The Chemistry Of The Cell


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Showing the importance of carbon, water And membranes

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The Chemistry Of The Cell

  1. 1. 2 The Chemistry of the Cell Biology is the study of chemistry systems that happen to be alive! <ul><li>Five topics: </li></ul><ul><li>The importance of carbon </li></ul><ul><li>The importance of water </li></ul><ul><li>The importance of selectively permeable membrances </li></ul><ul><li>The importance of synthesis by polymerization of small molecules </li></ul><ul><li>The importance of self-assembly </li></ul>
  2. 2. The Importance of Carbon <ul><li>The domain of organic chemistry is to study carbon-containing compounds </li></ul><ul><li>Biochemistry studies the chemistry of living systems </li></ul><ul><li>Carbon atom is the most important atoms in biological molecules </li></ul><ul><ul><li>Valence of four, lacking four electron at its outermost electron orbital </li></ul></ul><ul><ul><li>Methods of satisfaction of stable status: electron sharing with other electron deficient atoms (such as other carbon atoms) -- formation of covalent bonds with “light” elements (such as carbon, oxygen, hydrogen, and nitrogen) to form stable compounds as relative to their atom weight. </li></ul></ul><ul><li>Single bonds, double bonds and triple bonds </li></ul>Fig. 2-1 Electron configuration of some biologically important atoms and molecules
  3. 3. Carbon-Containing Molecules Are Stable Energies of biologically important transitions, bonds, and wavelengths of electromagnetic radiations <ul><li>Calorie: amount of energy needed to raise the temperature of one gram of water one degree centigrade </li></ul><ul><li>Bond energy: the amount of energy required to break 1 mole (about 6 x 10 23 ) of bonds: C-C (83 kilocalories/mole or kcal/mol), C-N (70), C-O (84), and C-H (99). Others, C=C (146), C C (212), and the diamonds! </li></ul>
  4. 4. The Carbon-carbon bonds are the fittest for the biological chemistry under solar radiation <ul><li>The relationship of electromagnetic radiation and the wavelength: E = 28,600/  (E, kcal/einstein;  , nm; 28,600, the constant with the units of kcal-nm/einstein, an einstein is equal to 1 mole of photons) </li></ul><ul><li>The ultraviolet light at a wavelength of 300 nm confers energy of ~95.3 kcal/einstein, sufficient to breakdown C-C bonds of ~83 kcal/mol -- pollution and ozone layer protection. </li></ul>The relationship between energy (E) and wavelength (  ) for electromagnetic radiation
  5. 5. The diversity of carbon-containing molecules Simple hydrocarbon compounds Common functional groups found in biological molecules <ul><li>Hydrocarbons are the major component of fuels (gasoline). However, with limited function in biological systems -- the phospholipid tail of membranes; </li></ul><ul><li>Functional groups </li></ul><ul><ul><li>Ionized or protonated </li></ul></ul><ul><ul><li>Uncharged at pH7, but “polarized” </li></ul></ul>
  6. 6. Stereoisomers of carbon-containing molecules Stereoisomers of biological molecules <ul><li>A tetrahedral structure of carbon atoms have geometric symmetry - when four different atoms or groups of atoms are bonded to the four corners of such a tetrahedral structure, two different spatial configurations are possible, but not superimposable </li></ul>An asymmetric carbon atom has four different substituents. Both L- and D-alanine present in nature but only L- type is present in proteins. D-glucose has four asymmetric carbon atom and has 2 4 or 16 kinds of possible stereoisomers.
  7. 7. The importance of water <ul><li>Water is the single most abundant component of cells and organisms. 75-85% of a cell is water (10-20 in spores and dry seeds) </li></ul><ul><li>The polarity of water molecules are caused by the angles that hydrogen atom bond to the oxygen atom (104.5 0 ), making the oxygen atom electronegative (  - ). This property accounts for the cohesiveness, the temperature-stabilizing capacity and the solvent properties of water . </li></ul>Hydrogen bonding between water molecules
  8. 8. <ul><li>Water molecules are cohesive -- Hydrogen bonds form between the hydrogen atoms and the oxygen atoms of water molecules and are responsible for its high boiling point, high specific heat, and high heat of vaporization . </li></ul><ul><li>Water has a high temperature-stabilizing capacity -- Specific heat is the amount of heat a substance absorb per gram to increase its temperature 1 0 C. The specific heat of water is 1.0 calorie per gram. </li></ul><ul><li>Water has a high heat of vaporization, the amount of energy required to convert one gram of a liquid into vapor. </li></ul><ul><li>Water is an excellent solvent. A solvent is a fluid in which another substance, called the solute , can be dissolved. </li></ul><ul><ul><li>Hydrophobic: “water fearing” </li></ul></ul><ul><ul><li>Hydrophilic: “water loving” </li></ul></ul>The solubilization of sodium chloride because water molecules form spheres of hydration More properties of water originated from its polarity
  9. 9. The importance of selectively permeable membranes <ul><li>Membranes are physical barriers of cells and subcellular compartments controlling material exchange between the internal environment and the extracellular environment </li></ul><ul><li>A membrane is essentially a hydrophobic permeability barrier consisting of phospholipids, glycolipids, and membrane proteins </li></ul><ul><li>Membranes contain amphipathic molecules such as phosphatidyl ethanolamine, an example of phosphoglycerides, the major class of membrane phospholipids in most cells. </li></ul><ul><ul><li>Polar head </li></ul></ul><ul><ul><li>Nonpolar tail </li></ul></ul>
  10. 10. The properties of membranes A membrane is a lipid bilayer with proteins embedded in it. Each layer is about 3-4 nm thick, with the hydrophobic tails facing each other in the middle. <ul><li>Functions of the associated proteins: transport proteins; enzymes, receptors, electron transport intermediates (mitochondria), or chlorophyll-binding proteins (chloroplast) </li></ul><ul><li>Membranes are selectively permeable . </li></ul><ul><ul><li>Freely diffusing molecules: H2O, CO2 or MW < 100 Dalton </li></ul></ul><ul><ul><li>However, ions like Na + and K + are effectively excluded (10 8 times less efficient). They need either hydrophilic channels or carriers for their crossing of the membrane </li></ul></ul>
  11. 11. The importance of synthesis by polymerization <ul><li>Macromolecules: proteins, ribonucleic acids (DNA or RNA), and polysaccharides (starch, glycogen, and cellulose), and lipid (?, with different synthesizing method) </li></ul><ul><li>Macromolecules are responsible for most of the form and function in living systems. They are, however, generated by polymerization of small organic molecules, a fundamental principle of cellular chemistry </li></ul><ul><li>The monomers: glucose, amino acids, nucleotides </li></ul><ul><li>Informational macromolecules: DNA and proteins </li></ul><ul><li>Storage macromolecules & structural macromolecules </li></ul>
  12. 12. Macromolecules are synthesized by stepwise polymerization of monomers The basic principles for the synthesis of macromolecules: 1. Macromolecules are synthesized by stepwise polymerization of similar or identical monomers 2. The addition of each monomeric units occurs with the removal of a H2O molecule -- condensation reaction 3. Momomeric units are activated 4. Activation usually involves coupling of monomers to carrier molecule 5. ATP (adenosine phosphate provides energy ) 6. Directionality of macromolecules
  13. 13. The importance of self-assembly The principle of self-assembly: the information required to specify the folding of macromolecules and their interactions to form more complicated structures with specific biological functions is inherent in the polymers themselves <ul><li>Many proteins self-assemble </li></ul><ul><ul><li>Polypeptide VS. protein </li></ul></ul><ul><ul><li>Denaturation VS. renaturation </li></ul></ul><ul><li>Molecular chaperones assist the assembly of some proteins </li></ul><ul><ul><li>Strictly self-assembly </li></ul></ul><ul><ul><li>Assisted self-assembly (by preventing the formation of incorrect confirmation) </li></ul></ul><ul><li>Noncovalent interactions are important in the folding of macromolecules. </li></ul><ul><ul><li>Covalent bonds: atoms share electrons </li></ul></ul><ul><ul><li>Noncovalent interactions: hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions </li></ul></ul>Heat Cool
  14. 14. Self-assembly of cellular structures <ul><li>Self-assembly of cellular structures: ribosome, membranes, and primary cell walls </li></ul><ul><li>The tobacco mosaic virus (TMV), a case study in self-assembly </li></ul><ul><ul><li>Structure: A RNA helical core surrounded by a cylinder of protein subunits (“coat proteins”) </li></ul></ul><ul><ul><li>17 subunits disc ring - conformational change to a helical shape and each binds 102 nt RNA, repeat... </li></ul></ul>
  15. 15. The limits of self-assembly and advantages of hierarchical assembly <ul><li>Some kinds of assembly requires preexisted structures such as addition of extra components to cell walls, membranes and chromosomes </li></ul><ul><li>Hierarchical assembly is the basic cellular strategy. The “alphabet of biochemistry” contains 20 amino acids, 5 aromatic bases, 2 sugars, and 3 lipid molecules </li></ul><ul><ul><li>Chemical simplicity </li></ul></ul><ul><ul><li>Efficiency of assembly -- the story of “Tempus Fugit and the fine art of watch-making” </li></ul></ul>