Crazy Carbon - Chapter 4 notes

Carbon is responsible for the large diversity of biological molecules Save me from Organic Chemistry!!! Carbon is responsible for the large diversity of biological molecules

Organic Molecules Compounds containing carbon These compounds can contain thousands of atoms. Overall percentages of major elements (C,H,O,N,S,P) are the same from one organism to the next. Because Carbon is so versatile, it can be used to build bzillions of organic molecules. Variations in organic molecules distinguish different species

History Jons Jakob Berzelius Made distinction between organic (found in living organisms) and inorganic (found in non living world). Gave rise to Vitalism – belief in a life force outside of physical and chemical laws

History Friedrich Wohler Attempted to make inorganic compounds Actually made urea – a compound found in urine (made without a living organism involved) Started chipping away at theory of vitalism

History Stanley Miller Tested whether organic molecules could arise spontaneously under conditions of early earth Led to theory of mechanism – the view that physical and chemical laws govern all natural phenomena – including the processes of life

Very Versatile Building Blocks

Chemical Structure Carbon has 6 electrons, 2 in the first shell, 4 in the outer shell. So....Valence of Carbon is 4 (tetravalence) It can bond to four other molecules Carbon completes its valence by sharing electrons, forming covalent bonds (NOT ionic) Shape is a tetrahedron (109˚) Most frequent partners are O, H, and N

Simple Carbon Molecules CH4--Methane-4 single bonds, tetrahedron shape

Simple Carbon Molecules CO2--Carbon Dioxide-source of Carbon for all organic molecules found in organisms (due to photosynthesis). Chemical formula O=C=O

Complex Carbon Molecules Carbon can bond to other carbon molecules forming long chains These are the skeletons of organic molecules Carbon skeletons can be straight, branched, or arranged in rings

Figure 4.4 Variations in carbon skeletons

Hydrocarbons Long chains containing only carbon and hydrogen Major component of petroleum Not prevalent in living things, but some organic molecules, like fat, have regions of hydrocarbons. Hydrocarbons are hydrophobic because the bonds are nonpolar. Store lots of energy (gas in a car, fat in animals)

Figure 4.5 The role of hydrocarbons in fats

Interesting Isomers Same molecular formula, but different structure and different properties.

Structural Isomers Differ in covalent arrangement of their atoms. The longer the carbon skeleton, the more structural isomers. Location of double bonds can also differ

Geometric Isomers Same covalent partnership, different spatial arrangements Result of inflexible double bonds (atoms attached to a double bond can’t rotate freely) The different shapes affect biological activities. ex. Vision involves light changing chemical rhodopsin from one geometric isomer to another.

Enantiomers Mirror images formed when carbon is attached to four different atoms. The middle Carbon is asymmetric!! Cells can distinguish enantiomers based on their different shapes. One is “active” and the other is “inactive”. ex. Pharmaceuticals....sometimes drug isomers produce no effect or harmful effects on patients

Figure 4.7 The pharmacological importance of enantiomers

What kind of isomer am I???

Functional Groups Components of organic molecules that are most commonly involved in chemical reactions. Number and arrangement of functional groups give molecules their unique properties. All are hydrophilic, so soluble in water Usually attached to a carbon on the skeleton ex. Estradiol and Testosterone--have same structural backbone, but different functional groups that cause one to take care of feminine qualities and other one mighty maleness.

Hydroxyl -OH or -HO Organic compounds containing hydroxyl groups are called ALCOHOLS Polar because O is really electronegative!!! This attracts water molecules and helps dissolve ex. Sugars

Carbonyl > CO Carbon atom joined to oxygen by a double bond Aldehydes: Carbonyl group on end of carbon skeleton Ketones: Carbonyl group in the middle of the skeleton Variations in location of carbonyl group is source of molecular diversity ex. Acetone (ketone) an Propanol (aldehyde) are structural isomers with different properties

Carboxyl -COOH Oxygen double bonded to carbon that is also bonded to a hydroxyl (-OH) Form carboxylic acids (organic acids) Has acidic properties because it is a source of H+ ions. Bond between O and H is so polar that hydrogen tends to dissociate. ex. Acetic Acid (vinegar), substance in ant stings

Amino -NH2 Nitrogen atom bonded to two hydrogen atoms and to carbon skeleton Compound with this group is called an amine Acts as a base because NH2 is able to pick up H+ ions from the surrounding solution and become NH3+. This lowers the H+ concentration!!! ex. Amino Acids...The building blocks of proteins!!

Sulfhydryl -SH Sulfur atom bonded to an atom of hydrogen Organic compounds with this group are called thiols ex. Help stabilize protein structure

Phosphate -OPO32- Anion formed by dissociation of phosphoric acid (H3PO4) Loss of hydrogen ions by dissociation leaves phosphate with a negative charge. Form organic phosphates ex. Function in transfer of energy between organic molecules, ATP (adenosine triphosphate)

Methyl -CH3 Methyl group attached to carbon skeleton ex. Methyl groups may be added to DNA to inactivate certain genes

Table 4.1 Functional Groups of Organic Compounds