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Basic Energy Concepts
Types of Catabolism
Feremented Foods
Catabolism of Fats
Catabolism of Proteins
Amazing Respirations
Membranes and
Energy Generation

Anaerobic Respiration
Summary of Catabolism
Collecting Elements
Synthesizing Monomers
Carbon Assimilation
Nitrogen Assimulation
Other Assimilation
Formation of
Amino Acids

Lipid Synthesis
Nucleotide Synthesis
Making Polymers
Structural Assembly
Amphibolic Pathways

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Assembly of Polymers

©2000 Timothy Paustian, University of Wisconsin-Madison

Building of the cell requires the assembly of needed macromolecular structures. Many of these structures are polymers made up of the building blocks we have just talked about, amino acids, nucleic acids, fatty acids, lipids, and sugars. Here we describe in the most general terms how each of these polymers are assembled.


Proteins are polymers and the average bacterial cell will require around 5000 different proteins to carry out cellular processes or to serve as part of structures in the cell. The sequence of each protein is unique, but the method of putting them together is identical. The cell has a tool and dye factory (ribosome) that assembles the amino acids based on the directions of a template, messenger RNA. The whole process is called translation and will be describe elsewhere in the textbook. [This section is not up yet - sorry]


The function of RNA in the cell can be boiled down to helping translate the recipes coded for in DNA into protein. The three types of RNA in the cell are ribosomal RNA, transfer RNA and messenger RNA. Their structures are described in the section on RNA. The process of creating these RNAs is similar and is carrier out by the enzyme RNA polymerase. A detail description of this process is available in the chapter on Transcription. [This section is not up yet - sorry]

DNA contains the list of instructions for how to make and maintain an organism. Accurate copying or replication of this DNA is critical to an organisms survival and the synthesis of DNA in the cell has been under intense study for decades. The replication of DNA is covered in the chapter on DNA Replication. [This section is not up yet - sorry]

Cell walls

Cell walls are synthesized from amino acids and the sugars N-Acetyl Glucosamine and N-Muramic Acid. The structure of bacterial cell walls and their make up was covered in the chapter on bacterial structure. The cell wall is made up of peptidoglycan and membranes and each of these structures has its own unique synthesis pathways.


Membranes are composed of lipids and proteins. Lipids are capable of spontaneously assembling into a bilayer while membrane proteins are guided into the membrane by ribosomes or other cellular machinery. The synthesis of membranes thus seems to consist of several systems guiding the spontaneous self assembly of the macromolecule.


In contrast to membranes, peptidoglycan (also called murein) synthesis and assembly is controlled by enzymes every step of the way. Peptidoglycan is a large molecule (3 x 109 to 6 x 109 daltons per cell) and assembling it is a complex process. Synthesis of peptidoglycan can be divided into two steps.

  • The formation of the NAG-NAM-peptide monomers that make up peptidoglycan. This process takes place in the cytoplasm and on the inner surface of the cytoplasmic membrane.

  • Polymerization of the NAG-NAM-peptide monomers into a nascent murein chain and then addition to the existing cell wall peptidoglycan.

Synthesis of the monomers of peptidoglycan begins with glucose which is readily converted into NAG. Synthesis begins by activating NAG with the addition of (uracil diphosphate) UDP, which serves as a carrier of the growing peptidoglycan during its synthesis in the cytoplasm. Phosphoenol pyruvate is then added to UDP-NAG and this is then converted into UDP-NAM. Next, the UDP-NAM-peptide is formed by four sequential additions of the appropriate amino acids (L-alanine, D-glutamic acid, diaminopimelic acid and finally two D-alanines). UDP-NAM-pentapeptide is then transported to the membrane and handed off to a membrane bound lipid, undecaprenyl phosphate to make NAM(pentapeptide)-pyrophosphoryl-undecaprenol. Undecaprenol is a 55 carbon alkyl chain that is highly hydrophobic. It serves as an anchor for the peptidoglycan unit. Finally, NAG is attached to NAM to finish the monomer.

The lipid moiety with its finished monomer flips to the outside of the membrane, resulting in the transport of the monomer across the membrane. The final polymerization reactions take place in the periplasm. Here the murein monomers are added to the growing peptidoglycan. Each monomer is attached to the cells peptidoglycan by a transglycosylation reaction. This adds the monomer to the cell wall by the sugar backbone. In the final step, the nascent peptidoglycan chain is cross-linked by transpeptidases that form covalent links between the peptide side chains. The D-alanine of one side chain is linked to the diaminopimelic acid of the next.

PeptidoSyn picture

Figure 1 - Assembly and Polymerization of peptidoglycan. M, N-acetylmuramic acid; G, N-acetylglucosamine; UDP, Uracil diphosphate; L-Ala, L-Alanine; D-Glu, D-Glutamate; DAP, diaminopimelic acid; D-Ala, D-Alanine.

Both the transglycosylation and transpeptidation reactions are catalyzed by a group of enzymes denoted as penicillin binding proteins (PCPs). They are called PCPs because they are the site of action for penicillin and other b-lactam antibiotics. E. coli has seven known PCPs and they have been an area of intense scientific interest; the more we learn about how they operate, the better we will be at making b-lactam antibiotics that fight bacterial infection. In the future it may be possible to design drugs that inhibit these proteins yet bacteria cannot readily develop a resistance to.

transpep picture

Figure 2 - Transpeptidation of peptidoglycan chains.

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