© Royalty-Free/CORBIS25 Nitrogen Acquisition and Amino Acid Metabolism Amino acids and nucleotides, as well as their polymeric forms proteins and nucleic acids, are nitrogen-containing
Trang 1Pregnenolone and Progesterone Are the Precursors of All Other
Steroid Hormones
Pregnenolone is transported from the mitochondria to the ER, where a hydroxyl
oxidation and migration of the double bond yield progesterone Pregnenolone
syn-thesis in the adrenal cortex is activated by adrenocorticotropic hormone (ACTH),
a peptide of 39 amino acid residues secreted by the anterior pituitary gland.
Progesterone is secreted from the corpus luteum during the latter half of the
menstrual cycle and prepares the lining of the uterus for attachment of a fertilized
ovum If an ovum attaches, progesterone secretion continues to ensure the
suc-cessful maintenance of a pregnancy Progesterone is also the precursor for
synthe-sis of the other sex hormone steroids and the corticosteroids Male sex hormone
steroids are called androgens, and female hormones, estrogens Testosterone is an
androgen synthesized in males primarily in the testes (and in much smaller
amounts in the adrenal cortex) Androgens are necessary for sperm maturation.
Even nongonadal tissue (liver, brain, and skeletal muscle) is susceptible to the
ef-fects of androgens.
Testosterone is also produced primarily in the ovaries (and in much smaller
amounts in the adrenal glands) of females as a precursor for the estrogens -Estradiol
is the most prominent estrogen (Figure 24.44)
O
HO
H3C
H3C
HO
H3C
H3C
O
H3C
H3C
O
O
H3C
H3C
O
OH
OH
H3C
HO
H3C
CH2OH
O
HO
CH
C O O
CH2OH C
O
H3C
H3C
O
OH HO
Pregnenolone Cholesterol
Desmolase (Mitochondria)
Isocaproic aldehyde
Progesterone (Endoplasmic reticulum)
Testosterone
-Estradiol
Aldosterone
Cortisol
FIGURE 24.44 The steroid hormones are synthesized from cholesterol, with intermediate formation of preg-nenolone and progesterone Testosterone, the principal male sex hormone steroid, is a precursor to -estradiol.
Cortisol, a glucocorticoid, and aldosterone, a mineralo-corticoid, are also derived from progesterone
Trang 2764 Chapter 24 Lipid Biosynthesis
Steroid Hormones Modulate Transcription in the Nucleus
Steroid hormones act in a different manner from most hormones we have consid-ered In many cases, they do not bind to plasma membrane receptors but rather pass easily across the plasma membrane Steroids may bind directly to receptors in the nucleus or may bind to cytosolic steroid hormone receptors, which then enter the nucleus In the nucleus, the hormone-receptor complex binds directly to spe-cific nucleotide sequences in DNA, increasing transcription of DNA to RNA (see Chapters 29 and 32).
Cortisol and Other Corticosteroids Regulate a Variety of Body Processes
Corticosteroids, including the glucocorticoids and mineralocorticoids, are made by the
cortex of the adrenal glands on top of the kidneys Cortisol (Figure 24.44) is rep-resentative of the glucocorticoids, a class of compounds that (1) stimulate
gluco-neogenesis and glycogen synthesis in liver (by promoting the synthesis of PEP carboxykinase, fructose-1,6-bisphosphatase, glucose-6-phosphatase, and glycogen synthase); (2) inhibit protein synthesis and stimulate protein degradation in pe-ripheral tissues such as muscle; (3) inhibit allergic and inflammatory responses; (4) exert an immunosuppressive effect, inhibiting DNA replication and mitosis and repressing the formation of antibodies and lymphocytes; and (5) inhibit formation
of fibroblasts involved in healing wounds and slow the healing of broken bones.
Aldosterone, the most potent of the mineralocorticoids (Figure 24.44), is
in-volved in the regulation of sodium and potassium balances in tissues Aldosterone increases the kidney’s capacity to absorb Na, Cl, and H2O from the glomerular fil-trate in the kidney tubules.
Anabolic Steroids Have Been Used Illegally to Enhance Athletic Performance
The dramatic effects of androgens on protein biosynthesis have led many athletes to
the use of synthetic androgens, which go by the blanket term anabolic steroids Despite
numerous warnings from the medical community about side effects, which include kidney and liver disorders, sterility, and heart disease, abuse of such substances is
epi-demic Stanozolol (Figure 24.45) was one of the agents found in the blood and urine
of Ben Johnson following his record-setting performance in the 100-meter dash in the 1988 Olympic Games Because use of such substances is disallowed, Johnson lost his gold medal and Carl Lewis was declared the official winner.
H3C
H3C
H
OH
CH3
N
HN
Stanozolol
FIGURE 24.45 The structure of stanozolol, an anabolic
steroid
SUMMARY
24.1 How Are Fatty Acids Synthesized? The synthesis of fatty acids
and other lipid components is different from their degradation Fatty
acid synthesis involves a set of reactions that follow a strategy different
in several ways from the corresponding degradative process:
1. Intermediates in fatty acid synthesis are linked covalently to the
sulf-hydryl groups of the acyl carrier proteins In contrast, fatty acid
break-down intermediates are bound to the OSH group of coenzyme A
2. Fatty acid synthesis occurs in the cytosol, whereas fatty acid
degrada-tion takes place in mitochondria
3. In animals, the enzymes of fatty acid synthesis are components of
one long polypeptide chain, the fatty acid synthase, whereas no
sim-ilar association exists for the degradative enzymes
4. The coenzyme for the oxidation–reduction reactions of fatty acid
syn-thesis is NADP/NADPH, whereas degradation involves the NAD/
NADH couple
24.2 How Are Complex Lipids Synthesized? A common pathway
oper-ates in nearly all organisms for the synthesis of phosphatidic acid, the
pre-cursor to other glycerolipids Glycerokinase catalyzes the phosphorylation
of glycerol to form glycerol-3-phosphate, which is then acylated at both the 1- and 2-positions to yield phosphatidic acid In eukaryotes, phosphatidic acid is converted directly either to diacylglycerol or to cytidine diphospho-diacylglycerol (or simply CDP-diphospho-diacylglycerol) From these two precursors, all other glycerophospholipids in eukaryotes are derived Phosphatidyl-ethanolamine synthesis begins with phosphorylation of Phosphatidyl-ethanolamine to form phosphoethanolamine The next reaction involves transfer of a cytidylyl group from CTP to form CDP-ethanolamine and pyrophosphate Diacylglycerol then displaces CMP to form phosphatidylethanolamine Eukaryotes also use CDP-diacylglycerol, derived from phosphatidic acid, as
a precursor for several other important phospholipids, including phos-phatidylinositol (PI), phosphatidylglycerol (PG), and cardiolipin
24.3 How Are Eicosanoids Synthesized, and What Are Their Functions?
Eicosanoids are ubiquitous breakdown products of phospholipids In re-sponse to appropriate stimuli, cells activate the breakdown of selected phospholipids Phospholipase A2selectively cleaves fatty acids from the C-2 position of phospholipids Often these are unsaturated fatty acids,
Trang 3among which is arachidonic acid Arachidonic acid may also be released
from phospholipids by the combined actions of phospholipase C
(which yields diacylglycerols) and diacylglycerol lipase (which releases
fatty acids) Animal cells can modify arachidonic acid and other
poly-unsaturated fatty acids to produce so-called local hormones These
substances include the prostaglandins, as well as thromboxanes,
leuko-trienes, and other hydroxyeicosanoic acids
24.4 How Is Cholesterol Synthesized? The cholesterol biosynthetic
pathway begins in the cytosol with the synthesis of mevalonate from
CoA The first step is the condensation of two molecules of
acetyl-CoA to form acetoacetyl-acetyl-CoA In the next reaction, acetyl-acetyl-CoA and
acetoacetyl-CoA join to form 3-hydroxy-3-methylglutaryl-CoA, which is
abbreviated HMG-CoA, in a reaction catalyzed by HMG-CoA synthase
The third step in the pathway is the rate-limiting step in cholesterol
biosynthesis; HMG-CoA undergoes two NADPH-dependent reductions
to produce 3R -mevalonate Biosynthesis of squalene involves conversion
of mevalonate to isopentenyl pyrophosphate and dimethylallyl
pyro-phosphate Condensation of these two 5-carbon intermediates produces
geranyl pyrophosphate; addition of another 5-carbon isopentenyl group
gives farnesyl pyrophosphate Both steps in the production of farnesyl
pyrophosphate occur with release of pyrophosphate, hydrolysis of which
drives these reactions forward Two farnesyl pyrophosphates join to
pro-duce squalene Squalene monooxygenase converts squalene to
squalene-2,3-epoxide A second ER membrane enzyme produces lanosterol, and
another 20 steps are required to convert lanosterol to cholesterol
24.5 How Are Lipids Transported Throughout the Body? Most lipids
circulate in the body in the form of lipoprotein complexes Simple,
un-esterified fatty acids are merely bound to serum albumin and other
pro-teins in blood plasma, but phospholipids, triacylglycerols, cholesterol, and cholesterol esters are all transported in the form of lipoproteins At various sites in the body, lipoproteins interact with specific receptors and enzymes that transfer or modify their lipid cargoes
24.6 How Are Bile Acids Biosynthesized? The formation of bile salts represents the major pathway for cholesterol degradation The first step involves hydroxylation at C-7 7-Hydroxylase is a mixed-function
oxi-dase involving cytochrome P- 450 Mixed-function oxioxi-dases use O2 as substrate One oxygen atom goes to hydroxylate the substrate while the other is reduced to water The function of cytochrome P- 450 is to acti-vate O2for the hydroxylation reaction Such hydroxylations are quite common in the synthetic routes for cholesterol, bile acids, and steroid hormones and also in detoxification pathways for aromatic compounds
24.7 How Are Steroid Hormones Synthesized and Utilized? Biosyn-thesis of steroid hormones begins with the desmolase reaction, which converts cholesterol to pregnenolone Desmolase activity includes two hydroxylases and utilizes cytochrome P-450 Pregnenolone is trans-ported from the mitochondria to the ER, where a hydroxyl oxidation and migration of the double bond yield progesterone Progesterone is also the precursor for synthesis of the sex hormone steroids and the cor-ticosteroids Testosterone is an androgen synthesized in males primarily
in the testes -Estradiol is the most prominent estrogen Aldosterone,
the most potent of the mineralocorticoids, is involved in the regulation
of sodium and potassium balances in tissues
PROBLEMS
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chapter at www.cengage.com/login
1.Carefully count and account for each of the atoms and charges in
the equations for the synthesis of palmitoyl-CoA, the synthesis of
malonyl-CoA, and the overall reaction for the synthesis of
palmitoyl-CoA from acetyl-palmitoyl-CoA
2.(Integrates with Chapters 18 and 19.) Use the relationships shown
in Figure 24.1 to determine which carbons of glucose will be
in-corporated into palmitic acid Consider the cases of both citrate
that is immediately exported to the cytosol following its synthesis
and citrate that enters the TCA cycle
3.Based on the information presented in the text and in Figures 24.4
and 24.5, suggest a model for the regulation of acetyl-CoA
carboxy-lase Consider the possible roles of subunit interactions,
phospho-rylation, and conformation changes in your model
4.Consider the role of the pantothenic acid groups in animal
FAS and the size of the pantothenic acid group itself, and estimate
a maximal separation between the malonyl transferase and the
-ketoacyl-ACP synthase active sites.
5.Carefully study the reaction mechanism for the stearoyl-CoA
desat-urase in Figure 24.14, and account for all of the electrons flowing
through the reactions shown Also account for all of the hydrogen
and oxygen atoms involved in this reaction, and convince yourself
that the stoichiometry is correct as shown
6.Write a balanced, stoichiometric reaction for the synthesis of
phos-phatidylethanolamine from glycerol, fatty acyl-CoA, and
ethanol-amine Make an estimate of the G° for the overall process.
7.Write a balanced, stoichiometric reaction for the synthesis of
cho-lesterol from acetyl-CoA
8.Trace each of the carbon atoms of mevalonate through the
synthe-sis of cholesterol, and determine the source (that is, the position in
the mevalonate structure) of each carbon in the final structure
9.Suggest a structural or functional role for the O -linked saccharide
domain in the LDL receptor (Figure 24.40)
10. Identify the lipid synthetic pathways that would be affected by ab-normally low levels of CTP
11. Determine the number of ATP equivalents needed to form palmitic acid from acetyl-CoA (Assume for this calculation that each NADPH is worth 3.5 ATPs.)
12. Write a reasonable mechanism for the 3-ketosphinganine synthase reaction, remembering that it is a pyridoxal phosphate–dependent reaction
13. Why is the involvement of FAD important in the conversion of stearic acid to oleic acid?
14. Write a suitable mechanism for the HMG-CoA synthase reaction What is the chemistry that drives this condensation reaction?
15. Write a suitable reaction mechanism for the -ketoacyl-ACP
syn-thase, showing how the involvement of malonyl-CoA drives this reaction forward
16. In the FAS megasynthase structures, the multiple functional sites must lie within reach of the ACP and its bound acyl group sub-strates Examine the mammalian FAS structure (see Figure 24.11) and determine the distances between the various functional sites You could approach this problem either by using a molecular
mod-eling program (such as PyMol at www.pymol.org) or by consulting
appropriate references (the following end-of-chapter reference is a good place to start: Maier, T., Leibundgut, M., and Ban, N., 2008
Science 321:1315–1322) You should convince yourself, with
quanti-tative arguments, that the intersite distances can be traversed ap-propriately by the ACP group
17. In the LDL receptor structure shown in Figure 24.41c, the
-propellor interaction with domains R4 and R5 is partly stabilized
by salt bridges between acidic residues on R4 and R5 that also coordinate Ca2ions Use a molecular modeling program or con-sult the literature to identify at least two such interactions Two
suit-able references are Beglova, N., and Blacklow, S C., 2005 Trends in
Biochemical Sciences 30:309–316; and Rudenko, G., Henry, L., et al.,
2002 Science 298:2353–2358.
Trang 4766 Chapter 24 Lipid Biosynthesis
18. Insights into the function of LDL receptors in displacing LDL
par-ticles in endosomes have come from an unlikely source: a study of
LDL receptor binding by a human rhinovirus HRV2 (a common
cold virus) Consult suitable references to learn how this study
pro-vided support for the model of LDL particle displacement
pre-sented in this chapter Good references are Blacklow, S C., 2004
Nature Structural and Molecular Biology 11:388–390; Verdaguer, N.,
Fita, I., et al., 2004 Nature Structural and Molecular Biology 11:
429–434; and Beglova, N., and Blacklow, S C., 2005 Trends in
Bio-chemical Sciences 30:309–316.
Preparing for the MCAT Exam
19.Consider the synthesis of linoleic acid from palmitic acid and iden-tify a series of three consecutive reactions that embody chemistry similar to three reactions in the tricarboxylic acid cycle
20.Rewrite the equation in Section 24.1 to describe the synthesis of be-henic acid (see Table 8.1)
FURTHER READING
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biol-ogy Nature Genetics 40:129–130.
Ohlrogge, J., and Browse, J., 1995 Lipid biosynthesis Plant Cell
7:957–970
Smith, W L., 2007 Nutritionally essential fatty acids and biologically
in-dispensable cyclooxygenases Trends in Biochemical Sciences 33:27–37.
Vance, D E., and Vance, J E., 2008 Biochemistry of Lipids, Lipoproteins
and Membranes, 5th ed., Amsterdam: Elsevier.
Wolfgang, M J., and Lane, M D., 2006 The role of hypothalamic
malonyl-CoA in energy homeostasis Journal of Biological Chemistry
281:37265–37269
Acetyl-CoA Carboxylase
Bilder, P., Lightle, S., et al., 2006 The structure of the
carboxyltrans-ferase component of acetyl-CoA carboxylase reveals a zinc-binding
motif unique to the bacterial enzyme Biochemistry 45:1712–1722.
Cho, Y S., Lee, J I., et al., 2007 Crystal structure of the biotin
carboxy-lase domain of human acetyl-CoA carboxycarboxy-lase 2 Proteins 70:
268–272
Munday, M R., 2002 Regulation of mammalian acetyl-CoA carboxylase
Biochemical Society Transactions 30:1059–1064.
Tong, L., 2005 Acetyl-coenzyme A carboxylase: Crucial metabolic
en-zyme and attractive target for drug discovery Cellular and Molecular
Life Sciences 62:1784–1803.
Tong, L., and Harwood, H J., Jr., 2006 Acetyl-coenzyme A carboxylases:
Versatile targets for drug discovery Journal of Cellular Biochemistry
99:1476–1488
Zhang, H., Tweel, B., et al., 2004a Crystal structure of the
carboxyl-transferase domain of acetyl-coenzyme A carboxylase in complex
with CP-640186 Structure 12:1683–1691.
Zhang, H., Tweel, B., et al., 2004b Molecular basis for the inhibition of
the carboxyltransferase domain of acetyl-coenzyme A carboxylase by
haloxyfop and diclofop Proceedings of the National Academy of Sciences
U.S.A 101:5910–5915.
Zhang, H., Yang, Z., et al., 2003 Crystal structure of the
carboxyl-transferase domain of acetyl-coenzyme A carboxylase Science 299:
2064–2067
Fatty Acid Metabolism
Asturias, F J., Chadick, J Z., et al., 2005 Structure and molecular
orga-nization of mammalian fatty acid synthase Nature Structural and
Molecular Biology 12:225–232.
Jakobsson, A., Westerberg, R., et al., 2006 Fatty acid elongases in
mam-mals: Their regulation and roles in metabolism Progress in Lipid
Re-search 45:237–249.
Jenni, S., Leibundgut, M., et al., 2007 Structure of fungal fatty acid
syn-thase and implications for iterative substrate shuttling Science 316:
254–261
Jump, D B., 2002 The biochemistry of n-3 polyunsaturated fatty acids.
Journal of Biological Chemistry 277:8755–8758.
Kim, H.-Y., 2007 Novel metabolism of docosahexaenoic acid in neural
cells Journal of Biological Chemistry 282:18661–18665.
Kresge, N., Simoni, R D., et al., 2006 Salih Wakil’s elucidation of the
animal fatty acid synthetase complex architecture Journal of
Biologi-cal Chemistry 281:e5–e7.
Leibundgut, M., Jenni, S., et al., 2007 Structural basis for substrate
de-livery by acyl carrier protein in the yeast fatty acid synthase Science
316:288–290
Maier, T., Jenni, S., and Ban, N., 2006 Architecture of mammalian fatty
acid synthase at 4.5Å resolution Science 311:1258–1262.
Maier, T., Leibundgut, M., and Ban, N., 2008 The crystal structure of a
mammalian fatty acid synthase Science 321:1315–1322.
Reshef, L., Olswang, Y., et al., 2003 Glyceroneogenesis and the
trigly-ceride/fatty acid cycle Journal of Biological Chemistry 278:30413–30416 Riezman, H., 2007 The long and short of fatty acid synthesis Cell 130:
587–588
Simard, J R., Zunszain, P A., et al., 2005 Locating high-affinity fatty acid–binding sites on albumin by X-ray crystallography and NMR
spectroscopy Proceedings of the National Academy of Sciences U.S.A 102:
17958–17963
Smith, S., and Tsai, S-C., 2007 The type I fatty acid and polyketide
syn-thases: A tale of two megasynthases Natural Product Reports 24:
1041–1072
White, S W., Zheng, J., et al., 2005 The structural biology of type II fatty
acid biosynthesis Annual Review of Biochemistry 74:791–831.
Zhang, Y.-M., White, S W., et al., 2006 Inhibiting bacterial fatty acid
syn-thesis Journal of Biological Chemistry 281:17541–17544.
Function and Synthesis of Eicosanoids and Essential Fatty Acids
Grosser, T., Fries, S., et al., 2006 Biological basis for the cardiovascular consequences of COX-2 inhibition: Therapeutic challenges and
op-portunities Journal of Clinical Nutrition 116:4–15.
Hunter, W N., 2007 The non-mevalonate pathway of isoprenoid
pre-cursor biosynthesis Journal of Biological Chemistry 282:21573–21577.
Kresge, N., Simoni, R D., et al., 2006 The prostaglandins, Sune
Bergström and Bengt Samuelsson Journal of Biological Chemistry
281:e9–e11
Kurumbail, R G., Stevens, A M., et al., 1996 Structural basis for
selec-tive inhibition of cyclooxygenase-2 by anti-inflammatory agents
Na-ture 384:644–648.
Lands, W E., 1991 Biosynthesis of prostaglandins Annual Review of
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276:37547–37555
Marszalek, J R., and Lodish, H F., 2005 Docosahexaenoic acid, fatty acid–interacting proteins, and neuronal function: Breastmilk and
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in-dispensable cyclooxygenases Trends in Biochemical Sciences 33:27–37.
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Jour-nal of Biological Chemistry 282:11613–11617.
Trang 5Phospholipid and Triacylglycerol Synthesis
Carman, G M., and Henry, S A., 1989 Phospholipid biosynthesis in
yeast Annual Review of Biochemistry 58:635–669.
Carman, G M., and Henry, S A., 2007 Phosphatidic acid plays a central
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37293–37297
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phos-phatidylcholine in bacteria Progress in Lipid Research 42:115–162.
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Biological Chemistry 283:1773–1777.
Structure and Function of Lipoproteins and Their Receptors
Beglova, N., and Blacklow, S C., 2005 The LDL receptor: How acid
pulls the trigger Trends in Biochemical Sciences 30:309–316.
Blacklow, S C., 2004 Catching the common cold Nature Structural and
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Trang 6© Royalty-Free/CORBIS
25 Nitrogen Acquisition and
Amino Acid Metabolism
Amino acids and nucleotides, as well as their polymeric forms (proteins and nucleic acids), are nitrogen-containing molecules upon which cell structure and function rely How do these various organic forms of nitrogen arise? As we look at these com-pounds, an obvious feature is that nitrogen atoms are typically bound to carbon and/or hydrogen atoms That is, the nitrogen atom is in a reduced state On the other hand, the prevalent forms of nitrogen in the environment are inorganic and oxidized; N2(dinitrogen gas) and NO3 (nitrate ions) being the principal species The two principal routes for nitrogen acquisition from the inanimate environment, nitrate assimilation and nitrogen fixation, lead to formation of ammonium ions (NH4 ) Reactions that incorporate NH4 into organic linkage (the reactions of am-monium assimilation) follow Among these, glutamine synthetase merits particular attention because it conveys several important lessons in metabolic regulation This chapter presents the pathways of amino acid biosynthesis and degradation; those in-volving the sulfur-containing amino acids provide an opportunity to introduce as-pects of sulfur metabolism.
on Inorganic Forms of Nitrogen?
Nitrogen Is Cycled Between Organisms and the Inanimate Environment
Nitrogen acquisition by biological systems is accompanied by its reduction to am-monium ion (NH4 ) and the incorporation of NH4 into organic linkage as amino
or amido groups (Figure 25.1) The reduction of NO3 to NH4 occurs in green plants, various fungi, and certain bacteria in a two-step metabolic pathway known
as nitrate assimilation The formation of NH4 from N2gas is termed nitrogen
fix-ation. N2fixation is an exclusively prokaryotic process, although bacteria in symbi-otic association with certain green plants also carry out nitrogen fixation No ani-mals are capable of either nitrogen fixation or nitrate assimilation, so they are totally dependent on plants and microorganisms for the synthesis of organic ni-trogenous compounds, such as amino acids and proteins, to satisfy their require-ments for this essential element.
Animals release excess nitrogen in a reduced form, either as NH4 or as organic nitrogenous compounds such as urea The release of N occurs both during life and
as a consequence of microbial decomposition following death Various bacteria re-turn the reduced forms of nitrogen back to the environment by oxidizing them The oxidation of NH4 to NO3 by nitrifying bacteria, a group of
chemoau-totrophs, provides the sole source of chemical energy for the life of these microbes Nitrate nitrogen also returns to the atmosphere as N as a result of the metabolic
Soybeans Only plants and certain microorganisms are
able to transform the oxidized, inorganic forms of
nitrogen available in the inanimate environment into
reduced, biologically useful forms Soybean plants can
meet their nitrogen requirements both by
assimilat-ing nitrate and, in symbiosis with bacteria, fixassimilat-ing N2
I was determined to know beans.
Henry David Thoreau (1817–1862)
The Writings of Henry David Thoreau, vol 2,
p 178, Houghton Mifflin (1906)
KEY QUESTIONS
25.1 Which Metabolic Pathways Allow
Organisms to Live on Inorganic Forms
of Nitrogen?
25.2 What Is the Metabolic Fate of Ammonium?
25.3 What Regulatory Mechanisms Act on
Escherichia coli Glutamine Synthetase?
25.4 How Do Organisms Synthesize Amino
Acids?
25.5 How Does Amino Acid Catabolism Lead
into Pathways of Energy Production?
ESSENTIAL QUESTIONS
Nitrogen is an essential nutrient for all cells Amino acids provide nitrogen for the synthesis of other nitrogen-containing biomolecules Excess amino acids in the diet can be converted into -keto acids and used for energy production.
What are the biochemical pathways that form ammonium from inorganic nitro-gen compounds prevalent in the inanimate environment? How is ammonium incorporated into organic compounds? How are amino acids synthesized and degraded?
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Trang 7activity of denitrifying bacteria These bacteria are capable of using NO3 and
sim-ilar oxidized inorganic forms of nitrogen as electron acceptors in place of O2in
energy-producing pathways The NO3 is reduced ultimately to dinitrogen (N2).
These bacteria thus deplete the levels of combined nitrogen, that is, N joined with
other elements in chemical compounds Combined nitrogen is important as
nat-ural fertilizer However, the denitrifying activity of bacteria is exploited in water
treatment plants to reduce the load of combined nitrogen that might otherwise
enter lakes, streams, and bays.
Nitrate Assimilation Is the Principal Pathway for Ammonium
Biosynthesis
Nitrate assimilation occurs in two steps: the two-electron reduction of nitrate to
ni-trite, catalyzed by nitrate reductase (Equation 25.1), followed by the six-electron
reduction of nitrite to ammonium, catalyzed by nitrite reductase (Equation 25.2).
(1) NO3 2 H 2 e⎯⎯→ NO2 H2O (25.1) (2) NO2 8 H 6 e⎯⎯→ NH4 2 H2O (25.2) Nitrate assimilation is the predominant means by which green plants, algae, and
many microorganisms acquire nitrogen The pathway of nitrate assimilation
ac-counts for more than 99% of the inorganic nitrogen (nitrate or N2) assimilated
into organisms.
Nitrate Reductase Contains Cytochrome b557and Molybdenum Cofactor
A pair of electrons is transferred from NADH via enzyme-associated sulfhydryl
groups, FAD, cytochrome b557, and MoCo (an essential molybdenum-containing
cofactor) to nitrate, reducing it to nitrite The brackets [ ] denote the
protein-bound prosthetic groups that constitute an e transport chain between NADH
and nitrate Nitrate reductases typically are cytosolic 220-kD dimeric proteins.
The structure of the molybdenum cofactor (MoCo) is shown in Figure 25.2a.
Molybdenum cofactor is necessary for both nitrate reductase activity and the
as-sembly of nitrate reductase subunits into the active dimeric holoenzyme form.
Molybdenum cofactor is also an essential cofactor for a variety of enzymes that
catalyze hydroxylase-type reactions, including xanthine dehydrogenase, aldehyde
oxidase, and sulfite oxidase.
(25.3)
NADH
NO3
NO2
[ SH FAD cytochrome b557 MoCo]
N2
Organic N
NH4+
NO–2
NO3–
NO– 2
NO
N2O
Nitrate respiration
(dissimilation)
Nitrogen fixa
tion
assimilatio
Nitrate
Nitrifiction
Denitrification
Aerobic
Anaerobic
FIGURE 25.1 The nitrogen cycle Organic nitrogenous compounds are formed by the incorporation of NH4
into carbon skeletons Note that denitrification and nitrogen fixation are anaerobic processes
Corn nitrate reductase cytochrome domain (FAD shown in yellow) (pdb id = 1CNE)
Fungal nitrate reductase molybdenum cofactor domain (Mo cofactor in gold)
(pdb id = 2BIH)
Nitrate reductase has two structural domains, the
cyto-chrome b domain (top) and the molybdenum cofactor domain (bottom).
Trang 8770 Chapter 25 Nitrogen Acquisition and Amino Acid Metabolism
Nitrite Reductase Contains Siroheme Six electrons are required to reduce NO2
to NH4 Nitrite reductases in photosynthetic organisms obtain these electrons from six molecules of photosynthetically reduced ferredoxin (Fdred).
Photosynthetic nitrite reductases are 63-kD monomeric proteins having a
tetranuclear iron–sulfur cluster and a novel heme, termed siroheme, as
pros-thetic groups The [4Fe-4S] cluster and the siroheme act as a coupled etransfer center Nitrite binds directly to siroheme, providing the sixth ligand, much as O2 binds to the heme of hemoglobin Nitrite is reduced to ammonium while lig-anded to siroheme The structure of siroheme is shown in Figure 25.2b.
In higher plants, nitrite reductase is found in chloroplasts, where it has ready ac-cess to its primary reductant, photosynthetically reduced ferredoxin Microbial ni-trite reductases closely resemble nitrate reductases in having essential OSH groups and FAD prosthetic groups to couple enzyme-mediated NADPH oxidation to nitrite reduction (Figure 25.3).
(25.4)
Light 6 Fdred
6 Fdox
NO2
NH4 [(4Fe-4S) siroheme]
COOH
Fe
COOH
COOH COOH
COOH
H3C COOH
HOOC
H3C HOOC
O
H2N
HN
H
H N
Mo
CHOH CH2OPO3–
FIGURE 25.2 The novel prosthetic groups of nitrate reductase and nitrite reductase (a) The molybdenum
cofactor of nitrate reductase (b) Siroheme, an essential prosthetic group of nitrite reductase Siroheme is
novel among hemes in having eight carboxylate-containing side chains These carboxylate groups may act
as Hdonors during the reduction of NO2 to NH4
Sequence Organization of the Nitrate Assimilation Enzymes
Plant and Fungal Nitrate Reductases (~200-kD homodimers) N-term MoCo/NO3– hinge cytochrome b hinge FAD NAD(P)H
Plant Nitrite Reductases (63-kD monomers)
e– donor FeS-siroheme/NO2–
473 518 566 Fungal Nitrite Reductases
(~250-kD homodimers)
FAD NAD(P)H Cys-rich FeS-siroheme/NO2–
26 60 183 215 496 600 715 763 1176
FIGURE 25.3 Domain organization within the enzymes of nitrate assimilation The numbers denote residue number along the amino acid sequence of the proteins
Spinach nitrite reductase (iron-sulfur
cluster in gold, siroheme in red)
(pdb id = 2AKJ)
Trang 9Organisms Gain Access to Atmospheric N2Via the Pathway
of Nitrogen Fixation
Nitrogen fixation involves the reduction of nitrogen gas (N2) via an enzyme system
found only in prokaryotic cells The heart of the nitrogen fixation process is the
en-zyme known as nitrogenase, which catalyzes the reaction
N2 10 H 8 e⎯⎯→ 2 NH4 H2 (25.5) Note that an obligatory reduction of two protons to hydrogen gas accompanies the
biological reduction of N2to ammonia Less than 1% of the inorganic N
incorpo-rated into organic compounds by organisms can be attributed to nitrogen fixation;
however, this process is the only way that organisms can tap into the enormous
reservoir of N2in the atmosphere.
Although nitrogen fixation is exclusively prokaryotic, N2-fixing bacteria may be
either free-living or living as symbionts with higher plants For example, Rhizobia are
bacteria that fix nitrogen in symbiotic association with soybeans and other
legumi-nous plants Because nitrogen in a metabolically useful form is often the limiting
nutrient for plant growth, such symbiotic associations can be an important factor in
plant growth and agriculture.
Despite the wide diversity of bacteria in which nitrogen fixation takes place, all
N2-fixing systems are nearly identical and all have four fundamental requirements:
(1) the enzyme nitrogenase; (2) a strong reductant, such as reduced ferredoxin;
(3) ATP; and (4) O2-free conditions In addition, several modes of regulation act to
control nitrogen fixation.
The Nitrogenase Complex Is Composed of Two Metalloproteins Two
metallopro-teins constitute the nitrogenase complex: the Fe-protein or nitrogenase reductase
and the MoFe-protein, which is another name for nitrogenase Nitrogenase
reduc-tase is a 60-kD homodimer possessing a single [4Fe-4S] cluster as a prosthetic group.
Nitrogenase reductase is extremely O2sensitive Nitrogenase reductase binds MgATP
and hydrolyzes two ATPs per electron transferred during nitrogen fixation Because
reduction of N2to 2 NH4 H2requires 8 electrons, 16 ATPs are consumed per N2
reduced.
This ATP requirement seems paradoxical because the reaction is
thermody-namically favorable: The Ᏹo for the reaction (N2 8 e 10 H→ 2 NH4
H2) is –0.314 V Ferredoxin, the most common edonor for nitrogen fixation, has
an Ᏹo that is more negative (see Table 20.1) The solution to the paradox is found
in the very strong bonding between the two N atoms in N2(Figure 25.4)
Sub-stantial energy input is needed to overcome this large activation energy and break
the NqN triple bond In this biological system, the energy is provided by ATP.
+
e –
8 10 H+ + N N 2 NH4+ + H2
N N
2 NH3
Very high energy
of activation
–ΔG
Reaction coordinate
FIGURE 25.4 The triple bond in N2must be broken dur-ing nitrogen fixation
Trang 10772 Chapter 25 Nitrogen Acquisition and Amino Acid Metabolism
Nitrogenase, the MoFe-protein, is a 240-kD 22-type heterotetramer An
-dimer serves as the functional unit, and each -dimer contains two types of
metal centers: an unusual 8Fe-7S center known as the P-cluster (Figure 25.5a) and the novel 7Fe-1Mo-9S cluster known as the FeMo-cofactor (Figure 25.5b) Nitroge-nase under unusual circumstances may contain an iron ⬊vanadium cofactor instead
of the molybdenum-containing one Like nitrogenase reductase, nitrogenase is very oxygen labile.
The Nitrogenase Reaction In the nitrogenase reaction (Figure 25.6), electrons from reduced ferredoxin pass to nitrogenase reductase, which serves as electron donor to nitrogenase, the enzyme that actually catalyzes N2fixation Electron trans-fer from nitrogenase reductase to nitrogenase takes place through docking of ni-trogenase reductase with an -subunit pair of nitrogenase (Figure 25.7) Nitroge-nase reductase transfers eto nitrogenase one electron at a time N2is bound within the FeMo-cofactor metal cluster until all electrons and protons are added; no free intermediates, such as HNPNH or H2NONH2are released Electron transfer takes place in the following sequence: Fe-protein → P-cluster → FeMo-cofactor → N2 ATP hydrolysis is coupled to the transfer of an electron from the Fe-protein to the P-cluster ATP hydrolysis leads to conformational change in the nitrogenase
reduc-(b)
Homocitrate
Cys275
His442
Cys88
Cys95
Cys70
Cys154
Cys153
Ser188
Cys62
(a)
FIGURE 25.5 Structures of the two types of metal
clus-ters found in nitrogenase (a) The P-cluster consists of
two Fe4S3clusters that share an S atom (b) The
FeMo-cofactor contains 1 Mo, 7 Fe, and 9 S atoms Homocitrate
provides two oxo ligands to the Mo atom.(Adapted from
Leigh, G J., 1995 The mechanism of dinitrogen reduction by
molybdenum nitrogenases European Journal of Biochemistry
229:14–20.)
e –
H2 Pyruvate
h
Reduced ferredoxin
Nitrogenase reductase (Fe-S) 16
+ 16 P
Nitrogenase (Fe-S, FeMoCo)
N2 + 10 H+
2 NH4 + H2
8
ATP 16 ADP
NADH
+
FIGURE 25.6 The nitrogenase reaction Depending on
the bacterium, electrons for N2reduction may come
from light, NADH, hydrogen gas, or pyruvate The
pri-mary edonor for the nitrogenase system is reduced
ferredoxin