A. Biological Chemistry(though water is the universal medium for life on earth, living organisms are made of chemicals based mostly on the element a. contain Carbon. total of 6e-, 2 in 1st shel , 4 in 2nd that holds 8 i. Carbon has 4 valence electrons that can join with an electron from another atom to form a strong covalent bond-usual y with C, H, O, or N ex/ CH4 (methane) ii. Carbon can bond with other carbon atoms to form large, complex molecules; can be straight, branched, or rings b. C chains form skeletons of most organic molecules c. each repeating unit is called a monomer d. long chain called a polymer; polymers are macromolecules-large, organic molecules i. macromolecules are formed by combining monomers by removing water; called dehydration synthesis or condensation reactions ii. macromolecules are broken down, separated, or digested by e. hydrocarbons-only contain C & H molecules ii. non-polar linkages; can release a lot of energy f. isomers-compounds with same molecular formula, but different structural arrangements (thus different properties) fig 4.7 p62 i. structural-different covalent arrangement of atoms, often ii. geometric-same sequence of covalently bonded atoms, but different spatial arrangements (cis vs. trans) iii. enantiomers-right & left handed versions of each other 3. Carbohydrates (starches & sugars) smal or large, can be monosaccharides, a. main energy source, fuel, & nutrients for cell ex/ glucose, fructose, galactose, deoxyribose, ribose c. simple unit (monomer)-monosaccharide (simple sugars) CH20 Exists in 2 interconvertable forms—alpha glucose (α), and beta glucose (β) (differ in placement of hydroxyl group 3. ID test: Benedict’s: monosaccharides turn green, yellow, d. double sugar-disaccharide (two monosaccharides bonded together by glycosidic linkage) 1. C6H12O6 + C6H12O6 --> C12H22O11 + H2O Water lost when bonded together: dehydration (Water added to break apart: hydrolysis) 2. C12H22O11 --sucrose; most common (table sugar) e. most complex-polysaccharides—many sugar units (macromolecules) 1. long polymers few hundred to few thousand monosaccharides joined 2. ID test: Iodine: polysaccharides turn blue a. plant starch found in breads/grains,potato (stores extra sugar as granules in plastids) 2 forms, amylose & amylopectin b. animal starch (called glycogen) stored in liver & muscle c. cellulose (gives plants their strength/rigidity; primary structure of cell wall; in wood, paper, cotton, d. chitin—cell wall of fungi & exoskeleton of arthropods *humans don’t have enzymes to digest cel ulose & chitin—our enzymes can only digest alpha glycosidic linkages & these have beta* 4. Lipids (fats)-usually small non-hydrocarbon part joined to 3 HC tails a. function-long term energy storage (contains twice as much energy as an equivalent weight of polysaccharide), parts of biological membranes, waterproof coverings, insulation b. composition: C, H, O, & often P (phospholipids) c. saturated-only single bonds (most often solids-animal) unsaturated-some double bonds; most often: oils/plants d. example: triglycerides: 1 glycerol + 3 fatty acids e. lipids don’t consist of polymers; grouped together because they have f. ID tests: translucent spot on brown paper, soluble in lighter fluid, g. phospholipids—phosphate group forms hydrophilic head h. steroids—lipids with a carbon skeleton of 4 fused rings 5. Proteins—examples: insulin, hemoglobin, antibodies, enzymes a. functions: (fig 5.1 p78) support, storage of amino acids, transport cell communication (hormones), movement, defense, growth & repair c. ID test: nitric acid turns proteins yellow (xanthoproteic test) d. monomer- amino acids; have amino group on one end (-NH2) with
basic properties, and carboxyl group on other end (-COOH) with acidic properties. At center is the α carbon, covalently bonded to a hydrogen atom. Other part is called R group (side chain) i. approx 20 found in nature (differ in their R-groups) ii. bonds between amino acids: peptide bonds—fig 5.18 p80 e. polymer-long chain (thousands of amino acids; called polypeptides) f. some function as enzymes-definition: biological catalysts
1. speed up reactions by lowering activation energy EA—the initial investment of energy for starting a reaction 2. very specific—only react on a certain substrate (‘lock & key’) 3. induced fit—enzyme actually changes its shape ii. active site (enzymes provide it, usually a groove on the if organic, called coenzymes ex/vitamins 4. inhibitors—if bind covalently, usually irreversible ex/sarin i. mimic normal substrate (competitive inhibition), ii. bind & cause enzyme to change shape (noncompetitive) 5. allosteric regulation—can inhibit or activate by binding 6. some factors affecting enzymatic activity 1. primary: sequence of amino acids (peptide bonds created) 2. secondary: spatial organization (ex. alpha helix, beta pleated sheet); due to H bonds between backbone, not amino acid side chains. amino acids can be twisted, folded 3. tertiary: shape of entire molecule; chain itself is folded. Level where interactions between R groups most important. Strong covalent bonds between amino acids maintain 3D shape. Example: can have disulfide bridges—from 2 cysteines 4. quaternary: # of chains; >1 chain → 3D structure 5. chaperonins: (chaperone proteins)—assist proper folding of 6, Denaturation: a change in a protein’s 3D shape/conformation due to disruption of H bonds, disulfide bridges, or ionic bonds. Can be due to pH, salt concentration, temp, chemicals, etc. Denatured protein becomes misshapen, and biologically inactive. h. Amino acid sequence of a polypeptide is programmed by a unit of inheritance called a GENE. Genes are made up of DNA, a nucleic acid. a. function: chemical activity & code for information. c. monomer-nucleotides. Nucleotides have 3 components pyrimidines-one ring (ex. thymine, uracil, cytosine) purines- double ring (ex. adenine, guanine) d. important examples: DNA (double strands—held together with H 7. ATP—organic phosphate—adenosine triphosphate a. primary energy transferring molecule in cell i. consists of an organic molecule (adenosine) attached to a b. one of ATP’s three phosphates may split off as an inorganic phosphate c. losing 1 phosphate, ATP becomes ADP; the reaction releases energy

Source: http://www.exeter.k12.pa.us/cms/lib6/PA01000700/Centricity/ModuleInstance/2883/Biological%20Chemistry%20Teacher%20Notes.pdf

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