Chemistry of life

The chemistry of life: Organic Compounds

  • Organic compounds are where carbon atoms covalently bond with one another to form the backbone of a molecule.

  • Compounds that are considered inorganic if the carbon isn’t covalently bonded with another carbon or to a hydrogen. So like the carbon dioxide we exhale as a waste product from the breakdown of organic molecules to obtain energy is an example of an inorganic compound.

Carbon atoms and organic molecules 

  • Since carbon has 4 electrons in its valence shell in either to fill the valence shell it would have to covalently bond 4 times.

  • Carbon to carbon bonds are strong which is why they make a great backbone for a molecule, though they still can be broken by cells. 

  • Cabins can form single bonds  (based on sharing one electron pair), double bonds and even triple bonds

  • Hydrocarbons are organic compounds consisting of only carbons and hydrogens and can exist in the shapes of unbranched or branched chains,or as rings. Rings and chains are joined in some compounds.

  • The arrangement of the electron orbitals of carbon project from the carbon atom towards the corners of a tetrahedron 

Isomer have the same molecular formula but different structures

  • Compounds with the same molecular formula but different sutures and having different properties are known as isomers

  • Isomers do not have identical physical or chemical properties and may have different common names. There are three types of isomers:

  • Structural isomers are compounds that are structured differently by the different covalent arrangement of their atoms. 

  • Geometric isomers are compounds that are identical in their arrangement of covalent bonds but different in the spatial arrangement of the atoms or groups of atoms. These isomers are sometimes present in carbon to carbon double bonds; double bonds are stronger and not as flexible as single bonds so the atoms are more fixed about the axis of the bonds. Geometric isomers exist as cis-trans isomers. Cis meaning its on the same side of the double bond, and trans meaning its on opposite sides of the double bond.

  • Enantiomers are isomers that are mirror images of each other.

Functional groups change the properties of organic molecules

  • covalent bonds between hydrogen and carbon are nonpolar lacking positive and negative charge, because of this are insoluble in water and cluster together through hydrophobic interactions. 

  • Functional group  is a group of atoms that help determine the types of chemical reactions and associations in which the chemical compound participates. Most readily form associations like ionic and hydrogen bonds, with other molecules. 

  • The methyl group is a non polar hydrocarbon group abbreviated by R—CH3

  • The hydroxyl group (R–OH) is polar because it has a presence of a highly electronegative oxygen atom. The use of OH- hydroxyl groups replacing the hydrogen atoms can significantly alter these molecules properties.

  • The carbonyl group consists of a carbon atom that has a double covalent bond with an oxygen atom and is hydrophilic because the double bond is polar because of the electronegativity of oxygen. The position of the carbonyl group determines its class.

  • An aldehyde has a carbonyl group positioned at the end of the carbon skeleton (R–CHO)

  • A ketone has an internal carbonyl group ( represented as R–CO–R)

  • Carboxyl groups (R–COOH) are represented with a carbon atom joined by a double covalent bond to an oxygen atom as well as by a single covalent bond to another oxygen, which is bonded to a hydrogen atom; this is if it is in its non-ionized form. When ionized it results in 1 unit of negative charge as its hydrogen atom can be stripped of its electron and be released as a hydrogen ion making R—COO- + H+. Carboxyl group is also weakly acidic.

  • An amino group (R–NH2) in its non ionized form contains an nitrogen atom covalently bonded to two hydrogen atoms. Amino groups are weakly basic because they accept hydrogen ions. The ionized for results in 1 unit of positive charge (R–NH3+)

  • A phosphate group (R– PO4H2) is weakly acidic. As a result of the attraction of electrons by the oxygen atoms results in the release of 1 or 2 units of negative charge. 

  • The sulfhydryl group (R — SH) consists of an atom of a sulfur that is covalently bonded to a hydrogen atom, and is found in molecules called thiols important to the structure of proteins.  

Many biological molecules are polymers

  • Large biological molecules consisting of thousands of atoms are referred to as macromolecules 

  • Most macromolecules are polymers, which are produced by small linking organic compounds referred to as monomers.

  • Monomers can be grouped in almost endless different ways to produce an endless variety of large molecules. For example, the 20 monomers referred to as amino acids can be linked end to end in endless ways to form polymers we call proteins.