Chapter 2 – The Chemical Basis of Life: Chemistry/Organic MoleculesPart 1: General Chemistry - Organisms mostly made of C, H, N, & Oo Other elements are required for life (ex. Na, Mg, P, Cl)- Pauling units; Relative Electronegativities: see slideso ∆E.N. = 0-.4: nonpolar covalent. ∆E.N. = .5 – 2; polar covalento Dipole – molecule that has poles- Hydrogen Bondso H atom (+) is attracted to the negative pole of another atom (F, O, N)o Individual H-bond is weak but several together is strong- Ionic Bondso ∆E.N= 2 – 3.3- Watero Attracted to more water (adhesion) & other molecules (cohesion)o Primary solvent in organisms Thermically stable (high specific heat)o Adding solute lowers FP- pHo pure H2O ionizes into H+ & OH-o Acids release H+ in solutiono Bases remove H+ from solutiono Organisms regulate their internal pH and it even varies within different components of cells (see slide for exact numbers)Part 2: Organic MoleculesI. General A. Contain carbonB. Can have both nonpolar & polar parts1. C-H bonds are nonpolar2. C-O bonds are polar3. O-H bonds are polarC. Fig. 2.14: Different ways of drawing molecules D. Isomers: same chemical formula; different structuresFour Major Types of Organic Molecules (Biochemistry)I. Proteins A. Contain C, H, O, N, and usually SB. Consist of 1 or more polypeptidesC. The building block (Monomer) (antithesis of polymer) of proteins is the amino acid1. Amino Acid Structure (picture): 2. R-Group Chemistry determines AA.a. Can be categorized 3 ways: Nonpolar, Polar(uncharged), & Polar (charged)i. This affects how the AA behaves in water and whatthe protein shape is. The shape of the protein has alarge affect on function.ii. Use electronegativity to determine polarity of AAside chainsD. Different from other 3 classes of organic moleculesE. Polypeptide – linear chains of covalently linked AA’s (Fig.2.17)1. Amino group at one end is called amino terminus or N-terminus2. Carboxyl group on other side is carboxyl terminus or C-terminus3. Count number of R-Groups, =O’s, or N’s to find out how many AA’s are inthe molecule4. Peptide Bonds form between the carboxyl group of one AA & the amino group of the next in the chainR-group (side chain/variable group) is the thing that changes, & subsequently determines what AA it is. ***Amino group accepts an H+ (base) – Nitrogen goes from NN+, and the carboxyl group donates an H+ (acid) – OHO-II. Nucleic Acids (DNA & RNA)A. Polymers of nucleotidesB. Store, express & transmit genetic informationC. Associate with proteins to form structures in the cell (rRNA)D. Structure1. Fig. 2.182. Bond between phosphate group & sugasr comes from dehydrating HPO4to PO4 (phosphate) groupE. Carbons in the sugar labeled “Prime” F. One source of variability is the structure of the base1. Pyrimidines ( Single-ring bases) a. Cytosineb. Thymine (DNA only)c. Uracil (RNA only)2. Purines ( Double-ring bases) a. Guanineb. AdenineG. Other source of variability: Structure of the Sugar1. Ex. at the 2’ carbon of the sugar in DNA, the carbon lacks an oxygen(deoxynucleic acid)2. Look at the 2’ carbon in the sugar to find if you’re in DNA or RNA. DNAhas H; RNA has OH.H. The 5’ Carbon of the sugar is not on the ring of the sugar. It’s on the endof the stick attached to the phosphate group1. There will always be 5 carbons in the sugarI. Strands of DNA: phosphate group of 21 nucleotide covalently bonds tothe 3’ carbon of the sugar on the next nucleotide1. Forms phosphodiester bond (Fig. 2.20) 2. A strand is linear, not branched3. All sugars in a given strand have the same orientation (Either 3’5’ or5’3’)III. CarbohydratesA. Structure: C(H2O)B. Simple: monosaccharides (MS)1. Hexoses (6C)a. Ex. Glucose (C6H12O6)2. Pentoses (5C)a. Ex. Ribose (C5H10O5), Deoxyribose (C5H10O4)3. Monosaccharide: unbranched carbon chains that form rings in solutionC. Monosaccharides link together covalently to form polysaccharides1. Can be digestible or indigestible (ex. cellulose [fiber])2. Don’t have to be a line of monosaccharaides – can be branched3. Can be made up of different monosaccharaides Base (thymine, etc.)Phosphate group5’ O 4’ 1’ 3’ 2’Sugar (Deoxyribose)Nucleotide Structure IV. LipidsA. General1. Contain lots of (primarily) H & C2. Nonpolar3. Insoluble in H2Oa. HydrophobicB. 3 types (Overview)1. Fats – energy storage, structural supporta. Structural support – ex. behind eye2. Steroids – cholesterol, hormonesa. “Communication molecules”3. Phospholipids – from cell membranesC. Fats1. Made from 3 fatty acids & a glycerola. Fatty acids: long C-H chains with a carboxyl group at the endi. Carboxyl group releases H+ in H2Ob. 2 types of fatty acidsi. Saturated – all C’s linked by single bonds (solid at room temp; straight chain)ii. Unsaturated – 1+ double bonds; (liquid at room temp, bent chain)D. Steroids1. 4 interconnected C-rings2. Ex. Cholesterol: 3. Differentiate from polysaccharides: no oxygen in steroidsE. Phospholipids1. [A charged, nitrogen-containing molecule] + [phosphate group] + [2 fatty acids]2.Saturated
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