1. Carbon-based compounds Chapter 4~ Carbon & The Molecular Diversity of Life

2. Organic chemistry… The Chemistry of Carbon Forms a tetrahedral shape when bound to 4 molecules Tetravalence- 4 e- in outer shell

3. Hydrocarbons Only carbon & hydrogen (petroleum; lipid ‘tails’) Covalent bonding; nonpolar High energy storage Isomers (same molecular formula, but different structure & properties) –structural~ differing covalent bonding arrangement –geometric~ differing spatial arrangement – enantiomers~ mirror images pharmacological industry (thalidomide)

4. Prefixes Organic compounds are named with prefixes Plain hydrocarbons end with –ane –Double bonds= ene –Side groups change names (ex: -OH = -ol)

5. Functional Groups Attachments that replace one or more of the hydrogens bonded to the carbon skeleton of the hydrocarbon Each has a unique property from one organic compound to another Hydroxyl Group –H bonded to O –alcohols –polar (oxygen) –solubility in water Carbonyl Group –C double bond to O –At end of H-C: aldehyde –Otherwise: ketone

6. Carboxyl Group –O double bonded to C to hydroxyl –carboxylic acids (dissociation= H+) –covalent bond between O and H –Polar Amino Group –N to 2 H atoms –“amines” –acts as a base Sulfhydral Group –sulfur bonded to H –Thiols –Can cross-link with each other

7. Methyl Group –C bonded to 3 H’s –Affects shape/configuration Phosphate Group –phosphate ion covalently attached by 1 O to the C skeleton –Negatively charged

8. ATP= NRG - ATP is the main energy source for cells. - One phosphate group is cleaved off to form ADP and energy is released

9. Macromolecules Chapter 5~ The Structure & Function of Macromolecules

10. Polymers Covalently bonded monomers Condensation (dehydration) reaction –One provides a –OH while the other provides a H to form a water molecule Hydrolysis –bonds between monomers are broken by adding water (ex:digestion)

11. Carbohydrates Monomer = Monosaccharides –CH 2 O formula –multiple hydroxyl (-OH) groups and 1 carbonyl (C=O) group: aldehyde (aldose) sugar- group at end ketone (ketose) sugar- group in center broken down during cellular respiration raw material for amino acids and fatty acids

12. Putting them together Disaccharides –glycosidic linkage (covalent bond between 2 monosaccharides) Sucrose (table sugar) –most common disaccharide

13. Functions of Carbohydrates Storage: –Starch= glucose monomers –Plants: roots/plastids –Animals: glycogen/fat Structure: –Cellulose~ most abundant organic compound –Chitin~ exoskeletons; cell walls of fungi; surgical thread

14. Lipids Monomers: Triacyglycerol (triglyceride) –Carboxyl group = fatty acid –Ester linkage: 3 fatty acids to 1 glycerol molecule Fats, phospholipids, steroids Hydrophobic Non-polar C-H bonds in fatty acid ‘tails’ Saturated vs. unsaturated fats; single vs. double bonds

15. Saturated vs. Unsaturated

16. Phospholipids Two fatty acids instead of three –phosphate group attaches to one -OH ‘Tails’ = hydrophobic ‘Heads’ = hydrophilic

17. Phospholipids in formation - Micelle (phospholipid droplet in water) -Bilayer (double layer) -cell membranes

18. Steroids Lipids with 4 fused carbon rings Ex: cholesterol... –cell membranes –precursor for other steroids (sex hormones) –“Good” (HDL) vs “Bad” (LDL) cholesterol atherosclerosis

19. Proteins Importance: –instrumental in nearly everything organisms do –50% dry weight of cells –most structurally sophisticated molecules known Monomer = amino acids (20) –central carbon atom –carboxyl (-COOH) group –amino group (NH 2 ) –H atom –variable group (R)

20. Amino Acid R- Groups Variable (R-) group characteristics: R- group interactions determine shape and function –Nonpolar (hydrophobic) Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro –Polar (hydrophilic) Ser, Thr, Cys, Tyr, Asn, Gln –Acids Asp, Glu –Bases Lys, Arg, His

21. Putting them together Polypeptides formed by a dehydration reaction. –peptide bonds~ covalent bond of carboxyl group to amino group

22. 3-D Structure Proteins function is determined by their structural conformation Amino acid sequence determines how it will fold –Affinity of A.A’s for each other, etc. Chaperonins- proteins that assist in folding of other proteins –Segregate and protect proteins and allow them to fold w/o any “bad influences” Four levels of protein structure

23. Primary Structure Linear structure of Amino Acids Molecular Biology: –each protein has a unique primary structure of amino acids Examples: –One amino acid substitution in hemoglobin causes sickle-cell anemia

24. Secondary Structure Coils & folds caused by hydrogen bonds Alpha Helix: –Coiling~ every 4 th AA fibrous proteins, keratin Pleated Sheet: –Parallel sheets w/ H bonding between them globular proteins, spider silk

25. Tertiary Structure Protein takes on irregular contortions from R group bonding –Hydrogen bonds between polar side groups –Hydrophobic molecules undergo van der Waals interactions –Disulfide bridges form between cystine –SH groups –Ionic bonds between + and -

26. Quaternary Structure 2 or more polypeptide chains aggregated into 1 macromolecule –Collagen (connective tissue that makes up 40% of body structure) –Hemoglobin (Oxygen binding protein in red blood cells) * 3-D structure of proteins discovered w/ X-ray crystallography and nuclear magnetic resonance (NMR)

27. Denaturation If protein shape is changed, it cannot function properly –Heat, pH change, chemical treatment, etc. Sometimes proteins can be “renatured” if environment is restored to normal (rare)

28. Nucleic Acids 2 types: –Deoxyribonucleic acid (DNA) –Ribonucleic acid (RNA) Storage and transmittance of genetic information DNA  RNA  protein

29. Monomers= nucleotides Each nucleotide is composed of: – nitrogenous base – pentose sugar – phosphate group

30. “Polynucleotides” Joined by phosphodiester linkages –covalent bonds between phosphate groups

31. Nitrogenous bases Purines always pair w/ Pyrimidines DNA- - A & T - G & C RNA- - A & U - G & C

32. DNA In nucleus Codes for proteins (like blueprints) Double helix –2 strands held together by H-bonds between bases –Complimentary base pairing Sugar = deoxyribose Bases- A, G, C, T

33. Watson and Crick James Watson and Francis Crick discovered the double helix structure of DNA in 1953.

34. RNA Single stranded Several types: –Ex: mRNA, rRNA, tRNA Acts as messenger between DNA in nucleus and ribosomes in cytoplasm Sugar= ribose Bases- A, G, C, U