Chemical Bonds

StudyBlue printing of Chemical Bonds html, body, div, span, applet, object, iframe, h1, h2, h3, h4, h5, h6, p, blockquote, pre, a, abbr, acronym, address, big, cite, code, del, dfn, em, font, img, ins, kbd, q, s, samp, small, strike, strong, sub, sup, tt, var, b, u, i, center, fieldset, form, label, legend, table, caption, tbody, tfoot, thead, tr, th, td { margin: 0; padding: 0; border: 0; outline: 0; font-size: 100%; background: transparent; } body { line-height: 1; } blockquote, q { quotes: none; } blockquote:before, blockquote:after, q:before, q:after { content: ''; content: none; } /* remember to define focus styles! */ :focus { outline: 0; } /* remember to highlight inserts somehow! */ ins { text-decoration: none; } del { text-decoration: line-through; } /* tables still need 'cellspacing="0"' in the markup */ table { border-collapse: collapse; border-spacing: 0; } /* end RESET */ .header { min-width:800px; } .logo { padding:6px 20px 2px 20px; margin:0; font-size:25px; font-weight:bold; color:#808285; position:relative; border-bottom: 1px solid #c5c5c5; } .logo-blue { color:#70adc4; } .logo-desc { font-weight:normal; font-size:19px; color:#cccccc; margin-top:50px; position:absolute; display: none; } .back-button { position:absolute; top:20px; right:20px; font-size:13px; line-height:25px; color:rgb(0,175,225); font-weight:normal; } .back-button a { color:rgb(0,175,225); } .instructions { padding:0; margin:0; width:100%; position:relative; color:rgb(100,100,100); } .step-holder { border-left:1px solid #ededed; margin-left:20px; } .steps { padding:15px 0; float:left; width:24%; border-right:1px solid #ededed; text-align:center; } .steps-01 { } .steps-02 { } .steps-03 { } .steps-04 { } .label { padding:5px 10px; } .print-button { } .print-button a { background-color:rgb(0,175,225); color:white; line-height: 19px; padding:9px 8px 5px 30px; font-size:14px; text-decoration:none; background-image: url(images/printer.png); background-repeat: no-repeat; background-position: 7px 50%; -moz-border-radius: 5px; -webkit-border-radius: 5px; } .print-button a:hover { background-color:black; } .theNote .content { width: 8.0in !important; margin: 5px auto; padding:20px; background-color:white; } .theNote .header { border-bottom: 1px dashed #C8C8C8; font-size: 17px; padding: 0 0 10px; line-height: 19px; color: #00ADE1; min-width:500px; } .theNote .body { font-size: 14px; line-height: 19px; padding: 10px 0; } .theNote{ padding:6px 0; clear:both; background-color: rgb(200,200,200); } .theNote h3{ color: rgb(100,100,100); } .theNote h1, .theNote h3{ background-color:white; padding:2px 20px; width:8.0in !important; margin: 0 auto; font-size: 15px; } .theNote h1{ padding-top: 10px; font-size: 15px; } .theNote h1:first-child{ font-size: 20px; } .theNote h3 { font-size: 14px; font-weight: normal; } #options { border: 3px double #ccc; padding: 5px 12px; margin: 10px 50px 10px 20px; float: left; } #info { border-top: 1px solid #ccc; padding-top: 5px; font-style: italic; } li { margin: 5px 10px 5px 25px; } ul li { list-style: disc; } ol li { list-style: decimal; } img { border: 0; } table { clear: both; width: 100%; border: 1px solid #c5c5c5; border-width: 1px 0; margin: 0; page-break-after: always; } table#page { page-break-after: auto; } td { text-align: center; font-size: 12px; border-bottom: 1px dashed #c5c5c5; height: 1.75in; width: 50%; padding-left: 15px; } .leftside { border-right: 1px solid #cccccc; padding: 0 15px 0 0; } .bottom td { border-bottom: none; } .clearfix { clear:both; line-height:1px; height:1px; } img { max-width:80%; max-height:150px; margin:20px; } @media print {.header { display: none; } .content .header{ display:inherit; } table { border: 1px dashed #bbb; border-width: 1px 0; } .theNote{ background-color:white; } } 1 1. Amongst the diversity of life there is at the cellular level evidence for common principles governing life. Whether they are prokaryotic or eukaryotic cells they share a common set of hydrocarbon-based biochemicals and use them in similar biochemical pathways for basic anabolism and catabolism, all use phospholipids bilayers to make the cellular compartments, have ATP for energy currency, use nucleic acid polymers for genetic information and must arise from a previous cell. 2. Only two basic types of cell exist: prokaryotic with few cell membranes and eukaryotic with multiple membrane-bounded organelles amongst many other more detailed differences. Compartments make reactions more efficient by concentrating substances and avoiding non-productive interactions. 3. Cells use 25 of 92 elements; 96 % being C ,H, O and N for the major macromolecules of proteins, lipids, nucleic acids, carbohydrates but Ca, P, K, Na, Cl, S are also relatively abundant. Some trace elements are very important for special functions of proteins and other molecules. 4. Radioisotopes like 14 C, 32 P, 3 H are used in biochemical research to trace molecules in reaction pathways. They give off detectable electrons ( β particles) as they decay to a lower energy state. 5. The number and distribution of valence electrons in the electron orbital shells determine the chemical properties (what kind and how many bonds can be formed) of an element. Five bonds are most important: the weak (0.6 to 1.0 kcal/mole Van der Waals for non-polar domains of molecules, the H bonds (1.5 to 3 kcal/mol) but relatively abundant and therefore important for maintaining structure shape, ionic bonds (3- 7 kcal/mol) are important in electrostatic interactions, single covalent bonds are very strong (averaging about 80 kcal/mol) but stronger double bonds can be made. 6. Water is a good solvent because it is a polar molecule capable of making H bonds with other water molecules and other hydrophilic and with ionic molecules. Hydrophobic molecules with C-H bonds (oils for instance) have nonpolar bonds, do not form H bonds and don’t dissolve readily in water. Water dissociates into reactive H + and OH - ions at a low rate in pure water of pH 7.0; H + at 10 -7 M. In the pH scale one unit represents a 10 fold change in hydrogen ion concentration. 7. Many biologically important molecules are acids or bases, which release or take up, respectively hydrogen ions in water. The pH must be maintained within a small range (cellular pH 7.3) by buffers because the shape and therefore function and solubility of proteins is sensitive (often very sensitive) to pH. Deviation of 0.4 unit up or down in blood is lethal. Blue Notes from Class 1. The rules of physics and chemistry govern life. Vitalism 2. All Cells use the same set of core hydrocarbon-based molecules in an aqueous solution 3. When available, only one enantiomer (=optical isomer) is used 4. Macromolecules are constructed of polymers 5. A core of multi-step biochemical pathways of synthesis anabolism, use and breakdown catabolism of molecules 6. All cells are bordered by a phospholipid membrane making possible a compartment of those core molecules of life 7. Only two cell types exist Prokaryotic Cell: two border membranes, no nucleus, limited internal membranes Eukaryotic Cell: single outer membrane but extensive internal membrane-bordered organelles, with a nucleus 8. Adenosine triphosphate (ATP) is universally used as energy currency 9. All Cells, and virused, use polymers of nucleic acids for inheritable genetic information 10. The central Dogma of information flow occurs in all cells. DNA then RNA then Protein 11. All cells must arise from a preexisting cell 12. Radioisotopes used in biomedical research: tritium, carbon 14, phosphorus 32 and sulphur 35 13. The number and distribution of electrons in the outer shell determines chemical properties of the elements 14. 5 types of Biochemical Bonds and where the bonds are in a protein 15. The number and kind of molecular bonds formed determines the shape and stability of the molecule and its interactions with other cellular molecules. 16. For a protein, shape determines function 17. Water is a polar molecule, therefore, it's a ood solvent for hydrophilic molecules 18. Water makes a hydration shell 19. Nonpolar molecules with nonpolar C-H bonds (greases and oils) are hydrophobic 20. ater dissociates at a low rate to hydrogen H+ and -OH hydroxide ions 21. Buffer like carbonic acid reversibly releases and accepts H+ ions