Chapter 4 Carbon and the Molecular Diversity of Life

Lecture Outline Overview: CarbonThe Backbone of Biolo ical Molecules

Although cells are 7095% water, the rest consists of mostly carbon-based compounds. arbon enters the biosphere when photosynthetic organisms use the sun!s energy to transform "# into organic molecules, which are transferred to primary consumers. arbon accounts for the di$ersity of biological molecules, which has made possible the wide $ariety of li$ing things. %roteins, &'A, carbohydrates, and other molecules that distinguish li$ing matter from inorganic material are all composed of carbon atoms bonded to each other and to atoms of other elements. o (hese other elements commonly include hydrogen )*+, o,ygen )"+, nitrogen )'+, sulfur )-+, and phosphorus )%+.

Concept 4!" Or anic che#istry is the study of carbon co#pounds!

Or anic che#istry focuses on organic compounds containing carbon. o "rganic compounds can range from simple molecules, such as * ., to comple, molecules such as proteins, which may ha$e molecular masses greater than /00,000 daltons. o 0ost organic compounds contain hydrogen atoms. (he o$erall percentages of the ma1or elements of life ) , *, ", ', -, and %+ are 2uite uniform from one organism to another. 3ecause of carbon!s $ersatility, these few elements can be combined to build an ine,haustible $ariety of organic molecules. 4ariations in organic molecules can distinguish e$en indi$iduals of a single species. (he science of organic chemistry began with attempts to purify and impro$e the yield of products obtained from organisms. o 5nitially, chemists learned to synthesi6e simple compounds in the laboratory but had no success with more comple, compounds. (he -wedish chemist 7ons 7acob 3er6elius was the first to ma8e a distinction between organic compounds that seemed to arise in only li$ing organisms and inorganic compounds that were found in the nonli$ing world. 9arly organic chemists proposed vitalis#$ the belief that physical and chemical laws do not apply to li$ing things. o -upport for $italism waned as organic chemists learned to synthesi6e comple, organic compounds in the laboratory. o 5n the early /:00s, the ;erman chemist <riedrich =>hler and his students synthesi6ed urea from totally inorganic materials. 5n /95?, -tanley 0iller at the @ni$ersity of hicago set up a laboratory simulation of
.-1 Aecture "utline for ampbellBCeece Biology, :th 9dition, D %earson 9ducation, 5nc.

possible chemical conditions on the primiti$e 9arth and demonstrated the spontaneous synthesis of organic compounds. o (he mi,ture of gases 0iller created probably did not accurately represent the atmosphere of the primiti$e 9arth. o *owe$er, similar e,periments using more accurate atmospheric conditions also led to the formation of organic compounds. o -pontaneous synthesis of organic compounds may ha$e been an early stage in the origin of life on 9arth. "rganic chemists finally re1ected $italism and embraced #echanis#$ the belief that the same physical and chemical laws go$ern all natural phenomena, including the processes of life. "rganic chemistry was redefined as the study of carbon compounds, regardless of their origin. o o "rganisms produce the ma1ority of organic compounds. (he laws of chemistry apply to both inorganic and organic compounds.

(he foundation of organic chemistry is not a mysterious life force but rather the uni2ue $ersatility of carbon-based compounds.

Concept 4!% Carbon ato#s can for# diverse #olecules by bondin to four other ato#s!
A carbon atom has a total of E electronsF # in the first electron shell and . in the second shell. arbon has little tendency to form ionic bonds by losing or gaining . electrons to complete its $alence shell. arbon usually completes its $alence shell by sharing electrons with other atoms in four co$alent bonds, which may include single and double bonds. arbon!s tetravalence ma8es large, comple, molecules possible. o =hen a carbon atom forms co$alent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond angles of /09.5G. o 5n molecules with multiple carbon atoms, e$ery carbon atom bonded to four other atoms has a tetrahedral shape. o =hen two carbon atoms are 1oined by a double bond, all bonds around those carbons are in the same plane and ha$e a flat, three-dimensional structure. o (he electron configuration of carbon enables it to form co$alent bonds with many different elements. (he $alences of carbon and its partners can be $iewed as the building code that go$erns the architecture of organic molecules. 5n carbon dio,ide, one carbon atom forms two double bonds with two different o,ygen atoms. o 5n the structural formula, "H H", each line represents a pair of shared electrons. (his arrangement completes the $alence shells of all atoms in the molecule. Although "# can be classified as either organic or inorganic, its importance to the li$ing
.-2 Aecture "utline for ampbellBCeece Biology, :th 9dition, D %earson 9ducation, 5nc.

world is clearF "# is the source of carbon for all organic molecules found in organisms. o "# is usually fi,ed into organic molecules by the process of photosynthesis. @rea, ")'*#+#, is another simple organic molecule in which each atom forms co$alent bonds to complete its $alence shell.

Molecular diversity arises from variations in the carbon skeleton.

arbon chains form the s8eletons of most organic molecules. o arbon s8eletons $ary in length and may be straight, branched, or arranged in closed rings. o o arbon s8eletons may include double bonds. Atoms of other elements can be bonded to the atoms of the carbon s8eleton. &ydrocarbons are organic molecules that consist of only carbon and hydrogen atoms.

*ydrocarbons are the ma1or component of petroleum, a fossil fuel that consists of the partially decomposed remains of organisms that li$ed millions of years ago. <ats are biological molecules that ha$e long hydrocarbon tails attached to a nonhydrocarbon component. %etroleum and fat are hydrophobic compounds that cannot dissol$e in water because of their many nonpolar carbon-hydrogen bonds. *ydrocarbons can undergo reactions that release a relati$ely large amount of energy. 'so#ers are compounds that ha$e the same molecular formula but different structures and, therefore, different chemical properties. (tructural iso#ers ha$e the same molecular formula but differ in the co$alent arrangement of atoms. o -tructural isomers may also differ in the location of the double bonds. )eo#etric iso#ers ha$e the same co$alent partnerships but differ in the spatial arrangement of atoms around a carbon-carbon double bond. o (he double bond does not allow the atoms to rotate freely around the bond a,is. o (he biochemistry of $ision in$ol$es a light-induced change in the structure of rhodopsin in the retina from one geometric isomer to another. *nantio#ers are molecules that are mirror images of each other. 9nantiomers are possible when four different atoms or groups of atoms are bonded to an asy##etric carbon. o (he four groups can be arranged in space in two different ways that are mirror images of each other. o o (hey are li8e left-handed and right-handed $ersions of the molecule. @sually one is biologically acti$e, while the other is inacti$e.

9$en subtle structural differences in two enantiomers may ha$e important functional significance because of emergent properties from specific arrangements of atoms. o <or e,ample, one enantiomer of the drug thalidomide reduced morning sic8ness, the desired effect, but the other isomer caused se$ere birth defects.
Aecture "utline for ampbellBCeece Biology, :th 9dition, D %earson 9ducation, 5nc. .-3

Concept 4!+ Characteristic che#ical roups help deter#ine how biolo ical #olecules function!
(he distincti$e properties of an organic molecule depend not only on the arrangement of its carbon s8eleton but also on the chemical groups attached to that s8eleton. 5f we start with hydrocarbons as the simplest organic molecules, characteristic chemical groups can replace one or more of the hydrogen atoms bonded to the carbon s8eleton of a hydrocarbon. (hese chemical groups may be in$ol$ed in chemical reactions or may contribute to the shape and function of the organic molecule in a characteristic way, gi$ing it uni2ue properties. o As an e,ample, the basic structure of testosterone )a male se, hormone+ and estradiol )a female se, hormone+ is the same. o 3oth are steroids with four fused carbon rings, but the hormones differ in the chemical groups attached to the rings. o As a result, testosterone and estradiol ha$e different shapes, causing them to interact differently with many targets throughout the body. 5n other cases, chemical groups 8nown as functional roups affect molecular function through their direct in$ol$ement in chemical reactions. -e$en chemical groups are most important to the chemistry of lifeF hydro,yl, carbonyl, carbo,yl, amino, sulfhydryl, phosphate, and methyl groups. (he first si, chemical groups are functional groups. (hey are hydrophilic and increase the solubility of organic compounds in water. 0ethyl groups are not reacti$e but may ser$e as important mar8ers on organic molecules. 5n a hydro,yl group )I"*+, a hydrogen atom forms a polar co$alent bond with an o,ygen atom, which forms a polar co$alent bond to the carbon s8eleton. o 3ecause of these polar co$alent bonds, hydro,yl groups increase the solubility of organic molecules. o "rganic compounds with hydro,yl groups are alcohols, and their names typically end in -ol. A carbonyl group )J "+ consists of an o,ygen atom 1oined to the carbon s8eleton by a double bond. o o o 5f the carbonyl group is on the end of the s8eleton, the compound is an aldehyde! 5f the carbonyl group is within the carbon s8eleton, the compound is a ketone! 5somers with aldehydes and those with 8etones ha$e different properties.

A carbo,yl group )I ""*+ consists of a carbon atom with a double bond to an o,ygen atom and a single bond to the o,ygen atom of a hydro,yl group. o ompounds with carbo,yl groups are carbo,ylic acids! o A carbo,yl group acts as an acid because the combined electronegati$ities of the two ad1acent o,ygen atoms increase the chance of dissociation of hydrogen as an ion )* K+. An a#ino group )I'*#+ consists of a nitrogen atom bonded to two hydrogen atoms and the carbon s8eleton. o "rganic compounds with amino groups are a#ines!
.-4

Aecture "utline for ampbellBCeece Biology, :th 9dition, D %earson 9ducation, 5nc.

o (he amino group acts as a base because it can pic8 up a hydrogen ion )* K+ from the solution. o Amino acids, the building bloc8s of proteins, ha$e amino and carbo,yl groups. A sulfhydryl group )I-*+ consists of a sulfur atom bonded to a hydrogen atom and to the bac8bone. o o o (his group resembles a hydro,yl group in shape. "rganic molecules with sulfhydryl groups are thiols! (wo sulfhydryl groups can interact to help stabili6e the structure of proteins.

A phosphate group )I"%"?#L+ consists of a phosphorus atom bound to four o,ygen atoms )three with single bonds and one with a double bond+. o A phosphate group connects to the carbon bac8bone $ia one of its o,ygen atoms. o %hosphate groups are anions with two negati$e charges because # protons dissociate from the o,ygen atoms. o "ne function of phosphate groups is to transfer energy between organic molecules.

ATP is an important source of energy for cellular processes.

Adenosine triphosphate, or A(%, is the primary energy transfer molecule in li$ing cells. A(% consists of an organic molecule called adenosine attached to a string of three phosphate groups. =hen one inorganic phosphate ion is split off as a result of a reaction with water, A(% becomes adenosine diphosphate, or A&%. 5n a sense, A(% MstoresN the potential to react with water, releasing energy that can be used by the cell.

Aecture "utline for ampbellBCeece Biology, :th 9dition, D %earson 9ducation, 5nc.

.-5