bioenergetics Flashcards

Question

Non-cyclic Phosphorylation

Answer 1

1. Absorption of light by photo system II When photo system II absorbs light, an electron excited to a higher energy level in the reaction centre chlorophyll P680 is captured by the primary electron acceptor of PS II. The oxidized chlorophyll is now a very strong oxidizing agent; its electron “hole” must be filled. 2. Photolysis of water This hole is filled by the electrons which are extracted, by an enzyme, from water. This reaction splits a water molecules into two hydrogen ions and an oxygen atom, which immediately combines with another oxygen atom to form O2. This water splitting step of photosynthesis that releases oxygen is called photolysis. The oxygen produced during photolysis is the main source of replenishment of atmospheric oxygen. 3. 1st Electron transport chain Each photoexcited electron passes from the primary electron acceptor of photo system II to photo system I via an electron transport chain. This chain consists of an electron carrier called plastoquinone (Pq), a complex of two cytochromes and a copper containing protein called plastocyanin (Pc). 4. Photophosphorylation As electrons move down the chain, their energy goes on decreasing and is used by thylakoid membrane to produce ATP. This ATP synthesis is called photophosphorylation because it is driven by light energy. Specifically, ATP synthesis during non-cyclic electron flow is called non-cyclic photophosphorylation. This ATP generated by the light reactions will provide chemical energy for the synthesis of sugar during the Calvin cycle, the second major stage of photosynthesis. 5. Filling of electron hole of PSI The electron reaches the “bottom” of the electron transport chain and fills an electron “hole” in P700, the chlorophyll a molecules in the reaction center of photosystem I. This hole is created when light energy is absorbed by molecules of P700 and drives an electron from P700 to the primary acceptor of photo system I. 6. 2nd electron transport chain The primary electron acceptor of photo system I passes the photoexcited electrons to a second electron transport chain, which transmits them to ferredoxin (Fd), an iron containing protein. An enzyme called NADP reductase then transfers theelectrons from Fd to NADP. This is the redox reaction that stores the high-energy electrons in NADPH. The NADPH molecule will provide reducing power for the synthesis of sugar in the Calvin cycle. The path of electrons through the two photosystems during non-cyclic photophosphorylation is known as Z-scheme from its shape.

Answer 2

Non-cyclic electron flow during photosynthesis generates ATP, NADPH and oxygen. (Each photon of light excite single electron).Non-cyclic electron flow during photosynthesis ATP, NADPH and oxygen are generated. The arrows trace the current of light-driven electrons from water to NADPH. Each photon of light excites single electron, but the diagram tracts two electrons at a time, the number of electrons required to reduce NADP+. The numbered steps are described in the text. Cyclic Phosphorylation Under certain conditions, photoexcited electrons take an alternative path called cyclic electron flow. This path uses photosystem I but not photosystem II.

Answer 3

Possibly it happens when i. The chloroplast runs low on ATP for the Calvin cycle. ii. The cycle slows down iii. NADPH accumulate in chloroplast. This rise in NADPH may stimulate a temporary shift from non-cyclic to cyclic electron flow until ATP supply meets the demand.

Answer 4

The cyclic flow is short circuit: The electrons cycle back from primary electron acceptor to ferredoxin (Fd) to the cytochrome complex and from there continue on to the P700 chlorophyll. ATP is generated by the coupling of ETC by chemiosomosis.

Answer 5

 There is no production of NADPH and no release of oxygen.  Cyclic flow does, however, generate ATP. This is called cyclic photosphosphorylation.

Answer 6

Chemiosmosis In both cyclic and non-cyclic photosphosphorylation, the mechanism for ATP synthesis is chemiosmosis, the process that uses membranes to couple redox reactions to ATP production. Pumping of protons (H+ ) Electron transport chain pumps protons (H+ ) across the membrane of thylakoids in case of photosynthesis into the thylakoids space. Energy for Proton Pumping The energy used for this pumping comes from the electrons moving through the electron transport chain. H + gradient establishment This energy is transformed into potential energy stored in the form of H+ gradient across the membrane. ATP synthase Next the hydrogen ions move down their gradient through special complexes called ATP synthase which are built in the thylakoid membrane. During this diffusion of H+ the energy of electrons is used to make ATP.

Answer 7

The dark reactions take place in the stroma of chloroplast. These reactions do not require light directly and can occur in the presence or absence of light provided the assimilatory power in the form of ATP and NADPH, produced during light reactions is available. Energy of these compounds is used in the formation of carbohydrates from CO2, and thus stored their in. Equation of Calvin cycle These reactions can be summarized as follows : 3CO2 + 6NADPH + 9ATP ⎯⎯→ (CH2O)3 + 6NADP + 9ADP + 9Pi + 3H2O Carbohydrate Discovery of Calvin Cycle The details of path of carbon in these reactions were discovered by Melvin Calvin and his colleagues at the University of California. Calvin was awarded Nobel Price in 1961. The cyclic series of reactions, catalyzed by respective enzymes, by which the carbon is fixed and reduced resulting in the synthesis of sugar during the dark reactions of photosynthesis is called Calvin Cycle. Phase of Calvin Cycle The Calvin cycle can be divided into three phases:  Carbon fixation  Reduction  Regeneration of CO2 acceptor (RUBP) (Fig 11.10). Phase 1: Carbon fixation Carbon fixation refers to the initial incorporation of CO2 into organic material. Keep in mind that we are following three molecules of CO2 through the reaction (because 3 molecules of CO2 are required to produce one molecule of carbohydrate, a triose). The Calvin cycle beings when a molecule of CO2 reacts with a highly reactive phosphorylated five – carbon sugar named ribulose bisphosphate (RUBP). Rubisco This reaction is catalyzed by the enzyme ribulose bisphosphate carboxylase, also known as Rubisco (it is the most abundant protein in chloroplasts, and probably the most abundant protein on Earth). The product of this reaction is an highly unstable, six – carbon intermediate that immediately breaks into two molecules of three – carboncompound called 3 – phosphoglycerate (phosphoglyceric acid-PGA). The carbon that was originally part of CO2 molecule is now a part of an organic molecule; the carbon has been “fixed”. Because the product of initial carbon fixation is a three – carbon compound, the Calvin cycle is also known as C3 pathway. Phase 2: Reduction: Each molecule of (PGA) receives an additional phosphate from ATP of light reaction, forming 1,3 – bisphosphoglycerate as the product. 1,3 bisphosphoglycerate is reduced to glyceraldehyde 3-phosphate (G3P) by receiving a pair of electrons donated from NADPH of light reactions. G3P is the same three-carbon sugar which is formed in glycolysis (first phase of cellular respiration) by the splitting of glucose. In this way fixed carbon is reduced to energy rich G3P with the energy and reducing power of ATP and NADPH (both the products of light-dependent reactions), having the energy stored in it. Actually G3P, and not glucose, is the carbohydrate produced directly form the Calvin cycle. For every three molecules of CO2 entering the cycle and combining with 3 molecules of five-carbon RuBP, six molecules of G3P can be counted as a net gain of carbohydrate. Out of every six molecule of G3P formed, only one molecule leaves the cycle to be used by the plant for making glucose, sucrose starch or other carbohydrates, and other organic compounds; the other five molecules are recycled to regenerate the three molecules of five-carbon RuBP, the CO2 acceptor. Phase 3: Regeneration of CO2 acceptor, RuBP: Through a complex series of reactions, the carbon skeletons of five molecules of three-carbon G3P are rearranged into three molecules of five-carbon ribulose phosphate (RuP). Each RuP is phosphorylated to ribulose bisphohate (RuBP), the very five-carbon CO2 acceptor with which the cycle started. Again three more molecules of ATP of light reactions are used for this phosphorylation to three RuP molecules. These RuBP are now prepared to receive CO2 again, and the cycle continues.

Answer 8

Living organisms need energy to carry on their vital activities. This energy is provided from within the cells by the phenomenon of respiration. Respiration is theuniversal process by which organisms’ breakdown complex compounds containing carbon in a way that allows the cells to harvest a maximum of usable energy. Two ways of Respiration In biology the term respiration is used in two ways.  External respiration  Cellular respiration External Respiration More familiarly the term respiration means the exchange of respiratory gases (CO2 and O2) between the organism and its environment. This exchange is called external respiration. Cellular Respiration The cellular respiration is the process by which energy is made available to cells in a step by step breakdown of C-chain molecules in the cells. Aerobic and Anaerobic Respiration The most common fuel used by the cell to provide energy by cellular respiration is glucose

Answer 9

Glycolysis (1st step of cellular respiration) The way glucose is metabolized depends on the availability of oxygen. Prior to entering a mitochondrion, the glucose molecule is split to form two molecules of pyruvic acid. This reaction is called glycolysis (glycolysis literally means splitting of sugar), and occurs in the cytosol and is represented by the equation: This reaction occurs in all the cells and biologists believe that an identical reaction may have occurred in the first cell that was organized on earth.The next step in cellular respiration varies depending on the type of the cell and the prevailing conditionsPyruvic Acid Cell processes pyruvic acid in three major ways:  Alcoholic fermentation  Lactic acid fermentation  Aerobic respiration. The first two reactions occur in the absence of oxygen and are referred to as anaerobic (without oxygen). The complete breakdown of glucose molecule occurs only in the presence of oxygen, i.e. in aerobic respiration. During aerobic respiration glucose is oxidized to CO2 and water and energy is released. (i) Alcoholic Fermentation: In primitive cells and in some eukaryotic cells such as yeast, pyruvic acid is further broken down by alcoholic fermentation into alcohol (C2 H5 OH) and CO2.(ii) Lactic acid fermentation: In lactic acid fermentation, each pyruvic acid molecule is converted into lactic acid C3 H6 O3 in the absence of oxygen gas: This form of anaerobic respiration occurs in muscle cells of humans and other animals during extreme physical activities, such as sprinting, when oxygen cannot be transported to the cells as rapidly as it is needed. Energy yield Both alcoholic and lactic acid fermentations yield relatively small amounts of energy from glucose molecule. Only about 2% of the energy present within the chemical bonds of glucose is converted into adenosine triphosphate (ATP). Aerobic respiration (Discussed in detail under cellular respiration)

Answer 10

Structure Mitochondria are large granular or filamentous organelles that are distributed throughout the cytoplasm of animals and plant cells. Each mitochondrion is constructed of an outer enclosing membrane and an inner membrane with elaborate folds or cristae that extend into the interior of the organelle.Function Mitochondria play a part in cellular respiration by transferring the energy of the organic molecules to the chemical bonds of ATP. A large “battery” of enzymes and coenzymes slowly release energy from the glucose molecules. Thus mitochondria are the “Power houses” that produce energy necessary for many cellular functions. Adenosine triphosphate and its importance Adenosine triphosphate, generally abbreviated ‘ATP’ is a compound found in every living cell and is one of the essential chemicals of life. It plays the key role in most biological energy transformations.Conventionally, ‘P’ stands for the entire phosphate group. The second and the third phosphate represent the so called “high energy” bonds. If these are broken by hydrolysis, far more free energy is released as compared to the other bond in the ATP molecule. Energy yield The breaking of the terminal phosphate of ATP releases about 7.3 K cal. of energy. The high energy ‘P’ bond enables the cell to accumulate a great quantity of energy in a very small space and keeps it ready for use as soon as it is needed.Use of ATP The ATP molecule is used by cells as a source of energy for various functions for example:  Synthesis of more complex compounds  Active transport across the cell membrane  Muscular contraction  Nerve conduction, etc.

Answer 11

The maintenance of living system requires a continual supply of free energy which is ultimately derived from various oxidation reduction reactions. Except for photosynthetic and some bacterial chemosynthetic processes, which are themselves oxidation reduction reactions, all other cells depend ultimately for their supply of free energy on oxidation reactions in respiratory processes. Dehydrogenase In some cases biological oxidation involves the removal of hydrogen, a reaction catalyzed by the dehydrogenases linked to specific coenzymes. Cellular respiration is essentially an oxidation process. Cellular Respiration Cellular respiration may be sub-divided into 4 stages: i. Glycolysis ii. Pyruvic acid oxidation iii. Krebs cycle or citric acid cycle iv. Respiratory chain Out of these stages the first occurs in the cytosol for which oxygen is not essential, while the other three occur within the mitochondria where the presence of oxygen is essential.

Answer 12

Glycolysis is the breakdown of glucose upto the formation of pyruvic acid. Glycolysis can take place both in the absence of oxygen (anaerobic condition) or in the presence of oxygen (aerobic condition). In both, the end product of glucose breakdown is pyruvic acid. The breakdown of glucose takes place in a series of step, each catalyzed by a specific enzyme. All these enzymes are founddissolved in the cytosol. In addition to the enzymes, ATP and coenzymes NAD (nicotinamide adenine dinucleotide) are also essential. Phases of glycolysis Glycolysis can be divided into two phases.  Preparatory phase  Oxidative phase In the preparatory phase breakdown of glucose occurs and energy is expended. In the oxidative phase high energy phosphate bonds are formed and energy is stored.

Answer 13

1. Phosphorylation of glucose The first step in glycolysis is the transfer of a phosphate group from ATP to glucose. As a result a molecule of glucose-6-phoshapte is formed. 2. Rearrangement (Isomerization) An enzyme catalyzes the conversion of glucose-6-phosphate to its isomer, fructorse-6-phosphate. 3. Phosphorylation of fructose 6-bisphosphate At this stage another ATP molecule transfers a second phosphate group. 4. Spliting of fructose 1, 6-bisphosphate The product is fructose 1,6-bisphosphate into two fragments. Each of these molecules contains three carbon atoms. One is called 3-phospo-glyceraldehyde, 3-PGAL or Glyceraldehyde 3-phosphate (G3P) while the other is dihydroxyacetone phosphate. 5. Interconvertion (isomerization) These two molecules (G3P and DAP) are isomers and in fact are readily interconverted by yet another enzyme of glycoslysis.

Answer 14

1. Oxidation and phosphorylation The next step in glycolysis is crucial to this process. Two electrons or two hydrogen atoms are removed form the molecule of 3-phosphoglyceraldehyde (PGAL) and transferred to a molecule of NAD. This is of course, an oxidation-reduction reaction, with the PGAL being oxidized and the NAD being reduced. During this reaction, a second phosphate group is donated to the molecule from inorganic phosphate present in the cell. The resulting molecule is called 1,3 Bisphosphoglycerate (BPG). 2. ATP formationThe oxidation of PGAL is an energy yielding process. Thus a “high energy” phosphate bond is created in this molecule. At the very next step in glycolysis this phosphate group is transferred to a molecule of adenosine diphosphate (ADP) converting it into ATP. The end product of this reaction is 3-phospho glycerate (3-PG). 3. Rearrangement (isomerization) In the next step 3-PG is converted to 2-Phosphoglycerate (2PG). 4. Dehydration and PEP formation From 2PG a molecule of water is removed and the product is phosphoenol. pyruvate (PEP). 5. Pyruvic acid formation PEP then gives up its ‘high energy’ phosphate to convert a second molecule of ADP to ATP. The product is pyruvate, pyruvic acid (C3 H4 O3).  It is equivalent to half glucose molecule that has been oxidized to the extent of losing two electrons (as hydrogen atoms).

Answer 15

Pyruvic acid (pyruvate), the end product of glycolysis, does not enter the Krebs cycle directly.  The pyruvate (3-carbon molecule) is first changed into 2-carbon acetic acid molecule. One carbon is released as CO2 (decarboxylation).  Acetic acid on entering the mitochondrion unites with coenzyme-A (CoA) to form acetyl CoA (active acetate).  In addition, more hydrogen atoms are transferred to NAD (Fig 11.13). Krebs Cycle or Citric Acid Cycle: Acetyl CoA now enters a cyclic series of chemical reactions during which oxidation process is completed. This series of reactions is called the Krebs cycle (after the name of the biochemist who discovered it), or the citric acid cycle. Citrate formation The first step in the cycle is the union of acetyl CoA with oxalocetate to form citrate. In this process, a molecule of CoA is regenerated and one molecule of water is used. Oxaloacetate is a 4-carbon acid. Citrate thus has 6 carbon atoms. Isocitrate formation After two steps that simply result in forming an isomer of citrate, isocitrate. Oxidative decarboxylation (ketoglutrate formation) It is conversion of isocitrate into ketoglutrate. Here NAD-mediated oxidation takes place. This is accompanied by the removal of a molecule of CO2. The result is ketoglutarate. Succinate formation ketoglutarate in turn, undergoes further oxidation (NAD + 2H → NADH2) followed by decarboxylation (CO2) and addition of a molecule of water. The product then has one carbon atom and one oxygen atom less. It is succinate. The conversion of -ketoglutarate into succinate is accompanied by a free energy change which is utilised in the synthesis of an ATP molecule. Oxidation of succinate The next step in the Krebs cycle is the oxidation of succinate to fumarate. Once again, two hydrogen atoms are removed, but this time the oxidizing agent is a coenzyme called flavin adenine dinucleotide (FAD), which is reduced to FADH2. Outline of the Kerbs cycle. The brackets give the number of carbon atom in each intermediate of the cycle. Malate Formation With the addition of another molecule of water, fumarate is converted to malate. Oxidation of Malate Another NAD mediated oxidation of malate produces oxaloacetate, the original 4-carbon molecule. This complete the cycle. The oxaloacetate may now combine with another molecule of acetyl CoA to enter the cycle and the whole process is repeated (Fig 11.13). Respiratory Chain In the Krebs cycle NADH and H+ are produced from NAD+ . NADH then transfers the hydrogen atom to the respiratory chain (also called electron transport system) where electrons are transported in a series of oxidation-reduction steps to react, ultimately, with molecular oxygen. (Fig. 11.14). Components of Respiration Chain The oxidation reduction substances which take part in respiratory chain are: i. A coenzyme called coenzyme Q ii. A series of cytochrome enzymes (b,c,a,a3) iii. Molecular oxygen (O2) Cytochrome Cytochromes are electron transport intermediates containing haem of related prosthetic groups, that undergo valency changes of iron atom. Heam is the same iron containing group that is oxygen carrying pigment in heamoglobin. The path of electrons in the reparatory chain appears to be as follows.

Answer 16

i. Oxidation of NADH NADH is oxidized by coenzyme Q. This oxidation yields enough free energy to permit the synthesis of a molecule of ATP from ADP and inorganic phosphate. ii. Oxidation of Co-enzyme Q Coenzyme Q is in turn oxidized by cytochrome b which is then oxidized by cytochrome c. This step also yields enough energy to permit the synthesis of a molecule of ATP. iii. Reduction of cytochrome c Cytochrome c then reduces a complex of two enzymes called cytochrome a and a3 (for convenience the complex is referred as cytochrome a). iv. Oxidation of cytochrome a Cytochrome a is oxidized by an atom of oxygen and the electrons arrive at the bottom end of respiratory chain. Oxygen is the most electronegative substance and the final acceptor of the electrons. A molecule of water is produced. In addition, this final oxidation provides enough energy for the synthesis of a third molecule of ATP. v. Oxidative phosphorylation Synthesis of ATP in the presence of oxygen is called oxidative phosphorylation. Normally, oxidative phosphorylation is coupled with the respiratory chain. As already described ATP is formed in three steps of the respiratory chain

Answer 17

The equation for this process can be expressed as follows: NADH + H+ + 3 ADP + 3Pi + ½ O2 → NAD+ +H2O + 3ATP Where Pi is inorganic phosphate. Mechanism of Oxidative Phosphorylation  The molecular mechanism of oxidative phosphorylation takes place in conjunction with the reparatory chain in the inner membrane of the mitochondrion.  Her also, as in photosynthesis, the mechanism involved is chemiosmosis by which electron transport chain is coupled with synthesis of ATP.  In this case, however the pumping/movement of protons (H+ ) is across the inner membrane of mitochondrion folded into cristae, between matrix of mitochondrion and mitochondrion’s intermembrane space.  The coupling factors in respiration are also different from those in photosynthesis.