هرباریومهای ایران

سه شنبه 26 اردیبهشت 1391 06:30 ب.ظ

نویسنده : عسکر اله قلی

 

 

1 – هرباریوم دانشکده کشاورزی کرج

اروین گائوبا استاد اتریشی همراه با شاگردانش با جمع آوری گیاهان ناحیه کرج، اولین قدم را در تاسیس هرباریوم مدرسه عالی فلاحت (کشاورزی) برداشتند. دو تن از شاگردان گائوبا، حبیب الله ثابتی (1316) و عین الله بهبودی  در امر گردآوری گیاهان و تکمیل موزه با او همکاری داشتند. محققینی که در اداره آن و گردآوری گیاهان سهیم بوده اند:

اروین گائوبا، دکتر اسفندیار اسفندیاری، مهندس عین الله بهبودی، مهندس اسماعیل میردامادی، دکتر زین العابدین ملکی، دکتر حبیب الله ثابتی، دکتر محمد صانعی شریعت پناهی، دکتر حسین لسانی، دکتر جواد میمندی نژاد، مهندس محمد صادق فخر طباطبائی، دکتر فوزیه طاهباز، مهندس تیمور رمک معصومی.

 

2 – هرباریوم موزه تاریخ طبیعی ایران

در همان سالهائی که گائوبا در کرج به گردآوری گیاهان مشغول بود، آقای دکتر احمد پارسا استاد گیاهشناسی دانشکده علوم از سال 1316 به اتفاق بعضی از شاگردان خود به جمع آوری گیاهان تفرش و نقاط دیگر پرداخت. در سال 1324 موزه علوم طبیعی را با بودجه وزارت فرهنگ آن زمان در بخشی از ساختمان دبستان حکیم نظامی سابق تاسیس کرد و گیاهان را به آن مکان به منظور تاسیس "هربیه ملی"  انتقال داد. بدینسان پایه "هرباریوم موزه علوم طبیعی ایران" گذاشته شد. در 1333 این موزه به ساختمان دانشکده علوم دانشگاه تهران منتقل شد. در این سالها آقایان دکتر صادق مبین استاد گیاهشناسی دانشکده علوم، دکتر زین العابدین ملکی عضو هیئت علمی دانشکده علوم، دکتر علی زرگری، خانم بتول بغایری، خانم پریگل دادجو درهرباریوم فعالیت می کردند. در سال 1335 مسئولیت هرباریوم به آقای دکتر زرگری واگذار شد. در همان سال با تاسیس موسسه مطعالعات مناطق خشک در دانشگاه تهران گیاهان این موزه به موسسه مزبور منتقل گردید (از فسیلها و سنگها اطلاعی در دست نیست) و بدینسان نام "هرباریوم موزه علوم طبیعی" از میان رفت. آقای دکتر زرگری مسئولیت هرباریوم موسسه مطالعات مناطق خشک را تا 1340 به عهده داشت.

با انحلات موسسه مذکور، گیاهان هربایوم آن به دانشسرای عالی و سپس به دانشکده داروسازی دانشگاه تهران منتقل شد و مبنای هرباریوم آن دانشکده قرار گرفت. بدینسان هربایوم مزبور که حاوی تقریبا همه گیاهان مذکور در "فلور ایران" دکتر پارسا بود (از جمله نزدیک به 250 گونه جدیدی که وی از ایران برای فلور دنیا تشخیص داده بود و به نام خود او بود و نمونه اول آنها در موزه کیو (انگلستان) هنوز به عنوان تایپ وجود دارد) در این انتقال ها از میان رفت.

 

3 – هرباریوم موسسه بررسی آقات و بیماریهای گیاهی (موسسه گیاهپزشکی اوین)

این هرباریوم در سال 1327 بنیانگذاری شد.

در آن سال دو نفر گیاهشناس خارجی به نامها دکتر رشینگر اتریشی و دکتر پل الن سوئیسی به ایران آمدند و به اتفاق دکتر اسفندیار اسفندیاری رئیس موسسه برای جمع آوری گیاه به استانهای جنوبی ایران مسافرتهائی انجام دادند. در سالهای 1328 – 1336 برخی از پژوهشگران وابسته به موسسه بویژه دکتر موسی ایرانشهر، مرحوم مهندس عین الله بهبودی، مرحوم دکتر علی منوچهری، دکتر قوام الدین شریف، مهندس هایک میرزایانس، مهندس میر صلواتیان، مهندس قدرت الله فرحبخش، دکتر فریدون ترمه، مهندس محمود موسوی، محققان موسسه مزبور سفرهای متعددی به منظور گردآوری نمونه های گیاهی و غنی ساختن هرباریوم آن انجام دادند. انتقال مجموعه گیاهان گردآوری شده وزارت کشاورزی، واگذاری شماری از نمونه های تکراری پابو (به توسط سازمان جنگلها) و نمونه هائی از مجموعه قدیم گائوبا به این هرباریوم محتویات آن را غنی تر ساخت. در سال 1354، نمونه های گیاهان شمال ایران نیز که آقای دکتر حبیب الله ثابتی و همکارانش در موسسه اکولوژی نوشهر گرد آورده بودند به این هرباریوم انتقال یافت.

در سالهای اخیر  آقایان دکتر اسفندیاری، دکتر ایرانشهر، دکتر حبیبی، دکتر ترمه، مهندس  موسوی، مهندس امینی راد، خانم فریده متین، خانم فاطمه آغابیگی، خانم جوادی و خانم ساجدی در هرباریوم موسسه گیاهپزشکی اوین فعالیت داشته اند.مسئولیت کنونی هرباریوم با آقای مهندس امینی راد است.

یکی از برتریهای این هرباریوم، مجموعه ارزشمند قارچهای آن است که در گردآوری و شناسائی آنها و تشکیل موزه قارچها، آقای دکتر جعفر ارشاد بسیار تلاش کرده اند. از محققان این بخش باید از آقایان مهندس بهمن دانش پژوه، مهندس جمشید فاتحی، مهندس مهرداد عباسی، و خانم مریم صابری را ذکر کرد.

 

4 – هرباریوم دانشکده علوم دانشگاه تهران

بنیاد این هرباریوم در سال 1338 توسط آقای دکتر صادق مبین، استاد گیاهشناسی این دانشکده نهاده شد. از بدو تاسیس آقای دکتر احمد قهرمان با ایشان همکاری داشتند.

از دیگر اعضای این هرباریوم باید از آقایان والتر آغوستین سنگر و مرحوم آقای دکتر غلامحسین طریقی نام برد. همچنین خانمها بتول بغایری، پریگل دادجو و فاطمه سعید آبادی با این هرباریوم همکاری داشته اند.

از آن پس تا سال 1357 آقای دکتر احمد قهرمان با همکاری برخی از آن افراد به اداره و تکمیل این هرباریوم پرداختند که مبنای هرباریوم مرکزی دانشگاه تهران شد. این مجموعه بخشی از هرباریوم مرکزی است كه از آن برای آموزش سیستماتیک گیاهی در بخش گیاهشناسی گروه زیست شناسی دانشکده علوم استفاده شده می گردد.

 

5 – هرباریوم دانشکده داروسازی دانشگاه تهران

بنیان این موزه گیاهی از 1341  با انتقال گیاهان هرباریوم دکتر پارسا به آن دانشکده نهاده شد. از همکاران آن هرباریوم، دکتر حسین گل گلاب، دکتر علی زرگری، بوده اند. در سالهای اخیر سرپرستی این هرباریوم با آقای دکتر غلامرضا امین از اعضای دانشکده داروسازی بوده است.یکی از جنبه های اهمیت این هرباریوم وجود برخی از نمونه های دکتر پارسا در آن است.

     

6 – هرباریوم موسسه تحقیقات جنگلها و مراتع

 این هرباریوم بخشی از موسسه تحقیقات جنگلها و مراتع كشور است که قبلا وابسته به وزارت کشاورزی، وزارت جهاد و اکنون وابسته به وزارت جهاد كشاورزی است.

هرباریوم کنونی از ادغام دو هرباریوم در سال 1358 بوجود آمد. یکی مجموعه پیشین موسسه تحقیقات جنگلها و مراتع و دیگری هرباریوم باغ ملی گیاهشناسی ایران. هرباریوم اخیر در سال 1346 که موسسه گیاهشناسی ایران تشکیل یافت، با نام "هرباریوم ملی" کار خود را شروع کرد. سرپرستی هرباریوم در بدو تاسیس با آقای هوشمند فروغی بود. سرپرستی هرباریوم موسسه تحقیقات جنگلها و مراتع از آغاز تاسیس با آقای مهندس پرویز باباخانلو بود. مسئول کنونی این هرباریوم با آقای دکتر علی اصغر معصومی است.

از بدو تشکیل هرباریوم باغ گیاهشناسی ملی ایران در زمانهای مختلف محققان متعددی در آن به همکاری و پژوهش اشتغال داشته اند:

آقایان دکتر حبیب الله ثابتی، مهندس هوشمند فروغی، مهندس منصور ریاضی، مرحوم دکتر وندلبو، دکتر رونه مارک خانم دکتر زیبا جمزاد، دکتر علی اصغر معصومی،  دکتر مصطفی اسدی،  مهندس عطاالله شیردلپور، دکتر ولی الله مظفریان، مهندس مصطفی قلی نوروزی ، مهندس محبوبه خاتمساز، مهندس فاطمه آقابیگی، مهندس خدیجه اخیانی، مهندس بهنام حمزه، مهندس رحمان آزادی، مهندس سید رضا صفوی.

7 – هرباریوم مرکزی دانشگاه تهران

این هرباریوم که در بهمن ماه 1367 رسما افتتاح شد، فعالیت علمی و تشكیلاتی خود را  از سال 1362 شروع کرده بود. بنبانگذار این هرباریوم مرحوم آقای دکتر احمد قهرمان استاد گیاهشناسی پردیس علوم  بوده و سرپرستی آن را تا سال 1386 به عهده داشتند. هسته اصلی گیاهان این هرباریوم بر اساس تدوین فلور رنگی ایران (طرح مشترك دانشگاه تهران و موسسه تحقیقات جنگلها و مراتع كشور) می باشد که طرح آن از سال 1354 شروع شده و هم اكنون نیز ادامه دارد. در جریان اجرای طرح فلور رنگی ایران، گیاهان جمع آوری شده نامگذاری و به هرباریوم مرکزی منتقل می شوند. بخش دیگری از گیاهان هرباریوم مربوط به طرحهای مطالعات فلورستیکی و پوشش گیاهی هرباریوم مرکزی است که توسط محققین آن در مناطق مختلف اجرا شده اند. بخش دیگری از گیاهان هرباریوم مربوط به رساله های کارشناسی ارشد و دکتری است که توسط دانشجویان جمع آوری شده اند.

Flora of Iran




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HERBARIUM

سه شنبه 26 اردیبهشت 1391 06:18 ب.ظ

نویسنده : عسکر اله قلی
A herbarium is a collection of plant samples preserved for long-term study. These materials may include pressed and mounted plants, seeds, wood sections, pollen, microscope slides, frozen DNA extractions, and fluid-preserved flowers or fruits; all are generally referred to as herbarium specimens. Worldwide there are over 300 million specimens preserved for research in herbaria (plural for herbarium).

Herbaria are usually associated with universities, museums, or botanical gardens. The first is believed to have been established in 1570 in Bologna, Italy, by Luca Ghini. There are now around 4,000 herbaria in over 165 countries. A world catalog of public herbaria, Index Herbariorum, is published periodically by the International Association for Plant Taxonomy and provided on the web at: http://sciweb.nybg.org/science2/IndexHerbariorum.asp. Each herbarium in Index Herbariorum is assigned an official acronym (code) that is used as a standard for referring to the institution and its specimens.

Approximate list of the ten largest herbaria in the world (also see List of Herbaria at Wikipedia and Index Herbariorum, the official registry):

acronymlocationnamespecimens (ca. millions)
P, PCParis, FranceMuséum National d'Histoire Naturelle9.5
NYNew York, USANew York Botanical Garden7.2
LESt. Petersburg, RussiaKomarov Botanical Institute7.2
KLondon, EnglandRoyal Botanic Gardens, Kew7
GGeneva, SwitzerlandConservatoire et Jardin botaniques de la Ville de Genève6
MOSt. LouisMissouri Botanical Garden5.9
L, U, WAGThe NetherlandsThe Nationaal Herbarium Nederland (NHN)5.5
BMLondon, EnglandBritish Museum of Natural History5.2
GH, A, AMES, ECON, FHCambridge, MassachusettsHarvard University Herbaria5
WVienna, AustriaNaturhistorisches Museum Wien5



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مقایسه تیپ های فتوسنتزی

سه شنبه 26 اردیبهشت 1391 05:21 ب.ظ

نویسنده : عسکر اله قلی

C3 Photosynthesis

Plants which use only the Calvin cycle for fixing the carbon dioxide from the air are known as C3 plants. In the first step of the cycle CO2 reacts with RuBP to produce two 3-carbon molecules of 3-phosphoglyceric acid (3-PGA). This is the origin of the designation C3 or C3 in the literature for the cycle and for the plants that use this cycle.

The entire process, from light energy capture to sugar production occurs within the chloroplast. The light energy is captured by the non-cyclic electron transport process which uses the thylakoid membranes for the required electron transport.

About 85% of plant species are C3 plants. They include the cereal grains: wheat, rice, barley, oats. Peanuts, cotton, sugar beets, tobacco, spinach, soybeans, and most trees are C3 plants. Most lawn grasses such as rye and fescue are C3 plants.

C3 plants have the disadvantage that in hot dry conditions their photosynthetic efficiency suffers because of a process called photorespiration. When the CO2 concentration in the chloroplastsdrops below about 50 ppm, the catalyst rubisco that helps to fix carbon begins to fix oxygen instead. This is highly wasteful of the energy that has been collected from the light, and causes the rubisco to operate at perhaps a quarter of its maximal rate.

The problem of photorespiration is overcome in C4 plants by a two-stage strategy that keeps CO2high and oxygen low in the chloroplast where the Calvin cycle operates. The class of plants calledC3-C4 intermediates and the CAM plants also have better strategies than C3 plants for the avoidance of photorespiration.

Energy cycle in living things
Index

Photosynthesis Concepts

Reference
Moore, et al. 
Ch 7
 
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C4 Photosynthesis

Sugarcane is a champion at photosynthesis under the right conditions and is a prime example of a C4 plant, one which uses C4 photosynthesis. Sugarcane has been recorded at 7% photosynthetic efficiency.

C4 plants almost never saturate with light and under hot, dry conditions much outperform C3 plants. They use a two-stage process were CO2 is fixed in thin-walled mesophyll cells to form a 4-carbon intermediate, typically malate (malic acid). The reaction involves phosphoenol pyruvate (PEP) which fixes CO2 in a reaction catalyzed by PEP-carboxylate. It forms oxaloacetic acid (OAA) which is quickly converted to malic acid. The 4-carbon acid is actively pumped across the cell membrane into a thick-walled bundle sheath cell where it is split to CO2 and a 3-carbon compound.

This CO2 then enters the Calvin cycle in a chloroplast of the bundle sheath cell and produces G3P and subsequently sucrose, starch and other carbohydrates that enter the cells energy transportsystem.

The advantage that comes from this two-stage process is that the active pumping of carbon into the bundle sheath cell and the blocking of oxygen produce an environment with 10-120x as much CO2available to the Calvin cycle and the rubisco tends to be optimally utilized. The high CO2concentration and the absence of oxygen implies that the system never experiences the detractive effects of photorespiration.

The drawback to C4 photosynthesis is the extra energy in the form of ATP that is used to pump the 4-carbon acids to the bundle sheath cell and the pumping of the 3-carbon compound back to the mesophyll cell for conversion to PEP. This loss to the system is why C3 plants will outperform C4 plants if there is a lot of water and sun. The C4 plants make some of that energy back in the fact that the rubisco is optimally used and the plant has to spend less energy synthesizing rubisco.

Moore, et al. say that only about 0.4% of the 260,000 known species of plants are C4 plants. But that small percentage includes the important food crops corn, sorghum, sugarcane and millet. Also inluded are crabgrass and bermuda. Many tropical grasses and sedges are C4 plants.

Energy cycle in living things
Index

Photosynthesis Concepts

Reference
Moore, et al. 
Ch 7
 
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C3-C4 Intermediate Photosynthesis

Moore, et al. point to Flaveria (Asteraceae), Panicum (Poaceae) and Alternanthera (Amarantheceae) as genera that contain species that are intermediates between C3 and C4 photosynthesis. These plants have intermediate leaf anatomies that contain bundle sheath cells that are less distinct and developed than the C4 plants.

These intermediates are characterized by their resistance to photorespirationso that they can operate in higher temperatures and dryer environments than C3 plants. At right, the ranges of CO2compensation points for the three types of plants are shown. These compensation points are the values at which the plants cease to provide net photosynthesis.

The connection to hot and dry conditions comes from the fact that all the plants will close their stomata in hot and dry weather to conserve moisture, and the continuing fixation of carbon from the air drops the CO2 dramatically from the atmospheric concentration of nominally 38,000 ppm. If the CO2compensation point is lower on the above scale, the plant can operate in hotter and dryer conditions. The limits are placed by the fact that rubisco begins to fix oxygen rather than CO2, undoing the work of photosynthesis. C4 plants shield their rubisco from the oxygen, so can operate all the way down to essentially zero CO2 without the onset of photorespiration.

Energy cycle in living things
Index

Photosynthesis Concepts

Reference
Moore, et al. 
Ch 7
 
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Crassulacean Acid Metabolism (CAM)

The CAM plants represent a metabolic strategy adapted to extremely hot and dry environments. They represent about 10% of the plant species and include cacti, orchids, maternity plant, wax plant, pineapple, Spanish moss, and some ferns. The only agriculturally significant CAM plants are the pineapple and an Agave species used to make tequila and as a source of fiber.

The sketch below of the day-night cycle of the CAM plants is patterned after Moore, et al. The name Crassulacean Acid Metabolism came from the fact that this strategy was discovered in a member of the Crassulaceae which was observed to become very acidic at night and progressively more basic during the day.

The acidity was found to arise from the opening of their stomata at night to take in CO2 and fix it into malic acid for storage in the large vacuoles of their photosynthetic cells. It could drop the pH to 4 with a malic acid concentration up to 0.3M . Then in the heat of the day, the stomata close tightly to conserve water and the malic acid is decarboxylated to release the CO2 for fixing by the Calvin cycle. PEP is used for the initial short-term carbon fixation as in the C4 plants, but the entire chain of reactions occurs in the same cell rather than handing off to a separate cell as with the C4 plants. In the CAM strategy, the processes are separated temporally, the initial CO2 fixation at night, and the malic acid to Calvin cycle part taking place during the day.

With stomata open only at night when the temperature is lower and the relative humidity higher, the CAM plants use much less water than either C3 plants or C4 plants. Some varieties convert to C3 plants at the end of the day when their acid stores are depleted if they have adequate water, and even at other times when water is abundant.

Energy cycle in living things
Index

Photosynthesis Concepts

Reference
Moore, et al. 
Ch 7
 
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Photorespiration

Respiration refers to the metabolism of oxygen and the release of carbon dioxide. In cellular respiration it is a positive term, a process vital to life. But photorespiration is an entirely negative term because it represents a severe loss to the process of using light energy in photosynthetic organisms to fix carbon for subsequent carbohydrate synthesis. By leading to the loss of up to half of the carbon that has been fixed at the expense of light energy, photorespiration undoes the work of photosynthesis.

Photorespiration happens in C3 plants when the CO2 concentration drops to about 50 ppm. The key enzyme that accomplishes the fixing of carbon is rubisco, and at low concentrations of CO2 it begins to fix oxygen instead.

Under moderate temperature conditions when C3 plants have sufficient water, the supply of carbon dioxide is abundant and photorespiration is not a problem. The CO2 concentration of the atmosphere as of 2004 was about 38,000 ppm and this CO2 freely diffuses through the stomata of leaves and across the membranes of the chloroplasts while water diffuses out through the stomata. But during hot and dry conditions, the stomata close to prevent excessive water loss and the continuing fixation of carbon in the Calvin cycle dramatically reduces the relative concentration of CO2. When it reaches a critical level of about 50 ppm the rubisco stops fixing CO2 and begins to fix O2 instead. Even though the detoured process feeds some PGA back into the cycle, the photorespiration process causes rubisco to operate at only about 25% of its optimal rate.

The C4 plants and CAM plants avoid photorespiration and therefore operate at much higher efficiencies in hot and dry climates




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دانستنیهای فتوسنتز

سه شنبه 26 اردیبهشت 1391 05:10 ب.ظ

نویسنده : عسکر اله قلی

Leaf Anatomy - The leaf is the primary photosynthetic organ of the plant

  • It is has a large surface area to maximize light harvesting
  • They are thin so that light will penetrate through to the bottom cells
  • Composed of the lamina (blade) and the petiole (stalk)
    • Leaf shape is highly variable - there are literally 1000's of different shapes of leaves
  • Simple leaf - developmentally it has one lamina per leaf
    • Look where the petiole meets the stem - you should see a bud
  • Compound leaf - developmentally it has many distinct lamina per leaf
    • Look where each leaflet meets the rachis, there is no bud.
    • Look where the rachis meets the stem, there is a bud
    • Therefore, the entire structure is a leaf

Leaf Epidermal Anatomy

  • The outer epidermis is covered with a waxy cuticle to prevent water loss
    • This also prevents gas exchange :(
  • Stomata (sing = stoma) are pores in the surface of leaves which allow for gas exchange
    • Pore surrounded by two guard cells
    • Guard cells open and close to allow gas exchange
    • The density of stomates is dependent upon ecological conditions like humidity and CO2 concentration
  • The underside of leaves is usually covered with hairs (trichomes).
    • Many functions:  catch water, reduce airflow, produce wax, etc.

Leaf Internal Anatomy

  • A "typical" leaf cross section


 

  • Upper and Lower Epidermis - protective function
    • Lower epidermis generally contains more stomates than upper epidermis (in dicots)
    • Epidermal cells lack chloroplasts
  • Palisade Mesophyll - tightly packed cells on the upper surface
    • Contain three to five times as many chloroplasts as those of the spongy parenchyma.
    • Chloroplasts remain usually near the cell wall, since this adjustment guarantees optimal use of light
  • Spongy Mesophyll - loosely arranged cells
    • Creates air spaces to facilitate gas exchange

Leaves can have other uses besides photosynthesis



C3 Photosynthesis

The photosynthetic pathway we discussed in the previous lecture is known as the C3 pathway
  • The first stable molecule formed after CO2 fixation is a 3-Carbon molecule
  • Most (>90%) of all angiosperms are C3 plants
  • Possess "typical" mesophyll arrangement
  • Rubisco is exposed to O2 and the plant loses energy due to photorespiration

C4 Photosynthesis - a Mechanism to Reduce the Effects of Photorespiration

Some plants have been observed to fix CO2 and initially form a 4-Carbon molecule.  What is up with that?
These same plants have an odd cross-sectional anatomy, called kranz anatomy (kranz is German for "wreath")

Cross Section of Zea mays displaying Kranz anatomy

  • The vascular bundles are surrounded by a special type of mesophyll cell which are collectively called the bundle sheath
    • The mesophyll cells do not have Rubisco
    • The bundle sheath cells have Rubisco and fix CO2 just like in C3 plants
    • But where do they get the CO2 ?
  • The mesophyll cells have another CO2-fixing enzyme, PEP carboxylase
    • CO2 + PEP (phosphoenol pyruvate) >>> OAA (Oxaloacetate), a 4-Carbon compound
    • PEP Carboxylase has NO affinity for O2
    • OAA >>> Malate
    • Malate is shuttled into the bundle sheath cell
    • The CO2 is removed, forming Pyruvate, a 3-Carbon compound
    • Pyruvate is shuttled back to the mesophyll cell where it is converted to PEP (requires ATP)
    • CO2 enters the Calvin-Benson cycle (exactly the same as in a C3 plant)


C4 Photosynthesis

C4 Photosynthesis is found in many plants, mostly in drier climates

  • C4 photosynthesis has evolved independently many times
  • All of the enzymes involved in C4 photosynthesis were already present in the plant, so nothing new needed to evolve, just the sequence of operation
  • Corn and sugar cane, two of the 10 most important crops worldwide, C4 plants
C4 plants are more efficient than C3 plants in hot, dry environments, but in moist or cold environments, C3 plants can be more efficient
  • PEP carboxylase has a much greater affinity for CO2 at high temps than does Rubisco, so it can assimilate carbon much more efficiently
  • However, the CO2 shuttling costs energy, so this efficiency is lost in cooler temperatures
  • Also, the CO2 shuttling becomes saturated at a much lower CO2 concentration than does Rubisco, so when CO2 levels are high (such as when the stomates are wide open in moist tropical plants) C3 is more efficient
  • C4 Photosynthesis and CAM animation


Carbon dioxide yield of C4 and C3 plants of open grasslands in different parts of the world



CAM Photosynthesis

As if C4 wasn't enough, there is yet another addition/modification to the typical C3 photosynthetic pathway, called Crassulacean Acid Metabolism (CAM)

  • Found almost exclusively in plants in xeric (dry) environments
    • mainly in succlents, cacti, etc.
  • Plants open stomates during the night - they are kept closed during the day to conserve water
  • The light-dependent reactions occur during the day, creating ATP and NADPH as expected
  • During the night, the stomates of a CAM plant open, CO2 is taken up into the plant and incorporated into a variety of organic acids
  • During the day, the light-dependent reactions proceed, making more ATP and NADPH - this promotes the release of CO2 from the organic acids and Rubisco operates as normal (but in a greatly CO2-enriched environment)
  • This is more of an adaptation to conserve water than to reduce the effects of photorespiration





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Photosynthesis

پنجشنبه 21 اردیبهشت 1391 04:35 ب.ظ

نویسنده : عسکر اله قلی

This tutorial will describe the mechanisms involved in photosynthesis. Photosynthesis occurs in the chloroplasts, where the energy derived from sunlight is used to excite electrons that are subsequently donated to a protein-mediated electron transport system analogous to the respiratory chain in the mitochondria. These electrons are finally donated to a reduced electron carrier. As electrons move through the transport chain, a hydrogen electrochemical gradient is generated and it drives the synthesis of ATP by ATP synthase. The ATP and reduced electron carriers generated from photosynthesis are used to convert CO2 into organic carbon in the form of sugars and carbohydrates.

By the end of this tutorial you should understand:

  • The features of a chloroplast
  • The role of chlorophyll in the light-gathering complexes
  • The mechanisms of the light-dependent reactions of photosynthesis, including the electron carrier NADP and water
  • How the energy of the light-dependent reactions is used to convert carbon dioxide into sugars

Photosynthesis Occurs In the Chloroplasts

Figure 1.  The structure of a chloroplast. A chloroplast has three distinct membranes: an outer membrane, an inner membrane and a thylakoid membrane. Stacks of disc-shaped invaginations of the thylakoid membrane are referred to as grana (singular: granum). The space surrounded by the inner membrane is referred to as the stroma. Photosynthesis occurs in the thylakoid membrane.

Photosynthesis is the conversion of the energy from sunlight into the chemical bonds of organic compounds synthesized from atmospheric CO2. There are two distinct pathways of reactions in photosynthesis: the light-dependent reactions and the light-independent reactions. In the light-dependent reactions, also referred to asphotophosphorylation, the energy of light is used to excite electrons that are transported through an electron transport chain analogous to the respiratory chain in the mitochondria. Chemiosmotic coupling links light-dependent electron transport and ATP synthesis with the electrons eventually donated to the high-energy molecule NADP. In addition, water is split, thus releasing oxygen. The light-independent reactions, also referred to as the carbon fixation cycle, use the energy of ATP and NADPH produced in the light reactions to convert CO2 into 5-carbon sugars. Both the light and dark reactions of photosynthesis occur in chloroplasts (illustrated in Figure 1). The chloroplast has an inner and outer membrane, separated by an intermembrane space, and the inner membrane surrounds a space termed the stroma (analogous to the matrix in mitochondria). A third membrane in the stroma, the thylakoid membrane, is unique to chloroplasts. It appears as stacks of disc-shaped invaginations that are referred to as grana. The light-gathering complexes, the electron transport chain and the ATP synthase of photosynthesis are all located in the thylakoid membrane. Like mitochondria, chloroplasts have their own genome. 

Chlorophyll absorbs light and transfers the energy to excited electrons

Figure 2.  Photosystems and the structure of chlorophyll. The light-gathering complexes, photosystems, are embedded in the thylakoid membrane of the chloroplast. A photosysytem (illustrated right) is composed of many molecules of pigments, mostly chlorophylls (shown in green), however, others such as carotenoids (shown in orange) are also present. The structure of chlorophyll is illustrated in the box on the lower left. Chlorophyll absorbs light with wavelengths of 450 nm, whereas carotenoids absorb light with wavelengths of 500 nm. When light is absorbed, electrons in chlorophyll (and the other pigments) are excited. As the electrons return to their ground energy state, the free energy released is funneled into a reaction center that contains special chlorophyll molecules (either P680 and P700) and it is used to excite these molecules. Once excited, these chlorophyll molecules can donate their electrons to the electron transport chain in the thylakoid membrane.

The two photosystems of the light-dependent reactions of photosynthesis are comprised of hundreds of molecules of chlorophyll. These light-absorbing molecules (see Figure 2) are embedded in the thylakoid membrane. A chlorophyll molecule absorbs photons of mostly red light (~ 450 nm), which excite electrons in the molecule to a higher energy level. Within a photosystem (illustrated inFigure 2), many chlorophyll molecules (and other pigment molecules) absorb light, and the energy of the excited electrons is passed from one molecule to another, funneling the energy into a reaction center that contains a special pair of chlorophyll molecules (P680 and P700). In the reaction center, the electrons of P680 and P700 are excited and then carried through an electron transport chain analogous to the respiratory chain in mitochondria.

Linear Photophosphorylation

Linear Photophosphorylation and ATP Synthesis In the Chloroplasts

Figure 3.  Linear photophosphorylation: electron transport and ATP synthesis.The respiratory chain is composed of three large protein complexes fixed in the membrane (colored green) and two mobile electron carriers (colored black). Light absorbed in photosystem II (PSII) excites the electrons of P680, which are donated to the mobile molecule plastoquinone (Q). The electron-depleted P680 chlorophylls are restored by the splitting of water, which liberates oxygen and donates electrons to P680. From Q, the electrons are donated to the cytochrome b6-f complex. In PSI, the electrons of the P700 chlorophylls are excited and donated to the protein ferredoxin (Fd). The electrons are then donated to Fd NADP reductase (FNR), which catalyzes the reduction of NADP+. The electron-depeleted P700 chlorophylls in PSI are restored by the electrons that are donated from the cytochrome b6-f complex via the small, mobile protein plastocyanin (PC). The hydrogen electrochemical gradient is generated by the proton pumping of the cytochrome b6-f complex, the release of protons into the thylakoid lumen by PSII, and the depletion of the protons from the stroma by Fd NADP reductase (FNR). This gradient drives protons back across the inner membrane through the ATP synthase (shown in gray) that catalyzes the synthesis of ATP from ADP and inorganic phosphate (Pi).

Electron transport in the thylakoid membrane of a chloroplast (illustrated schematically in Figure 3) involves two distinct, but linked, photosystems, and is referred to as linear photophosphorylation. Electrons are excited in both photosystems and donated to an ETC that links the two photosystems. Light energy is absorbed by chlorophyll (i.e. P680) in photosystem II (PSII), and the excited electrons are donated to plastoquinone (Q) (which is similar to CoQ in the respiratory chain of mitochondria). The electron deficit in chlorophyll P680 is filled by the electrons derived from splitting two molecules of water, which releases four electrons, protons and free oxygen. A component of PSII, a protein complex associated with manganese ions, catalyzes the splitting of water. The chlorophyll then returns to its low-energy state, ready to be activated once more. The excited electrons donated to the ETC travel from Q to the cytochrome b6-f complex, and subsequently, to plastocyanin (PC)(a small, copper-containing protein). The chlorophyll (i.e. P700) in photosystem I (PSI) also absorbs light, and the excited electrons are donated to ferredoxin (a small, iron/sulfur-containing protein). The electron deficit of PSI is filled by the electrons donated by Pc, which originated from PSII, thereby linking the two photosystems. To complete electron transport in the thylakoid membrane, the electrons from ferredoxin are finally donated to nicotinamide adenine dinucleotide phosphate (NADP+) in a reaction catalyzed by ferredoxin-NADP reductase to generate the high-energy molecule NADPH. Overall, the photoactivated electrons donated from PSII and PSI travel through an ETC and are ultimately donated to and reduce NADP+. In addition, a hydrogen gradient is generated across the thylakoid membrane, which is used to generate ATP via the ATP synthase. The gradient is generated in three places during electron transport: protons are moved from the stroma to the lumen of the thylakoid by PSII; the cytochrome b6-f complex pumps protons into the thylakoid lumen; and the reduction of NAD+ to NADPH + H+ depletes the free protons in the stroma, resulting in a higher concentration of protons in the lumen of the thylakoid than in the stroma. The hydrogen ions will flow from the thylakoid lumen into the stroma (down the electrochemical gradient), through the ATP synthase complex, and catalyze the synthesis of ATP in a fashion analogous to the ATP synthase found in mitochondria (described in the Oxidative Phosphorylation tutorial and illustrated in Figure 4).

Cyclic Photophosphorylation

Cyclic photophosphorylation is an alternative mechanism of electron transport in the thylakoid membrane, and it uses only PSI. This electron transport chain is cyclic: electrons in PSI are photoactivated and donated to ferredoxin; they are then transferred to the cytochrome b6-f complex (instead of Fd NADP reductase); and finally, they travel back to PSI via PC. This electron transport chain generates a hydrogen electrochemical gradient; therefore, ATP synthesis occurs. Unlike linear photophosphorylation, cyclic photophosphorylation does not generate NADPH or liberate oxygen. Chloroplasts use both linear and cyclic photophosphorylation to alter the relative levels of NADPH and ATP.

ATP Synthesis In Photophosphorylation

Figure 4.  Electron transport and ATP synthesis. A comparison of electron transport and ATP synthesis in a mitochondrion and a chloroplast.

ATP synthesis in chloroplasts is analogous to ATP synthesis in mitochondria; that is, electron transport is linked to ATP synthesis through chemiosmotic coupling (see Figure 4). Electron transport, for both linear and cyclic photophosphorylation, generates a hydrogen gradient across the thylakoid membrane. The lumen of the thylakoid is pH 4.5, whereas the stroma is pH 8.0. As a result of this gradient, hydrogen ions will flow through the ATP synthase from the lumen of the thylakoid into the stroma. The ATP synthase in the thylakoid membrane is composed of two subunits: CF0 subunit and CF1 subunit. Protons flow through CF0 and cause it to rotate. This rotation induces conformational changes in the stationary CF1 subunit that catalyzes ATP synthesis. The structure and mechanism of a chloroplast's ATP synthase is similar to that of the mitochondrial ATP synthase (described in detail in the previous tutorial). 

The chemiosmotic coupling of electron transport and ATP synthesis is analogous in mitochondria and chloroplasts. In both cases, the electron transport chain generates a hydrogen electrochemical gradient across the inner membrane of the mitochondria or the thylakoid membrane of the chloroplast. The ATP synthase (composed of F0 and F1 subunits in the mitochondria, and CF0 and CF1 subunits in the chloroplasts) uses the hydrogen electrochemical gradient to drive ATP synthesis. As the protons move through the F0 and CF0 subunits, these subunits rotate and induce conformational changes in the F1 and CF1 subunits, respectively, to activate ATP synthesis.

Carbon Fixation

The Light-Independent Reactions of Photosynthesis: Carbon Fixation

Figure 5.  The carbon fixation cycle (Calvin cycle).The carbon fixation cycle has three phases: phase I is carbon fixation (each molecule of ribulose 1,5-biphosphate + CO2 -> 2 molecules of 3-phosphoglycerate); phase II is reduction (each molecule of 3-phosphoglycerate + ATP + NADPH ->glyceraldehyde 3-phosphate + ADP + Pi + NADP+); and phase III is regeneration of ribulose 1,5-biphosphate (5 molecules of glyceraldehyde 3-phosphate + 3ATP -> 3 molecules of ribulose 1,5-biphosphate + 3ADP + 3Pi.) For each molecule of CO2 fixed, 3 ATPs and 2 NADPHs are consumed.

The high-energy molecules ATP and NADPH, synthesized in the light-dependent reactions of photosynthesis, are used to synthesize carbohydrates from carbon dioxide - hence the term carbon fixation. The carbon fixation cycle, also called the Calvin cycle, is a 3-phase cycle that occurs in the stroma and that converts CO2 into carbohydrates using the energy of ATP and the oxidation of NADPH (illustrated in Figure 5). The first phase of the cycle is carbon fixation, the combination of CO2 and ribulose 1,5-biphosphate(a 5-carbon sugar), resulting in two molecules of 3-phosphoglycerate (a 3-carbon sugar). The second phase is the reduction of 3-phosphoglycerate to glyceraldehyde 3-phosphate, which you may recall is essentially steps #6 and #7 of glycolysis in reverse (see tutorial entitled Glycolysis, Fermentation and the Citric Acid Cycle). This phase requires ATP hydrolysis and NADPH oxidation. The final phase of the cycle is ribulose 1,5-biphosphate regeneration. Some glyceraldehyde 3-phosphates are used to make common simple sugars or are stored as starch. The remainder of the glyceraldehyde 3-phosphates are used as intermediates in the carbon fixation cycle, ultimately regenerating ribulose 1,6-biphosphate. This phase also requires ATP. For each molecule of CO2 that is fixed, 3 ATPs and 2 NADPHs are consumed. 

Summary

Photosynthesis is the process of converting the energy of light into the energy of chemical bonds. This occurs in the chloroplasts of cells, specifically, in the thylakoid membranes. In photophosphorylation, or the light-dependent reactions, light is absorbed by chlorophyll and other pigment molecules. Light's energy is used to excite a pair of electrons in specialized chlorophyll molecules (P680 and P700) in the photosystems (PS). These electrons are donated to an electron transport chain embedded in the thylakoid membrane, which consists of large protein complexes and small, mobile electron carriers. In linear photophosphorylation, both photosystems I and II are used. The electrons that were excited and donated by PSII are replenished by a protein-mediated reaction that splits water to release electrons, protons and free oxygen. Eventually the electrons are donated to NADP+, which is reduced to NADPH. In cyclic photophosphorylation, only PSI is used and the excited electrons from P700 are donated to the electron transport chain and eventually returned to P700. In this case, no NADPH is generated and no oxygen is liberated. In both linear and cyclic photophosphorylation, ATP is generated from ADP + Pi. As electrons move through the electron transport chain, hydrogen ions are moved across the thylakoid membrane and they accumulate in the thylakoid lumen where they generate a hydrogen electrochemical gradient. This gradient drives the hydrogen ions back across the membrane through the ATP synthase, thereby driving the synthesis of ATP in a fashion analogous to the synthesis of ATP in the mitochondria. The products of linear photophosphorylation, ATP and NADPH, are used in the light-independent reactions of photosynthesis (also termed the carbon fixation cycle or the Calvin cycle). This cycle uses ATP and NADPH to convert CO2 into simple sugars. It has three phases: carbon fixation (the addition of CO2to ribulose 1,5-biphosphate); reduction of sugars to glyceraldehyde 3-phosphate (requiring NADPH and ATP); and regeneration of ribulose 1,5-biphosphate (requiring ATP).




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Overview of C3 Photosynthesis

پنجشنبه 21 اردیبهشت 1391 04:30 ب.ظ

نویسنده : عسکر اله قلی

 

 


 

The Calvin Cycle

During photosynthesis, light energy is used to generate chemical free energy, stored in ATP and NADPH. The light-independent Calvin ("dark") cycle uses the energy from short-lived electronically-excited carriers to convert carbon dioxide and water into organic compounds that can be used by the organism (and by animals which feed on it). This set of reactions is also called carbon fixation. The key enzyme of the cycle is called RuBisCO. In the following equations, the chemical species (phosphates and carboxylic acids) exist in equilibria among their various ionized states as governed by the pH.


 

The sum of reactions in the Calvin cycle is the following:

6 CO2 + 12 NADPH + 12 H2O + 18 ATP → C6H12O6 + 12 NADP+ + 18 ADP + 18 Pi


The steps in the Calvin cycle are:
1.  RuBisCO reacts with CO2, creating a 3-carbon compound, PGA.
2.  One ATP from the light reactions is used, producing an ADP and a Pi .
3.  An NADPH from the light reactions combines with an H+ and becomes NADP+.
4.  PGAL, a 3-carbon compound, is produced, which stores free energy.
5.  Another ATP is consumed, yielding an ADP and a Pi.
6.  RuBP is produced, which is a 5-carbon compound.

At high temperatures, RuBisCO will react with O2 instead of CO2 in photorespiration, an apparently-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. C4 plants use the enzyme PEP initially, which has a higher affinity for CO2. The process first makes a 4-carbon intermediate compound; hence the name C4 plants.

Photorespiration


 

C4 Pathway of Photosynthesis

 

C4 Photosynthesis : C4 plants.

  • Called C4 because the CO2 is first incorporated into a 4-carbon compound.
  • Stomata are open during the day.
  • Uses PEP Carboxylase for the enzyme involved in the uptake of CO2. This enzyme allows CO2 to be taken into the plant very quickly, and then it "delivers" the CO2 directly to RUBISCO for photsynthesis.
  • Photosynthesis takes place in inner cells (requires special anatomy called Kranz Anatomy)
  • Adaptive Value:
    • Photosynthesizes faster than C3 plants under high light intensity and high temperatures because the CO2 is delivered directly to RUBISCO, not allowing it to grab oxygen and undergo photorespiration.
    • Has better Water Use Efficiency because PEP Carboxylase brings in CO2 faster and so does not need to keep stomata open as much (less water lost by transpiration) for the same amount of CO2 gain for photosynthesis.
  • C4 plants include several thousand species in at least 19 plant families. Example: fourwing saltbush pictured here, corn, and many of our summer annual plants


 

CAM Photosynthesis : CAM plants. CAM stands for Crassulacean Acid Metabolism

  • Called CAM after the plant family in which it was first found (Crassulaceae) and because the CO2 is stored in the form of an acid before use in photosynthesis.
  • Stomata open at night (when evaporation rates are usually lower) and are usually closed during the day. The CO2 is converted to an acid and stored during the night. During the day, the acid is broken down and the CO2 is released to RUBISCO for photosynthesis
  • Adaptive Value:
    • Better Water Use Efficiency than C3 plants under arid conditions due to opening stomata at night when transpiration rates are lower (no sunlight, lower temperatures, lower wind speeds, etc.).
    • May CAM-idle. When conditions are extremely arid, CAM plants can just leave their stomata closed night and day. Oxygen given off in photosynthesis is used for respiration and CO2 given off in respiration is used for photosynthesis. This is a little like a perpetual energy machine, but there are costs associated with running the machinery for respiration and photosynthesis so the plant cannot CAM-idle forever. But CAM-idling does allow the plant to survive dry spells, and it allows the plant to recover very quickly when water is available again (unlike plants that drop their leaves and twigs and go dormant during dry spells).
  • CAM plants include many succulents such as cactuses and agaves and also some orchids and bromeliads

CAM plants keep their stomata (on the underside of the leaf) closed during the day, which conserves water but prevents photosynthesis, which requires CO2 to pass by gas exchange through these openings. Evaporation through the upper side of a leaf is prevented by a layer of wax.




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The Calvin cycle and Light reactions

پنجشنبه 21 اردیبهشت 1391 10:33 ق.ظ

نویسنده : عسکر اله قلی

 

What is obvious from that is the "connection" to the light reactions. The Calvin cycle needs NADPH and ATP from the light reactions. Thus the Calvin cycle is inseparable from the light reactions...they only occur in the light! This is why "dark reactions" is a poor name for the Calvin cycle. This relationship with the light reactions is reciprocal...the light reactions need a supply of ADP, Pi, and NADP+ which come directly from the Calvin cycle:

The Calvin cycle occurs in the stroma

With this knowledge, it is no surprise where the Calvin cycle takes place in a cell. Clearly the need for ATP and NADPH will put the Calvin cycle on the stroma side of the thylakoid membrane where these high-energy molecules are produced by the light reactions. The chemical reactions converting carbon dioxide to carbohydrate are enzymatic rather than electronic, so they are not associated with the thylakoid itself. Rather the Calvin cycle enzymes are dissolved in the stroma (the cytosol of the ancient endosymbiont).

The Calvin cycle is an enzymatic pathway

The enzymes that participate in the Calvin cycle form a cyclic pathway that perpetuates its own raw materials through multiple iterations of the cycle. The pathway is summarized in an overview:





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سنتز ATP

چهارشنبه 20 اردیبهشت 1391 07:25 ب.ظ

نویسنده : عسکر اله قلی




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زنجیره تنفسی

چهارشنبه 20 اردیبهشت 1391 07:24 ب.ظ

نویسنده : عسکر اله قلی



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گلیکولیز

چهارشنبه 20 اردیبهشت 1391 07:22 ب.ظ

نویسنده : عسکر اله قلی

 



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Transport in plant

چهارشنبه 20 اردیبهشت 1391 07:18 ب.ظ

نویسنده : عسکر اله قلی



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◦Na+, K+ -ATPase

چهارشنبه 20 اردیبهشت 1391 07:12 ب.ظ

نویسنده : عسکر اله قلی




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Respiration

چهارشنبه 20 اردیبهشت 1391 07:07 ب.ظ

نویسنده : عسکر اله قلی

 

 

Respiration is a metabolic process used by all organisms to break down fuel molecules in order to release the energy stored in them. Here, the glucose manufactured in photosynthesis is now ready to be cashed in for ATP molecules to drive the reactions of living cells. This is a very important metabolic process in cells.

Note: A plant may use its own glucose, but that glucose is also available to animals which eat the plants, and then to other animals.


Cellular respiration is the process of trading glucose for ATP since it takes place within the cell. Cellular respiration takes place in 3-stages:

  1. Glycolysis
  2. Krebs cycle
  3. Electron-transport chain

During the process of respiration the glucose molecule is split. Next, the hydrogen atoms are transferred from the carbon atoms to oxygen atoms. The energy released as a result of this transfer is used to convert ADP to ATP, which is the energy currency of the cell.

 

Glycolysis is the first phase of respiration where glucose is broken down with a small energy yield. This process takes place in the cell fluid or cytoplasm. Note what takes place during the above process:

  1. A 6-carbon glucose molecule is split up and changed into two molecules of a 3-carbon substance called pyruvic acid.
  2. Also during the process two ATPs are produced.

 

Two molecules of pyruvic acid are produced.

  1. Yeasts and other anaerobic organisms, those that do not utilize oxygen in their respiration, derive all their ATP from glycolysis.
  2. Pyruvic acid is not the end of the line in glycolysis. In yeasts, the respiratory products are carbon dioxide (CO2) and ethanol (CH3CH2OH).
  3. In animals, the product of respiration with oxygen is not alcohol, but lactic acid.
  4. In aerobic animals, some of their energy may be derived from glycolysis.

 

To see an animated form of glycolysis, click here.

 

The Krebs cycle is the phase of respiration in aerobic reactions where the fuel is broken down in CO2 and H2O. In aerobic respiration, glucose is broken down into CO2 and H2O, releasing the equivalent of 38 ATP in useable energy. Most of the energy is released in the form of hydrogen ions and electrons. Primitive organisms use anaerobic respiration. Anaerobic fermentation breaks down glucose into CO2, ethanol, and H2O. The rest of the energy is lost as heat. This is the process used to make alcoholic beverages and to raise bread.

 

More advanced animals, such as ourselves, can break down glucose into CO2, lactic acid, and H2O, releasing 2 ATP by a process called anaerobic muscle glycolysis. (Note: Build up of lactic acid is what causes muscle fatigue, muscle cramps commonly found within athletes.)

The last stage of aerobic respiration is the electron-transport chain. During this process, the electrons are passed along to a series of electron carriers similar to those referred to in photosynthesis. The energy that is released is used to form more ATP (See figure below).

 

To see an animation of the Krebs cycle, click here.


 

Diagram of an electron transport chain. As the electrons flow downhill from one carrier to the next, (which is at a lower energy level) the energy which the electrons possessed when they were held by the NAD is released in a stepwise manner. That energy goes to form ATP from ADP. Finally the spent electrons combine with protons and are accepted by an oxygen molecule (now you can see why you breathe) and water is formed. Some organisms, such as certain insects and desert rodents, can derive all the water they need from this "metabolic water".

 

To view an animation of the electron transport chain, click here.

 

 

Basic Life Cycle

The basic cycle of life on earth. Chloroplasts capture the sun's energy, convert it to glucose. The mitochondria utilize glucose. The mitochondria utilize the glucose to form ATP. the CO2 and water formed by the mitochondria is utilized by the chloroplast.




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Kreb's Cycle

چهارشنبه 20 اردیبهشت 1391 07:02 ب.ظ

نویسنده : عسکر اله قلی


 

The oxidation of pyruvic acid into CO2 and water is called Krebs cycle. This cycle is also citric acid cycle because the cycle begins with the formation of citric acid. Citric acid is a carboxylic acid containing 3 COOH groups. Hence this cycle is also called as tri carboxylic acid cycle or TCA cycle. This cycle was first described by Kreb's in 1936. This cycle occurs only in the presence of oxygen. Hence it is an aerobic process. It takes place in the mitochondria.

steps involved in krebs cycle



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Glycolysis, Fermentation and the Citric Acid Cycle

چهارشنبه 20 اردیبهشت 1391 06:49 ب.ظ

نویسنده : عسکر اله قلی

 

 


Introduction and Goals

This tutorial describes the breakdown of glucose into carbon dioxide and water. In cells, this occurs in a stepwise fashion that starts in the cytoplasm and ends in the mitochondria. As chemical bonds are broken, energy is captured and stored in the form of high-energy molecules. There are three major stages in the breakdown of glucose. In the first stage, six-carbon sugars are cleaved into three-carbon sugars. In the second stage, these three-carbon sugars are further broken down in two alternate pathways: one that requires oxygen and one that does not. In the third and final stage, sugars are further broken down, subsequently releasing carbon dioxide and generating more high-energy molecules.

By the end of this tutorial you should know:

  • The three phases and net yield of glycolysis
  • The oxidation and reduction reactions, especially the role of electron carriers
  • The allosteric regulation of glycolysis
  • The role of pyruvate as a branching point for different pathways
  • The pathways of lactate fermentation and ethanol fermentation
  • The citric acid cycle, especially the first step, last step and products
  • The role of the citric acid cycle in other metabolic pathways

Overview of Cellular Respiration

Figure 1.  High-energy molecules: ATP and NADH.The top panel illustrates the hydrolysis of ATP to ADP. The standard free energy of this reaction is ~ 7.3 kcal/mol. The lower panel illustrates the reduction of NAD+ to NADH + H+.

All cells require some source of energy to carry out their normal functions. The energy in cells is usually stored in the form of chemical bonds. In the next few tutorials you will learn about metabolic pathways (pathways of chemical reactions in a cell), including catabolic pathways, which describe reactions that breakdown molecules, and anabolic pathways, which describe reactions that build molecules. Often catabolic pathways release energy when chemical bonds are broken, whereas anabolic pathways may require energy to form chemical bonds. In plant cells, energy is derived from sunlight and used in anabolic pathways to synthesize simple sugars. These sugars can be stored and used later in either anabolic or catabolic pathways. In animal cells, energy is derived from the catabolism of ingested macromolecules such as starch and fat from other organisms (e.g. the hamburger you had for lunch). The large macromolecules are catabolized into simple sugars and other building blocks, releasing energy along the way. This energy is captured in the form of two types of high-energy molecules: ATP and electron carriers.

 This tutorial describes the catabolism of glucose, the most common simple sugar found in both animals and plants. Remember from a previous tutorial (Properties of Macromolecules II: Nucleic Acids, Polysaccharides and Lipids), glucose is found in both glycogen and starch. The complete catabolism of glucose into CO2 and H2O is referred to as cellular respiration because it requires oxygen. The net reaction for cellular respiration is C6H12O6 + 6O2 -> 6CO2 + 6H2O + 38ATP. The catabolism of glucose occurs through a series of oxidation reactions. Recall from Biology 110 that the oxidationof a molecule involves the removal of electrons. The oxidation of organic molecules occurs by the removal of electrons and protons (H+). In biological reactions, an oxidation reaction is coupled to a reduction reaction (the addition of electrons and protons) such that one molecule is oxidized and the other is reduced. In the catabolism of glucose, sugars are oxidized in reactions that are coupled to the reduction of the most common electron carrier, nicotinamide adenine dinucleotide (NAD+), (Figure 1). For instance, in the following reaction: malate + NAD+ -> oxaloacetate + NADH + H+, malate is oxidized and NAD->is reduced. Cellular respiration occurs in a stepwise fashion, initially producing many molecules of reduced electron carriers (NADH and FADH2). These reduced electron carriers will eventually be oxidized in the mitochondria in a process that is linked to ATP synthesis. It is only in this final step that oxygen is actually used. The reduced electron carriers donate their electrons to an electron transport chain, and eventually, oxygen is reduced to yield water. This final step of cellular respiration yields the largest amount of energy, in the form of ATP. 

There are four distinct stages of cellular respiration: glycolysis, the oxidation of glucose to the three-carbon sugarpyruvate; pyruvate oxidation, the oxidation of pyruvate to acetyl coenzyme A (acetyl CoA); the citric acid cycle(also referred to as the Kreb's cycle or TCA cycle), the complete oxidation of acetyl CoA; and finally, the oxidation of the reduced electron carriers linked to the synthesis of ATP. The first three stages (glycolysis, pyruvate oxidation and the citric acid cycle) will be described in this tutorial. In addition, we will consider the process of fermentation, which occurs in the absence of oxygen, whereby pyruvate is reduced and a variety of by-products are generated. The final step of cellular respiration, the oxidation of the electron carriers linked to ATP synthesis, will be covered in the next tutorial.

The Glycolytic Pathway

Glycolysis is a ten-step pathway that cleaves each glucose molecule (a 6-carbon sugar) into two molecules of pyruvate (a 3-carbon sugar) and that yields two molecules of ATP and two molecules of NADH. The pathway occurs in the cytoplasm, where each step is catalyzed by a different enzyme. Rather than memorize each step of glycolysis, we will categorize them into three distinct phases: Phase I: preparation of glucose; Phase II: cleavage of a 6-carbon sugar; and Phase III: oxidation and ATP generation (see animation below). The first phase of glycolysis requires the investment of ATP to prepare glucose for cleavage. This seems contrary to the previous statement that glycolysis results in the synthesis of two molecules of ATP per molecule of glucose. However, although two ATPs are used, an additional four ATPs are synthesized, resulting in a net yield of two ATPs per glucose molecule. The hydrolysis of ATP to ADP and Pi provides both the energy and the phosphate group required to phosphorylate the 6-carbon sugar; first, in reaction #1, by converting glucose to glucose-6-phosphate, and then, in reaction #3, by converting fructose-6-phosphate to fructose-1,6-biphosphate. The second phase of glycolysis involves the cleavage of one molecule of fructose-1,6-biphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate (in animation below, reaction 4), the latter of which is readily converted to glyceraldehyde-3-phosphate, resulting in two molecules of glyceraldehyde-3-phosphate. The third phase of glycolysis involves the oxidation of the 3-carbon sugars and the generation of NADH and ATP. In two steps (reaction 7 and reaction 10), ATP is synthesized by substrate-level phosphorylation; the high-energy phosphate bond on the 3-carbon sugar is broken and the phosphate is transferred to ADP to synthesize ATP. In this fashion, two molecules of ATP are synthesized for each glyceraldehyde-3-phosphate, and since there are two glyceraldehyde-3-phosphates generated per glucose, four molecules of ATP are synthesized per molecule of glucose. In addition, two molecules of NADH are generated per molecule of glucose. The reduced electron carrier NADH will further contribute to the synthesis of ATP in the mitochondria (reviewed in the next tutorial).  

Regulation of Glycolysis

Figure 2. The regulation of glycolysis. The glycolytic pathway is shown on the left. The enzymes (hexokinase, phosphofructokinase and pyruvate kinase) catalyzing three important exergonic steps are labeled in blue. For each of these pathways, the allosteric activators (labeled in green) and allosteric inhibitors (labeled in red) are indicated. Gluconeogenesis (shown on the right) is glycolysis in reverse, with the exception of steps 1, 3, and 10 and the enzymes that catalyze these steps.

Many of the steps of glycolysis are reversible, and, in fact, gluconeogenesis, which is the anabolic pathway that synthesizes glucose from pyruvate, is essentially glycolysis run in reverse (Figure 2). Most of the steps of gluconeogenesis are catalyzed by the same enzymes as glycolysis, with the exception of three important reactions that are strongly exergonic and that drive glycolysis in the forward direction. In glycolysis these three reactions are step #1 (glucose + ATP -> glucose-6-phosphate + ADP), which is catalyzed by the enzymehexokinase, step #3 (fructose-6-phosphate + ATP -> fructose-1,6-biphosphate), which is catalyzed by the enzyme phosphofructokinase 1 (PFK1), and the last step (phosphoenolpyruvate + ADP -> pyruvate + ATP), which is catalyzed by the enzyme pyruvate kinase. In gluconeogenesis these three reactions occur in the reverse direction and are catalyzed by different enzymes. 

The three steps listed above for glycolysis are regulated by allosteric regulation. Recall from the tutorial entitledEnzyme Kinetics and Catalysis, allosteric regulation of enzyme activity occurs due to a conformational change induced by the binding of both allosteric activators and inhibitors. Regulation of the rate of these three strongly exergonic reactions affects the overall rate of glycolysis. Their enzymes are regulated by the products of glycolysis (e.g. pyruvate kinase is activated by fructose-1,6-biphosphate), the products of other stages of cellular respiration (e.g. citrate, a product of the citric acid cycle, which inhibits phosphofructokinase 1) and the overall ratio of ADP/ATP (e.g. ATP inhibits phosphofructokinase 1, whereas ADP activates it). This mechanism balances the rate of glycolysis with the overall rate of cellular respiration and ATP synthesis. Therefore, when cellular respiration is running well and the levels of intermediates (e.g. citrate and acetyl CoA) and ATP are high, the rate of glycolysis is reduced. Conversely, when citrate, acetyl CoA and ATP levels are low, the rate of glycolysis is increased.

Another important allosteric activator of phosphofructokinase 1 is fructose-2-6-biphosphate (F2,6BP), which is generated from fructose-6-phosphate by the enzyme phosphofructokinase 2. Phosphofructokinase 2 (PFK-2) is a bifunctional enzyme that acts as a phosphatase or kinase, depending on its phosphorylation state, which is determined by hormone-regulated signal transduction cascades. In response to insulin production (activated by high blood sugar levels), PFK-2 is unphosphorylated and the kinase is activated, generating F2,6BP. F2,6BP activates phosphofructokinase 1 and stimulates glycolysis, thereby reducing the high levels of glucose. See Figure 2 for a summary of the allosteric regulation of glycolysis.

Pyruvate as a Branching Point

Figure 3. Pyruvate is a branching point. In the absence of oxygen, pyruvate undergoes either lactate or ethanol fermentation (top two panels) to yield lactate or ethanol, respectively. In both cases, NADH (labeled in pink) is oxidized to regenerate NAD+ (labeled in yellow). In the presence of oxygen (lower panel), pyruvate is oxidized to yield acetyl CoA, and NAD+ (labeled in yellow) is reduced to NADH (labeled in pink).

The end-point of glycolysis is the formation of pyruvate (2 molecules of pyruvate per molecule of glucose), which can enter several different metabolic pathways depending on the type of organism and the presence of oxygen. In the presence of oxygen, pyruvate enters the remaining stages of cellular respiration. Pyruvate is oxidized in a reaction that generates acetyl CoA, NADH and CO2 (Figure 3). Acetyl CoA is further oxidized to CO2 and H2O in the citric acid cycle (described in detail below). 

In organisms that can grow in the absence of oxygen (anaerobic organisms) and in aerobic organisms (oxygen-using organisms) that can grow when oxygen is insufficient, pyruvate has an alternative fate. Under these conditions pyruvate undergoes a process termed fermentation, whereby pyruvate is reduced and NADH is oxidized to regenerate NAD+. The regeneration of NAD+ is critical for the ability of the cell to undergo additional rounds of glycolysis and to generate additional energy in the form of ATP. Depending on the cell type, there are two types of fermentation reactions: lactate fermentation and alcohol fermentation (illustrated in Figure 3). When there is insufficient oxygen in muscles, pyruvate is converted to lactate. In some organisms (e.g. yeast) that can grow anaerobically, pyruvate is converted to ethanol and CO2. We enjoy the by-products of alcohol fermentation in the bread we eat and the alcoholic beverages we drink. Note, although fermentation allows the cell to continue to undergo glycolysis, the net energy yield from fermentation is much lower than that from cellular respiration. Fermentation does not yield any additional energy, so under anaerobic conditions the yield of ATP is only two ATPs/glucose. The yield of ATP for complete cellular respiration is thirty-eight nucleotides per molecule of glucose (two ATPs from glycolysis and an additional thirty-six ATPs from subsequent reactions; which will be described later in this tutorial and the next tutorial).

The Citric Acid Cycle

Figure 4. The citric acid cycle. The entry into the cycle is acetyl CoA (labeled in orange). The intermediates of the cycle are labeled in purple. The products of the cycle are four molecules of reduced electron carriers, three molecules of NADH (labeled in red), one FADH2 (also labeled in red) and one molecule of ATP (labeled in bright yellow).

The citric acid cycle, which takes place in the mitochondria, is the third stage of cellular respiration and it completes the oxidation of glucose. Recall that in glycolysis, glucose is converted to two molecules of pyruvate, and then pyruvate is further oxidized to acetyl CoA. In the citric acid cycle, acetyl CoA is completely oxidized to CO2 and reduced electron carriers are generated in the form of NADH and another molecule, flavin adenine dinucleotide (FAD). In addition, ATP is generated through substrate-level phosphorylation. The complete citric acid cycle is illustrated in Figure 4. In this tutorial we will focus on the first and last step, and the products of the citric acid cycle. 

Acetyl CoA is the entry point to the citric acid cycle, and while acetyl CoA will be oxidized and CO2released, this does not happen directly but occurs via an eight-step process. The first step of the citric acid cycle is the transfer of two carbons from acetyl CoA to the 4-carbon sugar oxaloacetate to generate the 6-carbon sugar citrate- hence, the name of the cycle. This first step seems contrary to the purpose of the citric acid cycle (sugar oxidation); however, in the subsequent step of the cycle, sugars are oxidized and carbon bonds are cleaved to release two molecules of CO2, three molecules of NADH, one molecule of FADH2, and one molecule of ATP. The end product of the citric acid cycle is oxaloacetate, which you should recall combines with acetyl CoA to start the cycle. These reactions are referred to as a cycle because oxaloacetate is used in the first step and is regenerated in the last step. The citric acid cycle is analogous to a hand-cranked generator, where one turn of the crank produces energy in the form of electricity, while the crank itself is unaltered. That is, no new energy is generated, rather it is transformed from one form to another; therefore, the hand turning the crank provides the energy that will be converted to electricity. Using this analogy, the citric acid cycle is the generator, acetyl CoA provides the energy to turn the crank, and the energy of the carbon bonds are converted to the reduced electron carriers and ATP (analogous to the electricity).

The level of acetyl CoA is critical to driving the citric acid cycle. The first step (oxaloacetate + acetyl CoA -> citrate) is strongly exergonic. In addition, it keeps the oxaloacetate levels low, driving the last step of the cycle (malate + NAD+ -> oxaloacetate + NADH + H+). So far we have considered acetyl CoA derived from pyruvate oxidation, however, there are other sources of acetyl CoA. In fact, an important source is the oxidation of fatty acids (recall the tutorial Properties of Macromolecules II: Nucleic Acids, Polysaccharides and Lipids), which are the macromolecules that store the most energy.

Finally, the citric acid cycle is not solely linked to cellular respiration. It is, in fact, amphibolic (both anabolic and catabolic). Many of the intermediates of the cycle are siphoned off and used in other pathways. For instance, citrate is used in pathways to synthesize fatty acids and cholesterol. Several intermediates, including oxaloacetate, are precursors of amino acids. In order to be able to run the citric acid cycle efficiently, there are pathways that replenish the intermediates of the cycle as well.

Summary

Figure 5. The net yields of ATP, NADH and FADH2 during glycolysis, pyruvate oxidation and the citric acid cycle.

Cellular respiration is a catabolic pathway in which glucose is completely oxidized, yielding CO2 and the high-energy, reduced electron carriers NADH and FADH2, and ATP. This tutorial reviewed the first three stages of cellular respiration: glycolysis, pyruvate oxidation and the citric acid cycle. Figure 5illustrates the net yield of ATP and reduced electron carriers for each of these stages. Glycolysis is the break down of glucose to give a net yield of two molecules of pyruvate, two ATPS and two NADH + H+. Glycolysis occurs in three phases: phase I: preparation of the sugar, which requires two ATPs to phosphorylate the 6-carbon sugar; phase II: cleavage of the 6-carbon sugar to two 3-carbon sugars; and phase III: oxidation of the sugars and generation of four ATPs and two NADH + H+ per glucose. Glycolysis is regulated by allosteric regulation of the enzymes hexokinase, phosphofructokinase and pyruvate kinase, which catalyze reactions at three steps that are highly exergonic. Gluconeogeneis is the generation of glucose, starting from pyruvate, and it is essentially glycolysis in reverse (with the important exception of three exergonic and highly regulated steps). Pyruvate is the end point of glycolysis and it is a branching point. In the absence of oxygen, pyruvate undergoes fermentation (either ethanol or lactate, depending on the organism). Fermentation does not generate any additional energy, however, NAD+ is regenerated. In the presence of oxygen, pyruvate is oxidized and acetyl CoA is formed, which feeds into the citrate acid cycle and the complete oxidation of glucose. The citric acid cycle begins when acetyl CoA combines with oxaloacetate to generate citric acid. One round of the cycle generates two CO2, three NAD+ + H+, FADH2and ATP, and oxaloacetate is regenerated. In addition to pyruvate, fatty acids are an important source of acetyl CoA. Finally, the citric acid cycle is amphibolic and is central to many other metabolic pathways.




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