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)