Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2010

Lecture Notes: 25 January

© R. Paselk 2006
 
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Biomolecules, cont.

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)

To give some perspective, lets look at the relative sizes of these objects. [overhead-sizes of molecules, one million times magnification]

All of these molecules together go to make up cells.

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. 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.) also occurs 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, though polymers have been synthesized under conditions which may have occurred on the early Earth.

The biggest problem for the origin of life is the issue of how we go from polymers to living "systems."

Pre-Cambrian Life:1


1A slightly enhanced treatment, with photos of specimens at our natural history museum is available by clicking on the link.


Cells and Organelles

There are two main cell types: prokaryote and eukaryote. A typical idealized prokaryote cell is shown in Figure 1-14 on p 17 of Text. [overhead- E. coli cell]

A prokaryote cell: size and composition

Let's look at E. coli for a moment just to get an idea of its size, and also to get an idea of the sizes of various molecules.

prokaryote cell image

public domain image via Wikipedia Creative Commons

Figure 1.14 [overhead- E. coli cell x 100,000] is an artists rendition of a typical E. coli cell, with the various components drawn to scale. Figure 1.17 [overhead- E. coli cytosol] magnifies a square section of that cell to 1,000,000 times so that particles such as ribosomes, proteins and DNA are readily visible. This view leaves out all of the small molecules though, to simplify the visualization. Finally a corner of the square is magnified a further ten times and water and small metabolites are shown in a very thin slice of our bacterial cell.

Cool facts about E. coli :70% water, 15% protein, 7% nucleic acids, 3% polysaccharides, 3%, lipids, 1% inorganic ions, & 0.2% metabolites.

Complex, generalized organisms such as E. coli exhibit an amazing level of redundancy in enzymes etc. For example, of the approximately 4,000 genes in E. Coli less than 300 have been found to be "essential," where essential means the organism cannot grow on rich medium if the gene is deleted. Many genes also appear to be "silent: under more restrictive conditions as well - that is the organism often has more than one pathway to accomplish a given metabolic activity. (Cornish-Bowden & Cárdenas, Nature 14 Nov 2002, p 129)

Compartmentation in Eukaryotes

As mentioned earlier we will be focusing on eukaryotes in the rest of this course. Eukaryotes differ from prokaryotes in having a nucleus and cell organelles (their cells are physically compartmentalized). As a point of reference, an E. coli cell is about the size of a typical mammalian mitochondria.

Let's look at where different major metabolic pathways occur in a "typical" liver cell. [overhead-Animal cell]

eukaryote cell image

public domain image via Wikipedia Creative Commons

A typical idealized eukaryote (animal) cell is shown in Figure 1-15 on p 19 of Text. [overheads- Animal cell, Plant cell]

Pathway Diagrams

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Last modified 25 January 2010