Carbon Chemistry and Life. Carbon is the central element in organic chemistry, the central chemistry of life
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ENERGY LEVEL DIAGRAM OF CARBON ATOMIC ORBITALS
sp hybrid orbitals of two carbon atoms positioned to form a bond; a second (and even a third) bond could be formed by p orbital overlap. Sp hybridization is advantageous for a carbon atom making a triple bond (as in alkynes like acetylene, propyne, etc of the form CnH(2n-2).
sp2 hybridization in carbon uses two of the three 2p orbitals and the s orbital to form hybrid orbitals. The 2pz orbital is available for p bonding. This scheme is used in carbon atoms making a double bond (e.g., alkenes such as butene of the form CnH2n).
three 2p orbitals and the 2s orbital
to form three hybrid orbitals pointing
at the vertices of a tetrahedron. This
is the scheme used by tetrahedral
carbon atoms that make four single
bonds (as in alkanes of the form CnH(2n+2)
such as methane, ethane, butane, etc.)
with C-C double bond
Benzene -AROMATIC- can be pictured
as having three delocalized C-C bonds
with two C-C double bonds
Cyclohexane- SATURATED- a six
membered ring like benzene, but not flat
because all bonds are single.
In saturated compounds all carbon bonds are single because enough bond partners, usually H atoms, are available to make four bonds per carbon. Unsaturated compounds have at least one multiple bond.
INCLUSION OF HEROATOMS (NOT C OR H)
FUSED RING SYSTEMS.
Ethanol AND OTHER ALCOHOLS HAVE A SINGLE OXYGEN THAT MAKES ONE BOND WITH CARBON AND ONE WITH A HYDROGEN ATOM (A HYDROXYL OXYGEN).
Pyrene has four fused rings
Amino acids all have an amino (NH2) group at one end and an organic acid group (COOH) at the other. The acid is different than an alcohol (CHOH), which has only one C-O bond. The central carbon (alpha carbon) carries a variable R group. In gycine this is just H, in alanine it’s CH3 and in aspartic acid it includes a second acidic group. Twenty amino acids with different R groups are the building blocks of proteins.
H R O
C C C
H H OH
NUCLEOTIDES are the monomeric building blocks of nucleic acids and have many functions in energy transfer and signaling. They are complex ‘small’ ( not macro) molecules that include a base ( ring structure with heteroatoms, a ribose sugar, and phospate groups). Adenine can be sequentially phosphorylated to AMP, ADP and ATP.
Fatty acids and phopholipids are examples of biomolecules that include hydrophobic alkylregions. Note the linear alkly hydrocarbon region in palmitic acid; in contrast, a single double bond in unsaturated oleic acid has introduced a pronounced kink. Phospholipids have multiple hydrocarbon tails.
Chlorophyll with central magnesium;
note similarity to heme
Carotene, an antenna pigment-
eat this if you want to see
well at night
Quinone, an electron ( and hydrogen) carrier
Some important biological cofactors/prosthetic groups
Pheophytin lacks a central
metal, but resembles chlorophyll
Carbohydrates tend to have approximately equal numbers of C and O and about twice as many hydrogens (differences caused by release of water when polymers are formed).