How many metabolic reactions required for synthesis of an ordinary bacterial cell?

Book says ~2000, but this number is a bit too high. Haemophilis influenzae (eubacterium) genome has about 1800 genes, and similar number found in Methanococcus jannaschii (archaeon). Not all of these genes are actually required. Probably ~1200 to 1300 genes for a free-living cell (less than 600 genes in Mycoplasma genitalium, but it is not free-living).

1. ASSEMBLY (Self- or Directed)

2. POLYMERIZATION of "Building Blocks"

3. BIOSYNTHETIC REACTIONS: production of building blocks and signalling molecules (ALARMONES); organized into PATHWAYS. All syntheses begin with one of 12 PRECURSOR METABOLITES to produce about 75 building blocks and coenzymes

4. FUELING REACTIONS produce the 12 precursor metabolites, protonmotive force and/or ATP, reducing power, and C-1 units.

CATABOLIC reactions: ENERGY

AMPHIBOLIC reactions: ENERGY and PRECURSORS

ANABOLIC reactions: biosynthesis

OTHER CATEGORIES: TRANSPORT (fueling); ASSIMILATION (N & S, biosynthetic; P, fueling). REPAIR (DNA) is polymerization; TURNOVER of RNA, Proteins, etc. is fueling/ polymerization. Chemotaxis???

The text is written from the point of view of E. coli and other related G- bacteria.

1. Not all bacteria can utilize glucose as sole carbon source; many prefer organic acids,etc.

2. Assume that many differences exist for other bacteria, since this will be true!

3. Lithotrophs/Autotrophs: using non-organic energy sources and assembling all building blocks from CO₂ is another matter altogether.

Not understood.

How are constrained domains created?

Roles of topoisomerases?

How attached to cytoplasmic membrane?

mRNA + ribosomes + protein chains [+tRNAs, etc.]

About 1000 polysomes (about 20 ribosomes + mRNA molecule) per cell.

Relatively little modification of mRNA compared to eucaryotes; there is some processing, however, including addition of poly-A tails to some mRNAs, and cutting mRNAs into segments

Number of ribosomes/cell depends on growth rate and is regulated.

Carbon source ribosomes/cell Doubling Time

Acetate 8000 3 h

Glucose 15-18,000 1 h

Rich Medium 27,000 0.3h

Assembly overlaps the initiation of TRANSLATION. Ribosome assembly takes only 2-5 minutes--very rapid

In E. coli, there are 7 rrn operons (rrnA-rrnH) encoding rRNA molecules. All have similar organization:

[16S rRNA]-[spacer tRNA(s)]-[23S rRNA]-[5S rRNA]-[distal tRNA]

50% of transcription can come from rrn operons; unusual to have multiple copies in DNA. Sequences of genes typically identical. Faster growing bacteria tend to have more rrn genes than slow-growing species. tRNAs are different for various copies, but overall organization is similar in all species.

Long 30 S RNA transcript is first formed, and ~20% of this RNA is discarded during processing.

Primary Processing: primary RNA is cut into precursor RNAs: p16S, p23S, p5S, and ptRNA(s). r-Proteins begin to bind to the processed RNA; in some species, the 23S rRNA is processed into two segments by removal of an intron without splicing two ends

Secondary Processing: ends are trimmed to final lengths; methylation of specific bases occurs. About 34 methylated bases are found in these rRNAs. Clustering of these in functionally important regions seems to indicate important role in translational decoding. Methylation of 16S rRNA is early and not necessary for 30 S subunit assembly; methylation of 23S rRNA is late, and seems to be required for assembly of proteins to occur

52 Genes encoding r-Proteins (r = ribosomal) are arranged in 21 transcription units!! How does coordination of synthesis occur??? Most made in small excess over rRNAs.

Assembly of 30S and 50S subunits can occur by mixing rRNAs with appropriate purified proteins. Complete assembly in vitro requires heating steps; in vivo, assembly probably requires some chaperone proteins. Some proteins interact directly with RNAs; others interact only through protein-protein interactions

CYTOSOL (CYTOPLASM): all that is not included in nucleoid, polysomes, cytoplasmic membrane, and cell wall/envelope

Includes proteins, tRNAs, storage polymers, metabolites, coenzymes, cofactor ions, etc.

Often there are no compartments in cells and no diffusion barriers. Exceptions: gas vesicles, chlorosomes, carboxysomes, intrcytoplasmic membranes?

Is cytosol organized or disorganized?? Probably some organization exists, but difficult to demonstrate in vitro since concentration of materials generally much lower when cells are disrupted

Assembly reactions include modification reactions of tRNAs and proteins.

About 40 enzymes are required to modify tRNA bases to final structures. Roles of modified bases: improve the specificity of charging reactions; improve anticodon-codon specificity;

Modification of proteins: less important in eubacteria than in eucaryotes. Bacteria use feedback inhibition and repression as primary control mechanisms rather than controlling activity through modification of protein.

Major exception: prosthetic group formation addition--required for formation of functional enzyme.