Prescotts 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:

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

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 Prescotts Microbiology, 9th Edition

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
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 phasethe enzyme ribulose 1,5-bisphosphate carboxylase oxygenase (Rubisco)
catalyzes the addition of carbon dioxide to ribulose 1,5-bisphosphate, forming two molecules of 3-
phosphoglycerate
3. The reduction phase3-phosphoglycerate is reduced to glyceraldehyde 3-
phosphate
4. The regeneration phasea 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

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manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
 Prescotts Microbiology, 9th Edition

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 glycolysisit
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
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

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 Prescotts Microbiology, 9th Edition

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 cycleused 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
A. Fatty acid synthesis is catalyzed by fatty acid synthetase using the substrates
acetyl-CoA and malonyl-CoA, 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
B. 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
C. 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.

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 Prescotts Microbiology, 9th Edition

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.