jimtrue.com : school : BSC2010 : CH 04: Carbon & the Molecular Diversity of Life

Posted by Jim True on January 26, 2004 6:03 AM. Last Updated October 22, 2006 9:23 PM

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CH 04: Carbon & the Molecular Diversity of Life

Carbon

• The major component of any cell (or living organism) is water, and the elements Hydrogen and Oxygen are two major constituents of any living thing.
• However, the central element of all of the structural components of living things is carbon.
• Originally, it was thought that only living things could produce and incorporate the element carbon, thus the field of chemistry associated with the study of carbon containing molecules was called organic chemistry.
• Because of its bonding properties, Carbon forms the "backbone" of organic molecules.
• It has four electrons in its valence shell and thus can form up to 4 single covalent bonds with other elements.
• Other elements most often bonded to carbon, and thus, most prevalent in organic molecules are Hydrogen (H), Oxygen (O) and Nitrogen (N). (see figures 4.2 & 4.3 on pg 54)
• The the four most important elements in living organisms are: N, O, C, H; 96% of the elements in the human body consist of these elements.
• These four are so abundant because:
  • Readily form gases
  • Are soluble in H₂O
  • Form breakable bonds with themselves and other elements.
• Because it can have up to four individual covalent bonds, and because it readily bonds with itself, Carbon as the "backbone" of an organic molecule "skeleton" can have a wide variety of shapes, even within the same number of atoms and elements within the molecule.
• The high degree of variability of the carbon "skeleton" means that there is tremendous diversity in organic molecules. Shape is related to function. (See figure 4.4 pg 55). Chitin is a massive assemblage of carbohydrates.
• This results in the formation of molecules of many different shapes, sizes and properties.
• The simplest form of organic molecules are hydrocarbons -- carbon bonds most easily with hydrogen and can form logn chains of Carbons & Hydrogens. Methane is the simplest hydrocarbon.
• Hydrocarbon may form the "backbone" of an organic molecule.
• Living organisms have very few molecules that are pure hydrocarbons.
• However, any Hydrogen in the hydrocaron can be replaced quite easily by another atom or even entire molecules, which may be quite large.
• Some organic molecules, e.g. fats, have long hydrocarbon structures attached to a non-hydrocarbon region.
• Molecules have distinctive shapes, so it is possible to have molecules whose molecular formulas are identical, but whose structures are different.
• These are called Isomers, ("iso" meaning equal and "mers" meaning part of something.

Isomers

• There are several different categories of isomers:
  • Structural Isomers: differ in structural arrangement of atoms and elements or bonds. Slightly different structure.
  • Geometric Isomers: due to arrangement of covalent bonds around double bonded carbons. ie. glucose and galactose.
  • Enantiomers: Structures are mirror images of one another. Often referred to as "left or right handed" molecules. Configurations around the central carbon are assymetrically different. (Figures 4.6 on p56, 5.3 on p.64).
• Enantiomers clearly demonstrate that in cellular processes and cellular structures, molecular shape may be critically important. Our bodies are designed to deal with specific enantiomeric forms and not others.
• e.g. Right and left handed sugars. Right handed sugar (naturally occuring digestive form of glucose is dextrose; right handed glucose is called dextrose) occur naturally and can be digested. Left handed are synthesized and taste the same, but cannot be digested. Splenda is a left-handed sugar to be used by diabetics as an example.
• e.g. Pharmaceutical agents: Critical functionality is also defined by function. May bind very specifically in the lab to the receptor sites in a mouse, but will not bind in a human.

Biomolecules

• The term biomolecule is used to refer to organic molecules that are associated with the structures and functions of life. When we talk about the large molecules necessary for large, we tend to call them biomolecules. 100,000 to 1,000,000's of atoms and repeating subunits.
• Most biomolecules tend to be quite large and constructed from repeating units of smaller molecules. The typical elemental composition for biomolecules include C,H, O in all groups, plus, N, P, and S in other biomolecular groups.
• Their construction and dismantling occurs in the same way regardless of biomolecular type.

Functional Groups

• Functional Group -- Special atoms or groups of atoms in all organic compounds.
• There are a number of different functional groups, and their attachment to a common molecular structure alters its properties, e.g. mammalian sex hormones. Different arrangements of different functional groups attached to different will impart all sorts of different 'functions' (Table 4.1, pg 58)
• In biochemical (metabolic) reactions, ALL functional groups function in the same way. Couplers and De-Couplers (See figure 4.8, pg 57). Structure will be a little different but can put them together and take them apart the same regardless of the molecule attached to. Oxygen and Hydrogen perform the primary connection characteristic.
• They serve as the site where organic molecules are built up or broken apart. Where biomolecules are built or broken.
• There are a variety of different functional groups, but we will deal with only 6 different types.
• All have their own properties as functional groups as well as serving as linking and detachment sites for organic molecules.
• We will examine the different types here and focus on their functions in Chapter 5.

1. Hydroxyl -- Its structure is --OH (notice that there is no charge, this is not the ion OH- (hydroxide ion !). And it is a terminal functional group, meaning that it projects off of organic molecules.
   • In sugars and alcohols (derived from sugars), hydroxyls are the main functional group.
2. Carbonyl -- an unusual functional group in that it can be either a terminal or internal functional group. (Carbon - KNEEL, pronounciation). (See figure 5.4 p 65). Different compounds based on internal or terminal.
   • If terminal, its structure is C=O (H branched off the Carbon).
   • If internal, its structure is -- C --, with the double-bonded Oxygen off of the C.
   • Both are associated with specific groups of sugars. Aldoses have terminal Carbonyl; internal Carbonyl belong to Ketoses. (See figure 5.3, p 64)
3. Carboxyl -- always terminal and abbreviated as --COOH.
• When present on an organic molecule, it forms a category of acids known as carboxylic or organic acids. Typically end in 'ic acid'.
• Carboxyls are associated with the fatty acids of lipids, and with the amino acids that form proteins.
4. Amine -- A terminal functional group, formed as --NH₂.
   • Amine groups are always associated with amino acids and associated collectively with proteins.
5. Sulfhydryl -- A simple terminal functional group containing Sulfur.
   • Only associated with certain proteins, these serve to stabilize the internal structure of the protein.
6. Phosphate -- Another terminal functional group consisting of 4 Oxygen atoms covalently bonded to a central Phosphorous atoms. The largest and one very critical to many facets of life; DNA, phospholipids.
   • One special group of lipids contain phosphate functional groups, as do all of the nucleic acids, and ATP (the battery of life).
   • As we will see, one important function of the phosphate groups themselves is the storage within and transfer of energy between organic molecules.

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