2. Organic Chemistry and Biochemistry Lecture Text Chapter 2

3. Organic Molecules Molecules containing both carbon and hydrogen Carbon –4 valence electrons in outer orbital –Needs 8 total for full complement

4. Carbon Can form 4 covalent bonds Can form 1-2 bonds with multiple atoms, including other carbon atoms –Form chains of carbons, rings, etc.

5. Reactive Groups Hydrocarbon chains may be linked to more reactive elements –E.g., oxygen, nitrogen

6. Chemical Formulas Molecular Formulas –Number of atoms of each element in the molecule E.g. water = H 2 O E.g. methane = CH 4 E.g. glucose = C 6 H 12 O 6 –Does not indicate how atoms bond together

7. 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 (C 3 H 6 O)

8. Chemical Formulas Condensed Structural Formulas –Not all bonds drawn –Central atoms shown with atoms bonded to them –E.g. Acetone (C 3 H 6 O) (CH 3 )CO(CH 3 ) (CH 3 ) 2 CO CH 3 CCH 3 O or

9. 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

10. Chemical Formulas Line-Angle Example Line-Angle Structural Formula

11. Biomolecules Complex organic molecules used in biological systems Polymers –Made up of repeated subunits Major Groups 1.Carbohydrates – energy sources, cell communication 2.Lipids – energy storage, cell membrane structure, cushioning, cell communication 3.Proteins – structure, cell function (enzymes), cell communication 4.Nucleic Acids – information storage

12. 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 = (CH 2 O) n –e.g. glucose – C 6 H 12 O 6

13. Carbohydrates (Sugars) monosaccharide - individual unit basic CH 2 O 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

14. Carbohydrates (Sugars) Disaccharide –two monosaccharides linked together e.g. sucrose = glucose + fructose e.g. maltose = glucose + glucose

15. Carbohydrates (Sugars) Polysaccharide –Many monosaccharides linked together E.g. glycogen –Polymer of glucose

16. 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

17. 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

18. Lipids (Fats, Oils, Waxes) very general category contain compounds that are not soluble in water (hydrophobic) Major classes –Triglycerides –Phospholipids –Steroids

19. Triglycerides fats and oils formed by dehydration synthesis combine glycerol with three molecules of fatty acid

20. 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

21. Phospholipids contain a phosphate group (PO 4 ) commonly a combination of a phosphate group to a glycerol molecule attached to two fatty acids –e.g. lecithin

22. 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

23. 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

24. 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)

25. Peptide Bonds Amino acids are joined together by dehydration synthesis NH 3 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

26. 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

27. 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

28. Protein Structure: Tertiary Structure Twisting and folding of a single protein chain due to chemical interactions among the different sidechain groups

29. Protein Structure: Quaternary Structure Bonding and interactions of multiple polypeptide chains –e.g. insulin = two separate chains –e.g. hemoglobin = four separate chains

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