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class3_w08 - Redox reactions in organic molecules-Oxidation...

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-Oxidation states of carbon – counting “owned” electrons provides a means of determining whether a reaction oxidizes or reduces the compound -The C in methane is least oxidized; that in carbon dioxide is most oxidized -Biomass synthesis (carbon cycle) can also be considered a redox reaction Redox reactions in organic molecules
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In metabolism, carbon compounds are oxidized and reduced stepwise, and the energy is conserved as ATP or used to generate reduced cofactors
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Rotation about single bonds is possible at low energy cost, because the cylindrical sigma orbitals can maintain overlap The different spatial arrangements of atoms in different rotational orientations are distinct conformations
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By contrast, rotation about a double bond is very unfavorable energetically because it is necessary to break the pi bond in the rotation
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Eclipsed conformations are at higher energy. This is called torsional strain . This means that the single-bond rotation is not fully free, but the energy barrier is small (12 kJ/mol; much smaller than covalent bond). The conformers interconvert rapidly at ambient T and the individual conformers cannot be separated.
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Boat vs. chair conformations of cyclohexane
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General structure of amino acids Zwitterionic form at pH 7.0 – pK a of COO - is about 2.0 pK a of NH 3 + is about 9.5 Example of an amino acid (alanine), where R is –CH 3 The central carbon atom is bonded to 4 different substituents This is an example of a chiral center The “L” and “D” forms are called stereoisomers They are nonsuperimposable mirror images In nature, the amino acids found in proteins are “L”
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Chirality – Right/left hands are mirror images that are not superimposable -The chair is achiral; its mirror image is an exactly superimposable copy -Organic molecules are chiral when the central atom is (most commonly) an asymmetric carbon bonded to 4 different substituent groups
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The chiral molecule and its nonsuperimposable mirror image are enantiomers of each other. “Superimposable” means that you can pick the molecule up and place it exactly on top of its mirror image by rotating/translating.
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Note – Glycine has no chiral center. Proline is a secondary rather than a primary amine Methionine has a “thioether” functionality (sulfur) All the side-chain carbons (and S) are sp 3 hybridized Isoleucine has a second chiral center
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Note that in tryptophan, the lone-pair electrons on the side-chain nitrogen atom are in a p-orbital, so there are 5 (odd #) pairs to satisfy the criterion for aromaticity.
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Note – Serine and threonine side-chains are alcohols The cysteine side-chain is a sulfhydryl group ( p K a = 8) Asparagine and glutamine side-chains are amides Like isoleucine, threonine has a second chiral center
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Note – Lysine is a primary amine (pKa = 10)
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