Basic organic chemistry of important macromolecules

1. Basic organic chemistry of important macromolecules

2. Structure • What are the organic molecules? • Polymer Principles • Carbohydrates – Fuel and Building Material. • Lipids – Diverse Hydrophobic Molecules. • Proteins – The Molecular Tools of the Cell • Nucleic Acids – Informational Polymers

3. 1. Organic molecules • Organic molecules are those that: • formed by the actions of living things; and/or • have a carbon backbone.

4. Carbon has four electrons in outer shell, and can bond with up to four other atoms (usually H, O, N, or another C). Since carbon can make covalent bonds with another carbon atom, carbon chains and rings that serve as the backbones of organic molecules are possible. Chemical bonds store energy.

5. The C-C covalent bond has 83.1 Kcal (kilocalories) per mole, while the C=C double covalent bond has 147 Kcal/mole. Energy is in two forms: kinetic, or energy in use/motion; and potential, or energy at rest or in storage. Chemical bonds are potential energy, until they are converted into another form of energy, kinetic energy (according to the two laws of thermodynamics).

6. 1. Organic molecules • Methane (CH4) is an example of this. • If we remove the H from one of the methane units below, and begin linking them up, while removing other H units, we begin to form an organic molecule. • (NOTE: Not all methane is organically derived, methane is a major component of the atmosphere of Jupiter, which we think is devoid of life). • When two methanes are combined, the resultant molecule is Ethane, which has a chemical formula C2H6. • Molecules made up of H and C are known as hydrocarbons.

7. The shapes of three simple organic molecules. Whenever a carbon atom has four single bonds, the bonds angle toward the corners of an imaginary tetrahedron.

8. The shapes of three simple organic molecules. When two carbons are joined by a double bond, all bonds around those atoms are in the same plane.

9. Variations in carbon skeletons Hydrocarbons

10. Three types of isomers Compounds with the same molecular formula but different structures. Isomers are a source of diversity in organic molecules.

11. The pharmacological importance of enantiomers. L-dopa is a drug used to treat Parkinson's disease, a disorder of the central nervous system. The drug's enantiomer, the mirror-image molecule designated d-dopa, has no effect on patients.

12. Functional groups in organic molecules. • Small groups of atoms that are frequently bonded to the carbon skeleton of organic molecules. • Have specific chemical and physical properties. • Are the regions of organic molecules which are commonly chemically reactive. • Behave consistently from one organic molecule to another. • Depending upon their number and arrangement, determine unique chemical properties of organic molecules in which they occur.

13. Functional groups in organic molecules. Hydroxyl group: Polar water soluble. Carbonyl group: Polar water soluble; Found in sugars.

14. Functional groups in organic molecules. Carboxyl group: Polar, water soluble; Donates protons, has acidic properties Amino group: Polar, water soluble; Act as weak base, The unshared pair of electrons on the N can accept a proton, giving the amino group a +1 charge.

15. Functional groups in organic molecules. Phosphate group: dissociated form of phosphoric acid (H3PO4); negatively charged and has acid properties; polar, water soluble. Important in cellular energy storage and transfer. Sulfhydryl group: stabilizes the protein structure; organic compounds with this group are called thiols.

16. 2. Polymer principles • A polymer is a long molecule consisting of many identical or similar parts linked by covalent bonds. • The repeating units are called monomers. • Macromolecules: large organic molecules formed from smaller building block molecules. • Four major classes: • Carbohydrates • Proteins • Lipids • Nucleic acids

17. Polymer principles Monomers are connected by a reaction in which two molecules are covalently linked to each other through loss of a water molecule: so called condensation (dehydration) reaction. Polymers are disassembled to monomers by hydrolysis: bonds between monomers are broken by the addition of water. Digestion is one form of hydrolysis.

18. Condensation reaction Formation of a peptide bond between two amino acids by the condensation (dehydration) of the amino end of one amino acid and the acid end of the other amino acid. The reverse reaction - hydrolysis

19. 3. Carbohydrates Carbohydrates – are organic molecules made of sugar and their polymers. They have the general formula [CH2O]n where n is a number between 3 and 6.

20. 3. Carbohydrates Carbohydrates function in short-term energy storage (such as sugar); as intermediate-term energy storage (starch for plants and glycogen for animals); and as structural components in cells (cellulose in the cell walls of plants and many protists), and chitin in the exoskeleton of insects and other arthropods.

21. Carbohydrates Sugars are structurally the simplest carbohydrates. They are the structural unit which makes up the other types of carbohydrates. Monosaccharides are single (mono=one) sugars. Important monosaccharides include ribose (C5H10O5), glucose (C6H12O6), and fructose (same formula but different structure than glucose).

22. The structure and classification of some monosaccharides

23. The structure and classification of some monosaccharides • Depending on the location of the carbonyl group (pink), sugars may be • aldoses (aldehyde sugars) or • ketoses (ketone sugars).

24. The structure and classification of some monosaccharides • According to the length of their carbon skeletons: • Triose • Pentose • Hexose • A third point of variation is in the spatial arrangement around asymmetric carbons (compare, for example, the gray portions of glucose and galactose).

25. Linear and ring forms of glucose. • Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. • To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.

26. Linear and ring forms of glucose. (b) In this abbreviated ring formula, the carbons in the ring are omitted. The ring's thicker edge indicates that you are looking at the ring edge-on; the components attached to the ring lie above or below the plane of the ring.

27. Carbohydrates In aqueous solution, glucose tends to have two structures, a and b, with an intermediate straight-chain form. The a form and b form differ in the location of one -OH group. Glucose is a common hexose in plants. The products of photosynthesis are assembled to make a glucose. Energy from sunlight is converted into the C-C covalent bond energy. One mole of glucose yields 673 Kcal of energy.

28. Disaccharidesare formed when two monosaccharides are chemically bonded together. Sucrose, a common plant disaccharide is composed of the monosaccharides glucose and fructose.Lactose (milk sugar) composed of glucose and themonosaccharide galactose. Formation of a disaccharide (top) by condensation

29. Polysaccharides are large molecules composed of individual monosaccharide units. They can be broadly divided to storage (starch) and structural (cellulose).

30. Polysaccharides Starch is a common plant polysaccharide, which is made up of many glucoses (in a polypeptide these are referred to as glucans). There are two forms of starch, amylose (unbranched) and amylopectin (branched).

31. Glycogen is an animal storage product that accumulates in the vertebrate liver and muscle cells. It is more extensively branched.

32. Structural polysaccharide – cellulose. Cellulose is a polysaccharide which forms the fibrous part in plant cell walls. Cellulose is indigestible, and thus forms an important, easily obtained part of dietary fiber. As compared to starch and glycogen, which are each made up of mixtures of a and b glucoses, cellulose (and the animal structural polysaccharide chitin) are made up of only b glucoses.

33. Cellulose The three-dimensional structure of the structural polysaccharides is constrained into straight microfibrils by the uniform nature of the glucoses. It resists the actions of enzymes (such as amylase) that breakdown storage polysaccharides (such a starch).

34. Cellulose Fibers from Print Paper (SEM x1,080).

35. Starch and cellulose structures compared. • Glucose forms two interconvertible ring structures, designated alpha and beta. • These two forms differ in the placement of the hydroxyl group attached to the number 1 carbon.

36. Starch and cellulose structures compared. (b) The  ring form is the monomer for starch. (c) Cellulose consists of glucose monomers in the  configuration. The angles of the bonds that link the rings make every other glucose monomer "upside down."

37. 4. Lipids • Lipids are compounds which grouped together because of following features: • little or no affinity for water; • they are not real polymers; • they consist of mostly hydrocarbons. • They are involved mainly with long-term energy storage. • Lipids are composed of three fatty acids (usually) covalently bonded to a 3-carbon glycerol.

38. Lipids • Diverse group of organic compounds that are insoluble in water, but will dissolve in nonpolar solvents (chloform, benzene). • The fatty acids are composed of CH2 units, and are hydrophobic/not water soluble. • The three most important families of lipids are: • -fats; • -phospholipids (the major building block in cell membranes); • -steroids ("messengers" (hormones) that play roles in communications within and between cells)

39. Fat A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids. Glycerol is an alcohol with three carbons, each bearing a hydroxyl group. A fatty acid has a long carbon sceleton with the “head” consisting of a carboxyl group at the end. Long non-polar hydrocarbon “tail” is the reason fats are hydrophobic.

40. The synthesis and structure of a fat, or triacylglycerol. • The molecular building blocks of a fat are one molecule of glycerol and three molecules of fatty acids. • One water molecule is removed for each fatty acid joined to the glycerol. • The result is a fat. • The attached fatty acids may be similar or different.

41. The synthesis and structure of a fat, or triacylglycerol. Fats are insoluble in water (hydrophobic because of the many nonpolar C-H bonds). Fatty acid composition is the source of variation among fat molecules Fatty acids in a fat may be the same or different Fatty acids may vary in length Fatty acids may vary in the number and location of carbon-to-carbon double bonds.

42. Saturated (top and middle) and unsaturated (bottom) fatty acids. Fatty acids can be saturated (meaning they have as many hydrogens bonded to their carbons as possible) or unsaturated (with one or more double bonds connecting their carbons, hence fewer hydrogens).

43. Difference in energy storage: plants versus animals Animals convert excess sugars (beyond their glycogen storage capacities) into fats. Most plants store excess sugars as starch, although some seeds and fruits have energy stored as oils (e.g. corn oil, peanut oil, palm oil, canola oil, and sunflower oil). Fats yield 9.3 Kcal/gm, while carbohydrates yield 3.79 Kcal/gm. Fats store six times as much energy as glycogen.

44. Difference in energy storage: plants versus animals Most animal fats are saturated (lard, butter) and are solid at r.t. In contrast, the fats of plants and fish are generally unsaturated – liquid at r.t. The reason: the kinks where the double bonds are located prevent the molecules from packing together closely enough to solidify at r.t.

45. Diet attempt • Diets are attempts to reduce the amount of fats present in specialized cells known as adipose cells that accumulate in certain areas of the human body. • By restricting the intakes of carbohydrates and fats, the body is forced to draw on its own stores to makeup the energy debt. • The body responds to this by lowering its metabolic rate, often resulting in a drop of "energy level.“ • Successful diets usually involve three things: • -decreasing the amounts of carbohydrates and fats; • -exercise; • -and behavior modification.

46. Phospholipids Phospholipids are similar to fats but have only two fatty acids attached to glycerol. Phospholipids are modified so that a phosphate group (PO4-) replaces one of the three fatty acids normally found on a lipidmaking a polar "head" and two nonpolar "tails". Additional variable group Phosphate Glycerole Fatty acids Space-filling model (left) and chain model (right).

47. Two structures of phospholipids in water (a) A micelle, in cross section. (b) A cross section of a phospholipid bilayer between two aqueous compartments.

48. Two structures of phospholipids in water Such bilayers are the main fabric of biological membranes. The hydrophilic heads (spheres) of the phospholipids are in contact with water, whereas the hydrophobic tails are in contact with each other and remote from water.

49. Function Phospholipids are important structural components of cell membranes. At the surface of a cell, phospholipids are arranged in a bilayer.

50. Steroids: are lipids characterised by a carbon skeleton consisting of four fused rings. Cholesterol is a common component of animal cell membrane, a precursor of other steroids.