Organic Chemistry and Biochemistry

1. Organic Chemistry and Biochemistry Lecture Text Chapter 2

2. Organic Molecules • Molecules containing both carbon and hydrogen • Carbon • 4 valence electrons in outer orbital • Needs 8 total for full complement Fig 2.1, p.25

3. Carbon • Can form 4 covalent bonds • Can form 1-2 bonds with multiple atoms, including other carbon atoms • Form chains of carbons, rings, etc. Figs 2.3a, p.26, 2.8, p.29, and 2.9. p.30

4. Reactive Groups • Hydrocarbon chains may be linked to more reactive elements • E.g., oxygen, nitrogen Figs 2.10-2.11, p.30

5. Chemical Formulas • Molecular Formulas • Number of atoms of each element in the molecule • E.g. water = H2O • E.g. methane = CH4 • E.g. glucose = C6H12O6 • Does not indicate how atoms bond together

6. Chemical Formulas • Structural Formulas • Indicate bonds among atoms within molecules • Single line indicates single covalent bond • Double line indicates double covalent bond • E.g. Acetone (C3H6O)

7. O CH3CCH3 Chemical Formulas • Condensed Structural Formulas • Not all bonds drawn • Central atoms shown with atoms bonded to them • E.g. Acetone (C3H6O) (CH3)CO(CH3) or (CH3)2CO or

8. Chemical Formulas • Line-Angle Formulas • Bonds represented by lines • Carbon atoms assumed to be present at the end of any line • Oxygen and Nitrogen shown, Hydrogen is not • Each carbon is assumed to have enough hydrogens bonded to it by single bonds to give it four bonds total

9. Chemical Formulas • Line-Angle Example Structural Formula Line-Angle

10. Biomolecules • Complex organic molecules used in biological systems • Polymers • Made up of repeated subunits • Major Groups • Carbohydrates– energy sources, cell communication • Lipids– energy storage, cell membrane structure, cushioning, cell communication • Proteins – structure, cell function (enzymes) , cell communication • NucleicAcids – information storage

11. Carbohydrates (Sugars) • molecules that contain H, O and C • relative amounts of each are the same in all simple carbohydrates • #C atoms = #O atoms • #H atoms = 2x the number of either C or O • general formula = (CH2O)n • e.g. glucose – C6H12O6

12. Carbohydrates (Sugars) • monosaccharide- individual unit • basic CH2O formula • name possesses the suffix –ose • e.g. glucose, galactose, fructose, ribose • Monosaccharides can have the same formula but different arrangements of atoms • Isomers – molecules of same formula but different structures Fig 2.13, p.32

13. Carbohydrates (Sugars) • Disaccharide • two monosaccharides linked together • e.g. sucrose = glucose + fructose • e.g. maltose = glucose + glucose Fig 2.15, p.33

14. Carbohydrates (Sugars) • Polysaccharide • Many monosaccharides linked together • E.g. glycogen • Polymer of glucose Fig 2.14, p.33

15. Carbohydrate Synthesis • Monosaccharides are linked together by dehydration synthesis • employs specific enzymes • H is removed from one monosaccharide, an -OH group from the other • covalent bond (glycosidic bond) formed between the two • water formed as an end-product Fig 2.15, p.33

16. Carbohydrate Digestion • polysaccharides are broken apart via hydrolysis • a water molecule is split • H+ added to one of the free monosaccharides • OH group added to the other Fig 2.16, p.34

17. Lipids (Fats, Oils, Waxes) • very general category • contain compounds that are not soluble in water (hydrophobic) • Major classes • Triglycerides • Phospholipids • Steroids Fig 2.17-2.23, p.35-38

18. Triglycerides • fats and oils • formed by dehydration synthesis • combine glycerol with three molecules of fatty acid Fig 2.17-2.18, p.35

19. Triglycerides • different types of fatty acids • Saturated • all carbons in chain linked by single bonds • Unsaturated • one or more carbons in chain linked by double bonds • Unsaturated fatty acids tend to be more fluid Fig 2.17, p.35

20. Phospholipids • contain a phosphate group (PO4) • commonly a combination of a phosphate group to a glycerol molecule attached to two fatty acids • e.g. lecithin Fig 2.20, p.36

21. Phospholipids • possess both polar an nonpolar ends (amphipathic) • nonpolar ends aggregate together • form micelles when mixed in water • interact with water – lowers surface tension of water Fig 2.21, p.37

22. Steroids • Consist of 3 six-carbon rings and a single five-carbon ring interlocked together • different functional groups attached to basic structure • e.g. sex steroids – produced by gonads (testosterone, progesterone) • e.g. corticosterones – produced by adrenal glands • e.g. cholesterol– precursor for hormones, regulation of cell membrane fluidity Fig 2.22, p.37

23. Proteins • Diverse in structure and function • Polymers of amino acids • 20 common amino acids each with: • an amino group • a carboxyl group • a functional side-group (differs among a.a.’s) Fig 2.24, p.39

24. Peptide Bonds • Amino acids are joined together by dehydration synthesis • NH3 group of one joined to the COOH group of another to form a peptide bond • two joined amino acids = dipeptide • many joined amino acids = polypeptide Fig 2.25, p.39

25. Protein Structure:Primary Structure • Sequence of amino acids in a polypeptide chain • From free amino end (N-terminus) to the free carboxyl end (C-terminus) • May be 1000’s of a.a.’s long Fig 2.26a, p.40

26. Protein Structure:Secondary Structure • Formation of helix or sheet shape in a protein chain • due to hydrogen bonds forming between the amino group of one peptide bond and the carboxyl group from another peptide bond Fig 2.26b+c, p. 40

27. Protein Structure:Tertiary Structure • Twisting and folding of a single protein chain • due to chemical interactions among the different sidechain groups Fig 2.26d, p.40, and 2.27, p.41

28. Protein Structure:Quaternary Structure • Bonding and interactions of multiple polypeptide chains • e.g. insulin = two separate chains • e.g. hemoglobin = four separate chains Fig 2.26e, p.40

29. Conjugated Biomolecules • Combinations of two or more types of biomolecules • Glycoprotein = carbohydrate + protein • Lipoprotein = lipid + protein • Glycolipid = carbohydrate + lipid