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

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Organic chemistry Definition – chemistry of reduced carbon compounds Primary non-aqueous components of biological systems

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: Carbon—The Backbone of Biological Molecules All living organisms – Are made up of chemicals based mostly on the element carbon Figure 4.1

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 4.1: Organic chemistry is the study of carbon compounds Organic compounds – Range from simple molecules to colossal ones

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

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9. 2. Bonding Angles The bonding versatility of carbon – Allows it to form many diverse molecules, including carbon skeletons (a) Methane (b) Ethane (c) Ethene (ethylene) Molecular Formula Structural Formula Ball-and- Stick Model Space- Filling Model H H H H H H H H H H HH H H C C C CC CH 4 C2H6C2H6 C2H4C2H4 Name and Comments Figure 4.3 A-C

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The electron configuration of carbon – Gives it covalent compatibility with many different elements H O NC Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) Figure 4.4

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 H H H H H H H H H H H HHH H H H H H H H H H H H H H H H H HH H H HH HHH H HH HH H H H H H H H C C CCC CCCCCCC CCCCCCCC C C C C C C C C C C C C H H H H H H H (a) Length (b) Branching (c) Double bonds (d) Rings Ethane Propane Butane 2-methylpropane (commonly called isobutane) 1-Butene2-Butene Cyclohexane Benzene HH HHH Figure 4.5 A-D

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ex. Hydrocarbons Hydrocarbons – Are molecules consisting of only carbon and hydrogen

14. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydrocarbons – Are found in many of a cell’s organic molecules (a) A fat molecule (b) Mammalian adipose cells 100 µm Fat droplets (stained red) Figure 4.6 A, B

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Isomer example

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Isomers – Are molecules with the same molecular formula but different structures and properties

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Three types of isomers are – 1. Structural – 2. Geometric – 3. Enantiomers H H HH H H H H HH H H H HH H H H H H H H H H H H H H CO 2 H CH 3 NH 2 C CO 2 H H CH 3 NH 2 XX X X C CCCC C C C C C C C C C C (a) Structural isomers (b) Geometric isomers (c) Enantiomers H Figure 4.7 A-C

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 1. Structural isomers (constitutional isomers) Isomers that display gross differences in the arrangement of carbons in the backbone.

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Geometric isomers (locational isomers) Only displayed by molecules that contain a double bond w/in the carbon backbone

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3. Enantiomers (sterioisomers) Only found in molecules that contain a ASYMETRIC (chiral) carbon Def. chiral – carbon w/4 different groups attached to it

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enantiomers Named D (R) if they rotatio plarized light to the right Named L (S) if they rotate polarized light to the left

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enantiomers – Are important in the pharmaceutical industry L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive) Figure 4.8

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

28. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings – Give organic molecules distinctive chemical properties CH 3 OH HO O CH 3 OH Estradiol Testosterone Female lion Male lion Figure 4.9

29. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Six functional groups are important in the chemistry of life – Hydroxyl – Carbonyl – Carboxyl – Amino – Sulfhydryl – Phosphate

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34. Some important functional groups of organic compounds FUNCTIONAL GROUP STRUCTURE (may be written HO ) HYDROXYL CARBONYL CARBOXYL OH 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 –.) 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). C OO C OH Figure 4.10 The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. 

35. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Some important functional groups of organic compounds Acetic acid, which gives vinegar its sour tatste NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton Carboxylic acids, or organic acids EXAMPLE Propanal, an aldehyde Acetone, the simplest ketone Ethanol, the alcohol present in alcoholic beverages H H H HH CC OH H H H H H H H C C H C C C CCC O H O H H HH H O H Figure 4.10

36. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Some important functional groups of organic compounds 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).  A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.  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,  In cells, found in the ionic form, which is called a carboxylate group. H H C H H C O OH H H C O C OO + H + Figure 4.10

37. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Some important functional groups of organic compounds The amino group (—NH 2 ) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. AMINO SULFHYDRYL PHOSPHATE (may be written HS ) The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. 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 (—OPO 3 2– ) is an ionized form of a phosphoric acid group (— OPO 3 H 2 ; note the two hydrogens). N H H SH O P O OH Figure 4.10

38. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Some important functional groups of organic compounds Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Glycine Ethanethiol Glycerol phosphate O C HO C H H N H H H CC SH H H H H H OH CCCOPOO OO HHH O H Figure 4.10

39. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Some important functional groups of organic compounds  Acts as a base; can pick up a proton from the surrounding solution:  Ionized, with a charge of 1+, under cellular conditions. (nonionized) (ionized) N H H H +N+NH H  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. Figure 4.10

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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. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Macromolecules A. Def. – large polymers of organic monomers 1. macromolecules are formed by dehydraton reaction (removal of a water molecule)

46. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 2. Bonds between monomers are broken by hydrolysis (add water, breaks bond)

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