Review

1. Review • Buffers • If H+ goes up (low pH), H+ is “soaked up” by carbonic acid • If H+ goes down (high pH), carbonic acid will dissociate to release more H+ into solution

2. Chapter 4 Carbon and the Molecular Diversity of Life

3. Organic chemistry • Definition – chemistry of reduced carbon compounds Primary non-aqueous components of biological systems

4. Figure 4.1 • Overview: Carbon—The Backbone of Biological Molecules • All living organisms • Are made up of chemicals based mostly on the element carbon

5. Concept 4.1: Organic chemistry is the study of carbon compounds • Organic compounds • Range from simple molecules to colossal ones

6. Why carbon? • Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms • 1. capacity to form 4 covalent bonds • 2. angles of available bonding orbitals afford optimal spacing for the addition of covalently bonded groups • 3. Carbon can be covalently bonded together to form long chains

7. 1. The Formation of Bonds with Carbon • Carbon has four valence electrons • This allows it to form four covalent bonds with a variety of atoms

9. Name and Comments Space-Filling Model Molecular Formula Structural Formula Ball-and-Stick Model H (a) Methane CH4 C H H H H H (b) Ethane C2H6 C H C H H H H H (c) Ethene (ethylene) C C C2H4 H H Figure 4.3 A-C 2. Bonding Angles • The bonding versatility of carbon • Allows it to form many diverse molecules, including carbon skeletons

10. Carbon (valence = 4) Nitrogen (valence = 3) Hydrogen (valence = 1) Oxygen (valence = 2) O H N C Figure 4.4 • The electron configuration of carbon • Gives it covalent compatibility with many different elements

11. H H C C C C H H C H H H H H H C H H H H H H H H H H H H C C C C C C C H H H H H H H H H H H H (a) Length H Ethane Propane H H H H H H H H H H H C C C C C C C C H H H H (b) Branching 2-methylpropane (commonly called isobutane) Butane H H H H C H (c) Double bonds H H C C C H H C C H H C C 1-Butene 2-Butene H H C C C (d) Rings Figure 4.5 A-D Cyclohexane Benzene 3. Molecular Diversity Arising from Carbon Skeleton Variation • Carbon chains (can form long chains) • Form the skeletons of most organic molecules • Vary in length and shape

12. Basic components of organic molecules • 1. Carbon backbone or skeleton • A. Primarily composed of C & H • B. Confers basic size & shape to molecule • C. May be in a chain or a ring shape

13. Ex. Hydrocarbons • Hydrocarbons • Are molecules consisting of only carbon and hydrogen

14. Fat droplets (stained red) 100 µm (b) Mammalian adipose cells (a) A fat molecule Figure 4.6 A, B • Hydrocarbons • Are found in many of a cell’s organic molecules

15. Basic components of organic molecules cont. • D. Many organic molecules share molecular formulas. These molecules differ in the arrangement of atoms w/in molecules. • 1. must be depicted as structural formulas Called ISOMERS.

16. Isomer example

17. Isomers • Isomers • Are molecules with the same molecular formula but different structures and properties

18. H H H C H H C H H H H H H H (a) Structural isomers H C C C C C H H C H C C H H H H H H H H H X X X C C C C (b) Geometric isomers X H H H CO2H CO2H C C (c) Enantiomers H H NH2 NH2 CH3 CH3 Figure 4.7 A-C • Three types of isomers are • 1. Structural • 2. Geometric • 3. Enantiomers

19. 1. Structural isomers (constitutional isomers) • Isomers that display gross differences in the arrangement of carbons in the backbone.

20. Geometric isomers (locational isomers) • Only displayed by molecules that contain a double bond w/in the carbon backbone

21. 3. Enantiomers (sterioisomers) • Only found in molecules that contain a ASYMETRIC (chiral) carbon Def. chiral – carbon w/4 different groups attached to it

22. Enantiomers • Differ in the arrangement of groups around the chiral carbon in such a way as to produce functional MIRROR images • *very similar to hands and feet • *enantiomers are chemically equivalent, but NOT BIOLOGICALLY equivalent

23. Enantiomers • Named D (R) if they rotatio plarized light to the right • Named L (S) if they rotate polarized light to the left

24. Biological significance • Living org’s can readily differentiate between enantiomers • Ex. Thalidomide • L enantiomer – safe • D enantiomer – teratogenic (causing major malformation of fetus) • Racemized mixture – equal parts D & L enantiomers

25. L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive) Figure 4.8 • Enantiomers • Are important in the pharmaceutical industry

27. Functional groups • Concept 4.3: Functional groups are the parts of molecules involved in chemical reactions

28. OH CH3 Estradiol HO Female lion OH CH3 CH3 O Testosterone Male lion Figure 4.9 • Give organic molecules distinctive chemical properties

29. Functional groups • A. Confer specific REACTIVITY to organic molecules • 1. most chemical rxn’s involving organic molecules do NOT involve the carbon backbone • 2. Most chemical rxn’s DO involve one or more of the functional groups on a molecule

30. Six functional groups are important in the chemistry of life • Hydroxyl • Carbonyl • Carboxyl • Amino • Sulfhydryl • Phosphate

34. FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O O OH C C OH (may be written HO ) STRUCTURE In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) The carbonyl group( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH).  Figure 4.10 • Some important functional groups of organic compounds

35. Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Carboxylic acids, or organic acids EXAMPLE H H H H O O C C H OH C C H C H C H OH H H H H C Ethanol, the alcohol present in alcoholic beverages H H Acetic acid, which gives vinegar its sour tatste Acetone, the simplest ketone H H O H C C C H H H Propanal, an aldehyde Figure 4.10 • Some important functional groups of organic compounds

36.  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). FUNCTIONALPROPERTIES  Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example,  A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. H H O O + H+ H C H C C C OH O H H  In cells, found in the ionic form, which is called a carboxylate group. Figure 4.10 • Some important functional groups of organic compounds

37. AMINO SULFHYDRYL PHOSPHATE O H SH N P OH O (may be written HS ) H OH In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO32–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. Figure 4.10 • Some important functional groups of organic compounds

38. OH O OH H H H H H O H C C C O P O N C C SH H C C HO H H H H O H H H Ethanethiol Glycine Glycerol phosphate Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Figure 4.10 • Some important functional groups of organic compounds

39.  Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).  Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules.  Acts as a base; can pick up a proton from the surrounding solution: H H N +N H H H (nonionized) (ionized)  Ionized, with a charge of 1+, under cellular conditions. Figure 4.10 • Some important functional groups of organic compounds

43. Important Functional Groups and properties • 1. OH (hydroxyl) – polar, attracts water molecules, help dissolve organic compounds • 2. CO (carbonyl) – ketones and aldehydes may be structural isomers with different properties • 3. COOH (carboxyl) – acidic properties b/c of H+, Covalent bond between O and H is polar so H+ tend to dissociate

44. Impt functional Group properties • 4. NH2 (amino)- acts as base, can pick up proton, ionized with +1 charge in cells (NH3) • 5. SH (Sulfydryl) – two sulfhydryl groups can interact to help stabilize protein structure • 6. OPO3 (phosphate) – make molecule anion (neg. charged), transfers energy btwn organic molecules.

45. Macromolecules • A. Def. – large polymers of organic monomers 1. macromolecules are formed by dehydraton reaction (removal of a water molecule)

46. 2. Bonds between monomers are broken by hydrolysis (add water, breaks bond)

47. Ex. Digestive system Macromolecules are broken down by Hydrolytic enzymes Hydrolytic enzymes are enzymes that catalyze hydrolysis Only monomers of macromolecules can be absorbed by small intestine.

48. B. Categories of Macromolecules • 1. Carbohydrates (sugars & sugar polymer) • 2. Lipids (fats, oils, waxes) • 3. Proteins (polymers of amino acids) • 4. Nucleic acids (DNA, RNA, polymers of nucleotides)