query: what process of photosynthesis occurs in the stroma of the chloroplast

pos: Stroma (fluid) the Calvin cycle or "light-independent reactions". There are three phases: carbon fixation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration. The stroma is also the location of chloroplast DNA and chloroplast ribosomes, and thus also the location of molecular processes including chloroplast DNA replication, and transcription/translation of some chloroplast proteins. Stroma (fluid) Stroma, in botany, refers to the colorless fluid surrounding the grana within the chloroplast. Within the stroma are grana, stacks of thylakoids, the sub-organelles, the daughter cells, where photosynthesis is commenced before the chemical changes are completed in the stroma. Photosynthesis occurs in two stages. In the first stage,

pos: Chloroplast and pyrenoids. Chloroplasts in plants are notable as they exhibit a distinct chloroplast dimorphism. Because of the H gradient across the thylakoid membrane, the interior of the thylakoid is acidic, with a pH around 4, while the stroma is slightly basic, with a pH of around 8. The optimal stroma pH for the Calvin cycle is 8.1, with the reaction nearly stopping when the pH falls below 7.3. CO in water can form carbonic acid, which can disturb the pH of isolated chloroplasts, interfering with photosynthesis, even though CO is used in photosynthesis. However, chloroplasts in living plant cells are

pos: Light-independent reactions from an alternative reaction of the RuBisCO enzyme, and its final byproduct is also another glyceraldehyde-3-P. The Calvin cycle, Calvin–Benson–Bassham (CBB) cycle, reductive pentose phosphate cycle or C3 cycle is a series of biochemical redox reactions that take place in the stroma of chloroplast in photosynthetic organisms. The cycle was discovered by Melvin Calvin, James Bassham, and Andrew Benson at the University of California, Berkeley by using the radioactive isotope carbon-14. Photosynthesis occurs in two stages in a cell. In the first stage, light-dependent reactions capture the energy of light and use it to make the energy-storage and transport molecules

pos: Chloroplast the thylakoids and intermembrane space. The protein-rich, alkaline, aqueous fluid within the inner chloroplast membrane and outside of the thylakoid space is called the stroma, which corresponds to the cytosol of the original cyanobacterium. Nucleoids of chloroplast DNA, chloroplast ribosomes, the thylakoid system with plastoglobuli, starch granules, and many proteins can be found floating around in it. The Calvin cycle, which fixes CO into sugar takes place in the stroma. Chloroplasts have their own ribosomes, which they use to synthesize a small fraction of their proteins. Chloroplast ribosomes are about two-thirds the size of cytoplasmic ribosomes (around 17 nm vs

pos: ATP synthase is integrated into thylakoid membrane; the CF-part sticks into stroma, where dark reactions of photosynthesis (also called the light-independent reactions or the Calvin cycle) and ATP synthesis take place. The overall structure and the catalytic mechanism of the chloroplast ATP synthase are almost the same as those of the bacterial enzyme. However, in chloroplasts, the proton motive force is generated not by respiratory electron transport chain but by primary photosynthetic proteins. The ATP synthase isolated from bovine ("Bos taurus") heart mitochondria is, in terms of biochemistry and structure, the best-characterized ATP synthase. Beef heart is used as a source for

pos: Chloroplast occur when the oxygen concentration is too high. RuBisCO cannot distinguish between oxygen and carbon dioxide very well, so it can accidentally add O instead of CO to RuBP. This process reduces the efficiency of photosynthesis—it consumes ATP and oxygen, releases CO, and produces no sugar. It can waste up to half the carbon fixed by the Calvin cycle. Several mechanisms have evolved in different lineages that raise the carbon dioxide concentration relative to oxygen within the chloroplast, increasing the efficiency of photosynthesis. These mechanisms are called carbon dioxide concentrating mechanisms, or CCMs. These include Crassulacean acid metabolism, carbon fixation,

pos: Ferredoxin—NADP(+) reductase The NADPH is then used as a reducing equivalent in the reactions of the Calvin cycle. Electron cycling from ferredoxin to NADPH only occurs in the light in part because FNR activity is inhibited in the dark. In nonphotosynthetic organisms, the FNR primarily works in reverse to provide reduced ferredoxin for various metabolic pathways. These pathways include nitrogen fixation, terpenoid biosynthesis, steroid metabolism, oxidative stress response, and iron–sulfur protein biogenesis. FNR is a soluble protein that is found both free in the chloroplast stroma and bound to the thylakoid membrane. This binding occurs opposite to the active site of the

pos: Chloroplast Chloroplast Chloroplasts are organelles that conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in plant and algal cells. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants

pos: Chloroplast species, recent results in tobacco plants are promising, showing a failed containment rate of transplastomic plants at 3 in 1,000,000. Chloroplast Chloroplasts are organelles that conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in plant and algal cells. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune

pos: Chloroplast they lack thylakoids organized into grana stacks—though bundle sheath chloroplasts still have free-floating thylakoids in the stroma where they still carry out cyclic electron flow, a light-driven method of synthesizing ATP to power the Calvin cycle without generating oxygen. They lack photosystem II, and only have photosystem I—the only protein complex needed for cyclic electron flow. Because the job of bundle sheath chloroplasts is to carry out the Calvin cycle and make sugar, they often contain large starch grains. Both types of chloroplast contain large amounts of chloroplast peripheral reticulum, which they use to get more surface area to transport

pos: Chloroplast the light reactions. The Calvin cycle takes place in the stroma of the chloroplast. While named ""the dark reactions"", in most plants, they take place in the light, since the dark reactions are dependent on the products of the light reactions. The Calvin cycle starts by using the enzyme RuBisCO to fix CO into five-carbon Ribulose bisphosphate (RuBP) molecules. The result is unstable six-carbon molecules that immediately break down into three-carbon molecules called 3-phosphoglyceric acid, or 3-PGA. The ATP and NADPH made in the light reactions is used to convert the 3-PGA into glyceraldehyde-3-phosphate, or G3P sugar molecules. Most of

pos: Carboxysome functional carboxysomes have not yet been constructed in plant chloroplasts. Nonetheless, successful improvement of photosynthesis in plants using this approach is ultimately dependent on the operation of transporter proteins in the chloroplast inner envelope membrane to help generate a high concentration of bicarbonate inside the chloroplast . Carboxysome Carboxysomes are bacterial compartments consisting of polyhedral protein shells filled with the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) -the predominant enzyme in carbon fixation and the rate limiting enzyme in the Calvin Cycle-and a carbonic anhydrase. Carboxysomes are thought to have evolved as a consequence of the increase in oxygen concentration in the ancient

pos: Chloroplast transformed into chemical energy, to subsequently produce food in the form of sugars. Water (HO) and carbon dioxide (CO) are used in photosynthesis, and sugar and oxygen (O) is made, using light energy. Photosynthesis is divided into two stages—the light reactions, where water is split to produce oxygen, and the dark reactions, or Calvin cycle, which builds sugar molecules from carbon dioxide. The two phases are linked by the energy carriers adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADP). The light reactions take place on the thylakoid membranes. They take light energy and store it in NADPH, a form

neg: Stroma (fluid) Stroma (fluid) Stroma, in botany, refers to the colorless fluid surrounding the grana within the chloroplast. Within the stroma are grana, stacks of thylakoids, the sub-organelles, the daughter cells, where photosynthesis is commenced before the chemical changes are completed in the stroma. Photosynthesis occurs in two stages. In the first stage, "light-dependent reactions" capture the energy of light and use it to make the energy-storage molecules ATP and NADPH. During the second stage, the "light-independent reactions" use these products to capture and reduce carbon dioxide. The series of biochemical redox reactions which take place in the stroma are collectively called

neg: Photosynthesis algae, photosynthesis takes place in organelles called chloroplasts. A typical plant cell contains about 10 to 100 chloroplasts. The chloroplast is enclosed by a membrane. This membrane is composed of a phospholipid inner membrane, a phospholipid outer membrane, and an intermembrane space. Enclosed by the membrane is an aqueous fluid called the stroma. Embedded within the stroma are stacks of thylakoids (grana), which are the site of photosynthesis. The thylakoids appear as flattened disks. The thylakoid itself is enclosed by the thylakoid membrane, and within the enclosed volume is a lumen or thylakoid space. Embedded in the thylakoid membrane are

neg: Light-independent reactions the stroma caused by its phosphorylation. Light-independent reactions The light-independent reactions, or dark reactions, of photosynthesis are chemical reactions that convert carbon dioxide and other compounds into glucose. These reactions occur in the stroma, the fluid-filled area of a chloroplast outside the thylakoid membranes. These reactions take the products (ATP and NADPH) of light-dependent reactions and perform further chemical processes on them. These reactions are closely coupled to the thylakoid electron transport chain as reducing power provided by NADPH produced in the photosystem I is actively needed. The process of photorespiration, also known as C2 cycle, is also coupled to

neg: Plastoquinone the cell membrane. One example of how it does this is by reacting with superoxides to form hydrogen peroxide and plastosemiquinone. The prefix "plasto-" means either plastid or chloroplast, alluding to its location within the cell. The role that plastoquinone plays in photosynthesis, more specifically in the light-dependent reactions of photosynthesis, is that of a mobile electron carrier through the membrane of the thylakoid. Plastoquinone is reduced when it accepts two electrons from photosystem II and two hydrogen cations (H) from the stroma of the chloroplast, thereby forming plastoquinol (PQH). It transfers the electrons further down the electron transport chain

neg: Chloroplast ATP synthase, phycobilisomes jut into the stroma, preventing thylakoid stacking in red algal chloroplasts. Cryptophyte chloroplasts and some cyanobacteria don't have their phycobilin pigments organized into phycobilisomes, and keep them in their thylakoid space instead. To fix carbon dioxide into sugar molecules in the process of photosynthesis, chloroplasts use an enzyme called RuBisCO. RuBisCO has a problem—it has trouble distinguishing between carbon dioxide and oxygen, so at high oxygen concentrations, RuBisCO starts accidentally adding oxygen to sugar precursors. This has the end result of ATP energy being wasted and being released, all with no sugar being produced. This is a

neg: Chloroplast membrane or the stroma of a chloroplast. A steep H gradient is formed, which allows chemiosmosis to occur, where the thylakoid, transmenbrane ATP-synthase serves a dual function as a "gate" or channel for H ions and a catalytic site for the formation of ATP from ADP + a PO ion. Experiments have shown that the pH within the stroma is about 7.8, while that of the lumen of the thylakoid is 5. This corresponds to a six-hundredfold difference in concentration of H ions. The H ions pass down through the ATP-synthase catalytic gate. This chemiosmotic phenomenon also occurs in mitochondria. Chloroplast

neg: Light-independent reactions Light-independent reactions The light-independent reactions, or dark reactions, of photosynthesis are chemical reactions that convert carbon dioxide and other compounds into glucose. These reactions occur in the stroma, the fluid-filled area of a chloroplast outside the thylakoid membranes. These reactions take the products (ATP and NADPH) of light-dependent reactions and perform further chemical processes on them. These reactions are closely coupled to the thylakoid electron transport chain as reducing power provided by NADPH produced in the photosystem I is actively needed. The process of photorespiration, also known as C2 cycle, is also coupled to the dark reactions, as it results

neg: Ferredoxin—NADP(+) reductase enzyme and does not seem to affect the structure of the active site or have a significant impact on the enzyme’s activity. When bound to the thylakoid membrane, the enzyme exists as a dimer, but when it is free in the stroma, it is monomeric. The binding of the FNR to the integral membrane proteins on the thylakoid membrane is enhanced under acidic conditions, so recruitment and binding of FNR to the thylakoid membrane may be a method of storing and stabilizing the enzyme in the dark when photosynthesis is not occurring. The chloroplast stroma varies from being slightly acidic

neg: Chloroplast the pyrenoids when CO is scarce. Pyrenoids can divide to form new pyrenoids, or be produced "de novo". Suspended within the chloroplast stroma is the thylakoid system, a highly dynamic collection of membranous sacks called thylakoids where chlorophyll is found and the light reactions of photosynthesis happen. In most vascular plant chloroplasts, the thylakoids are arranged in stacks called grana, though in certain plant chloroplasts and some algal chloroplasts, the thylakoids are free floating. Using a light microscope, it is just barely possible to see tiny green granules—which were named grana. With electron microscopy, it became possible to see the

neg: Chloroplast chloroplasts. Chloroplasts have no definite S-phase—their DNA replication is not synchronized or limited to that of their host cells. Much of what we know about chloroplast division comes from studying organisms like "Arabidopsis" and the red alga "Cyanidioschyzon merolæ". The division process starts when the proteins FtsZ1 and FtsZ2 assemble into filaments, and with the help of a protein ARC6, form a structure called a Z-ring within the chloroplast's stroma. The Min system manages the placement of the Z-ring, ensuring that the chloroplast is cleaved more or less evenly. The protein MinD prevents FtsZ from linking up and forming filaments.

neg: Malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) site. However, the inhibitory effect exhibits pH-dependence – existent at a pH of 7 but not a pH of 8. The control of enzyme activity due to pH changes align with the hypothesis that NADP-ME is most active while photosynthesis is in progress: Active light reactions leads to a rise in basicity within the chloroplast stroma, the location of NADP-ME, leading to a diminished inhibitory effect of malate on NADP-ME and thereby promoting a more active state. Conversely, slowed light reactions leads to a rise in acidity within the stroma, promoting the inhibition of NADP-ME by malate. Because the high

neg: Thylakoid more thylakoids membranes. The word "thylakoid" comes from the Greek word "thylakos" meaning "sac" or "pouch". Thus, "thylakoid" means "sac-like" or "pouch-like". Thylakoids are membrane-bound structures embedded in the chloroplast stroma. A stack of thylakoids is called a granum and resembles a stack of coins. The thylakoid membrane is the site of the light-dependent reactions of photosynthesis with the photosynthetic pigments embedded directly in the membrane. It is an alternating pattern of dark and light bands measuring each 1 nanometre. The thylakoid lipid bilayer shares characteristic features with prokaryotic membranes and the inner chloroplast membrane. For example, acidic lipids can

neg: Chloroplast to the required light. This process involves invaginations of the inner plastid membrane, forming sheets of membrane that project into the internal stroma. These membrane sheets then fold to form thylakoids and grana. If angiosperm shoots are not exposed to the required light for chloroplast formation, proplastids may develop into an etioplast stage before becoming chloroplasts. An etioplast is a plastid that lacks chlorophyll, and has inner membrane invaginations that form a lattice of tubes in their stroma, called a prolamellar body. While etioplasts lack chlorophyll, they have a yellow chlorophyll precursor stocked. Within a few minutes of light exposure,

neg: Chloroplast green algae, the nucleoids are dispersed throughout the stroma. Though chloroplast DNA is not associated with true histones, in red algae, similar proteins that tightly pack each chloroplast DNA ring into a nucleoid have been found. In chloroplasts of the moss "Physcomitrella patens", the DNA mismatch repair protein Msh1 interacts with the recombinational repair proteins RecA and RecG to maintain chloroplast genome stability. In chloroplasts of the plant "Arabidopsis thaliana" the RecA protein maintains the integrity of the chloroplast’s DNA by a process that likely involves the recombinational repair of DNA damage. The mechanism for chloroplast DNA (cpDNA) replication has

neg: Phototropism plant were dependent upon the age of the plant. This suggests that the phototropin expression levels change with the maturation of the leaves. Mature leaves contain chloroplasts that are essential in photosynthesis. Chloroplast rearrangement occurs in different light environments to maximize photosynthesis. There are several genes involved in plant phototropism including the "NPH1" and "NPL1" gene. They are both involved in chloroplast rearrangement. The "nph1" and "npl1" double mutants were found to have reduced phototropic responses. In fact, the two genes are both redundant in determining the curvature of the stem. In 2012, Sakai and Haga outlined how different auxin

neg: Ycf4 protein domain upon sucrose density gradient centrifugation of solubilised thylakoids. "Ycf" is an acronym standing for hypothetical chloroplast open reading frame. Ycf4 protein domain In molecular biology, the Ycf4 protein is involved in the assembly of the photosystem I complex which is part of an energy-harvesting process named photosynthesis. Without Ycf4, photosynthesis would be inefficient affecting plant growth. Ycf4 is located in the thylakoid membrane of the chloroplast. Ycf4 is important for the light dependent reaction of photosynthesis. To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified, these are as follows: The Ycf4 protein is firmly

neg: Chloroplast genes that code for a variety of things, mostly to do with the protein pipeline and photosynthesis. As in prokaryotes, genes in chloroplast DNA are organized into operons. Unlike prokaryotic DNA molecules, chloroplast DNA molecules contain introns (plant mitochondrial DNAs do too, but not human mtDNAs). Among land plants, the contents of the chloroplast genome are fairly similar. Over time, many parts of the chloroplast genome were transferred to the nuclear genome of the host, a process called "endosymbiotic gene transfer". As a result, the chloroplast genome is heavily reduced compared to that of free-living cyanobacteria. Chloroplasts may contain 60–100

neg: Magnesium in biology leads to an acidification of the stroma that inactivates key enzymes in carbon fixation, which all leads to the production of oxygen free radicals in the chloroplast that then cause oxidative damage. Magnesium in biology Magnesium is an essential element in biological systems. Magnesium occurs typically as the Mg ion. It is an essential mineral nutrient (i.e., element) for life and is present in every cell type in every organism. For example, ATP (adenosine triphosphate), the main source of energy in cells, must bind to a magnesium ion in order to be biologically active. What is called ATP is often

neg: Thylakoid antennae, the phycobilisomes. This macrostructure, as in the case of higher plants, shows some flexibility during changes in the physicochemical environment. Thylakoid A thylakoid is a membrane-bound compartment inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis. Thylakoids consist of a thylakoid membrane surrounding a thylakoid lumen. Chloroplast thylakoids frequently form stacks of disks referred to as grana (singular: granum). Grana are connected by intergranal or stroma thylakoids, which join granum stacks together as a single functional compartment. Thylakoids are flattened vesicles, which are stacked on each other like coins to form grana and intergrana

neg: ATP synthase or the plasma membrane in bacteria. During photosynthesis in plants, ATP is synthesized by ATP synthase using a proton gradient created in the thylakoid lumen through the thylakoid membrane and into the chloroplast stroma. ATP synthase consists of two main subunits, F and F, which has a rotational motor mechanism allowing for ATP production. Because of its rotating subunit, ATP synthase is a molecular machine. The F fraction derives its name from the term "Fraction 1" and F (written as a subscript letter "o", not "zero") derives its name from being the binding fraction for oligomycin, a type of naturally-derived

neg: Cytochrome b6f complex known as heme x). The inter-monomer space within the core of the cytochrome b6f complex dimer is occupied by lipids, which provides directionality to heme-heme electron transfer through modulation of the intra-protein dielectric environment. In photosynthesis, the cytochrome bf complex functions to mediate the transfer of electrons between the two photosynthetic reaction center complexes, from Photosystem II to Photosystem I, while transferring protons from the chloroplast stroma across the thylakoid membrane into the lumen. Electron transport via cytochrome bf is responsible for creating the proton gradient that drives the synthesis of ATP in chloroplasts. In a separate reaction, the cytochrome

neg: Thylakoid Thylakoid A thylakoid is a membrane-bound compartment inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis. Thylakoids consist of a thylakoid membrane surrounding a thylakoid lumen. Chloroplast thylakoids frequently form stacks of disks referred to as grana (singular: granum). Grana are connected by intergranal or stroma thylakoids, which join granum stacks together as a single functional compartment. Thylakoids are flattened vesicles, which are stacked on each other like coins to form grana and intergrana in the form of pile. Grana are green and intergrana are non-green. Each granum is composed a stack of 50 or

neg: Chloroplast cellular signals, reactive oxygen species are unstable molecules, so they probably don't leave the chloroplast, but instead pass on their signal to an unknown second messenger molecule. All these molecules initiate retrograde signaling—signals from the chloroplast that regulate gene expression in the nucleus. In addition to defense signaling, chloroplasts, with the help of the peroxisomes, help synthesize an important defense molecule, jasmonate. Chloroplasts synthesize all the fatty acids in a plant cell—linoleic acid, a fatty acid, is a precursor to jasmonate. One of the main functions of the chloroplast is its role in photosynthesis, the process by which light is

neg: Stomatal conductance stomatal opening occurs in many species and under many different conditions. Light is a major stimulus involved in stomatal conductance, and has two key elements that are involved in the process: the stomatal response to blue light, and photosynthesis in the guard cell's chloroplast. The stomata open when there is an increase in light, and they close when there is a decrease in light. This is because the blue light activates a receptor on the guard cell membrane which induces the pumping of protons of the cells, which creates an electrochemical gradient. This causes free floating potassium and other ions

neg: Chloroplast DNA 30–31 tRNAs, 21 ribosomal proteins, and four RNA polymerase subunits, involved in protein synthesis. For photosynthesis, the chloroplast DNA includes genes for 28 thylakoid proteins and the large Rubisco subunit. In addition, its genes encode eleven subunits of a protein complex which mediates redox reactions to recycle electrons, which is similar to the NADH dehydrogenase found in mitochondria. Over time, many parts of the chloroplast genome were transferred to the nuclear genome of the host, a process called "endosymbiotic gene transfer". As a result, the chloroplast genome is heavily reduced compared to that of free-living cyanobacteria. Chloroplasts may contain 60–100

neg: Light-dependent reactions is water, creating oxygen as a waste product. In anoxygenic photosynthesis various electron donors are used. Cytochrome b6f and ATP synthase work together to create ATP. This process is called photophosphorylation, which occurs in two different ways. In non-cyclic photophosphorylation, cytochrome b6f uses the energy of electrons from PSII to pump protons from the stroma to the lumen. The proton gradient across the thylakoid membrane creates a proton-motive force, used by ATP synthase to form ATP. In cyclic photophosphorylation, cytochrome b6f uses the energy of electrons from not only PSII but also PSI to create more ATP and to stop

neg: Chloroplast an electron transport chain. The molecules between the photosystems harness the electrons' energy to pump hydrogen ions into the thylakoid space, creating a concentration gradient, with more hydrogen ions (up to a thousand times as many) inside the thylakoid system than in the stroma. The hydrogen ions in the thylakoid space then diffuse back down their concentration gradient, flowing back out into the stroma through ATP synthase. ATP synthase uses the energy from the flowing hydrogen ions to phosphorylate adenosine diphosphate into adenosine triphosphate, or ATP. Because chloroplast ATP synthase projects out into the stroma, the ATP is synthesized there,

neg: RuBisCO in the compartment containing RuBisCO (chloroplast stroma). Several times during the evolution of plants, mechanisms have evolved for increasing the level of carbon dioxide in the stroma (see carbon fixation). The use of oxygen as a substrate appears to be a puzzling process, since it seems to throw away captured energy. However, it may be a mechanism for preventing overload during periods of high light flux. This weakness in the enzyme is the cause of photorespiration, such that healthy leaves in bright light may have zero net carbon fixation when the ratio of to reaches a threshold at which oxygen

neg: Chloroplast between their two cell membranes. These chloroplasts are called "muroplasts" (from Latin ""mura"", meaning "wall"). Other chloroplasts have lost the cyanobacterial wall, leaving an intermembrane space between the two chloroplast envelope membranes. The inner chloroplast membrane borders the stroma and regulates passage of materials in and out of the chloroplast. After passing through the TOC complex in the outer chloroplast membrane, polypeptides must pass through the TIC complex "(translocon on the inner chloroplast membrane)" which is located in the inner chloroplast membrane. In addition to regulating the passage of materials, the inner chloroplast membrane is where fatty acids, lipids, and

neg: Chloroplast as high atmospheric CO concentrations, these starch grains may grow very large, distorting the grana and thylakoids. The starch granules displace the thylakoids, but leave them intact. Waterlogged roots can also cause starch buildup in the chloroplasts, possibly due to less sucrose being exported out of the chloroplast (or more accurately, the plant cell). This depletes a plant's free phosphate supply, which indirectly stimulates chloroplast starch synthesis. While linked to low photosynthesis rates, the starch grains themselves may not necessarily interfere significantly with the efficiency of photosynthesis, and might simply be a side effect of another photosynthesis-depressing factor. Photorespiration can

neg: Chloroplast DNA protein (HC) coded by the chloroplast DNA that tightly packs each chloroplast DNA ring into a nucleoid has been found. In primitive red algae, the chloroplast DNA nucleoids are clustered in the center of a chloroplast, while in green plants and green algae, the nucleoids are dispersed throughout the stroma. The mechanism for chloroplast DNA (cpDNA) replication has not been conclusively determined, but two main models have been proposed. Scientists have attempted to observe chloroplast replication via electron microscopy since the 1970s. The results of the microscopy experiments led to the idea that chloroplast DNA replicates using a double displacement

neg: Chloroplast keeping it from folding prematurely. This is important because it prevents chloroplast proteins from assuming their active form and carrying out their chloroplast functions in the wrong place—the cytosol. At the same time, they have to keep just enough shape so that they can be recognized by the chloroplast. These proteins also help the polypeptide get imported into the chloroplast. From here, chloroplast proteins bound for the stroma must pass through two protein complexes—the TOC complex, or "translocon on the outer chloroplast membrane", and the TIC translocon, or "translocon on the inner chloroplast membrane translocon". Chloroplast polypeptide chains probably often

neg: Chloroplast each cell; they are star-shaped in "Zygnema", or may follow the shape of half the cell in order Desmidiales. In some algae, the chloroplast takes up most of the cell, with pockets for the nucleus and other organelles, for example, some species of "Chlorella" have a cup-shaped chloroplast that occupies much of the cell. All chloroplasts have at least three membrane systems—the outer chloroplast membrane, the inner chloroplast membrane, and the thylakoid system. Chloroplasts that are the product of secondary endosymbiosis may have additional membranes surrounding these three. Inside the outer and inner chloroplast membranes is the chloroplast stroma, a

neg: Ycf4 protein domain Ycf4 protein domain In molecular biology, the Ycf4 protein is involved in the assembly of the photosystem I complex which is part of an energy-harvesting process named photosynthesis. Without Ycf4, photosynthesis would be inefficient affecting plant growth. Ycf4 is located in the thylakoid membrane of the chloroplast. Ycf4 is important for the light dependent reaction of photosynthesis. To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified, these are as follows: The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain. Ycf4 co-fractionates with a protein complex larger than PSI

neg: Chloroplast not affected by this as much. Chloroplasts can pump K and H ions in and out of themselves using a poorly understood light-driven transport system. In the presence of light, the pH of the thylakoid lumen can drop up to 1.5 pH units, while the pH of the stroma can rise by nearly one pH unit. Chloroplasts alone make almost all of a plant cell's amino acids in their stroma except the sulfur-containing ones like cysteine and methionine. Cysteine is made in the chloroplast (the proplastid too) but it is also synthesized in the cytosol and mitochondria, probably because it

neg: Chloroplast carotenoids are synthesized. Some chloroplasts contain a structure called the chloroplast peripheral reticulum. It is often found in the chloroplasts of plants, though it has also been found in some angiosperms, and even some gymnosperms. The chloroplast peripheral reticulum consists of a maze of membranous tubes and vesicles continuous with the inner chloroplast membrane that extends into the internal stromal fluid of the chloroplast. Its purpose is thought to be to increase the chloroplast's surface area for cross-membrane transport between its stroma and the cell cytoplasm. The small vesicles sometimes observed may serve as transport vesicles to shuttle stuff between

neg: Chloroplast semi-porous membrane that small molecules and ions can easily diffuse across. However, it is not permeable to larger proteins, so chloroplast polypeptides being synthesized in the cell cytoplasm must be transported across the outer chloroplast membrane by the TOC complex, or "translocon on the outer chloroplast" membrane. The chloroplast membranes sometimes protrude out into the cytoplasm, forming a stromule, or stroma-containing tubule. Stromules are very rare in chloroplasts, and are much more common in other plastids like chromoplasts and amyloplasts in petals and roots, respectively. They may exist to increase the chloroplast's surface area for cross-membrane transport, because they are

neg: Chloroplast squeeze the chloroplast. This is when chloroplast constriction begins. In a few species like "Cyanidioschyzon merolæ", chloroplasts have a third plastid-dividing ring located in the chloroplast's intermembrane space. Late into the constriction phase, dynamin proteins assemble around the outer plastid-dividing ring, helping provide force to squeeze the chloroplast. Meanwhile, the Z-ring and the inner plastid-dividing ring break down. During this stage, the many chloroplast DNA plasmids floating around in the stroma are partitioned and distributed to the two forming daughter chloroplasts. Later, the dynamins migrate under the outer plastid dividing ring, into direct contact with the chloroplast's outer membrane, to

neg: Chloroplast DNA RNA editing resulting in a loss of function for photosynthesis genes. The movement of so many chloroplast genes to the nucleus means that many chloroplast proteins that were supposed to be translated in the chloroplast are now synthesized in the cytoplasm. This means that these proteins must be directed back to the chloroplast, and imported through at least two chloroplast membranes. Curiously, around half of the protein products of transferred genes aren't even targeted back to the chloroplast. Many became exaptations, taking on new functions like participating in cell division, protein routing, and even disease resistance. A few chloroplast genes

neg: Chemiosmosis is simply the negative of PMF(import). The spontaneity of proton import (from the P to the N side) is universal in all bioenergetic membranes. This fact was not recognized before the 1990s, because the chloroplast thylakoid lumen was interpreted as an interior phase, but in fact it is topologically equivalent to the exterior of the chloroplast. Azzone et al. stressed that the inside phase (N side of the membrane) is the bacterial cytoplasm, mitochondrial matrix, or chloroplast stroma; the outside (P) side is the bacterial periplasmic space, mitochondrial intermembrane space, or chloroplast lumen. Furthermore, 3D tomography of the mitochondrial inner

neg: Chloroplast many small circles. Most of the genome has migrated to the nucleus, and only critical photosynthesis-related genes remain in the chloroplast. The peridinin chloroplast is thought to be the dinophytes' "original" chloroplast, which has been lost, reduced, replaced, or has company in several other dinophyte lineages. The fucoxanthin dinophyte lineages (including "Karlodinium" and "Karenia") lost their original red algal derived chloroplast, and replaced it with a new chloroplast derived from a haptophyte endosymbiont. "Karlodinium" and "Karenia" probably took up different heterokontophytes. Because the haptophyte chloroplast has four membranes, tertiary endosymbiosis would be expected to create a six membraned chloroplast, adding

neg: Nucleoside-diphosphate kinase addition to this, plants have four types of NDPK isoforms. Cytosolic type I NDPK is involved in metabolism, growth, and stress responses in plants. Type II NDPK is concentrated in the chloroplast and it is believed to be involved in the photosynthesis process and the oxidative stress management, but its function is not yet known clearly. Type III NDPK targets both mitochondria and chloroplast, and it is mainly involved in energy metabolism. The localization and exact function of the type IV NDPK is not yet well known and needs further investigations. In addition, NDPK is associated with H2O2-mediated mitogen-activated protein

neg: Chloroplast both autotrophic and heterotrophic members. The most notable shared characteristic is the presence of cortical (outer-region) alveoli (sacs). These are flattened vesicles (sacs) packed into a continuous layer just under the membrane and supporting it, typically forming a flexible pellicle (thin skin). In dinoflagellates they often form armor plates. Many members contain a red-algal derived plastid. One notable characteristic of this diverse group is the frequent loss of photosynthesis. However, a majority of these heterotrophs continue to process a non-photosynthetic plastid. Apicomplexans are a group of alveolates. Like the helicosproidia, they're parasitic, and have a nonphotosynthetic chloroplast. They were once

neg: Photosynthesis that leads to the ultimate reduction of NADP to NADPH. In addition, this creates a proton gradient (energy gradient) across the chloroplast membrane, which is used by ATP synthase in the synthesis of ATP. The chlorophyll molecule ultimately regains the electron it lost when a water molecule is split in a process called photolysis, which releases a dioxygen (O) molecule as a waste product. The overall equation for the light-dependent reactions under the conditions of non-cyclic electron flow in green plants is: Not all wavelengths of light can support photosynthesis. The photosynthetic action spectrum depends on the type of accessory

neg: Chloroplast sheath cells are specialized for each stage of photosynthesis. In mesophyll cells, chloroplasts are specialized for the light reactions, so they lack RuBisCO, and have normal grana and thylakoids, which they use to make ATP and NADPH, as well as oxygen. They store in a four-carbon compound, which is why the process is called " photosynthesis". The four-carbon compound is then transported to the bundle sheath chloroplasts, where it drops off and returns to the mesophyll. Bundle sheath chloroplasts do not carry out the light reactions, preventing oxygen from building up in them and disrupting RuBisCO activity. Because of this,

neg: Chloroplast mature chloroplasts, it is rare for a starch granule to be completely consumed or for a new granule to accumulate. Starch granules vary in composition and location across different chloroplast lineages. In red algae, starch granules are found in the cytoplasm rather than in the chloroplast. In plants, mesophyll chloroplasts, which do not synthesize sugars, lack starch granules. The chloroplast stroma contains many proteins, though the most common and important is RuBisCO, which is probably also the most abundant protein on the planet. RuBisCO is the enzyme that fixes CO into sugar molecules. In plants, RuBisCO is abundant in all

neg: Elysia chlorotica activities. Although "Elysia chlorotica" are unable to synthesize their own chloroplasts, the ability to maintain the chloroplasts in a functional state indicates that "Elysia chlorotica" could possess photosynthesis-supporting genes within its own nuclear genome, possibly acquired through horizontal gene transfer. Since chloroplast DNA alone encodes for just 10% of the proteins required for proper photosynthesis, scientists investigated the "Elysia chlorotica" genome for potential genes that could support chloroplast survival and photosynthesis. The researchers found a vital algal gene, "psbO" (a nuclear gene encoding for a manganese-stabilizing protein within the photosystem II complex) in the sea slug's DNA, identical to the

neg: Photosystem to the chlorophyll via a redox-active tyrosine. Photoexcited electrons travel through the cytochrome b6f complex to photosystem I via an electron transport chain set in the thylakoid membrane. This energy fall is harnessed, (the whole process termed chemiosmosis), to transport hydrogen (H) through the membrane, into the thylakoid lumen, to provide a potential energy difference between the thylakoid lumen space and the chloroplast stroma, which amounts to a proton-motive force that can be used to generate ATP. The protons are transported by the plastoquinone. If electrons only pass through once, the process is termed noncyclic photophosphorylation. When the electron reaches

neg: Chloroplast DNA kilodaltons. The other two proteins, Toc64 and Toc12, are associated with the core complex but are not part of it. Toc34 is an integral protein in the outer chloroplast membrane that's anchored into it by its hydrophobic C-terminal tail. Most of the protein, however, including its large guanosine triphosphate (GTP)-binding domain projects out into the stroma. Toc34's job is to catch some chloroplast preproteins in the cytosol and hand them off to the rest of the TOC complex. When GTP, an energy molecule similar to ATP attaches to Toc34, the protein becomes much more able to bind to many chloroplast

neg: Chloroplast DNA explain the multiple A → G gradients seen in plastomes. This shortcoming is one of the biggest for the linear structure theory. The chloroplast genome most commonly includes around 100 genes which code for a variety of things, mostly to do with the protein pipeline and photosynthesis. As in prokaryotes, genes in chloroplast DNA are organized into operons. Introns are common in chloroplast DNA molecules, while they are rare in prokaryotic DNA molecules (plant mitochondrial DNAs commonly have introns, but not human mtDNA). Among land plants, the contents of the chloroplast genome are fairly similar—they code for four ribosomal RNAs,

neg: TIC/TOC complex protein. In the cytosol, a transit peptide that signals for transit of the protein to the chloroplast is exposed. This initiates transport and translocation through the TIC/TOC complexes into the stroma of the chloroplast. It is there that a signal peptidase cleaves the stromal transit peptide, only to reveal a second transit peptide sequence underneath; this time directing to the thylakoid membrane. TIC/TOC complex The TIC and TOC complexes are translocons located in the chloroplast of a eukaryotic cell, that is, protein complexes that facilitate the transfer of proteins in and out through the chloroplast's membrane. The TIC complex "(translocon

neg: Stomatal conductance to enter the guard cells via a channel. The increase in solutes within the guard cells leads to a decrease in the osmotic potential of the cells, causing water to flood in, the guard cell's to become enlarged, and therefore open.The second key element involved in light-dependent stomatal opening is the photosynthesis in the guard cell's chloroplast. This event also increases the amount of solutes within the guard cell. Carbon Dioxide enters the chloroplasts which increases the amount of photosynthesis. This increases the amount of solutes that are being produced by the chloroplast which are then released into the cytosol

neg: Gerontoplast Gerontoplast A gerontoplast is a plastid that develops from a chloroplast during the senescing of plant foliage. Gerontoplast development is generally seen to be the process of grana being unstacked, loss of thylakoid membranes, and large accumulation of plastoglobuli. The term "gerontoplast" was first introduced in 1977 to define the unique features of the plastid formed during leaf senescence. The process of senescence brings about regulated dismantling of cellular organelles involved in photosynthesis. Chloroplasts responsible for gas exchange in stomata are the last organelles to degrade during senescence, and give plants the green color. The formation of gerontoplasts from chloroplasts

neg: Thylakoid a CF1FO-ATP synthase similar to the mitochondrial ATPase. It is integrated into the thylakoid membrane with the CF1-part sticking into stroma. Thus, ATP synthesis occurs on the stromal side of the thylakoids where the ATP is needed for the light-independent reactions of photosynthesis. The electron transport protein plastocyanin is present in the lumen and shuttles electrons from the cytochrome b6f protein complex to photosystem I. While plastoquinones are lipid-soluble and therefore move within the thylakoid membrane, plastocyanin moves through the thylakoid lumen. The lumen of the thylakoids is also the site of water oxidation by the oxygen evolving complex associated

neg: Phase transition process of protein folding and DNA melting, liquid crystal-like transitions in the process of DNA condensation, and cooperative ligand binding to DNA and proteins with the character of phase transition. In "biological membranes", gel to liquid crystalline phase transitions play a critical role in physiological functioning of biomembranes. In gel phase, due to low fluidity of membrane lipid fatty-acyl chains, membrane proteins have restricted movement and thus are restrained in exercise of their physiological role. Plants depend critically on photosynthesis by chloroplast thylakoid membranes which are exposed cold environmental temperatures. Thylakoid membranes retain innate fluidity even at relatively low temperatures

neg: Magnesium in biology (1989) were unable to reproduce the result using older spinach chloroplasts. Deshaies "et al." had stated in their paper that older pea chloroplasts showed less significant changes in Mg content than those used to form their conclusions. The relative proportion of immature chloroplasts present in the preparations may explain these observations. The metabolic state of the chloroplast changes considerably between night and day. During the day, the chloroplast is actively harvesting the energy of light and converting it into chemical energy. The activation of the metabolic pathways involved comes from the changes in the chemical nature of the stroma on

neg: Pyrenoid of the biophysical CCM reliant upon a pyrenoid considers active transport of bicarbonate from the extracellular environment to the vicinity of RuBisCO, via transporters at the plasma membrane, the chloroplast membrane, and thylakoid membranes. Carbonic anhydrases in the periplasm and also in the cytoplasm and chloroplast stroma are thought to contribute to maintaining an intracellular pool of dissolved inorganic carbon, mainly in the form of bicarbonate. This bicarbonate is then thought to be pumped into the lumen of transpyrenoidal thylakoids, where a resident carbonic anhydrase is hypothesised to convert bicarbonate to CO, and saturate RuBisCO with carboxylating substrate. It is

neg: Chloroplast edges of the thylakoid disks or sheets. They are also more common on stromal thylakoids than on granal ones. Starch granules are very common in chloroplasts, typically taking up 15% of the organelle's volume, though in some other plastids like amyloplasts, they can be big enough to distort the shape of the organelle. Starch granules are simply accumulations of starch in the stroma, and are not bounded by a membrane. Starch granules appear and grow throughout the day, as the chloroplast synthesizes sugars, and are consumed at night to fuel respiration and continue sugar export into the phloem, though in

neg: Thylakoid nuclear genome need two targeting signals for proper localization: An N-terminal chloroplast targeting peptide (shown in yellow in the figure), followed by a thylakoid targeting peptide (shown in blue). Proteins are imported through the translocon of outer and inner membrane (Toc and Tic) complexes. After entering the chloroplast, the first targeting peptide is cleaved off by a protease processing imported proteins. This unmasks the second targeting signal and the protein is exported from the stroma into the thylakoid in a second targeting step. This second step requires the action of protein translocation components of the thylakoids and is energy-dependent. Proteins

neg: Chloroplast found in all chloroplasts, but become more common when the chloroplast is under oxidative stress, or when it ages and transitions into a gerontoplast. Plastoglobuli also exhibit a greater size variation under these conditions. They are also common in etioplasts, but decrease in number as the etioplasts mature into chloroplasts. Plastoglubuli contain both structural proteins and enzymes involved in lipid synthesis and metabolism. They contain many types of lipids including plastoquinone, vitamin E, carotenoids and chlorophylls. Plastoglobuli were once thought to be free-floating in the stroma, but it is now thought that they are permanently attached either to a thylakoid

neg: Protein targeting in positively charged amino acids and hydroxylated ones. Proteins are targeted to submitochondrial compartments by multiple signals and several pathways. Targeting to the outer membrane, intermembrane space, and inner membrane often requires another signal sequence in addition to the matrix targeting sequence. The preprotein for chloroplasts may contain a stromal import sequence or a stromal and thylakoid targeting sequence. The majority of preproteins are translocated through the Toc and Tic complexes located within the chloroplast envelope. In the stroma the stromal import sequence is cleaved off and folded as well as intra-chloroplast sorting to thylakoids continues. Proteins targeted to the

neg: Gilbert Morgan Smith Medal and energy transfer in the photosynthetic apparatus of red and blue-green algae. Jean-David Rochaix (1991) For his elegant, inventive studies in Chlamydomonas using genetics along with cell and molecular biology to explain molecular mechanisms of chloroplast biogenesis, photosynthesis, and nuclear-chloroplast interactions. Ruth Sager (1988) For her key role in the developing our understanding of genetic systems in organelles though her studies of chloroplast inheritance in the green alga Chlamydomonas Richard C. Starr (1985) For his important work, which explained the sexuality of desmids and green algae. This was the first time the details of meiosis had been set forth for

neg: Chloroplast and carotenoids that absorb light energy and use it to energize electrons. Molecules in the thylakoid membrane use the energized electrons to pump hydrogen ions into the thylakoid space, decreasing the pH and turning it acidic. ATP synthase is a large protein complex that harnesses the concentration gradient of the hydrogen ions in the thylakoid space to generate ATP energy as the hydrogen ions flow back out into the stroma—much like a dam turbine. There are two types of thylakoids—granal thylakoids, which are arranged in grana, and stromal thylakoids, which are in contact with the stroma. Granal thylakoids are pancake-shaped

neg: Magnesium in biology regularly stabilize membranes by the cross-linking of carboxylated and phosphorylated head groups of lipids. However, the envelope membrane of "E. coli" has also been shown to bind Na, K, Mn and Fe. The transport of ions is dependent on both the concentration gradient of the ion and the electric potential (ΔΨ) across the membrane, which will be affected by the charge on the membrane surface. For example, the specific binding of Mg to the chloroplast envelope has been implicated in a loss of photosynthetic efficiency by the blockage of K uptake and the subsequent acidification of the chloroplast stroma. The

neg: Magnesium in biology Mg-starved plants under low light conditions, the percentage of Mg bound to chlorophyll has been recorded at 50%. Presumably, this imbalance has detrimental effects on other cellular processes. Mg toxicity stress is more difficult to develop. When Mg is plentiful, in general the plants take up the ion and store it (Stelzer "et al.", 1990). However, if this is followed by drought then ionic concentrations within the cell can increase dramatically. High cytoplasmic Mg concentrations block a K channel in the inner envelope membrane of the chloroplast, in turn inhibiting the removal of H ions from the chloroplast stroma. This

neg: Chloroplast are not connected to the endoplasmic reticulum. The fact that apicomplexans still keep their nonphotosynthetic chloroplast around demonstrates how the chloroplast carries out important functions other than photosynthesis. Plant chloroplasts provide plant cells with many important things besides sugar, and apicoplasts are no different—they synthesize fatty acids, isopentenyl pyrophosphate, iron-sulfur clusters, and carry out part of the heme pathway. This makes the apicoplast an attractive target for drugs to cure apicomplexan-related diseases. The most important apicoplast function is isopentenyl pyrophosphate synthesis—in fact, apicomplexans die when something interferes with this apicoplast function, and when apicomplexans are grown in an isopentenyl pyrophosphate-rich

neg: Cyanobacteria cyanobacteria even display the circadian rhythms that were once thought to exist only in eukaryotic cells (see bacterial circadian rhythms). While contemporary cyanobacteria are linked to the plant kingdom as descendants of the progenitor of the endosymbiotic chloroplast, there are several features which are unique to this group. Cyanobacteria use the energy of sunlight to drive photosynthesis, a process where the energy of light is used to synthesize organic compounds from carbon dioxide. Because they are aquatic organisms, they typically employ several strategies which are collectively known as a "carbon concentrating mechanism" to aid in the acquisition of inorganic carbon

neg: Sucrose-phosphate synthase light stimulus. Glucose 6-phosphate binds to an allosteric site, resulting in conformational changes to SPS that increase the enzyme's affinity for the glucosyl accepting substrate. Inorganic phosphate can also bind to this allosteric site, preventing glucose 6-phosphate activation of SPS. Like regulation via phosphorylation, this regulation strategy is also closely related to photosynthesis, as high rates of photosynthesis will deplete levels of inorganic phosphate and increase concentrations of glucose 6-phosphate in the chloroplast. Overall, increased rates of photosynthesis will increase SPS activity. SPS plays a major role in partitioning carbon between sucrose and starch in photosynthetic and non-photosynthetic tissues, affecting

neg: Terrestrial biological carbon cycle soils remains there for some time before being respired by heterotrophs. Thus carbon is transferred in every step of the food chain from one organism to another. Autotrophs, such as trees and other green plants, use photosynthesis to convert carbon dioxide during primary production, releasing oxygen in the process. This process occurs most quickly in ecosystems with high amounts of growth, such as in young forests. Because carbon is consumed in the process of autotrophic growth, more carbon is consumed in spring and summer during daytime than in winter and at night, when photosynthesis no longer takes place in most

neg: Bienertia sinuspersici Bienertia sinuspersici Bienertia sinuspersici is a flowering plant that currently is classified in the family "Amaranthaceae", although it was previously considered to belong to the family Chenopodiaceae. "Bienertia sinuspersici" conducts C photosynthesis, but lacks the two cell types, bundle sheath and mesophyll cells, that are typical of Kranz anatomy in most C plants. "Bienertia sinuspersici" and three other former chenopods ("Suaeda aralocaspica", "Bienertia cycloptera", and "Bienertia kavirense") instead conduct single-celled C photosynthesis within individual chlorenchyma cells. Single-celled C photosynthesis is achieved in "Bienertia sinuspersici" by the subcellular partitioning of dimorphic chloroplasts into two distinct cellular compartments, the central chloroplast compartment

neg: Albinism or injury, however, this is contrary to definitions where the condition is inherited. In plants, albinism is characterised by partial or complete loss of chlorophyll pigments and incomplete differentiation of chloroplast membranes. Albinism in plants interferes with photosynthesis, which can reduce survivability. Some plant variations may have white flowers or other parts. However, these plants are not totally devoid of chlorophyll. Terms associated with this phenomenon are "hypochromia" and "albiflora". Biological pigments are substances produced by living organisms that have a colour resulting from selective colour absorption. What we perceive as "colour" are the wavelengths of light that are not

neg: Reclinomonas sequenced since, and the data were similar. It has been described as an excavate. "R. Americana" is a large protozoan that ingests bacteria. Such phagocytosis is thought to be how ancestral (two billion years ago) eucaryotes (true nucleus to hold DNA) acquired mitochondrial and chloroplast organelles to perform oxidative metabolism and photosynthesis. "R. Americana" has played a significant role in understanding the scope of antiquity of what bacterial DNA was captured because its mitochondrial DNA collection is more complete than that of other eukaryotes, which have discarded many and various genes . Reclinomonas Reclinomonas is a monotypic genus of jakobid

neg: Thylakoid to the lumen. During photosynthesis, the lumen becomes acidic, as low as pH 4, compared to pH 8 in the stroma. This represents a 10,000 fold concentration gradient for protons across the thylakoid membrane. The protons in the lumen come from three primary sources. The proton gradient is also caused by the consumptions of protons in the stroma to make NADPH from NADP+ at the NADP reductase. The molecular mechanism of ATP (Adenosine triphosphate) generation in chloroplasts is similar to that in mitochondria and takes the required energy from the proton motive force (PMF). However, chloroplasts rely more on the

neg: Thylakoid between the endoplasmic reticulum and inner membrane of the plastid envelope and transported from the inner membrane to the thylakoids via vesicles. The thylakoid lumen is a continuous aqueous phase enclosed by the thylakoid membrane. It plays an important role for photophosphorylation during photosynthesis. During the light-dependent reaction, protons are pumped across the thylakoid membrane into the lumen making it acidic down to pH 4. In higher plants thylakoids are organized into a granum-stroma membrane assembly. A granum (plural grana) is a stack of thylakoid discs. Chloroplasts can have from 10 to 100 grana. Grana are connected by stroma thylakoids,

neg: Micrasterias not used, taken up by many small round pyrenoids which are embedded in the chloroplast. They convert the sugar to a starch for storage. Micrasterias can produce both asexually and sexually. Asexual reproduction occurs via mitosis. When this occurs the genetic material of "Micrasterias" is duplicated and two small semi-cells grow between the original semi-cells, gradually increasing in size. Sexual reproduction occurs through a process called conjugation whereby two organisms come together and fuse their haploid cells to form a diploid zygote. This zygote typically forms a thick protective wall which can allow the organism to remain dormant for many

neg: Ferredoxin Ferredoxin Ferredoxins (from Latin "ferrum": iron + redox, often abbreviated "fd") are iron–sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co. and applied to the "iron protein" first purified in 1962 by Mortenson, Valentine, and Carnahan from the anaerobic bacterium "Clostridium pasteurianum". Another redox protein, isolated from spinach chloroplasts, was termed "chloroplast ferredoxin". The chloroplast ferredoxin is involved in both cyclic and non-cyclic photophosphorylation reactions of photosynthesis. In non-cyclic photophosphorylation, ferredoxin is the last electron acceptor thus reducing the enzyme NADP reductase. It accepts electrons

neg: Botany sequenced, small stature and short generation times. Corn has been used to study mechanisms of photosynthesis and phloem loading of sugar in plants. The single celled green alga "Chlamydomonas reinhardtii", while not an embryophyte itself, contains a green-pigmented chloroplast related to that of land plants, making it useful for study. A red alga "Cyanidioschyzon merolae" has also been used to study some basic chloroplast functions. Spinach, peas, soybeans and a moss "Physcomitrella patens" are commonly used to study plant cell biology. "Agrobacterium tumefaciens", a soil rhizosphere bacterium, can attach to plant cells and infect them with a callus-inducing Ti plasmid

neg: Chloroplast like "Arabidopsis" and wheat. A chloroplast is a type of organelle known as a plastid, characterized by its two membranes and a high concentration of chlorophyll. Other plastid types, such as the leucoplast and the chromoplast, contain little chlorophyll and do not carry out photosynthesis. Chloroplasts are highly dynamic—they circulate and are moved around within plant cells, and occasionally pinch in two to reproduce. Their behavior is strongly influenced by environmental factors like light color and intensity. Chloroplasts, like mitochondria, contain their own DNA, which is thought to be inherited from their ancestor—a photosynthetic cyanobacterium that was engulfed by an

neg: Thylakoid with known functions, 42% are involved in photosynthesis. The next largest functional groups include proteins involved in protein targeting, processing and folding with 11%, oxidative stress response (9%) and translation (8%). Thylakoid membranes contain integral membrane proteins which play an important role in light harvesting and the light-dependent reactions of photosynthesis. There are four major protein complexes in the thylakoid membrane: Photosystem II is located mostly in the grana thylakoids, whereas photosystem I and ATP synthase are mostly located in the stroma thylakoids and the outer layers of grana. The cytochrome b6f complex is distributed evenly throughout thylakoid membranes. Due

neg: Magnesium in biology for the efficiency of photosynthesis, allowing phase transitions to occur. Mg is probably taken up into chloroplasts to the greatest extent during the light-induced development from proplastid to chloroplast or etioplast to chloroplast. At these times, the synthesis of chlorophyll and the biogenesis of the thylakoid membrane stacks absolutely require the divalent cation. Whether Mg is able to move into and out of chloroplasts after this initial developmental phase has been the subject of several conflicting reports. Deshaies "et al." (1984) found that Mg did move in and out of isolated chloroplasts from young pea plants, but Gupta and Berkowitz

neg: Two-component regulatory system albicans", genes found in the nuclear genome likely originated from endosymbiosis and remain targeted to the mitochondria. Two-component systems are well-integrated into developmental signaling pathways in plants, but the genes probably originated from lateral gene transfer from chloroplasts. An example is the chloroplast sensor kinase (CSK) gene in "Arabidopsis thaliana", derived from chloroplasts but now integrated into the nuclear genome. CSK function provides a redox-based regulatory system that couples photosynthesis to chloroplast gene expression; this observation has been described as a key prediction of the CoRR hypothesis, which aims to explain the retention of genes encoded by endosymbiotic organelles. It

neg: Photosynthesis host cells and the genes in this chloroplast DNA resemble those found in cyanobacteria. DNA in chloroplasts codes for redox proteins such as those found in the photosynthetic reaction centers. The CoRR Hypothesis proposes that this Co-location of genes with their gene products is required for Redox Regulation of gene expression, and accounts for the persistence of DNA in bioenergetic organelles. The biochemical capacity to use water as the source for electrons in photosynthesis evolved once, in a common ancestor of extant cyanobacteria. The geological record indicates that this transforming event took place early in Earth's history, at least 2450–2320

neg: Hill reaction extraction of the chloroplasts from the plant cellular environment. The ferrocyanide is reduced (just as NADP is when the chloroplast is in vivo) while water (HO) is oxidized into oxygen (O) and hydrogen cations during the reaction. By using this technique to observe the reaction, Hill revealed a variety of valuable facts about photosynthesis. The Hill reaction confirms that oxygen (O) is produced by a reaction that is separate from carbon dioxide (CO) fixation. The reaction in which oxygen is released requires light; therefore the Hill reaction can be described as the light dependent reaction of photosynthesis. The reaction in

neg: Hill reaction which oxygen is released takes place within the chloroplast of plants and the Hill reaction demonstrated that the release of oxygen (O) is only a partial reaction which requires one step of photosynthesis. The Hill reaction implies that the light dependent reaction of photosynthesis is a result of a series of redox reactions and a suitable terminal electron acceptor is required for that reaction to occur. Plants have natural electron acceptors such as NADP, that play a major role in the oxidation of water. The Hill reaction also shows that the natural electron acceptors of the reaction can be substituted

neg: Photosynthesis plant populations. Gas exchange systems that offer control of CO levels, above and below ambient, allow the common practice of measurement of A/Ci curves, at different CO levels, to characterize a plant’s photosynthetic response. Integrated chlorophyll fluorometer – gas exchange systems allow a more precise measure of photosynthetic response and mechanisms. While standard gas exchange photosynthesis systems can measure Ci, or substomatal CO levels, the addition of integrated chlorophyll fluorescence measurements allows a more precise measurement of C to replace Ci. The estimation of CO at the site of carboxylation in the chloroplast, or C, becomes possible with the measurement

neg: Chloroplast large sheets that link multiple grana, or narrow to tube-like bridges between grana. While different parts of the thylakoid system contain different membrane proteins, the thylakoid membranes are continuous and the thylakoid space they enclose form a single continuous labyrinth. Thylakoids (sometimes spelled "thylakoïds"), are small interconnected sacks which contain the membranes that the light reactions of photosynthesis take place on. The word "thylakoid" comes from the Greek word "thylakos" which means "sack". Embedded in the thylakoid membranes are important protein complexes which carry out the light reactions of photosynthesis. Photosystem II and photosystem I contain light-harvesting complexes with chlorophyll

neg: Howard Griffiths (scientist) wasteful oxygenase activity and the salvage pathway, photorespiration, leading to improved radiation, water and nitrogen use by C₄ plants. his programmes are focusing on He has longstanding interests in Crassulacean Acid Metabolism (CAM photosynthesis) and has worked in Trinidad and Panama on tropical epiphytes such as the bromeliad and orchid and cacti families, and now has interests in bioenergy production by "Agave". He has investigated carbon concentrating mechanisms (see photosynthesis) in algae and hornworts, focusing on the molecular determinants of the chloroplast pyrenoid in "Chlamydomonas". He has a major collaboration funded by Biotechnology and Biological Sciences Research Council (BBSRC) and