Prescott’s Microbiology, 9th Edition
12
Anabolism: The Use of Energy in Biosynthesis
CHAPTER OVERVIEW
This chapter presents an overview of anabolism starting with the fixation of carbon dioxide. It then focuses on the
synthesis of carbohydrates and peptidoglycan; the assimilation of phosphorus, sulfur, and nitrogen; and the synthesis
of amino acids, purines and pyrimidines, and lipids.
LEARNING OUTCOMES
After reading this chapter you should be able to:
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describe in general terms the steps organisms use to convert a carbon source and inorganic molecules to cells
discuss the principles that govern biosynthesis
list the central metabolic pathways, noting which precursor metabolites are generated by each pathway
draw a simple diagram that lists all the precursor metabolites and illustrates how they are used in biosynthesis
list the six pathways used by microbe to fix CO2, noting the types of organisms that use each pathway
describe in general terms the three phases of the Calvin cycle
identify the steps of the Calvin cycle that consume ATP and NADPH
compare and contrast gluconeogenesis and Embden-Meyerhof pathway
describe the role of ATP and UTP in the synthesis of monosaccharides (other than glucose) and
polysaccharides
outline the major steps in peptidoglycan synthesis
evaluate the effectiveness of targeting antibiotics to peptidoglycan synthesis
discuss the three mechanisms microorganisms use to assimilate nitrogen and the role of transaminases in them
describe the two methods microbes use to assimilate sulfur
differentiate assimilatory nitrate reduction from dissimilatory nitrate reduction and assimilatory sulfate
reduction from dissimilatory sulfate reduction
evaluate the efficiency of using branched pathways for synthesizing amino acids
list the major types of anaplerotic reactions or pathways and explain their importance
distinguish a purine from a pyrimidine, and identify which nitrogenous bases are purines and which are
pyrimidines
draw a simple diagram that illustrates the chemical moieties found in nucleosides and nucloetides
discuss in general terms how phosphorous is assimilated
compare and contrast purine and pyrimidine biosynthesis
discuss the methods used to convert ribonucleotides to deoxyribonucleotides
describe the role of acetyl-CoA, acyl carrier protein (ACP), and fatty acid synthase in fatty acid synthesis
distinguish saturated fatty acids from unsaturated fatty acids
describe the roles of dihydroxyacetone phosphate and fatty acids in the synthesis of triacylglycerol
describe the roles of diacylglyerol and CTP in the synthesis of phospholipids
CHAPTER OUTLINE
I.
Principles Governing Biosynthesis
A. Biosynthetic metabolism follows a few general principles:
1. The synthesis of large, complex molecules (macromolecules) from a limited number of simple
structural units (monomers) saves much genetic storage capacity, biosynthetic raw material, and
energy
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Prescott’s Microbiology, 9th Edition
2.
The use of many of the same enzymes for both catabolism and anabolism saves additional materials
and energy
3. Many biosynthetic pathways are reversals of catabolic pathways; many steps of the pathway are
catalyzed by enzymes that participate in both catabolic and anabolic activities; however, some steps
are catalyzed by two different enzymes: one that functions in the catabolic direction and a second
that functions in the biosynthetic direction; this permits independent regulation of catabolism and
anabolism
4. Coupling some biosynthetic reactions with the breakdown of ATP (or other nucleoside
triphosphates) drives anabolic pathways irreversibly in the direction of biosynthesis
5. In eukaryotic cells, anabolic and catabolic reactions involving the same constituents are frequently
located in separate compartments for simultaneous but independent operation
6. Catabolic and anabolic pathways use different cofactors: catabolic oxidations produce NADH,
which is a substrate for electron transport, while NADPH acts as an electron donor for anabolic
pathways
B. Once macromolecules have been made from simpler precursors, cell structures (e.g., ribosomes) form
spontaneously from the macromolecules by a process known as self-assembly
II. Precursor Metabolites
A. Precursor metabolites are carbon skeletons used as building blocks for the synthesis of macromolecules;
many are intermediates in glycolytic pathways and the TCA cycle
III. CO2 Fixation
A. Autotrophs use CO2 as their sole or principal carbon source; carbon fixation requires much energy and
reducing power
B. Calvin cycle
1. The most widely used carbon fixation pathway is the Calvin cycle (reductive pentose phosphate
cycle or Calvin-Benson cycle); it consists of three phases that occur in the chloroplast stroma of
eukaryotes and possibly in the carboxysomes of certain bacteria
2. The carboxylation phase—the enzyme ribulose 1,5-bisphosphate carboxylase oxygenase (Rubisco)
catalyzes the addition of carbon dioxide to ribulose 1,5-bisphosphate, forming two molecules of 3phosphoglycerate
3. The reduction phase—3-phosphoglycerate is reduced to glyceraldehyde 3-phosphate
4. The regeneration phase—a series of reactions is used to regenerate ribulose 1,5-bisphosphate and to
produce carbohydrates such as fructose and glucose; this phase is similar to the pentose phosphate
pathway and involves transketolase and transaldolase reactions
5. The incorporation of one carbon dioxide takes three ATP molecules and two NADPH molecules;
thus the formation of a single glucose molecule requires six turns through the cycle with an
expenditure of 18 ATP molecules and 12 NADPH molecules; sugars formed in the Calvin cycle can
then be used to synthesize other essential molecules
C. Other CO2-fixation pathways are used by some bacteria and archaea including the reductive TCA cycle,
the 3-hydroxypropionate cycle, the acetyl-CoA pathway, and the 3-hydroxypropionate/4-hydroxybutyrate
pathway
IV. Synthesis of Carbohydrates
A. Synthesis of monosaccharides and polysaccharides
1. Heterotrophs synthesize glucose from noncarbohydrate precursors in a process called
gluconeogenesis; this pathway is a functional reversal of glycolysis—it shares seven enzymes with
the glycolytic pathway, reversing their catabolic direction, and uses several distinct enzymes or
multi-enzyme systems to catalyze steps that cannot be directly reversed
2. Once glucose and fructose are synthesized by gluconeogenesis, other sugars are manufactured;
several of these other sugars are synthesized while attached to a nucleoside diphosphate
3. Synthesis of polysaccharides also requires the use of nucleoside diphosphate sugars as precursors
B. Synthesis of peptidoglycan
1. A multistep process that involves two carriers: uridine diphosphate and bactoprenol; during the
process a peptidoglycan repeat unit is formed and is attached to the growing peptidoglycan chain
after being transported across the cytoplasmic membrane; cross-links are then formed by
transpeptidation
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Prescott’s Microbiology, 9th Edition
2.
Autolysins carry out limited digestion of peptidoglycan, and provide acceptor ends for the addition
of new peptidoglycan units
3. Peptidoglycan synthesis is very vulnerable to disruption by antimicrobial agents, including
antibiotics such as penicillin; inhibition of any step in the process weakens the cell wall and can
cause lysis
V. Synthesis of Amino Acids
A. Nitrogen assimilation
1. Ammonia incorporation
a. Many microorganisms use reductive amination to make alanine and glutamate, which are then
used as sources of amino groups; the amino groups are transferred from alanine or glutamate to
other carbon skeletons by transamination reactions
b. Other microorganisms use the enzymes glutamine synthetase and glutamate synthase to
synthesize glutamate, which then acts as an amino group donor in transaminase reactions
2. Assimilatory nitrate reduction involves the reduction of nitrate to nitrite, then to hydroxylamine, and
finally to ammonia, which can then be incorporated by the routes described above
3. Nitrogen fixation is the reduction of atmospheric nitrogen to ammonia; this is catalyzed by the
enzyme nitrogenase, which is found in only a few species of bacteria, archaea, and cyanobacteria;
nitrogen fixation requires an expenditure of 16 ATP molecules and 8 electrons per N 2 reduced; the
ammonia produced can be incorporated into organic molecules by the processes described above
B. Sulfur assimilation
1. Organic sulfur in the form of cysteine and methionine can be obtained from external sources
2. Assimilatory sulfate reduction is used to reduce inorganic sulfate before it is incorporated into
cysteine
C. Amino acid biosynthetic pathways
1. Involves attachment of an amino group to a carbon skeleton
2. Carbon skeletons are derived from acetyl-CoA and from intermediates of the TCA cycle, glycolysis,
and the pentose phosphate pathway
D. Anaplerotic reactions and amino acid biosynthesis
1. Biosynthetic functions of the TCA cycle are so important that many of its intermediates must be
synthesized even when the TCA cycle is not functioning to catabolize pyruvate or to provide NADH
for electron transport
2. Anaplerotic reactions replenish TCA cycle intermediates so that biosynthesis can occur; two major
types of anaplerotic reactions have been observed
a. Anaplerotic carbon dioxide fixation (e.g., pyruvate carboxylase reaction)
b. Glyoxylate cycle—used by microorganisms that can grow on acetate as a sole carbon source; is
a modified TCA cycle where carbons entering the cycle are not released as carbon dioxide
VI. Synthesis of Purines, Pyrimidines, and Nucleotides
A. These molecules are critical for all cells because they are used in the synthesis of ATP, several cofactors,
RNA, and DNA; two types of bases are required: purines (adenine and guanine) and pyrimidines (uracil,
cytosine, and thymine); a nucleoside includes the base and sugar, while a nucleotide also has the
phosphate group
B. Phosphorus assimilation
1. Inorganic phosphates are incorporated through the formation of ATP by photophosphorylation,
oxidative phosphorylation, and substrate-level phosphorylation
2. Organic phosphates obtained from the surroundings are hydrolyzed to release inorganic phosphates
by enzymes called phosphatases
C. Purine biosynthesis is a complex pathway in which seven different molecules (including folic acid)
contribute parts to the final purine skeleton; the first purine product is the nucleotide inosinic acid, from
which all other purine nucleotides can be made
D. Pyrimidine biosynthesis starts with aspartic acid and carbamoyl phosphate forming the initial pyrimidine
product (orotic acid), which can then be converted to pyrimidine nucleotides
VII. Lipid Synthesis
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Prescott’s Microbiology, 9th Edition
A.
B.
C.
Fatty acid synthesis is catalyzed by fatty acid synthetase using the substrates acetyl-CoA and malonylCoA, the electron donor NADPH, and a small protein called acyl carrier protein (ACP), which carries the
growing fatty acid chain; the fatty acid is lengthened by adding two carbons at a time to its carboxyl end
Triacylglycerols are formed from the reduction of dihydroxyacetone phosphate (a glycolytic pathway
intermediate) to glycerol 3-phosphate, which then undergoes esterification with two fatty acids to form
phosphatidic acid; this can then be used to produce triacylglycerol
Phospholipids also are produced from phosphatidic acid using a cytidine diphosphate (CDP) carrier
CRITICAL THINKING
1.
What would be the consequences for a cell if anaplerotic reactions did not exist? Consider in your discussion
the interrelationship between catabolic and anabolic reactions and the needs of an organism growing on limited
nutritional sources.
2.
There are a number of different ways to assimilate nitrogen. Only a relatively few species of bacteria, however,
are capable of utilizing gaseous atmospheric nitrogen (nitrogen fixation). Why do you think such a variety of
assimilatory pathways exist? Why do you think so few organisms are equipped to use gaseous atmospheric
nitrogen, even though it is quite abundant?
3.
Biosynthetic processes (e.g., gluconeogenesis) frequently are not direct reversals of the related catabolic
processes (e.g., glycolysis). However, some of the steps involved in the overall pathway may be direct
reversals. What is the advantage to the organism to have separate pathways for synthesis and degradation?
Furthermore, what is the advantage to the organism for the substantial overlap (i.e., directly reversed steps)
within these pathways?
4.
Organisms depend upon energy producing catabolic reactions in order to fuel energetically unfavorable
ones. Comment one how an organism can still build up new molecules when its supply of food is limited.
CONCEPT MAPPING CHALLENGE
Prepare a concept map that highlights the feedstock pathways that provide the molecular skeletons for carbohydrates,
nucleic acids (purines and pyrimidines), lipids and amino acids.
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.