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BIOLOGY II [COMPLETE NOTES] - 4.0ed the final exam

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CAS BI 108
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Lecture 2: What a cell needs to be a cell: water, macromolecules, ions and small molecules. Diagram: Chemical Properties making Bio-Molecules Water Soluble: ­ addition of functional groups ­ proteins, nucleic acids, carbs= soluble. ­ Lipids: usually are water soluble. Properties of Carbon: non polar (doesn’t like mixing with water) ­ 4 unpaired valence electrons so can form 4 separate covalent bonds. ­ Diagram: space-filling model shows true dimensions of molecular arrangement. Covalent Bond Diagram: Non-covalent bonds: 1. hydrogen bonds 2. hydrophobic interactions: nonpolar (Ethane) hydrophobic because has electron sharing. 3. van der waals 4. Ionic bonds: molecules attracted need to be charged. Diagram of Ionic Bonds: Hydrophobic: nonpolar molecules are more attracted to one-another than to H20. Chart of Covalent v. Noncovalent Bond Energy: Important Characteristics of All Biomolecules: -Solubility (in water) -Charge -Size: know something is hydrophilic because H2 and O2 is on surface so soluble. Amino Acids have multiple C,N,O (alanine and glucose is soluble). -Shape: space-filling, stick model, and ribbon model molecule -Environmental PH: Looking for: H ion concentration Lecture 2: Importance of Carbon in Biomolecules: -nonpolar -hydrophobic How Carbon-based molecules are made water soluble: -Add polar groups- covalently linked to C-containing molecules (functional groups) 1. Hydroxyl: R-OH added to compound making alcohols. Polar. H bonds with H20 to help dissolve molecules. Enables linkage to other molecules by dehydration. 2. Aldehyde: C=O is very reactive. Impt in building molecules and E-releasing reactions 3. Keto C=O groups important in Carbon and E rxns 4. Carboxylic: acidic, ionize so what they leave behind is negatively charged. Adds to electronegativity impot in E-releasing. 5. Amino: Basic, accepts proton in living tissues for NH3. Enters into dehydration synthesis by accepting H+. 6. Inorganic Phosphate: covalently linked to R. leaving other 2 O2 ionized. (-)charge. Enters into Dehydration synthesis by giving up OH, releases lots of E when bonded to another P. 7. Sulfhydrol Group: Found mainly in proteins. Plays roll in protein maintaing shape. By giving up H, 2-SH groups react to make a disulfide bridge. Stabilizing protein struction through covalent bond. -Organic Acids have a carboxyl group: weak acids are proton donors, not all acid molecules dissacioate into ions. --COOHCOO- + H+ -Amines: have amino group ---NH2+ H+NH3 + base=proton acceptor Macromolecules: formed by joining monomers (polymerization) Diagram: -polymers formed by joining monomers in condensation(dehydration=removal of water molecule) reactions. Produces water, universal. -takes minimum of two moners to make molecule of water. Always 2:1 ratio. Needs equivalent of a molecule of water. -2 water molecules needed to hydrolyze a trimer into 3 individual monomers=2 because water is added to the covalent bond. -Hydrolysis: how polymers are broken down. Require water, cells add enzymes to break down polymers by adding water back. Dehydration Diagram: Hydrolysis Diagram: Carbohydrates: 1. Monosaccharides=monomers. Glucose: C6H12O6. If aldehyde is off C1=aldo sugar. -3 addition structural monomers of glucose: mannose (diff at C2, C4) a-Galactose (diff at C2, C4) Fructose (diff at C1 and C2) ***a-d-glucose: monomer for starch and glycogen. b-d-glucose: monomer for cellulose both different from each other at C1 for isomers. Isomers: same chem formula, atoms arranged diff Structural (geometric)isomer: diff in how atoms joined together. Glucose ring closes at 1 and 5. Produces two isomers, two different ways in which you can close the ring. Alpha and beta d glucose are examples. Stereo (optical): “D” so shows that both are of same type in terms of stereo isomers and reflecting polarized light. Optical is mirror images of each other. At diagram: Carbon has covalently linked to four elements. Can arrange in one or two different ways. Arrange so carbon itself is asymmetric. (chiral carbon) Way to distinguish them: by forming an impression or mold that involved three of the elements linked to Carbon. Mirror images = D&L forms. Stereo isomers can only be distinguished from one another optically: by illuminating molecule with polarized light, one member of pair reflects light to one direction and vice versa. Result: two chemically different molecules although identical in atom type and make up. predominately D-Form: D&L, just has to do with reflecting light. Carbs: DISACCHARIDES= two monosachh linked covalently by dehydration (dimer) Dimer: two monomers linked covalently. Fig 3-15: Alpha and beta linked through condensation reaction Covalent form connected by reaction=glycosidic linkage. Sugar covalent linkage. Polarity of linkage: enzyme will look for alpha position hydroxyl group off of alpha-d and will look for hydroxyl group off of carbon 4, and produce linkage that. Alpha 1-4 glycosidic linkage. Heterodimer because monosachh are different. Specific nam
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