Microbiology, Lec 12.

Anabolic processes (Chapter 10)

Anabolic reactions in cells are almost always linked to catabolic reactions (via ATP, reducing power and common pathways)

We will not spend a lot of time memorizing individual pathways, but I'd like you to understand the overview of how anabolic and catabolic pathways are linked.

Figure 10.1 in the book gives an overview of this linkage in autotrophs and heterotrophs. Remember that ATP and NADH are also needed to build macromolecules and that these come from catabolic processes or from photosynthesis in photosynthetic organisms.

Figure 11.1 gives a global overview of anabolic reactions in a typical bacterium (E. coli).

We have already discussed how microbes take up nutrients (N, P, K etc.; lec. 10). For every type of nutrient taken up there are, of course, anabolic pathways for incorporating those nutrients into macromolecules (see above). We don't have time to discuss all of the pathways (for there are thousands) but I do want to say a little more about nitrogen. Most Bacteria, Archaea and Fungi are capable of taking up N (usually passively and actively) in the form of nitrate or ammonium from the environment. These organisms can then use this N to make amino acids and other N-containing compounds used to build cellular materials (anabolism). There are some Bacteria and Archaea, however that have the ability to also utilize N2 from the atmosphere as an N source for anabolism - we call this process N-fixation.

N-fixation is a very expensive proposition. Figure 10.15 shows a simplified diagram of how the nitrogenase enzyme complex catalyzes the reduction of N2 to NH3. Note that 16 ATP and 8 e- are needed to make two molecule of NH3. Given that N-fixation is so expensive, it is not surprising that it only occurs in environments where N is limiting (e.g. rotting logs, guts of herbivores and many soils). N-fixing bacteria will shut off their N-fixing machinery when there are adequate supplies of ammonia or nitrate in the environment.

Show overheads of bacteroids and then draw the interconnections among N-fixation and the rest of the metabolism in Rhizobium.........

Note that oxygen is delivered to the bacteroid by leghemoglobin. This molecule scavenges free oxygen and makes sure that it doesn't interfere with N-fixation (N-fixation is a very reducing process and is therefore sensitive to O2). All N-fixers have had to develop some adaptations to protect the N-fixing enzymes from O2. As another example, see Box 21.4 on page 534. Note that this N-fixing cyanobacterium has a special type of cell, the heterocyst, in which N fixation occurs. No photosynthesis (and therefore no O2 production) takes place in the heterocyst.

Remember that most Bacteria and Archaea (and all Fungi) don't fix N, but rather take up nitrate, ammonia or organic N, via transport proteins, just like they take up S, P etc.....

Some unique and newly understood types of metabolism....

Now that we understand catabolism and anabolism in typical bacteria let's look at some not so typical (and not so well understood) organisms. In what follows we will discuss both anabolic and catabolic reactions.

Methanogenesis -

Methanogens (Archaea, lec. 7) live in very reducing environments where e- acceptors like nitrate and sulfate are usually not found. Table 22.3 shows some of the creative ways that they have come up with to obtain energy. Most of the metabolic pathways used by these guys are still not well understood but we know quite a bit about the methanogens that use carbon dioxide and hydrogen to make methane. In general these organisms are using H2 as their e- donor and CO2 as their e- acceptor.

4 H2 + CO2 -----> CH4 + 2 H2O

See overhead; note that methanogens use a bunch of novel co-enzymes ("vitamins") in their metabolism.......

other CHEMOAUTOTROPHS (read pages 535-543).

There is a very broad diversity of organisms that fall under the heading of chemoautotrophs. Even the type of Methanogen that we just discussed is technically a chemoautotroph (although many other methanogens are heterotrophs, Table 22.3). We will cover some of the major types of chemoautotrophs, but we don't have time to cover all of the major groups.

Table 21.10 list some of the major groups of chemoautotrophic (= chemolithotrophic) Bacteria. We will discuss the major characteristics of just the Nitrifiers, Sulfur Oxidizers, and Acetogenic bacteria.

These guys are anaerobic bacteria, most of which are gram + (e.g. Clostridium aceticum and Acetobacterium woodii). In addition to carrying out the reaction shown below they can also ferment sugars to produce acetic acid. (don't confuse these guys with the gram - acetic acid or vinegar Proteobacteria, lec. 5). But the reaction the Acetogens are known for is the production of acetic acid via anaerobic respiration of hydrogen (with CO2 as the e- acceptor):

4 H2 + 2 CO2 -----> CH3COOH + 2 H2O

Note that this reaction is quite similar to the methanogenic reaction we discussed above, except that acetate is the end product rather than methane. There are other similarities between the acetogens and methanogens. Figure 10.11 shows details of how some Acetogens use the reductive acetyl CoA pathway to carry out the above reaction. You may want to compare the acetyl CoA pathway to the Calvin cycle that you learned in general Biology (see Fig. 10.8). Acetobacterium woodii is one bacterium that requires sodium for growth. It uses an NA+ (instead of H+) membrane gradient to generate ATP.

These organisms hold a keystone position in the global nitrogen cycle (see N-cycle, below). They are the organisms responsible for converting ammonia to nitrate. All known nitrifiers are gram - Proteobacteria (see lec. 5). The first step of nitrification is carried out by the ammonia oxidizers (Generic names all start with Nitroso e.g. Nitrosomonas Table 21.11) which convert ammonia to nitrite via the following overall redox reaction:

2 NH3 + 3 1/2 O2 -----> 2 NO2- + 3 H2O

The next step of nitrification is the conversion of nitrite to nitrate. The organisms that do this almost always live in close symbiotic relationships with the ammonia oxidizers. This is why nitrite (which is extremely toxic) almost never builds up in the environment. Nitrite oxidizers (Generic names all start with Nitro e.g. Nitrobacter Table 21.11) convert nitrite to nitrate via the overall rxn.:

NO2- + 1/2 O2 -----> NO3-

Figure 21.26 shows some nitrifying bacteria. Note the extensive internal membrane systems; many of the enzymes responsible for nitrification are concentrated in these membranes.