1. Chapter 4 Carbon & the Molecular Diversity of Life

2. The Backbone of Biological Molecules What compound makes up the majority of matter in cells? Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates Why is carbon so versatile?

3. 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?

5. Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms Hydrocarbons Quick Review: What are the elements that are most common in biological compounds? ◦O, H, S, P, and of course C

6. Organic chemistry is the study of carbon compounds Vitalism - the idea that organic compounds arise only in organisms Swedish scientist, Berzelius - The idea that there was a “life force” outside of physical & chemical laws Organic chemistry - study of carbon based compounds

7. Organic Chemistry - Origins Friedrich Wöhler accidentally created urea in his lab Hermann Kolbe created acetic acid from inorganic substance Stanley Miller demonstrated possible origin of life through synthesis of organic compounds

8. Vitalism  Mechanism ◦the view that all natural phenomena, are subject to physical & chemical laws Paradigm shift…

10. The Structure of Carbon Atoms What is the electron configuration of carbon? Why is the electron configuration important? What kind of bond is carbon going to form?

11. The Formation of Bonds with Carbon Four valence electrons = four covalent bonds (tetravalence)

12. Structure of Organic Molecules What shape is a carbon molecule with four single bonds? Why is the bond angle the same for each bond?

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

14. Structure of Organic Molecules Carbon most commonly forms bonds with: Oxygen Nitrogen Hydrogen Brainstorm: Why do you think that these elements are the most likely to form organic compounds?

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

16. Hydrocarbons Carbon is able to form long chains that vary in length and shape

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

18. Hydrocarbons Only contain carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Brainstorm: Why do you think that hydrocarbons might be important for biological processes?

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

20. Isomers Compounds with multiple possible structures and functions ◦Structural isomers- arrangement of bonds and atoms ◦Geometric isomers- same covalent placement, different spatial arrangements (e.g. cis/trans) ◦Enantiomers- mirror images

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. Enantiomers Thalidomide ◦Treatment for morning sickness ◦Causes limb deformities in newborns Ethambutol ◦Treatment for tuberculosis ◦Causes blindness Naproxen ◦Treatment for arthritis ◦Causes liver poisoning Why is thalidomide especially dangerous?

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

24. Functional Groups Molecular structures that are responsible for the chemical characteristics of a compound Most reactions (in organic chemistry) depend on the functional groups Methylamine

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

26. Know these functional groups! ◦Hydroxyl group OH ◦Carbonyl group CO ◦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. ATP: An Important Source of Energy for Cellular Processes Adenosine triphosphate (ATP)- primary energy-transferring molecule in the cell

34. The Chemical Elements of Life: A Review Why is the versatility of carbon so important for biological processes?

35. 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. Exam practice Hydrocarbons mainly consist of H-C nonpolar covalent bonds and thus not soluble in water The answer is B

37. Exam

38. Exam practice The two molecules shown in Figure 4.1 are best described as A) optical isomers (enantiomers). B) radioactive isotopes. C) structural isomers. D) nonradioactive isotopes. E) geometric isomers.

39. 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)

40. Functional Group Activity