Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes 2: January 25

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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
 

The following observations may be made regarding the elements of life:

Life is largely a phenomena of hydrogen and the second period of the Periodic Table. That is, the major component elements (red) in all known organisms are from these periods. Why these four 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 all of 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

There are a few critically important small molecular precursors to biomolecules found in the environment. Biomolecules can be looked at in two major categories:

  1. small molecules
  2. 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.

"Pecha Kucha" Power Point presentation of Chap 1 - Biomolecules.

So what have we learned?

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

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

structural diagram of a phospholipid

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. Also, biological systems chose a single chirality for each family (e.g. L-amino acids, D-sugars)

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© R. A. Paselk 2010; Last modified 25 January 2013