1 Carbon and the Molecular Diversity of Life chapter 4 Site: wikipedia.org

2 Carbon—The Backbone of Biological Molecules  Cells 70–95% water – remainder mostly carbon-based compounds  Unparalleled ability to form large, complex, diverse molecules  Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

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4 Organic chemistry -- the study of carbon compounds  Organic compounds -- simple molecules to colossal ones  simplest -- hydrogen atoms in addition to carbon atoms

5 Carbon atoms form diverse molecules by bonding to up to four other atoms

6 LE 2-8 First shell Hydrogen 1 H Lithium 3 Li Second shell Third shell Sodium 11 Na Beryllium 4 Be Magnesium 12 Mg Boron 5 B Aluminum 12 Al Silicon 14 Si Carbon 6 C Nitrogen 7 N Phosphorus 15 P Oxygen 8 O Sulfur 16 S Chlorine 17 Cl Fluorine 9 F Neon 10 Ne Argon 18 Ar Helium 2 He Atomic number Element symbol Electron-shell diagram Atomic mass 2 He 4.00

7 Carbon and partners (hydrogen, oxygen, and nitrogen) -- building blocks of organic molecules Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4)

8 Components of Carbon Diversity Skeleton Variation Skeleton Variation Isomerization Isomerization Functional Groups Functional Groups

9 Each carbon bonded to four other atoms has a tetrahedral shape Each carbon bonded to four other atoms has a tetrahedral shape  Two carbon atoms joined in a double bond, the molecule is flat

LE 4-3 Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Methane Ethane Ethene (ethylene)

11 Molecular Diversity Arising from Carbon Skeleton Variation Carbon chains form the skeletons of most organic molecules Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape Carbon chains vary in length and shape  single, double, or triple  straight or branched chains  rings Bond with many different elements Bond with many different elements

LE 4-5 Length Ethane Propane Butane 2-methylpropane (commonly called isobutane) Branching Double bonds Rings 1-Butene 2-Butene Cyclohexane Benzene

13 Fig. 3-1, p. 46 Cyclopentane Ethane 1-Butene Isobutane Propane 2-Butene Isopentane Histidine (an amino acid) Benzene

14 Isomers Isomers are compounds with the same molecular formula but different structures and properties Isomers are compounds with the same molecular formula but different structures and properties  Structural isomers -- different covalent arrangements of their atoms

15 Dimethyl ether (C 2 H 6 O)Ethanol (C 2 H 6 O) Isomers Structural isomers Structural isomers  different covalent arrangements

16 Isomers Isomers are compounds with the same molecular formula but different structures and properties Isomers are compounds with the same molecular formula but different structures and properties  Structural isomers -- different covalent arrangements of their atoms  Geometric isomers -- covalent arrangements but differ in spatial arrangements

17 Isomers Geometric isomers (cis – trans isomers) Geometric isomers (cis – trans isomers)  different spatial arrangements cis-2-butenetrans-2-butene

18 Isomers Isomers are compounds with the same molecular formula but different structures and properties Isomers are compounds with the same molecular formula but different structures and properties  Structural isomers -- different covalent arrangements of their atoms  Geometric isomers -- covalent arrangements but differ in spatial arrangements  Enantiomers -- mirror images of each other

19 Isomers Enantiomers Enantiomers  mirror images

20 Important in the pharmaceutical industry Important in the pharmaceutical industry Different enantiomers may have different effects Different enantiomers may have different effects Organisms are sensitive to even subtle variations Organisms are sensitive to even subtle variations Enantiomers

21 LE 4-7 Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane. Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon. cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. L isomer D isomer Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

22 Isomers Isomers are compounds with the same molecular formula but different structures and properties Isomers are compounds with the same molecular formula but different structures and properties  Structural isomers -- different covalent arrangements of their atoms  Geometric isomers -- covalent arrangements but differ in spatial arrangements  Enantiomers -- mirror images of each other SHAPE -- critical SHAPE -- critical

23 Molecular Shape and Function shape very important (can be critical) to function shape very important (can be critical) to function shape determined by the positions of its atoms’ valence orbitals shape determined by the positions of its atoms’ valence orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes

LE 2-16a s orbital z x y Three p orbitals Four hybrid orbitals Tetrahedron Hybridization of orbitals

25 Biological molecules (especially proteins) recognize and interact with each other with a specificity based on molecular shape Biological molecules (especially proteins) recognize and interact with each other with a specificity based on molecular shape Molecules with similar shapes can have similar biological effects Molecules with similar shapes can have similar biological effects

LE 2-17a Natural endorphin Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Structures of endorphin and morphine

27 Functional groups -- involved in chemical reactions Distinctive properties Distinctive properties  depend not only on the carbon skeleton  depend on the molecular components attached to it

LE 4-9 Estradiol Testosterone Male lion Female lion

29 Functional Groups Properties depend on functional groups: Properties depend on functional groups:  Polar -- hydroxyl and carbonyl groups  Non-polar -- alkyl  Acidic and Basic o carboxyl and phosphate groups (acidic) o amino groups (basic)

Most important Functional Groups Hydrocarbons -- Alkyl most common Hydrocarbons -- Alkyl most common  Alkenyl and Alkynyl Hydroxyl group -- ROH Hydroxyl group -- ROH Carbonyl group -- RCOR′ Carbonyl group -- RCOR′  Aldehyde group -- RCOH Carboxyl group -- RCOOH Carboxyl group -- RCOOH  Ester group -- RCOOR′ Amino group Amino group Phosphate group Phosphate group Sulfhydryl group Sulfhydryl group 30

31 Hydrocarbons Organic compounds Organic compounds  nonpolar  carbon and hydrogen only  hydrophobic Methyl group Methyl group

32 Polar and Ionic Functional Groups Partial charges on atoms Partial charges on atoms  at opposite ends of a bond  interact with one another  hydrophilic Hydroxyl and carbonyl groups Hydroxyl and carbonyl groups

LE 4-10aa STRUCTURE (may be written HO—) NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Ethanol, the alcohol present in alcoholic beverages FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

LE 4-10ab STRUCTURE NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton EXAMPLE Acetone, the simplest ketone A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Aldehydes if the carbonyl group is at the end of the carbon skeleton Acetone, the simplest ketone Propanal, an aldehyde FUNCTIONAL PROPERTIES RCOR ′ RCOH

35 Acidic and Basic Groups Acidic Acidic  release hydrogen ions  become negatively charged  carboxyl and phosphate groups

LE 4-10ac STRUCTURE NAME OF COMPOUNDS Carboxylic acids, or organic acids EXAMPLE Has acidic properties because it is a source of hydrogen ions. Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H + ) tend to dissociate reversibly; for example, Acetic acidAcetate ion In cells, found in the ionic form, which is called a carboxylate group. RCOOH -- /carboxyl group  makes acids RCOOR′ -- Ester group

LE 4-10bc STRUCTURE NAME OF COMPOUNDS Organic phosphates EXAMPLE Glycerol phosphate FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules. ATP – Adenosine TriPhosphate

38 Acidic and Basic Groups Acidic Acidic  release hydrogen ions  become negatively charged  carboxyl and phosphate groups Basic Basic  release hydroxide ions  become positively charged  amino group

LE 4-10ba STRUCTURE NAME OF COMPOUNDS Amine EXAMPLE Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES Acts as a base; can pick up a proton from the surrounding solution: (nonionized) Ionized, with a charge of 1+, under cellular conditions Glycine (ionized)

STRUCTURE (may be written HS—) NAME OF COMPOUNDS Thiols EXAMPLE Ethanethiol FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20). LE 4-10bb

41 Table 3-1a, p. 49 Also RCOOR′

42 Table 3-1b, p. 49

43 ATP: An Important Source of Energy for Cellular Processes One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell One 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 ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups

44 The Chemical Elements of Life: A Review The versatility of carbon makes possible the great diversity of organic molecules The versatility of carbon makes possible the great diversity of organic molecules Variation at the molecular level lies at the foundation of all biological diversity Variation at the molecular level lies at the foundation of all biological diversity