Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2010

Lecture Notes: 21 January

© R. Paselk 2006
 
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The Elements of Life, cont.

Periodic Table of Biologically Important Elements
 

 H
 

 He

 Li

Be
 

 B

C

N

O

F

Ne

Na

Mg

 Al

Si

P

S

Cl

Ar

K

Ca

Sc

Ti

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Ga

Ge

As

Se

Br

Kr
         

Mo
               Sn    

I
 

Recall that last time we looked at "life in the first and second Periods" (H, O, N, C) noting the special properties of these elements.

The next important elements to life occur in Period 3: P and S (orange). These are the smallest elements capable of multiple covalent bonds to C, O and N, and which also have available d-shells. The d-shells allow additional transition states and reaction mechanisms. P and S are particularly important in the capture, storage, and distribution of chemical energy.

Conveniently these elements are among the most abundant in the Universe. None-the-less, we hypothesize that these elements were chosen for their special properties, specifically strong covalent bond formation (to enable the formation of stable biomolecules), the ability of carbon to form large branched molecules, and for C, N, and O the formation of multiple bonds which provides chemical flexibility (step-wise oxidations, different hybridization geometries etc.).

(Aside: So why not have Si based life instead of C based?)

Elemental Ions:

 

Biomolecules to Cells

There are a few critically important small molecular precursors to biomolecules found in the environment. Biomolecules can be looked at in two major categories: 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) which are components of the nucleic acids (RNA and DNA-used for information storage and processing)

structural diagrams of the purine and pyrimidine rings
Both purines and pyrimidines are linked to a sugar, ribose or deoxyribose, and phosphate in their active, nucleotide, forms, as in ATP, below:
structural diagram of ATP
2. The amino acids.
structural diagram of common alpha amino acids elements in di-ionized form
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, 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.
Haworth structure of alpha-D-glucose

4. The fatty acids which, together with glycerol, 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:

structural diagram of palmitate


 

Pathway Diagrams

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Lecture Notes

Last modified 24 January 2010