water

1. Our first “functional group”: hydroxyl, -OH H O H Covalent bond (strength = ~100 kcal/mole) 1 E. coli molecule #1 water H2O HOH 105o

2. Waterdeltas Negative pole Positive pole 2 δ+ = partial charge, not quantified Not “ + ” , a full unit charge, as in the formation of ions by NaCl in solution: NaCl  Na+ + Cl- Water is a POLAR molecule (partial charge separation)

3. waterHbonds Hydrogen bond

4. Ethanol and Water 4 3 2 2 3

5. amide3 R= any group of atoms (the rest of the molecule) Note: carbon atoms always make 4 bonds R-CONH2 is an “amide”, -CONH2 is an amide group (another functional group) Note: Don’t think of the amide as a C=O and an –NH2; the whole thing is one functional group, the amide. It is highly polar but with no full charges

6. 6 ethanol, an alcohol an amide Hydrogen bonds between 2 organic molecules Water often out-competes this interaction (but not always)

7. Hydrogen bonds between 2 organic molecules ethanol, an alcohol an amide They face formidable competition from water

8. X Not all molecules are polar; e.g. octane, a non-polar, or apolar molecule CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3 H H H H H H H H | | | | | | | | H-C-C-C-C-C-C-C-C-H Note the absence of δ’s | | | | | | | | H H H H H H H H

9. Chemical Bonds • Bond: • Energy needed to break: • Comments: • Strength class-ification: • Covalent • ~100 • kcal/mole • Electrons • shared • strong

10. 1 calorie = amount of energy needed to raise the temperature of 1 gram of water (1 cc or ml. of water) one degree C 1 Calorie = dietary calorie = 1000 calories 1 kilocalorie (kcal) = 1000 calories

11. Chemical Bonds • Bond: • Energy needed to break: • Comments: • Strength class-ification: • Covalent • ~100 • kcal/mole • Electrons • shared • strong Hydrogen ~3 Water-water; Organic-water; Organic-organic(having polar functional groups) weak

12. Full loss or capture of an electron Full charge separation Full positive charge, or full negative charge (= charge of one electron) E.g. NaCl = Na+:::Cl-Strong bond between the ions in acrystal (e.g., rock salt) But: weak in aqueous solution So the ionic bond of NaCl becomes weak in water Is the bond between an Na+ ion and water ionic or an H-bond? Some characteristics of each: a “polar interaction” or an “ion-dipole interaction” Ionic bonds

13. BASES = amines Gain a proton R-NH2 + H+ R-NH3+ (net charge ≈ +1 at pH 7) Example: ethyl amine:CH3-CH2-NH2 ACIDS= carboxylic acids Lose a proton O O|| || R-C-OH  R-C-O-+ H+ (net charge ≈ -1 at pH 7) Example: acetic acid: CH3-COOH Organic IONS = acids and bases Carboxyl group = -COOH Amine group = -NH2 Where does the base get the proton? Are there any protons around in water at pH7?

14. Under the right conditions (to be seen later), two oppositely charged organic ions can form an ionic bond: O || R-C-O- - - - - - +H3N-R Weak, ~ 5 kcal/mole. But these weak bonds are VERY important for biological molecules …….

15. 15 The chemical structures of the functional groups used in this course must be memorized. See the Functional Groups handout. This is one of very few memorizations required. O || -C -- OH “carboxyl” Me You

16. Chemical Bonds • Bond: • Energy needed to break: • Comments: • Strength class-ification: • Covalent • ~100 • kcal/mole • Electrons • shared • strong Hydrogen ~3 Water-water; Organic-water; Organic-organic weak; orientation dependent Ionic ~5 Full charge transfer; Can attract H-bond; Strong in crystal weak

17. Van der Waals bonds First molecule • Can form between ANY two atoms that approach each other • “Fluctuating induced dipole” • Very weak (~ 1 kcal/m) • Effective ONLY at very close range (1A)(0.1 nm) “ “

18. Chemical Bonds • Bond: • Energy needed to break: • Comments: • Strength • Class- • ification: • Covalent • ~100 • kcal/mole • Electrons • shared • strong Hydrogen ~3 Water-water; Organic-water; Organic-organic weak Ionic ~5 Full charge transfer; Can attract H-bond; Strong in crystal weak Van der Waals ~1 Fluctuating induced dipole; Close range only weak Why are we doing all this now?

19. Chemical Bonds • Bond: • Energy needed to break: • Comments: • Strength class-ification: • Covalent • ~100 • kcal/mole • Electrons • shared • strong Hydrogen ~3 Water-water; Organic-water; Organic-organic weak Ionic ~5 Full charge transfer; Can attract H-bond; Strong in crystal weak Van der Waals ~1 Fluctuating induced dipole; Very close range only weak Hydro-phobic forces ~3 Not a bond per se; entropy driven; only works in water weak

20. Consider octane, C8H18, or: CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3 Electro-negativities of C and H are ~ equal No partial charge separation Non-polar (apolar), cannot H-bond to water, = “hydrophobic” Contrast: polar compounds = “hydrophilic”

21. Octane in water (These numbers are made up.)

22. (These numbers are made up.)

23. ENTROPY: related to the number of different states possible The water molecules around the non-polar molecule have a LOWER entropy (less choices, more ordered). Systems tend to change to maximize entropy (no. ofdifferent states possible to occupy). Aggregation of the non-polar molecules with each other minimizes the number of lower entropy water molecules that are on their surface, thus maximizing the entropy of the system

24. Admittedly, the non-polar octane molecules lose entropy when they coalesce. That is, they are more disordered when they are separate. • However, this loss of entropy apparently cannot counteract the gain in entropy of the system brought about by the freeing up of water molecule from the “cage” around the non-polar molecules.

25. Affects NON-polar molecules that find themselves in an aqueous environment (i.e., must be in water) They cannot H-bond with water molecules The water molecules around the non-polar molecule are not able to constantly switch partners for H-bonding The water molecules around the non-polar molecule are in a MORE ordered state. Hydrophobic “forces”, not really “bonds” per se Hydrophobic “bonds” (forces)

26. Water cages around methane: CH4 3 artists’ depictions

27. LARGE >= ~5000 daltons Called macromolecules Examples:proteins, polysaccharides, DNA SMALL <= ~500 daltons (~ 50 atoms) Called small molecules Size differences are rough, there are gray areas Examples:water, ethanol, glucose,acetamide, methane, octane End of bonds, and water, our molecule #1Now on to the next 4999 types of molecules found in an E. coli cell:First let’s categorize: Small vs. large molecules

28. Propylene CH3-CH=CH2 Polypropylene, a polymer, a large molecule

29. Large molecules are built up from small molecules One possibility: Poly ?

30. Or from many different small molecules? No

31. A great simplification: Large molecules are linearpolymers of small molecules. O-O-O-O-O-O-O-………

32. a monomer of the polymer Nomenclature for polymers monomer O O-O dimer trimer O-O-O tetramer O-O-O-O oligomer O-O-O-O-O-O-O oligomer O-O-O-O-O-O-O-O-O-O-O polymer

33. polysaccharides, lipids, nucleic acids, and proteins. Many important small molecules are the monomers of these polymers. Only about 50 of these monomers, a small number to learn about. About another dozen important small molecules are not monomers of polymers. Mostly vitamins. The large molecules, or macromolecules, of all cells can be grouped into 4 categories:

34. Monomers and polymersExample 1. Macromolecule: polysaccharide A monomer of many polysaccharides is glucose: Present in our minimal medium ) .

35. Getting the monomers CH3 C Example 2: Macromolecule: protein Monomer: amino acids Example at right = alanine Looks nothing like glucose Where does E. coli get alanine? COOH H2N H

36. E. coli makes all the monomers by biochemical transformations starting from glucose glucose →A → B→C →D →E →alanine →protein A, B, C, D, E, are “intermediates”: i.e., intermediate chemical structures (molecules) between glucose and alanine.

38. 50 monomers 15 non-monomer important small molecules (e.g., like vitamins) 65 total “end products” Average pathways to monomers and important small molecules starting from glucose:= ~ 10 steps, so ~9 intermediates per pathway 65 such pathways  65 x 9 = 585 intermediates 65 end-products + 585 intermediates = 650 total types of small molecules per E. coli cell A manageable number, and we ~know them all Very rough estimate of the total number of different small molecules in an E. coli cell:

39. Monomer = sugars Sugars = small carbohydrate molecules Carbohydrates ~= CnH2nOn Contain one C=O group and many –OH’s Can contain other functional groups as well (carboxyls, amines) Most common sugar and monomer is glucose Macromolecule class #1:Polysaccharides

40. C C Remember, always 4 bonds to carbon; Often even if not depicted Glucose, straight chain depictions Abbreviated With numbering

41. anomeric carbon Fisher view Haworth view Handout 2-7 Chair view

42. 11 10 7 5 8 9 6 4 1 2 3

43. 7 5 8 9 6 4 1 2 3

44. alpha-glucose beta-glucose

45. anomeric carbon Fisher view Haworth view Handout 2-7 Chair view

46. 5 3 4 1 From Handout 2-7

47. Relationship between Haworth (flat ring) depiction and chair-form Flat ring (Haworth projection) relative positions of the H and OH at each carbon, one “above” the other. But it does not tell the positions of the groups relative to the ring plane (up, down or out). (No room “in.”) Handout 2-8

48. Ball and stick models of glucose

49. Alpha or beta? You try it later. Glucose hydroxyl Gray = C White = H Red = O