Lecture – 2 cont.

1. Lecture – 2 cont. Functional Groups

2. Outline • Water • Structure - Review • Important properties • #4 Solvent properties • Carbon • Structure • Important properties • Functional Groups

3. #4 – Solvent Properties • Water can disassociate into hydronium and hydroxide ions +  2 H2O Hydronium ion (H3O+) Hydroxide ion (OH)

4. #4 Solvent Properties: Acids & Bases • The dissociation of water molecules has a great effect on organisms • Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell

5. #4 Solvent Properties: Acids & Bases • Acid – • donates a proton • Increases the number of Hydronium Ions in an aqueous solution • Base – • Accepts a proton • Reduces the number of Hydronium Ions in an aqueous solution

6. #4 – Solvent Properties: The pH scale • pH is a measure of the relative concentration of protons. • 0 < pH < 7 is an Acid ([H30+] > 10-7M) • 7 < pH < 14 is a Base ([H30+] < 10-7M) • pH 7 is neutral ([H30+] = [OH-] = 10-7M)

7. Figure 3.10 pH Scale 0 1 Battery acid 2 Gastric juice, lemon juice H+ H+ H+ Vinegar, wine, cola OH 3 H+ Increasingly Acidic [H+] > [OH] H+ OH H+ H+ H+ 4 Tomato juice Acidic solution Beer Black coffee 5 Rainwater 6 Urine OH Saliva Neutral [H+] = [OH] OH 7 Pure water OH H+ H+ OH OH Human blood, tears H+ H+ H+ 8 Seawater Neutral solution Inside of small intestine 9 10 Increasingly Basic [H+] < [OH] Milk of magnesia OH OH 11 OH H+ OH Household ammonia OH OH OH H+ 12 Basic solution Household bleach 13 Oven cleaner 14

8. #4 – Solvent Properties: Buffers • Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution. • They resist a change in pH when a small amount of acid or base is added to a solution. • Most buffers consist of an acid-base pair that reversibly combines with H+ • Buffers work within a specific pH range.

9. #4 – Solvent Properties: Buffers • Carbonic Acid – contributes to pH stability in blood and other biological solutions. • H2CO3 is formed when CO2 reacts with water.

10. Carbon

11. Carbon • The backbone of life • Living organisms consist mostly of carbon-based compounds. • Really good at forming large, complex, and diverse molecules. • Proteins, DNA, carbohydrates, and other molecules - all composed of carbon compounds.

12. Carbon • Electron configuration determines the kinds and number of bonds an atom will form with other atoms • Four valence electrons – Four covalent • Allows for the formation of large, complex molecules

13. Figure 4.3 Carbon bonds determine molecular shape Name andComment Structural Formula Space-Filling Model Molecular Formula Ball-and- Stick Model (a) Methane CH4 (b) Ethane C2H6 (c) Ethene (ethylene) C2H4

14. Figure 4.5 Diversity of carbon molecules (c) Double bond position (a) Length • Carbon chains form the skeletons of most organic molecules • Carbon chains vary in length and shape Ethane Propane 2-Butene 1-Butene (b) Branching (d) Presence of rings Benzene 2-Methylpropane (isobutane) Butane Cyclohexane

15. Figure 4.4 Valence Electrons • The electron configuration of carbon gives it covalent compatibility with many different elements • The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules Oxygen (valence  2) Hydrogen (valence  1) Nitrogen (valence  3) Carbon (valence  4)

16. Isomers • Compounds with the same molecular formula but different structures and properties • Structural isomers have different covalent arrangements of their atoms (constitutional) • Cis-trans isomers have the same covalent bonds but differ in spatial arrangements • Enantiomers are isomers that are mirror images of each other (they are chiral)

17. (a) Structural isomers Isomers – Three types Figure 4.7 (b) Cis-trans isomers cis isomer: The two Xsare on the same side. trans isomer: The two Xsare on opposite sides. (c) Enantiomers CO2H CO2H H NH2 H NH2 CH3 CH3 L isomer D isomer

18. Figure 4.8 Isomers - Enatomers Ineffective Enantiomer Effective Enantiomer Drug Condition Pain;inflammation Ibuprofen S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol http://www.youtube.com/watch?v=L5QbBYj_zVs

19. Functional Groups • The components of organic molecules that are most commonly involved in chemical reactions • The number and arrangement of functional groups give each molecule its unique properties

20. Female lion OH CH3 HO Estradiol Male lion OH CH3 CH3 O Testosterone The importance of functional groups

21. 7 most biologically important functional groups

22. Figure 4.9a Hydroxyl STRUCTURE Alcohols (Their specific names usually end in -ol.) NAME OF COMPOUND (may be written HO—) • Is polar as a result of the electrons spending more time near the electronegative oxygen atom. EXAMPLE FUNCTIONALPROPERTIES Ethanol • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

23. Figure 4.9b Carbonyl STRUCTURE Ketones if the carbonyl group is within a carbon skeleton NAME OF COMPOUND Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE • A ketone and an • aldehyde may be • structural isomers • with different properties, • as is the case for • acetone and propanal. FUNCTIONALPROPERTIES • Ketone and aldehyde • groups are also found • in sugars, giving rise • to two major groups • of sugars: ketoses • (containing ketone • groups) and aldoses • (containing aldehyde • groups). Acetone Propanal

24. Figure 4.9c Carboxyl STRUCTURE Carboxylic acids, or organic acids NAME OF COMPOUND EXAMPLE FUNCTIONALPROPERTIES Polar; can form H-bonds Weak acids; reversible dissociation in H2O Acetic acid Nonionized Ionized • Found in cells in the ionized form with a charge of 1– and called a carboxylate ion.

25. Figure 4.9d Amino Amines STRUCTURE NAME OF COMPOUND •Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms): EXAMPLE FUNCTIONALPROPERTIES Glycine Ionized Nonionized •Found in cells in the ionized form with a charge of 1.

26. Figure 4.9e Sulfhydryl Thiols STRUCTURE NAME OF COMPOUND (may be written HS—) •Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. EXAMPLE FUNCTIONALPROPERTIES •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 and then breaking and re-forming the cross-linking bonds. Cysteine

27. Figure 4.9f Phosphate Organic phosphates STRUCTURE NAME OF COMPOUND EXAMPLE •Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as at left; 1– when located internally in a chain of phosphates). FUNCTIONALPROPERTIES Glycerol phosphate •Molecules containing phosphate groups have the potential to react with water, releasing energy.

28. Figure 4.9g Methyl STRUCTURE Methylated compounds NAME OF COMPOUND •Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. EXAMPLE FUNCTIONALPROPERTIES •Arrangement of methyl groups in male and female sex hormones affects their shape and function. 5-Methyl cytidine

29. Lecture - 3 Biological Macromolecules

30. Outline • Monomers & Polymers • Four basic classes of biological macromolecules • Carbohydrates • Lipids • Proteins • Nucleic Acids • Form follows function

31. Polymers • Polymer is a large molecule build from similar building blocks • Legos! • Building blocks are monomers • Carbohydrates, Proteins, Nucleic acids are polymers

32. Polymer Synthesis • Usually, monomers are joined via a dehydration reaction. • Broken apart via hydrolysis.

33. Polymer Diversity • Thousands of different macromolecules • They vary • Cell to cell • Individuals • Species… • Can build an immense variety of polymers with a small set of monomers • legos

34. 4 Classes of Macromolecules • Carbohydrates • Lipids • Nucleic Acids • Proteins

35. #1 Carbohydrates

36. #1 Carbohydrates • Fuel & building blocks • Monosaccharides • Single sugars • One carbon ring • Polysaccharides • Polymers built from many sugar building blocks

37. #1 Carbohydrates: Simple Sugars • General Characteristics of Sugars • Generally have some multiple of CH2O • Have a carbonyl group (C=O) • Multiple hydroxyl groups (-OH) • Aldoses & Ketoses • Trioses (C3H6O3), Pentoses (C5H10O5) & Hexoses (C6H12O6) Glucose Glyceraldehyde Ribose (Fischer Projections)

38. Figure 5.3a #1 Carbohydrates: Simple Sugars Ketose (Ketone Sugar) Aldose (Aldehyde Sugar) • Aldoses vs. Ketoses • Aldoses – Carbonyl group at the end of carbon skeleton (aldehyde sugar) • Ketoses – Carbonyl group within the carbon skeleton (ketones) Trioses: 3-carbon sugars (C3H6O3) Glyceraldehyde Dihydroxyacetone

39. Figure 5.4 #1 Carbohydrates: Simple Sugars 6 6 1 2 5 5 3 • Most sugars exist as ring structures. 4 1 4 1 4 2 2 5 3 3 6 (a) Linear and ring forms Glucose 6 5 4 1 2 3 (b) Abbreviated ring structure

40. #1 Carbohydrates: Glucose vs. Fructose Glucose Fructose

41. Figure 5.5 #1 Carbohydrates: Disaccharide 1–4glycosidiclinkage 1 4 • 2 monosaccarides joined by a glycosidic linkage Glucose Glucose Maltose (a) Dehydration reaction in the synthesis of maltose 1–2glycosidiclinkage (important for making beer) 1 2 Sucrose Glucose Fructose (b) Dehydration reaction in the synthesis of sucrose (Table sugar)

42. #1 Carbohydrates: Polysaccarides • Hundreds to 1000s of monosaccarides held together via glycosidic linkages.

43. #1 Carbohydrates: Polysaccarides • Storage and structural roles • Storage - Carbohydrate “bank” - stored sugars can later by released by hydrolysis for use in metabolism. • Structure – Strong structural components are built from polysaccharides. • Structure and function are determined by its sugar monomers and the positions of glycosidic linkages

44. #1 Carbohydrates: Polysaccarides; Storage - Starch • Starch – Plants version of storage polysaccharides • Consists entirely of glucose monomers • Plants store surplus starch as granules within chloroplasts and other plastids • Most starches are built from 1-4 linkages – more complex starches can be linked differently amylose

45. #1 Carbohydrates: Polysaccarides; Storage - Starch

46. #1 Carbohydrates: Polysaccarides; Storage - Starch • Starches are stored in plasteds • Animals have enzymes that can hydrolyze starches • Major sources: • Potatoes • Grains • Wheat • Maize • Corn • Rice Chloroplast Starch granules 1 m

47. #1 Carbohydrates: Polysaccarides; Storage - Glycogen • Animals store glucose as a polysaccharide called glycogen. • Made up of glucose monomers – like Amylopectin but more extensively branched. • In vertebrates it is mostly stored in the liver and muscle cells. • Glycogen stores don’t last long. Glycogen granules Mitochondria 0.5 m

48. #1 Carbohydrates: Polysaccarides; Structure • Cellulose is a major component of the tough wall of plant cells • Cellulose is a polymer of glucose. • The glycosidic linkages differ from starch. • The difference is based on two ring forms for glucose: alpha () and beta ()

49. Figure 5.7a 1 1 4 4  Glucose  Glucose (a)  and  glucose ring structures

50. Figure 5.7b 1 4 (b) Starch: 1–4 linkage of  glucose monomers 1 4 (c) Cellulose: 1–4 linkage of  glucose monomers