LZ

Bio Chapter 4

  • ==Carbon: The Backbone of Life==
    • Living organisms are consisted of mostly carbon compounds (forms large, complex, varied molecules)
    • Proteins, DNA, carbohydrates, and other molecules that distinguish different beings are made of carbon compounds
    • Ex. amino acid structure
  • ==Organic Chemistry: The Study of Carbon Compounds==
    • Stanley Miller Experiment: Abiotic synthesis of organic compounds
    • Creating life by applying lightning and heat to seawater
      • Extremophiles, endosymbiotic theory (eukaryotic cells have developed when multiple cells joined together into one)
    • Potential stage of the origin of life
    • Overall percentages of C, H, O, N, S, P = uniform from one organism to another
    • We are made from carbon and not silicon because silicon holds on to compounds too tightly and does not let them react (we would be transparent)
    • Carbon has the right amount of hold to allow chemicals to react (only needs some energy to be broken apart - like in the metabolism)
    • Carbon’s ability to form 4 covalent bonds is the reason for its diversity in making different chem compounds
    • Electron configuration is the key to an atom’s characteristics and the reason for the number of and type of bonds the atom will make with other atoms.
  • ==The Formation of Bonds with Carbon==
    • Can form complex molecules
    • Molecules with a carbon each bonded to 4 other atoms can form a tetrahedral shape
      • When 2 carbons are joined in a double bond, atoms bonded to those carbons are in the same plane as them
    • Double/triple bonds prevent carbons from rotating around an axis (not dynamic anymore)
    • 1 bond = ane
    • 2 bonds = ene
    • 3 bonds = yne
    • The unpaired number of electrons is generally the number of bonds it can form (valence shell)
    • Carbon’s electron configuration increases its compatibility with many elements
      • Bonds with H, O, N is the building blocks of many molecules
  • @@Molecular Diversity Arising from Variation in Carbon Skeletons @@
    • Length, branching, double bond positions, and presence of rings
  • ==Hydrocarbons ==
    • Organic molecules with only carbon and hydrogen (ex. parts of fats)
    • Can undergo chemical reactions that release a lot of energy
    • Fat molecules are easier to break down than sugar (CnH2nOn)
    • Fat cells cannot be destroyed
    • Glyceride molecule bonded to 3 fatty acid molecules (not all the same size) = triglyceride
  • ==Isomers==
    • Compounds with the same chemical formula, but different structures/properties
    • ^^Structural isomers:^^ Different covalent arrangements (branching)
    • ^^Geometric (Cis-Trans) isomers:^^ Different spatial arrangements of compounds (ie. Trans isomers flip a part of the molecule into a different plane, whereas cis isomers remain in 1 plane)
      • ex. Alpha glucose and fructose have the same chemical formula, but different arrangement
      • Galactose = Alpha but 4th carbon is flipped
      • Beta glucose = Alpha but 1st carbon is flipped
      • Cis-trans must be around a double or a triple bond
      • Cis and trans isomers will react differently, but the single bonded isomers will react the same regardless of how it’s flipped
    • ^^Enantiomers (stereoisomers):^^ Isomers that are mirror images of each other
      • Enantiomers are important in the pharmaceutical industry
      • Different enantiomers may have different effects
      • Usually only one is biologically active
      • The difference in effects shows how sensitive organisms are to even subtle variations in molecules
      • Ex. Ibuprofen = reduces inflammation and pain (S-Ibu = effective, R-Ibu = ineffective)
      • Albuterol = Relaxes bronchial airways (R-Alb = effective, S-Alb = ineffective)
  • ==Chemical Groups==
    • Distinctive properties of organic molecules depend on the carbon skeleton and the functional groups attached to it
    • Enzymes add groupings to hydrocarbons to make them more effective
    • Ex. Estradiol vs. Testosterone (T has additional methyl + double bonded oxygen and no benzene ring) (E has additional hydroxyl and benzene ring)
    • Hormones dissolve in fat molecules and not in water (non-polar)
    • Water-based hormones act on the outside of cells, not inside
    • ^^Functional groups^^ change the behaviour of a molecule and are most commonly involved in chemical reactions (+ gives unique properties)
  • %%Functional Groups:%%
    • %%Hydroxyl group%% (-OH)
    • Alcohol
    • %%Carbonyl group%% (C=O)
    • Ketone (double bonded O to a carbon)
      • Must be anywhere not at the end of the molecule (“sandwiched between the alkyl groups”)
    • Aldehyde (double bonded O to a carbon)
      • Must be at the end of the molecule
    • %%Carboxyl group%% (-COOH)
    • Carboxylic acid
      • Usually at the end of a molecule (carbonyl + hydroxyl)
    • %%Amino group%% (-NH2)
    • Doesn’t have to have H
      • Amine (-NH2)
      • Amide (C=O, NH2)
    • %%Sulfhydryl group%% (-SH)
    • Thiol
    • %%Phosphate group%% (-OPO3)
    • Organic phosphate
    • Phosphate have 5 bonds (oxygen has 1 free bond, making it negative)
      • Can add H to O to make oxygen stable
    • %%Methyl group%% (CH3)
    • Methylated compound
    • Can affect how tightly wound DNA is
      • Causes mutations
    • %%Alkane%% (CH3) - single bonded
    • %%Ester%% (-COO)
    • %%Ether%% (-O)
    • In the middle single-bonded
    • %%Halide%%
    • B, F, I, Cl
  • ==ATP: Source of Energy for Cellular Processes==
    • Adenosine attached to 3 phosphate groups
    • ATP stores the potential to react with water
    • This reaction releases energy that can be used by the cell (made in mitochondria)