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 Cells are 70–95% H 2 O, the rest is mostly Carbon based compounds C can form large, complex, and diverse molecules Protein/DNA/carbs/other molecules that distinguish living matter are all composed of C compounds Organic compounds range from simple to colossal molecules Most organic compounds contain H atoms in addition to C atoms

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 4.1: Organic chemistry is the study of carbon compounds Vitalism (idea that organic compounds arise only in organisms) was disproved when chemists synthesized these compounds Mechanism is the view that all natural phenomena are governed by physical and chemical laws Figure 4.2: Could organic compounds have been synthesized abiotically on the early Earth?

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration - key to atom’s characteristics as it determines the kinds/number of bonds an atom will form with other atoms With 4 valence electrons, C can form 4 covalent bonds with a variety of atoms – This tetravalence makes lg, complex molecules possible In molecules with multiple carbons, each carbon bonded to 4 other atoms has a tetrahedral shape However, when 2 C atoms are joined by a double bond, the molecule has a flat shape

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Methane Ethane Ethene (ethylene) Figure 4.3: The shapes of three simple organic molecules.

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings C’s electron configuration gives it covalent compatibility w/many different elements (H, O, N) Figure 4.4: Electron shell diagrams showing valences for the major elements of organic molecules Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4)

7. 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 C chains vary in length and shape Figure 4.5: Variations in carbon skeletons Length Ethane Propane Butane 2-methylpropane (commonly called isobutane) Branching Double bonds Rings 1-Butene2-Butene CyclohexaneBenzene

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydrocarbons Hydrocarbons - organic molecules with only C & H – Many organic molecules (ex: fats) have hydrocarbon components Hydrocarbons can undergo reactions that release a lg amount of energy

9. A fat molecule Mammalian adipose cells 100 µm Fat droplets (stained red) Figure 4.6: The role of hydrocarbons in fats.

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Isomers Isomers = compounds w/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 Enantiomers are important in the pharmaceutical industry Two enantiomers of a drug may have different effects

11. 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. Figure 4.7: Three types of isomers.

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Differing effects of enantiomers show that organisms are sensitive to subtle variations in molecules L -Dopa (effective against Parkinson’s disease) D -Dopa (biologically Inactive) Figure 4.8: The pharmocological importance of enantiomers.

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 4.3: Functional groups are the parts of molecules involved in chemical reactions Properties of organic molecules depend on the C skeleton AND on the molecules attached to it – Certain groups of atoms are often attached to skeletons of organic molecules Functional 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

14. Estradiol Testosterone Male lion Female lion Figure 4.9: A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones.

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 6 functional groups important in the chem of life: – Hydroxyl group – Carbonyl group – Carboxyl group – Amino group – Sulfhydryl group – Phosphate group

16. 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). Figure 4.10: Some Important Functional Groups of Organic Compounds

17. 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

18. 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.

19. 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)

20. 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).

21. 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.

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