Carbon Chemistry and Life. Carbon is the central element in organic chemistry, the central chemistry of life The properties of carbon emerge from its

Carbon Chemistry and Life

• Carbon is the central element in organic chemistry, the

central chemistry of life• The properties of carbon emerge from its atomic

structure, which leads to its position in the middle of the second row of the periodic table. Carbons n=2 shell is half full, so it has four electrons and four ‘holes’ in its outer (n=2) shell. It has a strong tendecy to share, rather than donate or accept, electrons

• The most stable carbon compounds are those that make 4 strong covalent bonds. The ability to make four bonds makes carbon uniquely flexible, and organic chemistry uniquely important and rich.

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BOHR ATOM REPRESENTATION OF CARBON ATOM

ENERGY LEVEL DIAGRAM OF CARBON ATOMIC ORBITALS

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sp hybrid 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).



sp3 hybridization in carbon uses allthree 2p orbitals and the 2s orbitalto form three hybrid orbitals pointingat the vertices of a tetrahedron. This is the scheme used by tetrahedral carbon atoms that make four singlebonds (as in alkanes of the form CnH(2n+2) such as methane, ethane, butane, etc.)








Methane and ethane










Propane, butane, pentane and hexane





Butadiene-UNSATURATEDwith two C-C double bonds (diene).

Ethylene-UNSATURATED with C-C double bond



Benzene -AROMATIC- can be pictured as having three delocalized C-C 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.

SOME OTHER EXAMPLES OF CARBON CHEMISTRY IMPORTANT IN BIOLOGY:

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






are needed to see this picture.Glycine

Alanine

Aspartic acid

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.





palmitic

Oleic



Fatty acids and phopholipids are examples of

biomolecules that include hydrophobic alkyl regions. 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.











Carotene, an antenna pigment- eat this if you want to see well at night

Quinone, an electron ( and hydrogen) carrier

Heme with central iron

Pheophytin lacks a centralmetal, but resembles chlorophyll

Chlorophyll with central magnesium; note similarity to heme

Some important biological cofactors/prosthetic groups





d-glucose

l-glucose



sucrose

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).

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Carbon Chemistry and Life. Carbon is the central element in organic chemistry, the central chemistry of life The properties of carbon emerge from its