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)

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