Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431

Biochemistry

Fall 2008

Lecture Notes: 3 September

© R. Paselk 2008
 
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Cells to Biomolecules

Two major categories of biomolecules: small molecules and macromolecules.

The small molecules are going to be either metabolites or monomers from which the macromolecules are built.

First let's note the "inorganic" (sometimes called mineral) molecules and molecular ions: oxygen (O2), water (H2O), carbon dioxide (CO2) ammonia or ammonium ion (NH3 or NH4+), nitrate ion (NO3-), nitrogen (N2), phosphate ion (PO43-) and sulfate ion (SO42-). These are mostly metabolites, though the ions can also serve as counter ions along with chloride in creating the intracellular media.

These molecules and ions in turn can be made into metabolites, small organic molecules used in energy transformation and as precursors to monomers and macromolecules.

Right now we'll focus on the monomers and the associated macromolecules. There are four major categories:

1. The nitrogenous bases (purines and pyrimidines, text Figure 1-10b) which are components of the nucleic acids (RNA and DNA-used for information storage and processing)

Both purines and pyrimidines are linked to a sugar, ribose or deoxyribose, and phosphate in their active, nucleotide, forms (ATP - text Figure 1-25), as in ATP, below:
2. The amino acids (text Figure 1-10a).
Amino acids are components of proteins, which comprise the machinery of life [enzymes] and much of the structure of life-proteins are the molecules that do things.
 
3. The sugars (text Figure 1-10d), which are components of the polysaccharides (together comprising the carbohydrates, which are used for energy storage and structure). Glucose, the most common sugar, is shown in a cyclic form. Note that a sugar must have an aldehyde or ketone and two or more alcohol functional groups by definition.

4. The fatty acids which, together with glycerol (text Figure 1-10c), make up the fats (used mostly for energy storage) and the phospholipids (the major component of cell membranes). The 16 carbon fatty acid palmitate is shown below:

A typical phospholipid is shown here, replacement of the phosphate ester group with a third fatty acid would give a fat instead:

The amino acids, nucleotides, and sugars can all be polymerized to give the macromolecules characteristic of life: proteins, nucleic acids, and polysaccharides, respectively. We will come back to each of these macromolecules in our study, focusing particularly on proteins. Briefly, proteins comprise the machinery and much of the structure of life; nucleic acids provide the information required to specify the proteins, and polysaccharides provide structural fibers and energy storage molecules.

Note that all of these families of molecules exhibit chirality in some, and generally most, of their members (text Figure 1-19). Also, biological systems chose a single chirality for each family (e.g. L-amino acids, D-sugars).

All of these molecules together go to make up cells.

Pathway Diagrams

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Last modified 3 September 2008