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Carbon Chemistry and Life. Carbon is the central element in organic chemistry, the central chemistry of life

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  • 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.


BOHR ATOM REPRESENTATION OF CARBON ATOM central chemistry of life

ENERGY LEVEL DIAGRAM OF CARBON ATOMIC ORBITALS

http://www.edinformatics.com/math_science/c_energy.gif


sp hybrid orbitals central chemistry of life

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).


sp central chemistry of life2 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).


sp central chemistry of life3 hybridization in carbon uses all

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.)


Methane and ethane central chemistry of life


Propane, butane, pentane and hexane central chemistry of life


Ethylene-UNSATURATED central chemistry of life

with C-C double bond

Benzene -AROMATIC- can be pictured

as having three delocalized C-C bonds

Butadiene-UNSATURATED

with two C-C double bonds

(diene).

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 BIOLOGY: 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 (NH BIOLOGY: 2) 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.

Glycine

Alanine

H R O

C C C

H H OH

Aspartic acid


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 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.

Oleic


Heme with central iron 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.

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


d-glucose 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.

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).

l-glucose


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