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The Chemistry Of The Cell
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The Chemistry Of The Cell


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Showing the importance of carbon, water And membranes

Showing the importance of carbon, water And membranes

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  • 1. 2 The Chemistry of the Cell Biology is the study of chemistry systems that happen to be alive!
    • Five topics:
    • The importance of carbon
    • The importance of water
    • The importance of selectively permeable membrances
    • The importance of synthesis by polymerization of small molecules
    • The importance of self-assembly
  • 2. The Importance of Carbon
    • The domain of organic chemistry is to study carbon-containing compounds
    • Biochemistry studies the chemistry of living systems
    • Carbon atom is the most important atoms in biological molecules
      • Valence of four, lacking four electron at its outermost electron orbital
      • 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.
    • Single bonds, double bonds and triple bonds
    Fig. 2-1 Electron configuration of some biologically important atoms and molecules
  • 3. Carbon-Containing Molecules Are Stable Energies of biologically important transitions, bonds, and wavelengths of electromagnetic radiations
    • Calorie: amount of energy needed to raise the temperature of one gram of water one degree centigrade
    • 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!
  • 4. The Carbon-carbon bonds are the fittest for the biological chemistry under solar radiation
    • 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)
    • 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.
    The relationship between energy (E) and wavelength (  ) for electromagnetic radiation
  • 5. The diversity of carbon-containing molecules Simple hydrocarbon compounds Common functional groups found in biological molecules
    • Hydrocarbons are the major component of fuels (gasoline). However, with limited function in biological systems -- the phospholipid tail of membranes;
    • Functional groups
      • Ionized or protonated
      • Uncharged at pH7, but “polarized”
  • 6. Stereoisomers of carbon-containing molecules Stereoisomers of biological molecules
    • 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
    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. The importance of water
    • 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)
    • 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 .
    Hydrogen bonding between water molecules
  • 8.
    • 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 .
    • 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.
    • Water has a high heat of vaporization, the amount of energy required to convert one gram of a liquid into vapor.
    • Water is an excellent solvent. A solvent is a fluid in which another substance, called the solute , can be dissolved.
      • Hydrophobic: “water fearing”
      • Hydrophilic: “water loving”
    The solubilization of sodium chloride because water molecules form spheres of hydration More properties of water originated from its polarity
  • 9. The importance of selectively permeable membranes
    • Membranes are physical barriers of cells and subcellular compartments controlling material exchange between the internal environment and the extracellular environment
    • A membrane is essentially a hydrophobic permeability barrier consisting of phospholipids, glycolipids, and membrane proteins
    • Membranes contain amphipathic molecules such as phosphatidyl ethanolamine, an example of phosphoglycerides, the major class of membrane phospholipids in most cells.
      • Polar head
      • Nonpolar tail
  • 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.
    • Functions of the associated proteins: transport proteins; enzymes, receptors, electron transport intermediates (mitochondria), or chlorophyll-binding proteins (chloroplast)
    • Membranes are selectively permeable .
      • Freely diffusing molecules: H2O, CO2 or MW < 100 Dalton
      • 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
  • 11. The importance of synthesis by polymerization
    • Macromolecules: proteins, ribonucleic acids (DNA or RNA), and polysaccharides (starch, glycogen, and cellulose), and lipid (?, with different synthesizing method)
    • 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
    • The monomers: glucose, amino acids, nucleotides
    • Informational macromolecules: DNA and proteins
    • Storage macromolecules & structural macromolecules
  • 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. 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
    • Many proteins self-assemble
      • Polypeptide VS. protein
      • Denaturation VS. renaturation
    • Molecular chaperones assist the assembly of some proteins
      • Strictly self-assembly
      • Assisted self-assembly (by preventing the formation of incorrect confirmation)
    • Noncovalent interactions are important in the folding of macromolecules.
      • Covalent bonds: atoms share electrons
      • Noncovalent interactions: hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions
    Heat Cool
  • 14. Self-assembly of cellular structures
    • Self-assembly of cellular structures: ribosome, membranes, and primary cell walls
    • The tobacco mosaic virus (TMV), a case study in self-assembly
      • Structure: A RNA helical core surrounded by a cylinder of protein subunits (“coat proteins”)
      • 17 subunits disc ring - conformational change to a helical shape and each binds 102 nt RNA, repeat...
  • 15. The limits of self-assembly and advantages of hierarchical assembly
    • Some kinds of assembly requires preexisted structures such as addition of extra components to cell walls, membranes and chromosomes
    • Hierarchical assembly is the basic cellular strategy. The “alphabet of biochemistry” contains 20 amino acids, 5 aromatic bases, 2 sugars, and 3 lipid molecules
      • Chemical simplicity
      • Efficiency of assembly -- the story of “Tempus Fugit and the fine art of watch-making”