I.  Nitrogen Cycle
  A.  Nitrogen Sources (Cyclic Salts)
    1.  RAIN: Ammonium (NH4+), Nitrate (NO3-) 
    2.  Industrial Burning, Volcanic Activity, Forest Fires: (NH4+)
    3.  Oxidation of N2 by O2 or ozone in the presence of lightning
or ultraviolet radiation: (NO3-) 4. Ocean aerosols B. 90% of the total nitrogen in soils may be in organic matter. 1. Nitrogen reservoir from which NH4+ and NO3- arise. 2. Manure, dead plants, microorganisms, animals are important
sources of nitrogen returned to the soil. 3. Most of this nitrogen is insoluble. Not immediately available
for the plant. C. Ammonification: conversion of organic nitrogen to NH4+ by soil
bacteria & fungi 1. Cool temperatures., various pH 2. Warm, moist soils: near neutral pH D. Nitrification: NH4+ is oxidized by bacteria to nitrite (NO2-)
and NO3- 1. Nitrosomonas: oxidation of ammonia to nitrite 2. Nitrobacter: reduce nitrite to nitrate a. cold, acidic, or hypoxic soils: nitrifying bacteria are less
effective b. NH4+ becomes a more important nitrogen source than NO3-: arctic soils and anaerobic bogs. c. Forest trees absorb NH4+ because of the low pH common to
forest soils d. Positive Charge: NH4+ is absorbed to soil colloids whereas
NO3- is not absorbed and is much more readily leached. E. Denitrification: N2, NO, H2O, and NO2 are formed from NO3- by
anaerobic bacteria F. Oxidized forms of nitrogen in the atmosphere are important
ecologically because when converted to NO3- they contribute
HNO3 to acidic rainfall (acid rain) II. Nitrogen Fixation A. Plants require nitrogen to produce proteins, nucleic acids and
other organic molecules. B. The nitrogen cannot be in gaseous form for plant use, but must
be in the form of ammonium (NH4+) or nitrate (NO3-) C. Nitrogen fixation = The process of converting atmospheric nitrogen
(gaseous state) to nitrogenous compounds that can be directly used by plants (nitrate or ammonia). 1. The process is catalyzed by the enzyme nitrogenase: nitrogenase N2+ 6H+ + 6e- 2NH3 2. Some soil bacteria possess nitrogenase. 3. Very energy consuming process, costing the bacteria at least
12 ATPs for each ammonia molecule synthesized. 4. In the soil, ammonia is converted to the ammonium ion which
plants can absorb: NH3 + H+ NH4+ 5. Plants acquire most of their nitrogen in the form of nitrate
(NO3 which is produced in soil by nitrifying bacteria that
oxidize ammonium. B. Symbiotic Nitrogen Fixation 1. Legumes (e.g. peas, beans, soybeans, peanuts, alfalfa, clover)
have a built-in source of fixed nitrogen because their roots
have nodules. 2. Nodules = Root swellings composed of plant cells that contain
nitrogen-fixing bacteria of the genus Rhizobium. 3. Nodules form as follows: a. Root hairs curl to prepare for bacterial infection after
recognizing a specific molecular tag on the bacterial surface. (Each legume is associated with a particular Rhizobium species.) b. Bacteria enter root through an "infection thread" that carries
them to the root cortex. c. Bacteria become enclosed in vesicles and assume a form called
bacteroids. d. Bacteroids produce a chemical that induces the host's cells to
divide and form a nodule. 4. This association is mutualistic; the bacteria supplies fixed
nitrogen, and the plant supplies carbohydrates and other
organic compounds. 5. Leghemoglobin = An iron-containing protein that binds oxygen. a. The plant and the bacteroids each make a part of the molecule. b. Releases oxygen for the intense respiration needed to produce
ATP for nitrogen fixation. c. Keeps the free oxygen concentration low in root nodules so
that the oxygen cannot inhibit the function of nitrogenase. 6. The basis for crop rotation is that, under favorable conditions,
root nodules fix more nitrogen than the legume uses. The
excess is secreted into the soil. a. One year a nonlegume crop is planted, and the next year a
legume is planted to restore the fixed nitrogen content of the soil. b. Legume may be plowed under to further increase the fixed
nitrogen content of the soil. 7. Some non-legumes host nitrogen-fixing symbionts. a. Alders and tropical grasses may host nitrogen-fixing
actinomycetes. b. Rice farms culture a fern (Azolla),containing symbiotic
nitrogen-fixing cyanobacteria, with the rice. III. Assimilation of Nitrate and Ammonium Ions A. Sites of Nitrate Assimilation 1. Most NO3- reduction occurs at the site (roots or shoots) at which
the most nitrate reductase activity occurs. 2. Plants do not translocate detectable amounts of NH4+ to the shoots.
Transport large quantities of organic nitrogen compounds derived
from NH4+, especially amino acids and amides. 3. Reduction of NO3- in the roots cannot keep pace with transport to
the shoots. Reduction then occurs in leaves and stems, especially during sunny days. B. Processes of Nitrate Reduction 1. NO3- + 8 e- + 10H+ Þ NH4+ + 3H2O 2. Use of H+ causes the cell pH to rise 3. About half of the H+ are neutralized when NH4+ is subsequently
converted into protein because that process releases one H+ for each nitrogen atom involve. 4. Nitrate reduction occurs in two distinct reactions catalyzed
by different enzymes. a. Nitrate Reductase (NR) NO3- + NADH + H+ => NO2- + NAD+ + H2O b. occurs in the cytosol c. NR activity controls the rate of protein synthesis in plants
that absorb NO3- as the major nitrogen source. NR is affected by several factors including the rate of synthesis and the
rate of degradation of the enzyme d. Light also increases NR activity when NO3- is available. C. Reduction of Nitrite to Ammonium Ions 1. Second reaction of the overall process of nitrate reduction
involves conversion of nitrite to NH4+. Nitrite transported into chloroplasts in leaves or into proplastides in roots. 2. Catalyzed by Nitrite Reductase. D. Conversion of Ammonium into Organic Compounds 1. Whether NH4+ is absorbed directly from the soil or produced by
energy-dependent nitrogen fixation or NO3- reduction, it does not accumulate anywhere in the plant. 2. Toxic: inhibits ATP formation, uncoupling agent. 3. NH4+ seems to be converted first into the amide group of
glutamine. This conversion and other reactions leading to
glutamic acid, aspartic acid, and asparagine. E. Transamination 1. glutamate transfers its amino group directly to a variety of
a-keto acids in several reversible transamination reactions 2. all transaminations involve freely reversible donation of an
alpha-amino group from one amino acid to the alpha-keto group
of an alpha-keto acid, accompanied by formation of a new amino acid and a new alpha-keto acid. IV. Photorespiratory Nitrogen Cycle A. For every CO2 released during photorespiration, an equivalent molar
amount of NH4+ is released from glycine, and this NH4+ must be
recaptured into organic combination B. Photorespiratory nitrogen cycle C. Three organelles are involved (chloroplast, peroxisomes, and
mitochondria) Traffic to and from via the cytosol. V. Nitrogen Transformations During Plant Development A. Nitrogen Metabolism of Germinating Seeds 1. In storage cells in all kinds of seeds, the reserve proteins are
deposited in membrane bound structures called protein bodies. 2. Phytin 3. Imbibition of water by a dry seed sets off a variety of chemical
reactions that lead to germination (radicle protrusion through
the seed coat) and subsequent seedling development. Proteins
in protein bodies are hydrolyzed by proteinases (proteases) and pepetidases to amino acids and amides. 4. Membranes surrounding disintegrating protein bodies are not
destroyed: rather they fuse to form the tonoplast around the
growing central vacuole. B. Movement of Nitrogen Compounds During Vegetative and
Reproductive Stages 1. In herbaceous plants there is extensive recirculation of nitrogen
from roots to leaves and back. 2. Changes largely reflect degradation and synthesis of proteins
because most of the nitrogen in any plant part is in protein 3. One of the major leaf proteins that contains this nitrogen is
the abundant photosynthetic enzyme RuBisCo. Photosynthetic
activity decreases considerably during fruit and seed production in essentially all crops because RuBisCo is
hydrolyzed by proteinases. 4. In cereal grains and many other annuals that do not fix N2,
transfer of nitrogen from vegetative parts to seeds is sometimes
more extensive than in legumes. Even through their seeds contain
lower percentages of protein than do legume seeds. 5. Transport of nitrogen from vegetative organs occurs partly at the
expense of RuBisCo degradation. This degradation is more of a growth limitation in C3 plants then C4 plants because use C4
plants contain only about 10% as much of this enzyme as C3 plants. 6. In perennial herbaceous plants, much of the nitrogen and other
elements that are mobile in the phloem moves into the crown
and roots after seed demands are satisfied. These elements are
available for the next season's growth. Decay of dead plant
parts returns less to the soil than otherwise would have occurred. 7. RNA molecules are degraded in mature and senescing leaves and in
seed storage tissues by Ribonucleases. VI. Assimilation of Sulfate A. SO42- absorbed by roots provides the necessary sulfur for plant growth. SO42- + ATP + 8 e- + 8 H+ => S2- + 4 H2O + AMP + PPi Sulfate reduction occurs in both roots and shoots of some species,
but most of the sulfur transported in the xylem to the leaves is
in nonreduced SO42-. Some transport back to roots and to other parts
of the plant occurs through phloem, and both free SO42- and organic
sulfur compounds are transported. Entire process occurs in
chloroplast. In roots occurs in proplastids. B. First step of SO42- assimilation in all cells is reaction of SO42-
with ATP, producing adenosine-5'-phosphosulfate (APS) and pyrophosphate (ppi). The enzyme involved is ATP sulfurylase. C. APS sulfotransferase creates glutathione which is a thioredoxin. D. APS does not accumulate, is rapidly converted into organic sulfur
compounds, especially cysteine and methionine. Most of the plant's sulfur (90%) is in cysteine or methionine of proteins, coenzyme A,
S-adenosylmethionine. E. S-adenosylmethionine helps form lignins and pectins of cell walls,
flavonoids such as the brightly colored anthocyanins, and chlorophylls; another importance is its role as a precursor of
the plant hormone ethylene. F. Sulfur is also found in mercaptans of onion, garlic and cabbage. G. Also H2S is released by trees when the reduced sulfur (cysteine)
supply of the leaf is already adequate, in daylight, when the SO42- supply is plentiful. VII. Improving the Protein Yield of Crops A. Most people depend mainly on plants for protein. B Ways in which to increase the protein content of plants are: 1. Plant breeding to create new varieties enriched in protein. a. Unfortunately these "super" varieties require very much
nitrogen in the form of commercial fertilizer too expensive
for many countries to afford. 2. Improving the productivity of symbiotic nitrogen fixation. a. Mutant strains of Rhizobium have been isolated that continue
to produce nitrogenase even after fixed nitrogen accumulates. b. Rhizobium varieties may be selected that fix N2 at a lower cost
in photosynthetic energy, yielding a higher total food content
in the plant. 3. Genetic Engineering a. May create varieties of Rhizobium that can infect nonlegumes. b. May transfer some genes required for nitrogen-fixation directly
into plant genomes, using bacterial plasmids as vectors. VIII. SOME NUTRITIONAL ADAPTATIONS OF PLANTS Modifications for nutrition have evolved among many plants. A. Parasitic Plants 1. Some arc photosynthetic but supplement nutrition by using
haustoria (not homologous to those of parasitic fungi) to absorb
from its host plant (e.g. mistletoe). 2. Some have ceased photosynthesis entirely, drawing all nutrients
from its host (e.g. dodder). 3. Epiphytes grow on the surface of other plants, anchored by roots,
but nourish themselves and are not parasitic. B. Carnivorous Plants 1. Live in habitats with poor soil conditions. 2. Are photosynthetic, but obtain some nitrogen and minerals by
killing and digesting insects. 3. Most insect traps evolved by modifications of leaves and usually
are equipped with glands that secrete digestive juices. C. Mycorrhizae: Symbiotic associations between plant roots and fungi.
The fungus either forms a sheath around the root or penetrates root tissue. 1. Helps the plant absorb water. 2. Absorbs minerals and may secrete acid that increases mineral
solubility and converts minerals to forms easily used by
the plant. 3. May help protect the plant against certain soil pathogens. 4. The plant nourishes the fungus with photosynthetic products. 5. Almost all plants are capable of forming mycorrhiza and
grow more vigorously when mycorrhiza are present.