The structure of a plant cell and organelles

American Society of Plant Biologists

Abstract
The phototropism is flavoprotein kinases that control phototropic bending,
light-induced chloroplast movement, and stomatal opening in plants. Two
Flavin mononucleotide binding light, oxygen, or voltage (LOV) domains are the
sites for initial photochemistry in these blue light photoreceptors. We have
determined the steady state, photo excited crystal structure of a Flavin-bound
LOV domain. The structure reveals a unique photochemical switch in the Flavin
binding pocket in which the absorption of light drives the formation of a
reversible covalent bond between a highly conserved Cys residue and the Flavin
cofactor. This provides a molecular picture of a cysteinyl-flavin covalent adduct,
the presumed signaling species that leads to phototropic kinase activation and
subsequent signal transduction. We identify closely related LOV domains in two
eubacterial proteins that suggests the light-induced conformational change
evident in this structure is an ancient biomolecular response to light, arising
before the appearance of plants.

A "MICROTUBULE" IN PLANT CELL FINE STRUCTURE

Abstract
This paper reports an electron microscope examination of the cortices of some
plant cells engaged in wall formation. Previous studies of similar material fixed
in OSO4 alone have disclosed discontinuities in the plasma membrane and
other evidence of inadequate fixation. After glutaraldehyde, used as a fixative
in this present study, the general preservation of cortical fine structure is
greatly improved. This is shown, for example, by the first evidence of slender
tubules, 230 to 270 A in diameter and of indeterminate length, in plant cells of
this type. They have been found in the cortical regions of cells of two
angiosperms and one gymnosperm, representing all the material so far studied
following this method of fixation. The tubules are identical in morphology to
those also observed here in the mitotic spindles of plant cells, except that the
latter have a somewhat smaller diameter. It is noted that the cortical tubules
are in a favored position to govern cytoplasmic streaming and to exert an
influence over the disposition of cell wall materials. In this regard it may be of
some significance that the tubules just beneath the surface of the protoplast
mirror the orientation of the cellulose micro fibrils of the adjacent cell walls.
Photosynthesis.
https://www.cabdirect.org/cabdirect/abstract/19700703082
Author(s) : RABINOWITCH, E.; GOVINDJEE.
Book : Photosynthesis 1969 pp.273 pp. ref.Bibl. 73
Abstract :
The authors' preface points out that advances in knowledge of photosynthesis
in the 15 years since Rabin witchs Photosynthesis and related processes (of
2000 pages and 3 volumes) have been so great that no one person could now
produce an up-to-date work of a similar nature. This book deals "more
modestly only with the physicochemical mechanism of the primary process in
photosynthesis and the enzymatic mechanisms closely associated with it. No
attempt is made to cover these topics exhaustively, to describe all the related
experiments, or to discuss the suggested physical and chemical hypotheses.
Instead, only the main lines are traced. On the other hand, a broad
introduction [is provided] by discussion of the basic physical and chemical
concepts relevant to the understanding of photosynthesis, such as energy,
entropy, free energy, bond strength and oxidation-reduction potentials. The
role of photosynthesis in the chemical household of the earth, in total yield,
the carbon and oxygen cycles in nature, the origin and evolution of life, and its
different modes-photoautotrophic, chemoautotrophic and heterotrophic [are
dealt with]." The authors hope the book will be suitable as an "introduction
into the field of photosynthesis for students of varying backgrounds-from
physics to plant physiology-and also for interested general readers and for
high-school students with advanced interests in biology." The book should
stand a very good chance of achieving this aim, provided the readers can
stomach its occasional lapses into a story-book style (there is a particularly rich
example on p. 44). Happily, the book is otherwise eminently readable and
explains many highly sophisticated ideas clearly and economically. As well as
the subjects already mentioned, chloroplast structure and function, the
photosynthetic pigments, absorption of light and energy transfer, the two
photochemical systems and their separation and, finally, enzymatic pathways
and phosphorylation, are dealt with. The final chapter considers future
developments, and poses some intriguing questions in doing so. The
bibliography is classified into books (18 between 1945 and 1968) symposia (22;
1935-69), reviews (24; 1958-68) and articles in Scientific American (5; 1948-65).
The authors are meticulous in crediting work to its original author, but
complete references are not given, presumably for reasons of length. There
are a few misprints, but none likely to confuse an intelligent reader. Paper and
binding are of very good quality, the diagrams and photographs are clear and
well reproduced, the index is adequate and the price not excessive for these
days. -R. D. Williams.
 Essential nutrients for plant growth
http://www.src.gov.jm/wp-content/uploads/2013/02/pnm3.pdf
This pdf site explains the nutrient functions of plants.

Essential Nutrients
There are 15 essential elements that plants must have in order to grow properly.
18 Essential Nutrients
Nutrient elements obtained from atmosphere through photosynthesis
o Hydrogen
o Carbon
o Oxygen
Nutrient elements obtained from the soil
o Nitrogen
o Phosphorus
o Potassium
o Sulphur
o Magnesium
o Calcium
o Iron
o Boron
o Manganese
o Zinc
o Molybdenum
o Copper
Out of the 15 essential elements that come from the soil, we deal with only the 12 that are generally
managed by the growers. These 12 elements are mineral nutrients and are obtained from the soil.
We further divide mineral nutrients into 3 groups: primary, intermediate, and micronutrients. Our
presentation will exclude cobalt, chlorine, and nickel from our discussion on the management of
essential mineral nutrients, though are included by many as essential nutrients.
The primary nutrients are nitrogen, phosphorus and potassium. You may be most familiar with
these three nutrients because they are required in larger quantities than other nutrients. These
three elements form the basis of the N-P-K label on commercial fertilizer bags. As a result, the
management of these nutrients is very important. However, the primary nutrients are no more
 important than the other essential elements since all essential elements are required for plant
growth. Remember that the Law of the Minimum tells us that if deficient, any essential nutrient
can become the controlling force in crop yield.
The intermediate nutrients are sulphur, magnesium, and calcium. Together, primary and
intermediate nutrients are referred to as macronutrients. Macronutrients are expressed as a certain
percentage (%) of the total plant uptake. Although sulphur, magnesium, and calcium are called
intermediate, these elements are not necessarily needed by plants in smaller quantities. In fact,
phosphorus is required in the same amount as the intermediate nutrients, despite being a primary
nutrient. Phosphorus is referred to as a primary nutrient because of the high frequency of soils
that are deficient of this nutrient, rather than the amount of phosphorus that plants actually use for
growth.
The remaining essential elements are the micronutrients and are required in very small quantities.
In comparison with macronutrients, the uptake of micronutrients is expressed in parts per million
(ppm, where 10,000 ppm = 1.0%), rather than on a percentage basis. Again, this does not infer that
micronutrients are of lesser importance. If any micronutrient is deficient, the growth of the entire
plant will not reach maximum yield (Law of the Minimum).
Since the soil provides most essential nutrients, it is crucial that we understand the soil processes
that determine the availability of each essential nutrient for plant uptake.
Table 4. Forms of Essential Elements Taken up by Plants

Element Abbreviation Form absorbed

Nitrogen N NH4+ (ammonium) and

NO3- (nitrate)

Phosphorus P H2PO4- and HPO4-2

(orthophosphate)

Potassium K K+

Sulfur S SO4-2(sulphate)

Calcium Ca Ca+2

Magnesium Mg Mg+2

Iron Fe Fe+2 (ferrous) and Fe+3

(ferric)

Zinc Zn Zn+2
 Manganese Mn Mn+2

Molybdenum Mo MoO4-2 (molybdite)

Copper Cu Cu+2

Boron B H3BO3 (boric acid) and

H2BO3- (borate)

In this website, we will discuss major factors that affect the availability of the essential nutrients.
In the tropics, the management of nitrogen and phosphorus can be problematic. Thus, it is
appropriate that we discuss management issues of each nutrient separately.
In a second section, we will collectively discuss the availability of potassium, calcium, and
magnesium in Hawaii soils.
Lastly, we will address issues of micronutrient management in the tropics.
We will omit a discussion on sulphur, since it is seldom deficient in Hawaii soils.

Calvin Cycle

Letters to Nature
Nature 432, 779-782 (9 December 2004) | doi:10.1038/nature03145; Received 13
August 2004; Accepted 1 November 2004
Rubisco without the Calvin cycle improves the carbon efficiency of developing
green seeds
Jrg Schwender, Fernando Goffman, John B. Ohlrogge & Yair Shachar-Hill
1. Plant Biology Department, Michigan State University, East Lansing, Michigan
48824, USA
Correspondence to: Jrg Schwender Email: schwend2@msu.edu
Top of page
Efficient storage of carbon in seeds is crucial to plant fitness and to agricultural
productivity. Oil is a major reserve material in most seeds1, and these oils provide
the largest source of renewable reduced carbon chains available from nature.
However, the conversion of carbohydrate to oil through glycolysis results in the
loss of one-third of the carbon as CO2. Here we show that, in developing embryos
of Brassica napus L. (oilseed rape), Rubisco (ribulose 1,5-bisphosphate
carboxylase/oxygenase) acts without the Calvin cycle2 and in a previously
undescribed metabolic context to increase the efficiency of carbon use during the
formation of oil. In comparison with glycolysis, the metabolic conversion we
describe provides 20% more acetyl-CoA for fatty-acid synthesis and results in 40%
less loss of carbon as CO2. Our conclusions are based on measurements of mass
balance, enzyme activity and stable isotope labelling, as well as an analysis of
elementary flux modes.
 Nutrient summary

Executive Summary
The nutrient cycle describes how nutrients move from the physical environment into living organisms, and
subsequently are recycled back to the physical environment. This movement of nutrients, essential for life,
from the environment into plants and animals and back again, is a vital function of the ecology of any
region. In any particular environment, the nutrient cycle must be balanced and stable if the organisms that
live in that environment are to flourish and be maintained in a constant population (MARTIN 2010).
Currently, large parts of humankind influence the nutrient cycle in such a way that we remove nutrients
from the land and discharge them into aquatic environments. On the one hand, this leads to soil depletion
on the land, and on the other hand, an overabundance of nutrients and pollution of water sources.

Nutrients the Fuel of Life

Nutrients are chemical elements that all plants and animals require for growth. On the earth, there is a constant and natural
cycle how these elements are incorporated when an organism grows, and degraded if an organism dies. The nutrients used in
the largest amounts are the non-mineral elements, i.e. carbon (C), hydrogen (H) and oxygen (O). These elements are mainly
taken up as carbon dioxide (CO2) from the air, and water (H2O) by the roots (JOENSSON et al. 2004). They make up 95-98% of
the mass of all living beings (MAHENDRAPPA 2007). But they are, however, not sufficient for life to exist. Further elements are
important to fuel life on earth: Nitrogen (N) and Phosphorus (P), Potassium (K) as well as Calcium (Ca) and Magnesium (Mg) are
highly important, in particular for plant growth and agriculture. These elements are often referred to as macro nutrients.
Their uptake is about 100 times that of micro nutrients. Further nutrients, that plants take up in a much smaller amount and
that are essentially consumed by humans, include Boron (Bh), Copper (Cu), Iron (Fe), Chloride (Cl), Manganese (Mn),
Molybdenum (Mo) and Zinc (Zn) and others. These are called micro nutrients (JOENSSON et al. 2004).

Natural Nutrient Cycles

The basic nutrient cycle. Source: USDA NRCS & NSTA (2010)

These nutrients essentially chemical elements are continuously in a circular movement, the nutrient cycle. The nutrient
cycle is hence a general term that describes how nutrients move from the physical environment into living organisms, and are
subsequently recycled back to the physical environment (MARTIN 2010). Nutrients in the soil are taken up by plants, which are
consumed by humans or animals, and excreted again by them or they are released back into the environment when
organisms die (e.g. plants lose their leaves). Microorganisms in the soil break this matter down, and again make nutrients
available in their mineral form, which makes it possible for plants to take them up again (see also nutrient requirements of
plants).

Essentially, all nutrients that plants and also human beings require to survive are cycled in this way. In relation to water
management and sanitation, it is mainly N, P and K that are of high priority. They are the most important nutrients to sustain
plant growth and agriculture, and thus humanity.

How Humans Influence Nutrient Cycles

Nutrient removal by harvesting crops. Source: (unknown)

As described above, nutrients are continuously recycled in a natural ecosystem. In recent decades, population growth and
resulting human activities such as large-scale farming have caused some significant changes in nutrient cycles.

With harvesting crops, nutrients are removed from the soil. For centuries, dung from animals has been used as a fertiliser to
restore the nutrients back to the soil, and in many cultures e.g. in Europe, or also in China, also human excreta have been
recycled back to agricultural fields. Hence, nutrients went back into the soil at roughly the rate they had been withdrawn.
However, with the introduction of water-borne sewage, this cycle was interrupted and replaced by a linear system that
transports nutrients away from soils and into watercourses (see also water pollution).
Degraded Soils. Source: REKACEWICZ (2002)

Furthermore, agriculture also influences the nutrient cycle in another way: agriculture accelerates land erosion because
ploughing and tilling disturb and expose the soil so more nutrients drains away with runoff (see also soil degradation). And
flood control contributes to disrupting the natural nutrient cycle. Typically river floods would redistribute nutrient-rich
sediments to lower lands where it is again available for ecosystems. Instead dams trap sediment or embankments confine it to
the river until it washes out to sea. So too much nutrients from eroded soil and from human and animal waste ends up in lakes
and oceans, where it spurs massive, uncontrolled blooms of algae. Once they die and fall to the bottom, their decay starves
other organisms of oxygen, creating dead zones and contributing to the depletion of fisheries (VACCARI 2009).

Essentially, the human alterations to the nutrient cycle leads to an excess of nutrients in aquatic ecosystems and a serious lack
of nutrients in agriculture. Worldwide, more and more soils are deplete of nutrients, with serious consequences to agricultural
production and food security.

The lack of nutrients in agriculture is often made up by applying artificial fertilisers. However there are several problems
related to this strategy:

Artificial fertilisers usually contain only the most important macro nutrients nitrogen, phosphorus and potassium and lack
other essential trace elements. This eventually leads to a soil deplete in micro nutrients.
Phosphorus is a finite resource. "China, Morocco and the United States alone currently produce almost two thirds of global
phosphate. Estimates on the remaining amount of phosphorus vary, as do projections about how long it will take to deplete
the irreplaceable resource entirely. Figures for easily exploitable reserves range from 60-130 years (TIESSEN 1995; STEEN
1998), but all sources agree that continued phosphorus production will decline in quality and increase in cost. It imperative
that we begin recycling phosphorus and returning it to the soil to decrease the need for mined phosphorus as artificial
fertiliser. Within a half century, the severity of this crisis will result in increasing food prices, food shortages and
geopolitical rifts."
Nitrogen, on the other hand, is available abundantly. 78% of the air is composed of nitrogen. However, the process of
producing nitrogen is highly energy consuming and relies mostly on fossil fuels which, on the other hand, are finite.
The element potassium is available abundantly, and reserves are predicted to last for a long time. However, most of the
potassium is contained in small proportions in a large number of mineral formations which makes extraction laborious.
Essentially, the problem with the human alterations to natural nutrient cycle is the one that we are extracting nutrients from
the soil, and discharging them essentially in aquatic environment this leads to a heavy imbalance with severe consequences.

Consequences

Sites with dead zones, February 2008. As visible on the picture, the problem is crucial In particular in the so called "developed countries" in
North America and Europe - where sewer-based wastewater management is common. Source: AHLENIUS (2008)

These human-induced alterations in the nutrient cycles lead to an imbalance in the availability of nutrients, whose
consequences, in particular with regard to water, are grave:

Depletion of soils: The accumulation of nutrients in the seas means that they are depleted elsewhere, i.e., to a large
extent from soils. This leads to the fact that many of the fruit and vegetables that animals and humans are consuming,
essentially contain less nutrients, minerals, vitamins etc. that they have some decades ago. Applying more artificial
fertilisers is not the solution: it is energy and cost intensive; it can lead to salinisation, and, because artificial fertilisers
which are mainly based on the three main components Nitrogen, Phosphorus and Potassium, are essentially incomplete.
Furthermore, soils that do not contain adequate amounts of organic material (e.g. from compost, dead plant material
etc.), are not able to adsorb much of the nutrients added, and also have a low water holding capacity.
Depletion of nutrient sources: While nitrogen can be gained from the air, it is an energy intensive process that is mainly
based on the use of fossil fuels. Other components of artificial fertiliser, are based on fossil resources, such as
phosphorus. The amount that is easily mined, is limited (see above). If these easily mineable resources are deplete, this
means that phosphorus prices will increase drastically.
Affordability & food security: "Fertilisers are bound to world market prices which are already substantially high for many
farmers from developing countries. An increase in price, as is to be expected in the case of phosphorus, will make them
unavailable for many farmers. This may make agricultural products, especially in developing countries, more expensive and
thus lead to a decreased food security." (CONRADIN 2007).
Eutrophication of waterways and dead zones: "Fertiliser runoff and wastewater discharge contribute to eutrophication,
uncontrolled blooms of algae in rivers, lakes and oceans, feeding on nitrogen and phosphorus from fertilisers. When they
die, their decomposition depletes the water of oxygen and slowly chokes aquatic life, producing dead zones. The largest
dead zone in American waters, topping 20,000 square kilometres in July 2008, is off the Mississippi delta. More than 400
dead zones now exist worldwide, covering a combined area of more than 245,000 square kilometres." (CASTELVECCHI 2009)
(see also water pollution).

Outlook
At the moment, humans influence natural nutrient cycles in an unsustainable way, and in a one-way direction. Too many
nutrients end up in the sea, and are lacking on the land, leading to the above mentioned consequences. A new approach in
nutrient management is needed, essentially incorporating a new way to look at what we commonly call wastewater too: this
is, not to consider wastewater as a waste, but as a resource, full of nutrients that can be recycled and reused (see recharge
and reuse).

http://www.sswm.info/category/concept/nutrient-cycle

Bibliography
Crosson, Sean, and Keith Moffat. "Photo excited Structure of a Plant
Photoreceptor Domain Reveals a Light-Driven Molecular Switch." The Plant
Cell. American Society of Plant Biologists, 29 Apr. 2002. Web. 31 Jan. 2017.
http://www.plantcell.org/content/14/5/1067.short.

Ledbetter, M. C., and K. R. Porter. "A "MICROTUBULE" IN PLANT CELL FINE

STRUCTURE." Rockefeller University Press. Rockefeller University Press, 1 Oct.
1963. Web. 31 Jan. 2017. http://jcb.rupress.org/content/19/1/239.

Rabinowitch, Govindjee E. "Welcome to CAB Direct." CAB Direct. John

Wiley and Sons Inc., 1966. Web. 3 Feb. 2017.
https://www.cabdirect.org/cabdirect/abstract/19700703082.