Chapter 3: Organic Molecules

1. Chapter 3: Organic Molecules Biology 100 Spring 2009

2. Carbon: The Central Atom • Organic Molecules contain Carbon, and are usually complex. • Carbon atoms can be arranged in rings or chains

3. Carbon: The Central Atom • Carbon is the central atom in all organic molecules. • Can bond to one another, creating long chains or rings. • Carbon likes to have ______ covalent bonds. • When several carbon are present, they form the backbone to which other elements or molecules attach.

4. Carbon: The Central Atom • C-C and C-H bonds are rich in______. The simplest hydrocarbon is methane (CH4), which is dominant in natural gas. • A major component of gasoline is the 8-carbon molecule called octane.

5. Carbon: The Central Atom • In addition, carbon can also form double and triple bonds. • A double bond is indicated by two lines between atoms. • C=O or C=C • Triple bonds are denoted by three lines between atoms.

6. Carbon: The Central Atom • Empirical Formula of a chemical formula is a simple expression of the relative number of atoms in it. • C2H6O • Structural Formula is the graphic arrangement and bonding of atoms.

7. Isomers • An isomer has the same empirical formula, but different structural formulas. • Example is the empirical formula C3H8O, but can be structurally different. Propan-2-ol Methoxyethane Propan-1-ol

8. Isomers • Structural isomers may also involve differences in the carbon backbone itself.

9. Isomers • Geometric isomers have the same carbon backbone and even the same elements or functional groups attached to the same carbons. • But they differ from each other in ______________ these elements or groups are located around a C=C bond.

10. Isomers • While we draw biological molecules as if they were two-dimensional, they are actually three-dimensional. • Enantiomers are ________ images of one another, like a right hand and left hand.

11. Functional Groups • As mentioned earlier, carbon is the backbone of organic molecules. However, attached to these carbon atoms are combinations of other elements, including carbon. These are known as functional groups.

13. Macromolecules • Macromolecules are very large, organic molecules. • Macromolecules are organized into four major classes because of similarities in structure and form Carbohydrates Proteins Nucleic Acids Lipids

14. Macromolecules • Monomer is a small molecule • Monomers may have their own specific functions and/or can be linked by covalent bonds to form larger molecules. • Polymers are composed of identical or similar monomers linked together by covalent bonds. • Glucose is a monomer, but when many glucose molecules chemically bond to one another, it can become the polymer, starch.

15. Carbohydrates • Carbohydrates are also known as sugars and their names often end in –ose (fructose, sucrose, cellulose). • Carbohydrates are composed of carbon, hydrogen, and oxygen. • They have a typical chemical formula: CnH2nOn, with twice as many hydrogen atoms as carbon and equal numbers of carbon and oxygen atoms. • Is it a carbohydrate? • C6H1206 • C2H6O

16. Monosaccharide • Glucose, C6H12O6, is a very common monosaccharide • It has a terminal carbonyl group • And 5 hydroxyl groups • Glucose and many other monosaccharides are an important sources of fast energy.

17. Monosaccharide • Important 5C monosaccharides are ribose (C5H10O5) and deoxyribose (C5H10O4). • Glucose is the most common 6C monosaccharide, but its structural isomer, fructose, is common as well. • An enzyme, isomerase (ase = enzymes), converts one isomer to the other.

18. Disaccharide • A disaccharide is formed by a dehydration reaction between two monosaccharides. • Disaccharides function in extracellular transport of sugars (e.g., sucrose in plant sap, lactose in mammalian milk). The monosaccharides glucose and fructose combine to form the disaccharide, sucrose (plant sugar). Disaccharides function in extracellular transport of sugars (e.g., sucrose in plant sap, lactose in mammalian milk).

19. Disaccharide • While most babies are able to digest lactose into glucose and fructose, many people have a hard time digesting lactose as they age. • Unfortunately, intestinal bacteria will take advantage of this food source, producing gas, and inducing diarrhea, bloating, and nausea. • One major reason for this problem is that levels of the key enzyme for this hydrolysis, lactase, decline as we age, starting as early as age 2. • There are also geographic differences in lactose intolerance.

20. web.lemoyne.edu/~hevern/psy340/graphics/lactose.intolerance.jpgweb.lemoyne.edu/~hevern/psy340/graphics/lactose.intolerance.jpg

21. Polysaccharide • Polysaccharides are long chains with hundreds or thousands of monosaccharides. • Polysaccharides have two functions: • Energy Storage (e.g. glycogen, starch) • Extracellular Structural Materials (cellulose)

22. Proteins • Proteins are polymers composed of amino acids. • Amino acids have C, N, O, and H in their structure. Made of fourdifferent parts. H Hydrogen H OH C C N _________ group H O R ________ group “R” group or variable side chain

23. Amino Acids • There are 20 different R groups and these produce the 20 amino acids that are used for producing proteins.

24. Amino Acids • Humans cannot synthesize 8 of the 20 amino acids. • While a diet with animal products provides all these essential amino acids, a purely ______________ diet may lead to problems because some plants are deficient in these 8. • Since the body does not store amino acids, a single deficiency of an essential amino acid, can lead to a protein deficiency.

25. Polypeptides • Peptide bond is a bond formed by two molecules when a carboxyl group of one molecule reacts with an amine group in another molecule. • Polypeptides are polymers of amino acids linked by peptide bonds.

26. Polypeptides • Proteins are polypeptides that fold into complex 3-D shapes. • There are four different structures of proteins. • Primary • Secondary • Tertiary • Quartenary

27. Proteins • Primary structure of a protein, the order of the amino acids will ultimately determine it’s shape. • Secondary structure of a protein are from amino acids forming weak bonds with other amino acids.

28. Proteins • Tertiary structure of proteins is shaped due interactions of side chains. • Quaternary structure is caused by interactions among separate polypeptides, each with their own tertiary structure. • Hemoglobin has 2 alpha and 2 beta globin proteins

29. Small Changes Add Up • The genetic disease, sickle-cell anemia, is due to a change of a single amino acid in the oxygen-carrying protein hemoglobin. • In individuals with sickle-cell anemia, valine (a non-polar AA) replaces the sixth amino acid, glutamine (a polar AA) of a normal globin.

30. Protein Shape • Protein shape depends on the primary structure of polypeptides and also on the physical environment and the presence of other proteins. • Smaller proteins “self-assemble” into their functional shape. • Others require ________________ proteins to assist in proper folding. • Changes in the environment or binding (or release) of other molecules cause proteins to change shape.

31. Protein Shapes • Two proteins may have the same amino acid sequence, but do not fold in the same way. This can cause them to function differently. • Prions are misfolded proteins, and when they enter the body, they can cause normal proteins to fold differently.

32. Prions • Mad cow disease (BSE or bovine spongiform encephalopathy) and related illnesses (scrapie in sheep, variant Creutzfeldt-Jakob disease in humans) are caused by an abnormal protein which can alter the shape of normal proteins. • In humans, the disease leads to neurological problems and death within a year of the onset of symptoms.

33. Mad-Cow Disease www.cnn.com/interactive/world/europe/0010/cjd/bse.gif

34. Functions of Proteins • Structural proteins (e.g., collagen) are intra- and extracellular supports. • Storage proteins (e.g., ovalbumin) are a source of amino acids to support the synthesis of new proteins during development. • Transport proteins either carry materials around the organism (e.g., hemoglobin) or carry molecules past biological membranes (e.g., Na+-K+ pump). • Hormonal proteins (e.g., insulin) are intercellular messengers.

35. Function of Proteins • Receptor proteins detect chemical signals (e.g., hormones) and alter the intracellular environment. • Contractile proteins (e.g., myosin) are responsible for organismal and cell movement. • Defensive proteins (e.g., antibodies) attack foreign molecules like viruses, bacteria, and other parasites. • Enzymatic proteins control specific chemical reactions.

36. . Fig. 3.15, pg. 57 Nucleotides • Nucleotides are molecules that comprise the structural units of DNA and RNA A 5C sugar Nitrogen Base Phosphate Group

37. Nucleotides • The 5-carbon sugar in nucleotides can be either ribose or deoxyribose. • Ribose (C5H10O5) is found in ribonucleotides. • Deoxyribose (C5H10O4) is found in deoxyribonucleotides.

38. Nucleotides • There are five possible nitrogenous bases. • In DNA there is Adenine, Guanine, Cytosine, and Thymine. • In RNA Thymine is replaced with Uracil.

39. Classes of Nucleic Acids • Polynucleotides (ribonucleic acid: RNA and deoxyribonucleic acid: DNA) carry the information for and participate in protein synthesis. • ATP (adenosine triphosphate) and GTP (guanine triphosphate) store and release energy to support normal metabolic activities. • Nucleotides coenzymes transport high energy electrons from one site in the cell to another.

40. A Closer Look at Nucleotides • RNA (Ribonucleic Acid) is a __________ strand. • In single strands of RNA and DNA, the sugar group of one nucleotide bonds to the phosphate of the next. • RNA will only have Guanine, Adenine, Uracil,and Cytosine bases.

41. RNA • RNA molecules have multiple roles • rRNA (ribosomal RNA) combines with proteins to form ribosomes which synthesize new proteins • mRNA (messenger RNA) sets the order with which amino acids should be bonded to synthesize a polypeptide • tRNA (transfer RNA) transfers or carries specific amino acids to the ribosome

42. A Closer Look at Nucleotides • DNA molecules are ___________ stranded. • The two strands are linked together by hydrogen bonds between nitrogen bases on the two strands. • Specific bases on one strand match up with specific bases on the other strand • ______ with C and ______ with T

43. The order of a section of nucleotides on DNA (a gene) contains the information for producing a __________________. • Each of the 100,000 different proteins synthesized by humans begins with a section of DNA. • This gene is transcribed from DNA to _______________. • The mRNA is complementary to the nucleotides of DNA. • At the ribosome, the order of nucleotides on mRNA directs the addition of amino acids to form a protein during translation. Fig. 3.19, pg. 59

44. Lipids • Lipids are large, nonpolar organic molecules that don’t dissolve in polar solvents well. • They are not polymers, and do not have the same ratio of C, H, O as carbohydrates do. They usually have fewer oxygen in their empirical formula. • Classes of Lipids: • Fats • Phospholipids • Steroids

45. Fatty Acids • Fatty Acids are the monomers of fats. • Fatty acids have lots of C & H atoms and two O atoms. • There is a long backbone of C & H with a carboxyl (COOH) group at one end.

46. Fatty Acids • Saturated Fatty Acids lack the C=C in the backbone. • Most saturated fats are solid at room temperature. (animal fats) • It has as many Hydrogens attached to it as possible.

47. Fatty Acids • Unsaturated Fatty Acids have one (monounsaturated) or more (polyunsaturated) C=C bonds in the backbone. • Most unsaturated fatty acids are liquid at room temperature (plant oils). • Fatty acids are a major source of ________________ in cells.

48. Fatty Acids • While your body can synthesize most of the fatty acids that it requires, it cannot synthesize two essential fatty acids. • These fatty acids are used in the production of hormones that control cell growth and specialization. A lack of them can cause impaired growth, skin problems and neurological problems. • Omega-3 fatty acids are also linked with reduced risk of heart attack.

49. Fatty Acids • Normally, polyunsaturated and monounsaturated fats, from plant oils have positive effects on health. • However, in the many processed foods (cookies, fried foods, candies, crackers), some natural fats are converted to trans fats. • Trans fats elevate levels of cholesterol and LDL (low density lipoprotein) in the blood. • This can lead to elevated risk of heart attacks. Now manufacturers are required to list trans fat content.

50. Triacylglycerides • Triacylglycerides are a fat that has one glycerol molecule, attached to three fatty acids. • Account for 95% of fat stored in human tissue.