Editing Botany (section)

== Plant biochemistry ==

Plant biochemistry is the study of the chemical processes used by plants. Some of these processes are used in their [[primary metabolism]] like the photosynthetic [[Calvin cycle]] and [[crassulacean acid metabolism]].{{sfn|Lüttge|2006|pp = 7–25}} Others make specialised materials like the [[cellulose]] and [[lignin]] used to build their bodies, and [[Secondary metabolism|secondary products]] like [[resin]]s and [[aroma compounds]].

[[File:Chromatography rev.jpg|thumb|upright=2|[[Paper chromatography]] of some [[spinach]] leaf extract shows the various pigments present in their chloroplasts: yellowish xanthophylls, greenish chlorophylls ''a'' and ''b''.]]

Plants and various other groups of photosynthetic eukaryotes collectively known as "[[algae]]" have unique organelles known as [[chloroplast]]s. Chloroplasts are thought to be descended from [[cyanobacteria]] that formed [[endosymbiotic]] relationships with ancient plant and algal ancestors. Chloroplasts and cyanobacteria contain the blue-green pigment [[chlorophyll a|chlorophyll ''a'']].{{sfn|Campbell|Reece|Urry|Cain|2008|pp=190–193}} Chlorophyll ''a'' (as well as its plant and green algal-specific cousin [[chlorophyll b|chlorophyll ''b'']]){{efn|Chlorophyll ''b'' is also found in some cyanobacteria. A bunch of other chlorophylls exist in [[cyanobacteria]] and certain algal groups, but none of them are found in land plants.{{sfn|Kim|Archibald|2009|pp=1–39}}{{sfn|Howe|Barbrook|Nisbet|Lockhart|2008|pp=2675–2685}}{{sfn|Takaichi|2011|pp=1101–1118}}}} absorbs light in the blue-violet and orange/red parts of the [[visible spectrum|spectrum]] while reflecting and transmitting the green light that we see as the characteristic colour of these organisms. The energy in the red and blue light that these pigments absorb is used by chloroplasts to make energy-rich carbon compounds from carbon dioxide and water by [[Carbon fixation#Oxygenic photosynthesis|oxygenic photosynthesis]], a process that generates [[molecular oxygen]] (O<sub>2</sub>) as a by-product.

The light energy captured by [[chlorophyll a|chlorophyll ''a'']] is initially in the form of electrons (and later a [[proton gradient]]) that is used to make molecules of [[Adenosine triphosphate|ATP]] and [[NADPH]] which temporarily store and transport energy. Their energy is used in the [[light-independent reactions]] of the Calvin cycle by the enzyme [[rubisco]] to produce molecules of the 3-carbon sugar [[glyceraldehyde 3-phosphate]] (G3P). Glyceraldehyde 3-phosphate is the first product of photosynthesis and the raw material from which [[glucose]] and almost all other organic molecules of biological origin are synthesised. Some of the glucose is converted to starch which is stored in the chloroplast.{{sfn|Lewis|McCourt|2004|pp=1535–1556}} Starch is the characteristic energy store of most land plants and algae, while [[inulin]], a polymer of [[fructose]] is used for the same purpose in the sunflower family [[Asteraceae]]. Some of the glucose is converted to [[sucrose]] (common table sugar) for export to the rest of the plant.

Unlike in animals (which lack chloroplasts), plants and their eukaryote relatives have delegated many biochemical roles to their [[chloroplast]]s, including synthesising all their [[fatty acids]],{{sfn|Padmanabhan|Dinesh-Kumar|2010|pp=1368–1380}}{{sfn|Schnurr|Shockey|De Boer|Browse|2002|pp=1700–1709}} and most [[amino acids]].{{sfn|Ferro|Salvi|Rivière-Rolland|Vermat|2002|pp=11487–11492}} The fatty acids that chloroplasts make are used for many things, such as providing material to build [[cell membrane]]s out of and making the polymer [[cutin]] which is found in the [[plant cuticle]] that protects land plants from drying out.{{Sfn|Kolattukudy|1996|pp=83–108}}

Plants synthesise a number of unique [[polymer]]s like the [[polysaccharide]] molecules [[cellulose]], [[pectin]] and [[xyloglucan]]{{sfn|Fry|1989|pp=1–11}} from which the land plant cell wall is constructed.{{sfn|Thompson|Fry|2001|pp=23–34}}
Vascular land plants make [[lignin]], a polymer used to strengthen the [[secondary cell walls]] of xylem [[tracheid]]s and [[Xylem vessel element|vessels]] to keep them from collapsing when a plant sucks water through them under water stress. Lignin is also used in other cell types like [[Ground tissue#Sclerenchyma|sclerenchyma fibres]] that provide structural support for a plant and is a major constituent of wood. [[Sporopollenin]] is a chemically resistant polymer found in the outer cell walls of spores and pollen of land plants responsible for the survival of early land plant spores and the pollen of seed plants in the fossil record. It is widely regarded as a marker for the start of land plant evolution during the [[Ordovician]] period.{{sfn|Kenrick|Crane|1997|pp=33–39}}
The concentration of carbon dioxide in the atmosphere today is much lower than it was when plants emerged onto land during the [[Ordovician]] and [[Silurian]] periods. Many [[monocots]] like [[maize]] and the [[pineapple]] and some [[dicots]] like the [[Asteraceae]] have since independently evolved{{sfn|Gowik|Westhoff|2010|pp=56–63}} pathways like [[Crassulacean acid metabolism]] and the [[C4 carbon fixation|{{C4}} carbon fixation]] pathway for photosynthesis which avoid the losses resulting from [[photorespiration]] in the more common [[C3 carbon fixation|{{C3}} carbon fixation]] pathway. These biochemical strategies are unique to land plants.

=== Medicine and materials ===
[[Phytochemistry]] is a branch of plant biochemistry primarily concerned with the chemical substances produced by plants during [[secondary metabolism]].{{sfn|Benderoth|Textor|Windsor|Mitchell-Olds|2006|pp = 9118–9123}} Some of these compounds are toxins such as the [[alkaloid]] [[coniine]] from [[conium|hemlock]]. Others, such as the [[essential oil]]s [[Peppermint#Oil|peppermint oil]] and lemon oil are useful for their aroma, as flavourings and spices (e.g., [[capsaicin]]), and in medicine as pharmaceuticals as in [[opium]] from [[Papaver somniferum|opium poppies]]. Many [[medication|medicinal]] and [[recreational drugs]], such as [[tetrahydrocannabinol]] (active ingredient in [[Cannabis (drug)|cannabis]]), [[caffeine]], [[morphine]] and [[nicotine]] come directly from plants. Others are simple [[Derivative (chemistry)|derivatives]] of botanical natural products. For example, the pain killer [[aspirin]] is the acetyl [[ester]] of [[salicylic acid]], originally isolated from the [[Bark (botany)|bark]] of [[willow]] trees,{{sfn|Jeffreys|2005|pp = 38–40}} and a wide range of [[opiate]] [[analgesics|painkillers]] like [[diamorphine|heroin]] are obtained by chemical modification of [[morphine]] obtained from the [[opium poppy]].{{sfn|Mann|1987|pp = 186–187}} Popular [[stimulant]]s come from plants, such as [[caffeine]] from coffee, tea and chocolate, and [[nicotine]] from tobacco. Most alcoholic beverages come from [[fermentation (food)|fermentation]] of [[carbohydrate]]-rich plant products such as [[barley]] (beer), rice ([[sake]]) and grapes (wine).{{sfn|University of Maryland Medical Center|2011}} [[Native Americans in the United States|Native Americans]] have used various plants as ways of treating illness or disease for thousands of years.{{sfn|Densmore|1974}} This knowledge Native Americans have on plants has been recorded by [[Ethnobotany|enthnobotanists]] and then in turn has been used by [[Pharmaceutical industry|pharmaceutical companies]] as a way of [[drug discovery]].{{sfn|McCutcheon|Ellis|Hancock|Towers|1992}}

Plants can synthesise coloured dyes and pigments such as the [[anthocyanin]]s responsible for the red colour of [[red wine]], yellow [[Reseda luteola|weld]] and blue [[Isatis tinctoria|woad]] used together to produce [[Lincoln green]], [[indoxyl]], source of the blue dye [[indigo]] traditionally used to dye denim and the artist's pigments [[gamboge]] and [[rose madder]].

Sugar, [[starch]], cotton, [[linen]], [[hemp]], some types of [[rope]], wood and [[particle board]]s, [[papyrus]] and paper, [[vegetable oil]]s, [[epicuticular wax|wax]], and [[natural rubber]] are examples of commercially important materials made from plant tissues or their secondary products. [[Charcoal]], a pure form of carbon made by [[pyrolysis]] of wood, has a long [[charcoal#History|history]] as a metal-[[smelting]] fuel, as a filter material and [[activated carbon#Applications|adsorbent]] and as an artist's material and is one of the three ingredients of [[gunpowder]]. [[Cellulose]], the world's most abundant organic polymer,{{sfn|Klemm|Heublein|Fink|Bohn|2005}} can be converted into energy, fuels, materials and chemical feedstock. [[cellulose#products|Products made from cellulose]] include [[rayon]] and [[cellophane]], [[methyl cellulose|wallpaper paste]], [[Butanol fuel#Using Alternate Carbon Sources|biobutanol]] and [[nitrocellulose|gun cotton]]. [[Sugarcane]], [[rapeseed]] and [[soy]] are some of the plants with a highly fermentable sugar or oil content that are used as sources of [[biofuel]]s, important alternatives to [[fossil fuel]]s, such as [[biodiesel]].{{sfn|Scharlemann|Laurance|2008|pp = 52–53}} Sweetgrass was used by Native Americans to ward off bugs like [[mosquitoes]].{{sfn|Washington Post 18 Aug 2015}} These bug repelling properties of sweetgrass were later found by the [[American Chemical Society]] in the molecules [[phytol]] and [[coumarin]].{{sfn|Washington Post 18 Aug 2015}}