1. AP Biology 2007-2008 Chemistry of Carbon Building Blocks of Life

2. AP Biology Why study Carbon?  All of life is built on carbon  Cells  ~72% H 2 O  ~25% carbon compounds  Carbohydrates  Lipids  Proteins  Nucleic Acids  ~3% salts  Na, Cl, K…

3. AP Biology Chemistry of Life  Organic chemistry is the study of carbon compounds  C atoms are versatile building blocks  bonding properties  4 stable covalent bonds HH C H H

4. AP Biology Complex molecules assembled like TinkerToys

5. AP Biology 2007-2008 Fig. 4-7b (b) Geometric isomers cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides.

6. AP Biology Hydrocarbons  Combinations of C & H  Methane  not soluble in H 2 O  stable  very little attraction between molecules  a gas at room temperature methane (simplest HC)

7. AP Biology Hydrocarbons can grow

8. AP Biology Isomers  Molecules with same molecular formula but different structures (shapes)  different chemical properties  different biological functions 6 carbons

9. AP Biology Form affects function  Structural differences create important functional significance  amino acid alanine  L-alanine used in proteins  but not D-alanine  medicines  L-version active  but not D-version  sometimes with tragic results… stereoisomers

10. AP Biology Form affects function  Thalidomide  prescribed to pregnant women in 50s & 60s  reduced morning sickness, but…  stereoisomer caused severe birth defects

11. AP Biology Diversity of molecules  Substitute other atoms or groups around the carbon  ethane vs. ethanol  H replaced by an hydroxyl group (–OH)  nonpolar vs. polar  gas vs. liquid  biological effects! ethane (C 2 H 6 ) ethanol (C 2 H 5 OH)

12. AP Biology Functional groups  Parts of organic molecules that are involved in chemical reactions  give organic molecules distinctive properties hydroxyl amino carbonyl sulfhydryl carboxyl phosphate  Affect reactivity  increase solubility in water

13. AP Biology Viva la difference!  Basic structure of male & female hormones is identical  identical carbon skeleton  attachment of different functional groups  interact with different targets in the body  different effects

14. AP Biology Hydroxyl  –OH  organic compounds with OH = alcohols  names typically end in -ol  ethanol

15. AP Biology Carbonyl  C=O  O double bonded to C  if C=O at end molecule = aldehyde  if C=O in middle of molecule = ketone

16. AP Biology Carboxyl  –COOH  C double bonded to O & single bonded to OH group  compounds with COOH = acids  fatty acids  amino acids

17. AP Biology Amino  -NH 2  N attached to 2 H  compounds with NH 2 = amines  amino acids  NH 2 acts as base  ammonia picks up H + from solution

18. AP Biology Sulfhydryl  –SH  S bonded to H  compounds with SH = thiols  SH groups stabilize the structure of proteins

19. AP Biology Phosphate  –PO 4  P bound to 4 O  connects to C through an O  lots of O = lots of negative charge  highly reactive  transfers energy between organic molecules  ATP, GTP, etc.

20. AP Biology 2007-2008 Fig. 4-10a Hydroxyl CHEMICAL GROUP STRUCTURE NAME OF COMPOUND EXAMPLE FUNCTIONAL PROPERTIES Carbonyl Carboxyl (may be written HO—) 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 an —OH group, the entire assembly of atoms is called a carboxyl group (—COOH). Carboxylic acids, or organic acids Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton Alcohols (their specific names usually end in -ol) Ethanol, the alcohol present in alcoholic beverages Acetone, the simplest ketone Acetic acid, which gives vinegar its sour taste Propanal, an aldehyde Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion). Acetic acid Acetate ion A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. These two groups are also found in sugars, giving rise to two major groups of sugars: aldoses (containing an aldehyde) and ketoses (containing a ketone). Is polar as a result of the electrons spending more time near the electronegative oxygen atom. Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars. The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond.

21. AP Biology 2007-2008 Fig. 4-10b CHEMICAL GROUP STRUCTURE NAME OF COMPOUND EXAMPLE FUNCTIONAL PROPERTIES AminoSulfhydrylPhosphate Methyl A methyl group consists of a carbon bonded to three hydrogen atoms. The methyl group may be attached to a carbon or to a different atom. 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. The phosphate group (—OPO 3 2–, abbreviated ) is an ionized form of a phosphoric acid group (—OPO 3 H 2 ; note the two hydrogens). P The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. (may be written HS—) The amino group (—NH 2 ) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. AminesThiolsOrganic phosphatesMethylated compounds 5-Methyl cytidine 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes. Glycerol phosphate Cysteine Cysteine is an important sulfur-containing amino acid. Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function. Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates). Has the potential to react with water, releasing energy. Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds. Acts as a base; can pick up an H + from the surrounding solution (water, in living organisms). Ionized, with a charge of 1+, under cellular conditions. (nonionized) (ionized)

22. AP Biology 2007-2008 Fig. 4-10c STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Carboxyl Acetic acid, which gives vinegar its sour taste Carboxylic acids, or organic acids Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion). Acetic acidAcetate ion

23. AP Biology 2007-2008 Fig. 4-10d STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Amino Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Amines Acts as a base; can pick up an H + from the surrounding solution (water, in living organisms). Ionized, with a charge of 1+, under cellular conditions. (ionized)(nonionized) Glycine

24. AP Biology 2007-2008 Fig. 4-10e STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Sulfhydryl (may be written HS—) Cysteine Cysteine is an important sulfur-containing amino acid. Thiols Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds.

25. AP Biology 2007-2008 Fig. 4-10f STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Phosphate In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes. Glycerol phosphate Organic phosphates Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates). Has the potential to react with water, releasing energy.

26. AP Biology 2007-2008 Fig. 4-10g STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Methyl 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. 5-Methyl cytidine Methylated compounds Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function.

27. AP Biology 2007-2008 Macromolecules Building Blocks of Life

28. AP Biology Macromolecules  Smaller organic molecules join together to form larger molecules  4 major classes of macromolecules:  Proteins  Carbohydrates  Lipids  Nucleic Acids

29. AP Biology H2OH2O HO H HH Polymers  Long molecules built by linking repeating building blocks in a chain  Monomers  building blocks  repeated small units  Dehydration synthesis

30. AP Biology H2OH2O HO H HH How to build a polymer  Chemical reaction that  joins monomers by “taking” H 2 O out  one monomer donates OH –  other monomer donates H +  together these form H 2 O enzyme Dehydration synthesis Condensation reaction or

31. AP Biology H2OH2O HOH H H How to break down a polymer  Chemical Reaction that breaks polymers  use H 2 O to breakdown polymers  reverse of dehydration synthesis  cleave off one monomer at a time  H 2 O is split into H + and OH –  H + & OH – attach to ends Hydrolysis enzyme

32. AP Biology 2007-2008 Any Questions??