Organic Molecules

1. Organic Molecules

2. Essential Knowledge 4.A.1 • The subcomponents of biological molecules and their sequence determine the properties of that molecule • a. Structure and function of polymers are derived from the way their monomers are assembled • b. Directionality influences structure and function of the polymer

3. Organic Molecules • Carbon—The Backbone of Biological Molecules • All living organisms • Are made up of chemicals based mostly on the element carbon

4. Organic chemistry is the study of carbon compounds, chemistry of organisms • Organic compounds range from simple molecules to very large ones

5. Organic moleculescontain both carbon and hydrogen atoms. Four classes of organic molecules (biomolecules) exist in living organisms: Carbohydrates Lipids Proteins Nucleic Acids 3.1 Organic Molecules

6. Carbon atoms can form diverse molecules by bonding to four other atoms • Life’s molecular diversity is based on Carbon’s properties

7. The carbon atom is small with only 6 electrons, two in the first shell and four in the outer shell. Carbon has four valence electrons Carbon can form four covalent bonds. Bonds with carbon, nitrogen, hydrogen, oxygen, phosphorus and sulfur. The C-C bond is very stable. Besides single bonds, double bonds, triple bonds and ring structures are also possible. Branches at any carbon make carbon chains more complex. The Carbon Atom

8. Molecular Diversity Arising from Carbon Skeleton Variation • Carbon chains • Form the skeletons of most organic molecules

9. Hydrocarbons • Hydrocarbons • Are chains of carbon bonded only to hydrogen

10. Hydrocarbons • Are found in many of a cell’s organic molecules

11. Isomers • Isomers • Are molecules with the same molecular formula but different structures and properties

12. Functional Groups • Functional groups are the parts of molecules involved in chemical reactions, they have a specific combination of atoms that always react in the same way • The unique properties of organic compounds depend on the functional groups attached to the carbon skeleton • Determine the chemical reactivity and polarity of organic molecules

13. Functional groups give organic molecules distinctive chemical properties

14. The Functional Groups Most Important in the Chemistry of Life • Four functional groups are important in the chemistry of life • Hydroxyl • Carbonyl • Carboxyl • Amino

15. Sugars contain a hydroxyl and carbonyl group, making them alcohols and ketones • These functional groups are polar (because of nitrogen and oxygen), thus making compounds with them hydrophilic or water soluble

16. R R SH OH O O R R C C OH H O R R C H R N H O R-O OH P OH Biologically ImportantFunctional Groups • Group • Structure • Compound • Significance • Alcohols • Hydroxyl • Polar, forms H-bonds; some sugarsand amino acids Example: Ethanol • Aldehydes • Polar; some sugarsExample: Formaldehyde • Carbonyl • Ketones • Polar; some sugarsExample: Acetone • CarboxylicAcids • Polar, acidic; fats and amino acidsExample: Acetic acid • Carboxyl • Amines • Polar, basic; amino acidsExample: Tryptophan • Amino • Thiols • Sulfhydryl • Disulfide Bonds; some amino acidsExample: Ethanethiol • OrganicPhosphates • Polar, acidic; some amino acidsExample: Adenosine triphosphate • Phosphate

17. Macromolecules are very large molecules • Carbohydrates, lipids, proteins, and nucleic acids are called biomolecules. • Usually consist of many repeating units • Each repeating unit is called a monomer.

18. Most macromolecules are polymers, long molecules consisting of many similar building blocks called monomers • Three of the classes of life’s organic molecules are polymers • Carbohydrates • Proteins

19. Adehydration reactionis a chemical reaction in which subunits are joined together by the formation of a covalent bond and water is produced during the reaction. Example: formation of starch (polymer) from glucose subunits (monomer) A hydrolysis reaction is a chemical reaction in which a water molecule is added to break a covalent bond. Example: digestion of starch into glucose monomers Synthesis and Degradation

20. The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration reactions

21. Polymerscan disassemble by • Hydrolysis (digestion)

22. Special molecules called enzymes are required for cells to carry out dehydration synthesis and hydrolysis reactions. An enzymeis a molecule that speeds up a chemical reaction. Enzymes are not consumed in the reaction. Enzymes are not changed by the reaction. Synthesis and Degradation-1

23. The Diversity of Polymers • Each class of polymer • Is formed from a specific set of monomers • Nucleic acids are formed by monomers called nucleotides • Carbohydrates are built from monosaccharides 1 3 2

24. Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers • An immense variety of polymers can be built from a small set of monomers (40-50)

25. Trillions of different proteins are constructed from only 20 different amino acids linked into chains several hundred long

26. Macromolecules have directionality. • Nucleic acids and proteins share a characteristic, directionality, which affects how other molecules interact with them. Directionality exists when each end of the molecule is different from the other. This characteristic of some macromolecules can affect how they function and how other molecules interact with them. • Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a molecule such as DNA • A polynucleotide therefore has directionality: the two ends of the molecule have very different biochemical properties, and behave very differently in molecular genetic processes.  It is therefore critical to recognize which end is which.

27. The directionality of nucleic acids affects their function. • In DNA and RNA, one end has a sugar molecule while the other has a phosphate part • In the sugar-phosphate backbone, the end with a phosphate group attached to it is known as the 5’ (five prime) end, while the one with the sugar is known as the 3’ end • The nitrogenous bases branch off from an end where they may pair with their complementary bases on another nucleic acid that runs antiparallel to the first nucleic acid—its 5’ to 3’ backbone is going in the opposite direction

28. During DNA replication, directionality impacts how the new DNA strands are put together. Elongation must take place in a 5’ to 3’ direction. • The directionality of proteins affects their function • Proteins also utilize directionality: one end is always a carboxyl group while the other is an amino group. There are enzymes in our bodies that only work on one end or the other of a polypeptide. This is the case with some digestive enzymes.

29. Carbohydrates • Carbohydrates serve as fuel and building material • Carbohydrates include both sugars and their polymers

30. Sugars • Monosaccharides • It has a backbone of 3 to 7 carbon atoms • Main source of fuel for cells • Can be converted into other organic molecules • Molecular formulas are multiples of CH2O (C:H:O ratio = 1:2:1) • Trademarks of sugars: hydroxl group andcarbonyl

31. Hexoses - 6 carbon sugars • Glucose • Fructose • Galactose • Pentoses - five carbon sugars • Ribose • Deoxyribose

32. Monosaccharides • May be linear • Can formrings (happens in aqueous solutions) • Can switch back and forth between linear and rings

33. Disaccharides - double sugar • Are joined by a dehydration synthesis reaction • Types: • Sucrose = glucose + fructose • Maltose = glucose + glucose • Lactose = glucose + galactose • Lactose-intolerant individuals lack the enzyme lactose which breaks down lactose into galactose and glucose.

34. Polysaccharides • Polysaccharides • Are polymers of sugars (from a few hundred to a few thousand linked monosaccharides)

35. Storage Polysaccharides • Starch • Is a polymer consisting entirely of glucose monomers • Broken down (hydrolyzed) into glucose to provide energy or building blocks for other molecules • Potatoes, grains (wheat, corn, rice) are major starch source in human diet

36. Storage Polysaccharides STARCH is the major storage form of glucose in plants

37. Storage Polysaccharides • Glycogen • Consists of glucose monomers • Is the major storage form of glucose in animals • Stored in liver and muscle cells

38. Structural Polysaccharides • Cellulose • Is a polymer of glucose • Found in cell walls, major component of wood • Most abundant organic compound found on Earth

39. Cellulose • Is a major component of the tough walls that enclose plant cells

40. Cellulose is difficult to digest • Cows, termites have microbes in their stomachs to facilitate this process

41. Cellulose • Has different glycosidic linkages than starch

42. The main structural difference comes from the difference in the sequence of bonds in glycogen and cellulose and starch where the three of them composed mainly of glucose and its derivatives. Starch, glycogen and cellulose are all polymers of glucose. They differ in the type of glucose present and the bonds which link those glucose monomers together.

43. Starch and glycogen are made from alpha-glucose. This is an isomer of glucose in which the hydroxyl (-OH) group attached to carbon number 1 is below the plane of the ring. • Starch is itself composed of two types of polymer: amylose and amylopectin. In amylose, the glucose monomers are linked by 1,4 glycosidic bonds. This means that the bond connects carbon atom number 1 in one glucose to carbon atom number 4 in the other glucose. This produces an unbranched chain of glucose which then folds up to form a coil or helix.

44. In amylopectin there are two types of glycosidic bonds: 1,4 and 1,6. Some glucose molecules have a glycosidic link from carbon atom number 6 to carbon atom number 1 in a new glucose molecule. This produces a branch point in the amylopectin molecule. Amylopectin is therefore a branched polymer.

45. Glycogen is similar in structure to amylopectin, but branches more frequently. • Cellulose is an unbranched polymer composed of beta glucose molecules. Beta glucose is an isomer of glucose in which the hydroxyl group attached to carbon 1 is above the plane of the ring. The glucose monomers are linked by 1,4 glycosidic bonds.

46. Structural Polysaccharides • Chitin, another important structural polysaccharide containing nitrogen • Is found in the exoskeleton of arthropods, cell walls in fungi

47. Peptidoglycan Polysaccharide found in bacterial cell walls (D.Bacteria) Contains glucose monomers with attached amino acids

48. Lipids • Lipids are a diverse group of hydrophobic molecules, composed mostly of carbon and hydrogen linked in non-polar covalent bonds • Lipids • Share the common trait of being hydrophobic - they are not attracted to water molecules and are non-soluble in water (oil and water)

49. 3.3 Lipids • Varied in structure • Large, nonpolar molecules that are insoluble in water • Functions: • Long-term energy storage • Structural components • Cell communication and regulation • Protection • Varieties: fats, oils, phospholipids, steroids, waxes

50. Lipids • Insoluble in water • Long chains of repeating CH2 units • Renders molecule nonpolar • Types of Lipids • Type • Organismal Uses • Human Uses • Fats • Long-term energy storage & thermal insulation in animals • Butter, lard • Oils • Long-term energy storage in plants and their seeds • Cooking oils • Phospholipids • Component of plasma membrane • No-stick pan spray • Steroids • Component of plasma membrane; hormones • Medicines • Waxes • Wear resistance; retain water • Candles, polishes