Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431	Biochemistry	Fall 2001
Lecture Notes:: 29 August	© R. Paselk 2001
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BIOMOLECULES TO CELLS

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.

There are a few critically important small molecular precursors to biomolecules found in the environment: oxygen (O₂), water (H₂O), carbon dioxide (CO₂) ammonia or ammonium ion (NH₃ or NH₄⁺), nitrate ion (NO₃^-, and nitrogen (N₂).

These molecules and atoms 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)

Both purines and pyrimidines are linked to a sugar, ribose or deoxyribose, and phosphate in their active, nucleotide, forms, as in ATP, below:

2. the amino acids which are components of the proteins (proteins comprise the machinery of life [enzymes] and much of the structure of life-these 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.

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:

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.

 

All of these molecules together go to make up cells.

The Origin of Life

The oldest fossil evidence for life on Earth dates to about 3.7 by (billion years ago). The Earth itself formed about 4.5 by with the formation of our solar system. It is thought that the Earth was too hot and chaotic to support life until perhaps 3.8 by (intense bombardment of the earth did not end until 3.9 by, thus life arose quite quickly, essentially as soon as possible!

How did this occur? Obviously guess work - no one was there, and there is no record in the rocks that we could even be certain of. However, we have good guesses as to Earth's early environment (atmosphere of H₂O, NH₃, CO₂ and smaller amounts of CH₄, NH₃, SO₂, and H₂. If you treat such an atmosphere with any high energy source in the laboratory, as was first done by Miller in 1953) you will get a mixture of organic molecules including many important to organisms today (Tables 1-2, p 5 in Voet). Interestingly, we also find small precursor molecules all over the Universe - in ancient rocks, meteors, comets etc. Evidence of small precursor molecules (amino acids, nitrogenous bases etc) in interstellar space, the atmospheres of carbon stars, gas giant planets etc.

The formation of polymers is more problematic. A major difficulty is that biopolymers are all thermodynamically unstable relative to their hydrolysis products. Some theories, but no certainty as to how polymers may have formed.

"RNA World"

Pre-Cambrian Life:

• 3.8 - microfossils?
• 3.46 - stomatolites (Australia) [3.5-3.3 microfossils of cyanobacteria?]
• 2.8 kerogens with low ¹³C/¹²C indicative of O₂ use by methanogens
• 2.7-2.5 2-methyl-hopane "fossils" (cyanobacterial markers); steranes (eukaryotic molecular marker, oxygen needed for synthesis)
• 2.5 -> stromatolite reefs rivaling modern reefs in size and architecture
• 0.6 Ediacaran fauna
• 0.54-0.53 "Cambrian explosion"

Pathway Diagrams

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Last modified 30 August 2001