Chapters 10, 11 Timberlake biochemistry

1. Chapters 10, 11 Timberlake biochemistry Unit Topic —introduction to the chemistry of Life, organic (living) chemistry

2. March 31 intro to organic chemistry—why are names & structures so important—intro to isomers homework: read 10.2 & do red questions in blue box April 1 naming & representing simple hydrocarbons • full structural formulas, • molecular formulas, • condensed formulas, • organic shorthand formulas; • using organic prefixes & suffixes to describe structure of a compound homework: practice worksheet April 2naming & representing substituted hydrocarbons • functional groups (structure & names) substituted for H side chains • identifying positions along the backbone of org’c compoundshomework—practice worksheet April 3 importance of structural, geometric , & stereoisomers—e.g, methamphetamine vs decongestant or trans- vscis- fats Homework—practice worksheet April 4 building and naming isomers—lab; activity—physiological importance of isomers—research + present (review 4/8, quiz 4/9)

3. LG1 Students will understand how only S P O N C and H can comprise millions of functionally different organic compounds and will be able to distinguish between : A Explain how the chemical properties of C make it the idea element for building diverse molecules. B Describe similarities and differences between organic compounds; explain how only 6 elements comprise so many functionally different molecules. LG2 Students will be able to draw complete structural and Lewis dot formulas for straight chain, cyclic, & branched chain hydrocarbon alkanes, alkenes, and alkynes. LG 3 Students will be able to apply the specialized system of organic nomenclature &structural representation to name hydrocarbons given their structures or to draw hydrocarbons given their names. A Draw condensed and organic shorthand structural formulas for organic compounds, given the IUPAC name of a compound or given the full structural formula for the compound. B Use IUPAC nomenclature rules plus organic prefixes & suffixes to name straight chain, cyclic, & branched chain hydrocarbon alkanes, alkenes, and alkynes. LG 4 Students will be able to apply the specialized system of organic nomenclature &structural representation to name substituted hydrocarbons given structures or to draw substituted hydrocarbons given names. A Identify these functional groups: Carboxyl, amino, carbonyl, phosphate, sulfahydrol, hydroxyl, ether, ester. B Use IUPAC C backbone numbering rules to name substituted hydrocarbons with these functional groups, so that the name can be used to generate the structure of the compound. LG5 Students will be able to understand the biological importance of isomerism. A Identify structural, geometric, and stereo-isomers of compounds. B Explain the biologically and medically significant impacts of isomerism.

4. Organic chemistry—the study of covalently bonded carbons containing at least C and H Biochemistry—application of organic chemistry to understanding the structure and function of organisms. 96% of the dry mass of organisms is made of organic compounds Other elements commonly found in organic compounds: C H O N P S

5. The biochemist’s Mantra pays homage to the ability of only 6 elements to construct nearly all organisms. SHAPE CHARGE CONCENTRATION And RATE RULE THE WORLD! AND THE MOST IMPORTANT OF THESE is…. SHAP E! CHNOPS! CHNOPS! CHNOPS!

6. L.G. 1Explain how chemical properties of C make it the ideal element for building diverse molecules. By promoting one of its 2s electrons to the 3rd 2p position, C opens up 4 half filled valence orbitals. C can form 4 different side chains! It’s a hub.

7. Carbon can link to other C’s in a “carbon backbone”, as well as to side group—here in these hydrocarbons, the only side chain is H..

8. C backbones are variable in • Length • Shape (branched, linear, cyclic) • #, locations of double and triple bonds (no C=C: saturated—as many H as it can hold; 1 or more C=C, unsaturated—could bond more H’s if the double bonds were single bonds instead) • Side groups (H or functional groups)

9. LG 2 Draw complete structural and Lewis dot formulas for straight chain, cyclic, & branched chain hydrocarbon alkanes, alkenes, and alkynes. Whatever the shape of the backbone & whatever the nature of its side chains, these rules will help you assess whether a structural formula is drawn correctly. # covalent bonds allowed—in this priority H 1 never violated C 4 never violated O 2 hardly ever violated P, N 3 unless part of a charged functional group (the normally unbonded pair can form a coordinate covalent bond) S 2 unless part of a charged functional group

10. Stop—take 5 minutes to examine the ball and stick models of atoms, on your white boards identify them by color and H, P, S, O, N, and C or halogens place whiteboards on the ledge up front, then return to your seat for class discussion

11. Which balls represent which elements? Black C 4 holes needs to share 4 ve- Red S, O 2 holes needs to share 2 ve- Yellow H 1 hole (lots of them) 1 ve- shared Green halogens 1 hole (few of them) 1 ve- shared Blue P, N 3 or 4 holes shares 3 ve- but can also use coordinate covalent bonds in charged ions (it donates BOTH of its normally lone pair to the bond in such a case)

12. LG 3Draw condensed and organic shorthand structural formulas for organic compounds, given the IUPAC name of a compound or given the full structural formula for the compound.

13. Organic compounds can be represented by: IUPAC names—describe C backbone and all of its side chains, such that the shape of the molecule can be determined from the name. Full structures—showevery atom & covalent bond Condensed structures—use the organization of the atoms in a word-like format to convey structure Organic shorthand—the C backbone and H side chains are not shown, but functional groups (side chains that are not H but one of several groups of atoms) are shown Ball and stick models Space filling models

14. C2H6O 1-ethanol or ethan-1-ol (dicarbon-hexahydrogen monoxide)Full structure condensed organic shorthandCH3CH2OHC4H8O2 butyric acid or 1-butanoic acidFull structure condensed organic shorthandCH3(CH2)2COOH

15. Organic prefixes to show #s Carbons in longest uninterrupted backbone of an unbranced hydrocarbon # C Name Molec FormulaStruct Formula 1 Methane CH4CH4 2 Ethane C2H6 CH3CH3 3 Propane C3H8 CH3CH2CH3 4 Butane C4H10 CH3CH2CH2CH3 5 Pentane C5H12 CH3CH2CH2CH2CH3 6 Hexane C6H14 CH3(CH2)4CH3 7 Heptane C7H16 CH3(CH2)5CH3 8 Octane C8H18 CH3(CH2)6CH3 9 Nonane C9H20 CH3(CH2)7CH3 10 Decane C10H22 CH3(CH2)8CH3

16. Why is it so important to represent an organic compound so that its shape is revealed? Whereas each different ionic compound is unique—hence the need for use of a simplest ratio formula (empiracle) like CaO instead of Ca2O2—for organic compounds, one molecular formula can represent many functionally very different substances called isomers.

17. Examples for C4H10O

18. C3H6 Prop-1-eneCH2CHCH3

19. Formula rules for drawing an organic compound’s: • Full structural formula • Lewis formula • Condensed formula • Organic shorthand formula

20. Summary: different shapes, lengths, #s, and arrangements of allows tremendous molecular diversity Proper representation identifies which isomer is being described, whereas the molecular formula alone provides only minimal information.

21. Isomers are compounds of the same molecular formula, but different atomic organization. Isomers have different shapes, so they also have different properties. a) butane is linear, isobutane is branched—butane boils at a lower temperature. b) cis-isomers: larger side chains (X) attached to C at ends of a C=C are on the same plane (double C=C bonds are stiff, whereas atoms rotate around single covalent bonds) trans-isomers: different sized side chains attached Cs at either end of C=C are on the same plane of the double bond c) d (right) & l (left) hand mirror images form stereoisomers (enantiomers) around chiral C (4 different side groups on the same C)

22. The broadest class of isomer is structural isomers. This is the general term to describe molecules having the same molecular formula but different arrangements of the atoms and covalent bonds. Geometric and stereoisomers are subgroups of structural isomers.

23. Example of how subtle rearrangements of atoms between isotopes affects shape and function:C5H10O has more than 10 structural isomers—some toxins, others pleasant tasting food additives. You can use the Merck index to look up properties of common organic compounds. Look under the index of chemical formulas. Isoprenol is a flammable gas that causes severe eye irritation—industrial solvent But, Valeraldehyde is a food flavoring or perfume scent http://www.alibaba.com/promotion/promotion_c5h10o-promotion-list.html

24. More C5H10O isomers • Pain reliever (analgesic) • Industrial solvent

25. Examples for C4H10O isomers

26. Geometric isomers have different properties because of their shapes. Cis-fatty acids are healthier for eating than trans fatty acids because they are less likely to clog blood vessels

27. 9/2/2010 Which of these are cis isomers? Which are trans isomers? Which are not geometric isomers?Build and draw (complete and shorthand structures) cis and trans isomers of CHOHCHOH

28. A third class of isomers is stereoisomers, also called enantiomers. They are termed d or l according to how they rotate a plane of polarized light shown through their crystals. d-isomers: right handed rotation of polarized light. l-isomers: left handed rotation of polarized light)

29. Even though visually, stereoisomers seem nearly identical—just mirror images—cells are very specific about which form use. Cells use d-sugars but l-amino acids. L-valine amino acid

30. For example, one stereoisomer of carvone tastes like spearmint, the other like caraway seeds.

31. Huge molecules can be stereoisomers at more than one site. D and l configuration is described for a particular, stated chiral C. In this small molecule, only C b is chiral (attached to 4 different side groups)

32. Still another way to increase diversity of organic compounds is to use functional groups • http://www.chemistry-drills.com/functional-groups.php?q=simple • A functional group is a covalently bonded group of atoms that tends to give organic compounds characteristic types of chemical reactions • Molecules in the same class (like amino acids, sugars, fats, nucleotides) have similar cell functions because they have similar functional groups • You need to recognize these functional groups • Carboxyl • Carbonyl • Amino (also called amine) • Phosphate • Sulfahydryl • Ester • hydroxyl

33. R means the rest of the molecule other than the R group of interest

34. Most functional groups render an organic compound polar covalent if they are asymmetric in their organization. This is because they often contain both highly electronegative O or N bonded to either C or H atoms that have lower electronegativity. For example, when a hydroxyl group replaces one H of nonpolar ethane (a hydrocarbon), polar ethanol is formed. Ethane is poorly soluble in water—is very hydrophobic—while ethanol is highly soluble in water—is very hydrophilic.

35. Finally, polymerization or use of conserved motifs (ch 12+ topics) increases diversity Simpler subunits are joined into chains (e.g., glucose chains form glycogen, starch, and cellulose; amino acid subunits form chains called proteins; nucleotide chains form nucleic acids DNA & RNA)

36. Homework due for Friday 9/3/2010 Be prepared for a quiz on all of the info found in this powerpoint—from chapter 4--tomorrow (Friday, 9/3). We’ll head into chapter 5 as soon as the quiz ends, so preview the power point posted for chapter 5. The unit test for chapters 1—5 will occur Friday, 9/10/2010.