1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Chapter 4 Carbon and the Molecular Diversity of Life

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: Carbon—The Backbone of Biological Molecules Although cells are 70–95% water, the rest is mostly C-based compounds Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Where do we ultimately get carbon to make the molecules necessary for life? What about life elsewhere? Do you think it is carbon-based life?

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

5. Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 4.1: Organic chemistry is the study of carbon compounds Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized the compounds Organic chem-study of carbon based compounds; 1 st built on the idea of vitalism The idea that there was a “life force” outside of physical & chem laws This was disproven by later experiments

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Mechanism-the view that all natural phenomena, are subject to physical & chem laws

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

9. Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration is the key to an atom’s characteristics E- configuration determines the kinds & # of bonds an atom will form with other atoms

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Formation of Bonds with Carbon W/ 4 valence e-s, carbon can form 4 covalent bonds w/ a variety of atoms This tetravalence makes large, complex molecules possible

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape This is b/c of the arrangement of its orbitals When 2 C atoms are joined by a dbl bond, the molecule has a flat shape

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

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The electron configuration of carbon gives it covalent compatibility w/ many diff elements The valences of C and its most frequent partners (H, O, & N) are the “building code” that governs the architecture of living molecules

14. LE 4-4 Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4)

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular Diversity Arising from Carbon Skeleton Variation C chains form the skeletons of most organic molecules Carbon chains vary in length and shape Animation: Carbon Skeletons Animation: Carbon Skeletons

16. LE 4-5 Length Ethane Propane Butane 2-methylpropane (commonly called isobutane) Branching Double bonds Rings 1-Butene2-Butene CyclohexaneBenzene

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydrocarbons Hydrocarbons- organic molecules of only C & H Many organic molecules, such as fats, have hydrocarbon components * rxns w/these release a lg amt of energy

18. LE 4-6 A fat moleculeMammalian adipose cells 100 µm Fat droplets (stained red)

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Isomers Isomers- cmpds w/ the same molecular formula but diff structures & properties: – Structural isomers- diff covalent arrangements of their atoms – Geometric isomers- same covalent arrangements, differ in spatial arrangements – Enantiomers- mirror images of each other Animation: Isomers Animation: Isomers

20. 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.

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enantiomers- impt in the pharmaceutical industry 2 enantiomers of a drug may have diff effects Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules Animation: L-Dopa Animation: L-Dopa

22. LE 4-8 L -Dopa (effective against Parkinson’s disease) D -Dopa (biologically Inactive)

23. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 4.3: Functional groups are the parts of molecules involved in chemical reactions Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it Certain groups of atoms are often attached to skeletons of organic molecules

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Functional Groups Most Important in the Chemistry of Life Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The # & arrangement of funct grps give each molecule its unique properties

25. LE 4-9 Estradiol Testosterone Male lion Female lion

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 6 functional groups that are most impt in biochemistry: – Hydroxyl group OH – Carbonyl group COO – Carboxyl group COOH – Amino group NH 2 – Sulfhydryl group SH – Phosphate group PO 4

27. 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).

28. 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

29. 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.

30. 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)

31. LE 4-10bb 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).

32. 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.

33. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ATP: An Important Source of Energy for Cellular Processes A phosphate molecule- adenosine triphosphate (ATP), is primary energy- transferring molecule in the cell ATP is an organic molecule called adenosine attached to a string of 3 phosphate groups

34. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Chemical Elements of Life: A Review 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

35. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exam practice What is the reason why hydrocarbons are not soluble in water? A) The majority of their bonds are polar covalent carbon to hydrogen linkages. B) The majority of their bonds are nonpolar covalent carbon-to-hydrogen linkages. C) They are hydrophilic. D) They exhibit considerable molecular complexity and diversity. E) They are lighter than water.

36. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exam practice Hydrocarbons mainly consist of H-C nonpolar covalent bonds and thus not soluble in water The answer is B

37. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exam

38. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exam practice The two molecules shown in Figure 4.1 are best described as A) optical isomers. B) radioactive isotopes. C) structural isomers. D) nonradioactive isotopes. E) geometric isomers.

39. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exam practice The answer is C structural isomers This is because structural isomers differ in covalent patterns Geometric isomers differ in arrangement about a double bond Enantiomers differ in spatial arrangement around an asymmetric carbon (mirror images)