Campbell and Reece Chapter 4

Organic Chemistry  study of carbon compounds (most also have hydrogen)  range from small molecules (methane has 4 atoms) to very large one (proteins can have thousands of atoms)

Major Elements of Life  Carbon  Hydrogen  Oxygen  Nitrogen  Sulfur  Phosphorus

Carbon is very Versatile  because C can form 4 covalent bonds these 6 elements can form an almost limitless # organic molecules

VITALISM  Some credit Hippocrates  Simply stated: there is a life force outside physical & chemical laws

Jons Jakob Berzelius  Swedish chemist in early 1800’s  “Organic compounds come from living things” (only )  so inorganic compounds found only in nonliving things

Fredrich WÖhler  German chemist  1828: synthesized urea in lab (normally made in kidney)  Did not convince Vitalists because he 1 reactant he used came from animal blood

Urea

Hermann Kolbe  Student of Wohler  Synthesized urea using only inorganic reactants…..  Crushed Vitalism…..sorry Yoda

Origin of Life on Earth  Stanley Miller, 1953  Designed experiment trying to re- create conditions on early Earth  Hypothesized : abiotic synthesis of organic compounds possible

Miller’s Experiment  Closed system  Flask of water (early seas) heated  Water vapor rose to another higher chamber containing “atmosphere”  Sparks added (lightening)  “rain” formed, cooled  material collected analyzed

Miller’s Experiment

Miller’s Conclusion  Complex organic compounds could form spontaneously under conditions thought to exist on early Earth

Miller’s Results  2008: re-analyzed some samples from Miller’s experiments in the 1950’s  Additional organic compounds identified

Organic Chemistry  Definition changed to:  Study of Carbon Compounds (regardless of origin)

Bonding with Carbon  C has 4 valence e-  Bonds possible:  4 single covalent bonds  2 single & 1 double covalent bond  2 double covalent bonds  1 single & 1 triple covalent bond

Bonding with Carbon

Carbon Skeletons  Carbon chains form the backbone of most organic molecules  These skeletons can be  Straight  Branched

Carbon Skeleton Variation  In rings:

Carbon Skeleton Variation  1 important source of molecular complexity & diversity that characterizes living organisms

Hydrocarbons  C & H  Major components of petroleum products (fossil fuels)  When organism dies all water soluble compounds wash away as it decays.  Fats stay behind  hydrocarbons  Burn fossil fuels because they release a large amount of energy

Fossil Fuels

Isomers  Cpds with same # and types of atoms but they are arranged differently  Different structures behave differently  3 types: 1. Structural Isomers 2. Cis/trans Isomers 3. enantiomers

Structural Isomers  Differ in covalent arrangements of their atoms  Molecular formula same, structure different

Structural Isomers  # possibilities for different arrangements of atoms increases dramatically as carbon skeleton increases in size

Cis-trans Isomers  aka geometric isomers  Carbons have covalent bonds with same atoms but these atoms differ in their spatial relationship

Cis-trans Isomers  In cis groups are on same side of Carbon  In trans groups are across from each other

Cis-trans Isomers  The difference in cis-trans can dramatically affect the biological behavior of the molecule

Enantiomers  Isomers that are mirror images of each other  Differ in shape due to having asymmetric carbon

Enantiomers  Usually only 1 is biologically active  Other 1 may have much milder effect

Functional Groups  Portion of molecule that participates in chemical reactions in a characteristic way  7 common, & very important functional groups in organic chemistry

HYDROXYL -OH  Make alcohols  Properties: 1. Polar 2. Can for H-Bonds with water (help cpd dissolve in water)

CARBONYL -C=O  Makes: 1. Ketones: if in middle of molecule 2. Aldehyde: if at end of molecule  Properties: 1. can be isomers 2. ketoses/aldoses

CARBOXYL -COOH  Makes: organic acids  Properties: 1. Can donate H+  COO- 2. Mostly found in cells in ionized form (charge of -1) & called a carboxylate ion 3. In amino acids

CARBOXYL

AMINO -NH 2  Makes: Amines  Properties: 1. Acts as a base (can take H+) 2. Found in cells in ionized form with +1 charge 3. in amino acids

AMINE

SULFHYDRYL -SH  Makes: thiols  Properties: 1. 2 –SH can react forming disulfide bridges  These bridges make hair curly

PHOSPHATE -PO 4  Structure:  2 O have (-) charge  Makes:  Organic phosphates  Properties:  Makes molecule polar (-1) charge when in middle, (-2) when on end  Can react with water  energy

PHOSPHATE

METHYL -CH 3  Makes:  Methylated compounds  Properties:  When attached to DNA, affects expression of genes  Attachment to Testosterone changes biological effect compared to Estrogen (without methyl group)

METHYL

ADENOSINE TRIPHOSPHATE ATP  Made of adenosine + 3 phosphate groups  When 3 phosphates in series, easy to remove 3 rd group with water

Hydrolysis of ATP