The Chemistry of Carbon

Introduction Compounds that contain carbon  Organic Compounds Organic molecules are the most prevalent molecules in biological systems because carbon forms the backbone of so many of the large molecules in these systems.

Carbon… Carbon is a very special element and is the main element of organic molecules. Can form so many shapes and structures like rings, diamonds, long-chains and acts as a branching point for other molecules to branch off from.  

Carbon How is carbon so unique and useful in biological systems? Carbon has 4 electrons in its valence shell (which is the outer shell of electrons) Carbon atomic number: 6 6 protons and 6 neutrons within the nucleas and 6 electrons total: 2 on the inner ring and 4 on the outer ring or valence shell

Carbon Bonding The 4 valence electrons of Carbon allow for many bonding options and make carbon capable of bonding with many other elements to form a variety of organic compounds. Each electron is like a connecting point. 4 Valence electrons = 4 bonds can form single, double or triple bonds. The elements that most frequently bond with carbon in organic molecules are nitrogen, hydrogen, oxygen and sulfur. Carbon atoms can also bond to each other which creates long chains, rings or branched structures.

Carbon Bonding

example of carbon-carbon bonds and also carbon hydrogen bonds.

Carbon Bonding Hydrocarbons organic molecules that consists of carbon bonded only to hydrogen.  

Hydrocarbons The smallest hydrocarbon = methane (CH4)

Monomer  a single molecule (such as methane) Polymer  many small subunits or monomers joined together to form a larger molecule Linear Polymer Branched Polymer

Ring Structures When carbons are joined into these carbon backbones, the chemical symbol (C) is left out when drawing the structures. Each point in the structure represents a carbon. Hydrogens are also left out when drawing organic molecules for simplicity.

Carbon Bonding This is a carbon carbon single bond. Each carbon has 3 bonding sites.

Carbon Bonding This is a carbon carbon double bond. It leaves each carbon with only two bonding sites rather than three.

Carbon Bonding This is a carbon carbon triple bonds. It leaves each carbon with only one bonding spot rather than three.

Nitrogen Bonding Nitrogen is found to have 5 valence electrons and lies at the top of Group 5 on the periodic table. Nitrogen usually forms 3 bonds because it has 5 valence electrons. 3 bonds would give nitrogen a complete octet.

Nitrogen Bonding Ma 3 bonds, 2 lone pair electrons = complete octet

Oxygen Bonding Oxygen needs two electrons to complete its octet. Oxygen is found in group 6 of the periodic table and has 6 valence electrons. There is space for two more electrons around the oxygen atom. Oxygen needs two electrons to complete its octet. Oxygen forms two bonds.

Oxygen Bonding 2 bonds, 4 lone pair electrons = complete octet

Sulfur Bonding Sulfur needs two electrons to complete its octet. Sulfur is found in group 6 of the periodic table and has 6 valence electrons. There is space for two more electrons around the sulfur atom. Sulfur needs two electrons to complete its octet. Sulfur forms two bonds (but can sometimes form up to 6!!  H2SO4

Sulfur Bonding Range between 2-6 bonds formed between sulfur and neighboring molecules

Hydrogen Bonding Oxygen is found in group 1 of the periodic table and has 1 valence electron Hydrogen can form one bond with other atoms

Carbon Containing Molecules Biological molecules in the body have different functional properties and give rise to the four main categories of biological molecules: Carbohydrates (CHO) Lipids Proteins Nucleic acids Functional Groups  Various elemental groups that join to carbon in a molecule allow that molecule special properties to undergo chemical reactions.

Functional Groups These groups attach to long hydrocarbon chains which allow for interaction in chemical reactions. Usually ionic or very polar unlike the non-polar hydrocarbon chain. These very polar functional groups act as the hook which allows the hydrocarbons to react! Fig. 4 Pg. 26 – Common Functional Groups in biological molecules Memorize these common functional groups, their classes and be able to give an example.

Polar Functional Groups Polar molecules are able to dissolve in water, while non polar hydrocarbons cannot! Ex- ETHANE compared (C2H6) to ETHANOL (C2H5OH) The hydroxyl group is very polar which allows this molecule to dissolve in water and it can therefore be dissolved in the cytosol of the cell.

Carboxyl Groups -COOH Can release proton in solution and become a negatively charged, acidic molecule (-COO-) Acts like an ACID

Amino Group -NH2 Can bond to, and gain an H+ proton to become NH3+ which turns the acid into a weak base Acts like a BASE

Phosphate Groups -PO42- These are acidic and make up nucleic acids which compose DNA. Can lose their H+ ions to become negatively charged (phosphate groups have 2 H+ to loose) acts like an ACID

Dehydration and Hydrolysis Rxns. Dehydration  removes a water molecule (HOH) usually during the assembly of a larger molecule from smaller subunits. Also knows as a Dehydration Synthesis Reaction Ex- the formation of large sugar molecules from glucose monomers The hydroxyl groups interact and the oxygen atom forms a link between the two cyclic monomer sugars.

ATP ~ Anhydride Linkage