Chapter 3

1. Chemistry of Organic Molecules Chapter 3

2. Organic Molecules • Organic chemistry—chemistry of organisms • Inorganic chemistry—chemistry of the nonliving world • Organic molecules—molecule that always contains carbon and hydrogen, and often contains oxygen as well; organic moleucles are associated with living things.

3. Inorganic vs. Organic Molecules Inorganic molecules Organic Molecules Always contain carbon and hydrogen. Always covalent bonding. Often quite large, with many atoms. Usually associated with living organisms. • Usually contain positive and negative ions. • Usually ionic bonding. • Always contain a small number of atoms. • Often associated with nonliving matter.

4. Organic Molecules • 4 classes of organic compounds in any living thing: • Carbohydrates • Lipids • Proteins • Nucleic acids

5. The Carbon Atom • Only contains 6 electrons. • 2 electrons in the 1st energy level. • 4 electrons in the 2nd energy level. • Carbon atom needs 4 electrons to have a complete outer energy level. • It can share electrons with up to 4 different atoms.

6. Carbon Functional Group • Carbon chain of an organic molecule is called skeleton or backbone. • Functional group—specific combination of bonded atoms that always reacts in the same way.

7. Isomers • Isomers—organic molecules that have identical molecular formulas but a different arrangement of atoms.

8. Macromolecules of Cells • Macromolecules—carbohydrates, lipids, proteins, and nucleic acids. • Polymers—largest of the macromolecules • Monomers—small molecule that is a subunit of a polymer. • Ex: glucose is a monomer of starch

9. Macromolecules of Cells • Dehydration reaction—chemical reaction resulting in a covalent bond with accompanying loss of a water molecule. • Hydrolysis reaction—splitting of a compound by the addition of water, with the H+ being incorporated in one fragment and the OH- in the other.

10. Enzymes—a molecule that speeds a reaction by bringing the reactants together causing the reaction to occur.

11. Carbohydrates • Carbohydrates used for: • Energy • Energy storage • Structure • Classes of carbohydrates: • Monosaccharides • Disaccharides • ploysaccharides

12. Monosaccharides • Monosaccharides—consist of only a single sugar molcule or a simple sugar. • Building block of a carbohydrate.

13. Monosaccharides • Composition of monosaccharides consist of carbon, hydrogen, and oxygen. • Simple sugar can have a carbon backbone of 3-7 Carbons. • Named according to number of carbon atoms • Most common: • hexose sugar—glucose • Contains 6 carbon atoms. • Pentose sugars—ribose and deoxyribose • Contains 5 carbon atoms

14. Disaccharides • Disaccharides—two monosaccharides that have joined during a dehydration reaction.

15. Polysaccharides • Polysaccharides—more than two monosaccharides linked together. • Characteristics: • Short-term energy storage molecules. • Cannot easily pass through the plasma membrane, because they are not soluble in water.

16. Polysaccharides • Plant cells store glucose as starch. • Starch can exists in two forms: • Non-branched • Branched • Animal cells store glucose as glycogen. • The storage and release of glucose from liver cells is under the control of hormones. • After we eat, the release of the hormone insulin from the pancreas promotes the storage of glucose as glycogen.

17. Polysaccharides as Structural Molecules • Some polysaccharides function as structural components of cells. • Cellulose is the most abundant of all the carbohydrates. • Cellulose has long glucose chains that are held parallel to each other by hydrogen bonding to form microfibrils and then fibers. • The fibers crisscross within the plant cell walls for even more strength.

18. Polysaccharides as Structural Molecules • Chitin is found in the exoskeleton of crabs and related animals, such as lobsters and insects, is also a polymer of glucose. • Chitin is not digestible by humans.

19. Lipids • Lipid—class of organic compounds that tends to be soluble in nonpolar solvents. • Utilized for both insulation and long-term energy storage by animals. • Fat below the skin of marine mammals is called blubber. • Plants use oil instead of fat for long-term energy storage.

20. Triglycerides: Long-term Energy Storage • Fats and oils contain two types of unit molecules: glycerol and fatty acids. • Building blocks of lipids are glycerol and fatty acids. • Glycerol is a compound with three hydroxide (OH) groups. • OH groups are polar = glycerol is soluble in water.

21. Triglycerides: Long-term Energy Storage • Fatty acids consist of a long hydrocarbon chain with a COOH (carboxyl) group at one end. • Fatty acids are either saturated or unsaturated. • Saturated fatty acids have no double bonds between the carbon atoms (fats). • Unsaturated fatty acids have double bonds in the carbon chain (oils).

22. Triglycerides: Long-term Energy Storage • Nearly all animals use fat in preference to glycogen for long-term energy storage. • Gram per gram, fat stores more energy than glycogen. • C—H bonds of fatty acids make them a richer source of chemical energy than glycogen, because glycogen has several C—OH bonds.

23. Phospholipids • Phospholipids • contain a phosphate group • Constructed like a fat, except that in place of the third fatty acid attached to glycerol, there is a polar phosphate group. • The phosphate group is usually bonded to another organic group, indicated by R. • This portion of the molecule becomes the polar head, while the hydrocarbon chains of the fatty acids become the nonpolar tails.

24. Phospholipids

26. Steroids: Four Fused Rings • Steroids—are lipids that have entirely different structures from those of fats. • Skeletons of four fused carbon rings. • Each skeleton differs based on the type functional group attached to the carbon skeleton.

27. Steroids • Cholesterol is a component of an animal cell’s plasma membrane, and is a precursor of several other steroids. • A diet high in saturated fats and cholesterol can lead to circulatory disorders. • The fatty material accumulates inside the lining of blood vessels, and reduces blood flow.

28. Waxes • Waxes—long-chained fatty acids bond with long-chain alcohols. • Waxes are solid at normal temperatures because they have high melting points. • Waxes are hydrophobic, resulting in them being waterproof and resistant to degradation.

29. Waxes • In plants • Form a protective cuticle that slows the loss of water for all exposed parts. • In animals • Waxes are involved in skin and fur maintenance. • Earwax contains an organic compound that at the very least repels insects, and in some cases even kills them.

30. Proteins • Building Blocks—Amino Acids

31. Amino Acids: Subunits of Proteins • Amino acid—organic molecule composed of an amino group (NH2), an acid group (COOH), and a R (side group—differs for each of the 20 different kinds of amino acids). • Covalent bonds to produce peptide molecule.

32. Peptides • Peptide—two or more amino acids bonded together. • Peptide bond—covalent bond between two amino acids. • Dipeptide—two amino acids linked together by a peptide bond. • Polypeptides—three or more amino acids linked together.

33. Proteins Functions • Support • Some proteins make up hair, nails, and collagen. • Lend support to ligaments, tendons, and skin • Enzymes • Enzymes bring reactants together and speed up chemical reactions in cells. • They are specific for one particular type of reaction and can function at body temperature.

34. Proteins • Transport • Channel and carrier proteins in the plasma membrane allow substances to enter and exit cells. • Some other proteins transport molecules in the blood of animals. • Hemoglobin is a complex protein that transports oxygen.

35. Proteins • Defense • Antibodies are proteins. • They combine with foreign substances called antigens. • Prevents antigens from destroying cells and upsetting homeostasis.

36. Proteins • Hormones • Hormones are regulatory proteins. • Serve as intercellular messengers that influence the metabolism of cells. • The hormone insulin regulates the content of glucose in the blood and in cells. • The presence of growth hormone determines the height of an individual.

37. Proteins • Motion • The contractile proteins actin and myosin allow parts of cells to move and cause muscles to contract.

38. Shape of Proteins • The final shape of a protein determines its function in the cells and body of an organism. • A protein can have up to four levels of structure, but not all proteins have all four levels.

39. Primary Structure • One protein is its own particular sequence of amino acids. • Primary structure is determined by code within nucleic acid molecules. • The level of structure is determined by the sequence of amino acids that join to form polypeptide.

40. Secondary Structure • Occurs when the polypeptide coils or folds in a particular way. • Linus Pauling and Robert Corey, who began studying the structure of amino acids in the late 1930s, concluded the coiling they called an alpha helix and a pleated sheet the beta sheet.

41. Secondary Structure • Hydrogen bonds often holds the secondary structure of a polypeptide in place. • Fibrous proteins—structural proteins that exist as helices or pleated sheets that hydrogen-bond to each other.

42. Tertiary Structure • The tertiary structure is a folding and twisting that results in the final three-dimensional shape of a polypeptide called globular proteins. • Then to ball up into rounded shapes.

43. Enzymes are globular proteins. • Each enzyme works best at a specific temperature and pH. • When the protein loses its natural shape its called denatured. • If the shape of the protein changed they cannot work like they are suppose to in the chemical reaction.

44. Quaternary Structure • Quaternary structure of a protein consists of more than one polypeptide. • Hemoglobin is a globular protein that consists of four polypeptides.

45. Nucleic Acids • Nucleic acids—polymers of nucleotides with very specific functions in cells. • Building blocks—nucleotides. • Composition of nucleotides—pentose sugar (ribose or dexoyribose), phosphate, and organic base. • Organic bases—adenine, thymine, cytosine, and guanine or uracil.

46. DNA • DNA—deoxyribonucleic acid • double stranded helix with sugars and phosphates forming backbone and bases paired in complementary fashion forming “rungs of ladder”. • Function—genetic material that stores information regarding its own replication and the order in which amino acids are to be joined to make a protein.

47. RNA • RNA—Ribose nucleic acid • Single stranded • 3 types— • ribosomal (rRNA) • transfer (tRNA) • messenger (mRNA)

48. DNA RNA Made of four nucleotides A,U,G,C Single-stranded Temporary Copies of gene Information, or code, found in nucleotide sequence (order) • Made of four nucleotides A,T,G,C • Double-stranded • Permanent • Contains all genes • Information, or code, found in nucleotide sequence (order)

49. Structure of DNA and RNA • Complementary base pairing—hydrogen bonding between particular purines and pyrimidines in DNA. • The number of purine and pyrimidines in DNA, regardless or order, are always equal. • Purine bases—adenine (A) and guanine (G) • Pyrimidine bases—cytosine (C) and thymine (T).

50. Adenosine Triphosphate (ATP) • Adenosine composed of adenine and ribose. • Triphosphate stands for the three phosphate groups that are attached together and to ribose (pentose sugar). • ATP—high-energy molecule because the last two phosphate bonds are unstable and are easily broken.