsynthetic rganisms use the sun s energy t transfrm CO 2 int rganic mlecules, which are transferred t primary cnsumers. Carbn accunts fr the diversity f bilgical mlecules, which has made pssible the wide variety f living things. Prteins, DNA, carbhydrates, and ther mlecules that distinguish living matter frm inrganic material are all cmpsed f carbn atms bnded t each ther and t atms f ther elements. These ther elements cmmnly include hydrgen (H), xygen (O), nitrgen (N), sulfur (S), and phsphrus (P). Cncept 4.1 Organic chemistry is the study f carbn cmpunds. Organic chemistry fcuses n rganic cmpunds cntaining carbn. Organic cmpunds can range frm simple mlecules, such as CH 4, t cmplex mlecules such as prteins, which may have mlecular masses greater than 100,000 daltns. Mst rganic cmpunds cntain hydrgen atms. The verall percentages f the majr elements f life (C, H, O, N, S, and P) are quite unifrm frm ne rganism t anther. Because f carbn s versatility, these few elements can be cmbined t build an inexhaustible variety f rganic mlecules. Variatins in rganic mlecules can distinguish even individuals f a single species. The science f rganic chemistry began with attempts t purify and imprve the yield f prducts btained frm rganisms. Initially, chemists learned t synthesize simple cmpunds in the labratry but had n success with mre cmplex cmpunds. The Swedish chemist Jns Jacb Berzelius was the first t make a distinctin between rganic cmpunds that seemed t arise in nly living rganisms and inrganic cmpunds that were fund in the nnliving wrld. Early rganic chemists prpsed vitalism, the belief that physical and chemical laws d nt apply t living things. Supprt fr vitalism waned as rganic chemists learned t synthesize cmplex rganic cmpunds in the labratry. In the early 1800s, the German chemist Friedrich Wöhler and his students synthesized urea frm ttally inrganic materials. Lecture Outline fr Campbell/Reece Bilgy, 8 th Editin, Pearsn Educatin, Inc. 4-1

2 In 1953, Stanley Miller at the University f Chicag set up a labratry simulatin f pssible chemical cnditins n the primitive Earth and demnstrated the spntaneus synthesis f rganic cmpunds. The mixture f gases Miller created prbably did nt accurately represent the atmsphere f the primitive Earth. Hwever, similar experiments using mre accurate atmspheric cnditins als led t the frmatin f rganic cmpunds. Spntaneus synthesis f rganic cmpunds may have been an early stage in the rigin f life n Earth. Organic chemists finally rejected vitalism and embraced mechanism, the belief that the same physical and chemical laws gvern all natural phenmena, including the prcesses f life. Organic chemistry was redefined as the study f carbn cmpunds, regardless f their rigin. Organisms prduce the majrity f rganic cmpunds. The laws f chemistry apply t bth inrganic and rganic cmpunds. The fundatin f rganic chemistry is nt a mysterius life frce but rather the unique versatility f carbn-based cmpunds. Cncept 4.2 Carbn atms can frm diverse mlecules by bnding t fur ther atms. A carbn atm has a ttal f 6 electrns: 2 in the first electrn shell and 4 in the secnd shell. Carbn has little tendency t frm inic bnds by lsing r gaining 4 electrns t cmplete its valence shell. Carbn usually cmpletes its valence shell by sharing electrns with ther atms in fur cvalent bnds, which may include single and duble bnds. Carbn s tetravalence makes large, cmplex mlecules pssible. When a carbn atm frms cvalent bnds with fur ther atms, they are arranged at the crners f an imaginary tetrahedrn with bnd angles f In mlecules with multiple carbn atms, every carbn atm bnded t fur ther atms has a tetrahedral shape. When tw carbn atms are jined by a duble bnd, all bnds arund thse carbns are in the same plane and have a flat, three-dimensinal structure. The electrn cnfiguratin f carbn enables it t frm cvalent bnds with many different elements. The valences f carbn and its partners can be viewed as the building cde that gverns the architecture f rganic mlecules. In carbn dixide, ne carbn atm frms tw duble bnds with tw different xygen atms. In the structural frmula, O=C=O, each line represents a pair f shared electrns. This arrangement cmpletes the valence shells f all atms in the mlecule. Althugh CO 2 can be classified as either rganic r inrganic, its imprtance t the living wrld is clear: CO 2 is the surce f carbn fr all rganic mlecules fund in rganisms. CO 2 is usually fixed int rganic mlecules by the prcess f phtsynthesis.

3 Urea, CO(NH 2) 2, is anther simple rganic mlecule in which each atm frms cvalent bnds t cmplete its valence shell. Mlecular diversity arises frm variatins in the carbn skeletn. Carbn chains frm the skeletns f mst rganic mlecules. Carbn skeletns vary in length and may be straight, branched, r arranged in clsed rings. Carbn skeletns may include duble bnds. Atms f ther elements can be bnded t the atms f the carbn skeletn. Hydrcarbns are rganic mlecules that cnsist f nly carbn and hydrgen atms. Hydrcarbns are the majr cmpnent f petrleum, a fssil fuel that cnsists f the partially decmpsed remains f rganisms that lived millins f years ag. Fats are bilgical mlecules that have lng hydrcarbn tails attached t a nnhydrcarbn cmpnent. Petrleum and fat are hydrphbic cmpunds that cannt disslve in water because f their many nnplar carbn-hydrgen bnds. Hydrcarbns can underg reactins that release a relatively large amunt f energy. Ismers are cmpunds that have the same mlecular frmula but different structures and, therefre, different chemical prperties. Structural ismers have the same mlecular frmula but differ in the cvalent arrangement f atms. Structural ismers may als differ in the lcatin f the duble bnds. Gemetric ismers have the same cvalent partnerships but differ in the spatial arrangement f atms arund a carbn-carbn duble bnd. The duble bnd des nt allw the atms t rtate freely arund the bnd axis. The bichemistry f visin invlves a light-induced change in the structure f rhdpsin in the retina frm ne gemetric ismer t anther. Enantimers are mlecules that are mirrr images f each ther. Enantimers are pssible when fur different atms r grups f atms are bnded t an asymmetric carbn. The fur grups can be arranged in space in tw different ways that are mirrr images f each ther. They are like left-handed and right-handed versins f the mlecule. Usually ne is bilgically active, while the ther is inactive. Even subtle structural differences in tw enantimers may have imprtant functinal significance because f emergent prperties frm specific arrangements f atms. Fr example, ne enantimer f the drug thalidmide reduced mrning sickness, the desired effect, but the ther ismer caused severe birth defects. Cncept 4.3 Characteristic chemical grups help determine hw bilgical mlecules functin. Lecture Outline fr Campbell/Reece Bilgy, 8 th Editin, Pearsn Educatin, Inc. 4-3

4 The distinctive prperties f an rganic mlecule depend nt nly n the arrangement f its carbn skeletn but als n the chemical grups attached t that skeletn. If we start with hydrcarbns as the simplest rganic mlecules, characteristic chemical grups can replace ne r mre f the hydrgen atms bnded t the carbn skeletn f a hydrcarbn. These chemical grups may be invlved in chemical reactins r may cntribute t the shape and functin f the rganic mlecule in a characteristic way, giving it unique prperties. As an example, the basic structure f teststerne (a male sex hrmne) and estradil (a female sex hrmne) is the same. Bth are sterids with fur fused carbn rings, but the hrmnes differ in the chemical grups attached t the rings. As a result, teststerne and estradil have different shapes, causing them t interact differently with many targets thrughut the bdy. In ther cases, chemical grups knwn as functinal grups affect mlecular functin thrugh their direct invlvement in chemical reactins. Seven chemical grups are mst imprtant t the chemistry f life: hydrxyl, carbnyl, carbxyl, amin, sulfhydryl, phsphate, and methyl grups. The first six chemical grups are functinal grups. They are hydrphilic and increase the slubility f rganic cmpunds in water. Methyl grups are nt reactive but may serve as imprtant markers n rganic mlecules. In a hydrxyl grup ( OH), a hydrgen atm frms a plar cvalent bnd with an xygen atm, which frms a plar cvalent bnd t the carbn skeletn. Because f these plar cvalent bnds, hydrxyl grups increase the slubility f rganic mlecules. Organic cmpunds with hydrxyl grups are alchls, and their names typically end in -l. A carbnyl grup (>CO) cnsists f an xygen atm jined t the carbn skeletn by a duble bnd. If the carbnyl grup is n the end f the skeletn, the cmpund is an aldehyde. If the carbnyl grup is within the carbn skeletn, the cmpund is a ketne. Ismers with aldehydes and thse with ketnes have different prperties. A carbxyl grup ( COOH) cnsists f a carbn atm with a duble bnd t an xygen atm and a single bnd t the xygen atm f a hydrxyl grup. Cmpunds with carbxyl grups are carbxylic acids. A carbxyl grup acts as an acid because the cmbined electrnegativities f the tw adjacent xygen atms increase the chance f dissciatin f hydrgen as an in (H + ). An amin grup ( NH 2) cnsists f a nitrgen atm bnded t tw hydrgen atms and the carbn skeletn. Organic cmpunds with amin grups are amines. The amin grup acts as a base because it can pick up a hydrgen in (H + ) frm the slutin.

5 Amin acids, the building blcks f prteins, have amin and carbxyl grups. A sulfhydryl grup ( SH) cnsists f a sulfur atm bnded t a hydrgen atm and t the backbne. This grup resembles a hydrxyl grup in shape. Organic mlecules with sulfhydryl grups are thils. Tw sulfhydryl grups can interact t help stabilize the structure f prteins. A phsphate grup ( OPO 3 2 ) cnsists f a phsphrus atm bund t fur xygen atms (three with single bnds and ne with a duble bnd). A phsphate grup cnnects t the carbn backbne via ne f its xygen atms. Phsphate grups are anins with tw negative charges because 2 prtns dissciate frm the xygen atms. One functin f phsphate grups is t transfer energy between rganic mlecules. ATP is an imprtant surce f energy fr cellular prcesses. Adensine triphsphate, r ATP, is the primary energy transfer mlecule in living cells. ATP cnsists f an rganic mlecule called adensine attached t a string f three phsphate grups. When ne inrganic phsphate in is split ff as a result f a reactin with water, ATP becmes adensine diphsphate, r ADP. In a sense, ATP stres the ptential t react with water, releasing energy that can be used by the cell. Lecture Outline fr Campbell/Reece Bilgy, 8 th Editin, Pearsn Educatin, Inc. 4-5