bio - module 9

Energy Derived from Food 

  • Aerobe – organism that grows or metabolizes only in the prescence of oxygen (plants and animals) 

  • Anaerobe – organism that grows only in the absece of oxygen (sulphate-reducing bacteria) 

  • Facultative anaerobe – organism capable of carrying out aerobic respiration but able to switch to fermentation when oxygen is unavailable (e coli. and yeast) 

  • Cellular respiration – the process by which cells generate ATP through a series of redox reactions; electrons are removed from various molecules such as glucose and passed through intermediate electron carriers to a final electron acceptor 

    • When this acceptor molecule is oxygen, the process is called aerobic respiration 

    • When it is a chemical substance (inorganic molecule) in the absence of oxygen, the process is called anaerobic respiration 

    • When it is an organic molecule, the process is called fermentation 

  • During aerobic cellular respiration, the fuel (such as glucose) is oxidized and oxygen is reduced. Cellular respiration can be summarized as the following equation: 

 

Mitochondrion – structure and function 

  • The power station of the cell, an organelle in eukaryotic cells where cellular respiration and ATP synthesis occur 

  • Double-membrane mitochondrion forms two different compartments 

    • Outer membrane 

    • Inner membrane  

    • Intermembrane space 

    • Matrix 

    • Folds (cristae) 

 

Aerobic Respiration – a redox process 

  • Most cells of plant, animals, protists, fungi and bacteria use aerobic respiration to gain energy from glucose 

  • The overall reaction pathway for the aerobic respiration of glucose is summarized as follows: 

  • Includes four stages: 

    • Glycolysis 

    • Formation of acetyl-CoA 

    • Krebs cycle 

    • Electron transport chain/chemiosmosis 

 

Glycolysis 

  • The multistep chemical breakdown of a 6-C glucose molecule into two, 3-C molecules of pyruvate 

  • Consists of a series of reactions divided into two major phases with 10 steps, each of which is catalyzed by a specific enzymes 

    • The first phase includes endergonic reaction requiring an investment of ATP  

    • The second phase includes exergonic reactions yielding ATP and NADH 

  • The first stage of cellular respiration in all organisms 

  • Occurs in the cytoplasmic fluid 

  • An ancient and universal metabolic system does not require oxygen  

  • Starting materials; glucose, ADP+Pi, NAD+, ATP and enzymes 

  • Produces 2 pyruvates, 2 ATP and 2 NADH 

 

Formation of Acetyl-CoA 

  • The conversion of pyruvate to acetyl-CoA 

  • Occurs in mitochondria  

  • A carbon atom in pyruvate is removed and released in CO2 

  • A molecular of NAD+ is reduced to NADH (total 2NADH) 

  • A coenzyme- A (CoA) is attached 

  • An acetyl-CoA is produced 

  • The reaction is catalyzed by pyruvate dehydrogenase 

 

Kreb's Cycle  

  • the metabolic cycle that is fueled by acetyl-CoA formed after glycolysis in cellular respiration; chemical reactions in the Krebs cycle complete the metabolic breakdown of glucose molecules to CO2 

  • Occurs in the matrix of mitochondria 

  • The four carbon molecule oxaloacetrate accepts two carbon acetyl group from acetyl-CoA 

  • The first product is citric acid 

  • Includes eight steps each of which is catalyzed by a specific enxyme 

  • The cycle completely disassembles acetyl-CoA, stripping away its electrons and producing CO2 

  • At the end of each cycle, the oxaloacetate has been regenerated 

  • High energy extraction steps produce 2 ATP, 6 NADH and 2 FADH2 per a glucose molecule 

  • NADH and FADH2 molecules carry most of the energy (in form of high-energy electrons) of the original glucose molecule to the electron transport chains 

 

Electron Transport Chain 

  • A sequence of electron-carrier molecules that shuttle electronds during redox reactions, with the release of energy 

  • The electron transport chain is embedded in the inner mitochondrial membrane (comparable to bacterial plasma membrane) 

  • The chain contains three large enzyme complexes and several (mobile) electron carriers: 

    • I  NADH-Q reductase complex 

    • II  (succinate-Q reductase complex) 

    • III cytochrome b/c1 reductase complex 

    • IV cytochrome c oxidase complex 

    • Flavin mononucleotide (FMN) 

    • Ubiquinone (Q) 

    • Cytochrome (b, c, c1, a, a3)  

  • All of the carriers can exist in an oxidized form or reduced form, bind and release electrons in redox reactions 

  • The electrons from NADH or FADH2 entering the electron transport chain have a relatively high energy content, and lose some of their energy at each step as they pass along the chain 

  • As redox occurs, the electron carriers use some of the energy released as electron pass down the electron transport chain to actively transport proton (hydrogen ion, H+) from one side of the inner mitochondrial membrane to the other, which results in H+ gradient 

  • In the end, the electrons are simultaneously united with H+ from the surrounding medium to form hydrogen which reacts with oxygen to produce water 

  • NADH and FADH2 are the primary electron donors 

  • O2 is the final electron acceptor  

 

Chemiosmosis 

  • The production of ATP using the energy of proton gradient across membrane to phosphorylate ADP; it powers the most ATP synthesis in cells 

  • The activity of electron transport chains establishes the proton gradient between the intermembrane space and the matrix 

  • The proton gradient is a form of potential energy that can be harnessed to provide the energy of ATP synthesis 

  • Diffusion of protons from the intermembrane space through the inner mitochondrial membrane to the matrix is through specific channels formed by an enzyme complex, ATP synthase 

  • Diffusion of the protons down their gradient, through the ATP synthase complex, is an exergonic process 

  • This exergonic process drives the endergonic reaction, in which ATP is produced by phosphorylating ADP – oxidative phosphorylation  

 

Oxidative Phosphorylation 

  • Mitochondria are called the power plants of the cell because most of a cell's ATP is produced there in the process of oxidative phosphorylation 

 

Aerobic Respiration of One Glucose Yields a Maximum of 36 to 38 ATPS 

  • Glycolysis – 2 ATP + 2 NADH 

  • Pyruvate grooming – 2 NADH 

  • Kreb's cycle – 2 ATP + 6 NADH + 2 FADH2  

  • Total = 4 ATP, 10 NADH, and 2 FADH2 

  • The oxidation of NADH in the electron transport chain yields up to 3 ATP. However, the 2 NADH molecules produced through glycolysis in the cytosol yields either 2 ATPs (eukaryotes) or 3 ATPs (prokaryotes). Thus, the maximum number of ATPs formed using the energy from NADH is 28 to 30 

  • The oxidation of FADH2 yields 2 ATPs per molecule, so the 2 FADH2 molecules produced in the Kreb's cycle yield 4 ATPs 

 

Other Organic molecules as Fuels 

  • Carbohydrates – glucose and other sugars; entering glycolysis  

  • Proteins – amino acids; eg. alanine – pyruvate, glutamate – ketoglutarate, aspartate – oxaloacetate 

  • Fats – glycerol + fatty acids. Glycerol – glycerol 3-phosphate, fatty acids – acetyl-CoA 

  • Each gram of lipid in the diet contains 9 kcal 

  • Each gram of sugars or amino acids has about 4 kcal 

 

Fermentation 

  • An ATP-generating process in which organic compounds act as both donors and acceptors of electrons; occurs in the absence of O2 

    • Some organisms are able to survive without O2 

    • Organisms survive on the energy base of two molecules of ATP per glucose molecule that come from glycolysis by substrate-level phosphorylation 

    • Excess cytosolic NADH produced during glycolysis tends to be toxic to the cells 

    • In fermentation, NADH molecules transfer their hydrogen atoms to organic molecules, thus regeneration of the NAD+ enables cells to keep glycolysis going 

 

Fermentation – Anaerobic Respiration 

  • Alcoholic fermentation – yeasts and certain bacteria convert the pyruvate produced by glycolysis to CO2 and ethanol 

  • Lactic Acid Fermentation – in some fungi and bacteria, lactic acid, rather than alcohol, is produced when NADH from glycolysis is oxidized 

    • Lactic acid fermentation is used in the dairy industry to make cheese and yogurt 

    • Human muscle cells can also make ATP by this metabolic pathway when oxygen is scarce 

  • Functions of fermentation: 

    • It is an inefficient way to use fuel 

    • It allows organisms to survive without oxygen 

    • It removes toxic excess NADH in the cytosol 

    • It replenishes the supply of NAD+ 

  • Energy derived from light 

    • All organisms can be classified on the basis of two aspects of their nutrition: their carbon source and their energy source  

    • Organisms obtain carbon in one of two ways: 

      • Autotrophs (Greek auto, "self", and trophos, "nourishing"– are able to carry out carbon fixation using CO2 as a carbon source; also called primary producer 

      • Hetetrophs – are unable to synthesize its own organic carbon-based compounds from inorganic sources and as a result, they feed on organic matter produced by, or available in, other organisms 

    • Organisms obtain energy in one of two ways: 

      • Phototrophs – are photosynthetic organisms that use light as their energy source 

      • Chemotrophs – are organisms that contain energy by the oxidation of reduced compounds (electron donors) in their environments 

    • Photoautotrophs – plants, algae and cyanobacteria  

    • Photosynthesis – the process by which all photoautotrophs use light energy to make sugars and other organic food molecules from CO2  and water. It creates the biomass on earth and the atmospheric oxygen (O2) 

 

  • Photosynthesis can be summarized as the following equation: 


  • Two unique reactions in chloroplasts: 

    • Light reactions – the light driven production of ATP (photophosphorylation) and NADPH 

    • Carbon fixation – the conversion of CO2 to carbohydrates 

  • Chloroplast – an organelle found in plants and photosynthetic protists absorbs sunlight and uses it to power the synthesis of organic food molecules (sugars) 

    • In plants, chloroplasts are located mainly in the mesophyll cells. In non-green tissues, the equivalent organelles are called plastids (etioplast, chromoplast, leucoplast, amyloplast) 

  • Structure of chloroplast: 

    • Out and inner membranes  

    • Stroma 

    • Thylakoid (granum) 

      • Thylakoid membrane 

      • Thylakoid lumen 

 

Light Energy 

  • Basic physics of light 

    • Most life on our planet depends on sunlight 

    • Light is composed of small particles call photons 

    • Light carries electromagnetic energy (solar energy or radiation), which travels in space as rhythmic waves and can be measured in photons  

    • The energy of a photon is inversely proportional to its wavelength: the shorter the wavelength of light, the greater the energy of a photon 

    • The visible light spectrum ranges from 380 to 760 nm 

    • Plants absorb light mainly in the blue (422-492nm) and red (647-760nm) regions of visible light (plant leaves turn green) 

 

Light reaction  

  • Solar energy absorption and conversion to chemical energy in the form of ATP and NADPH, which powers the sugar-producing calvin cycle 

  • Photosynthetic pigments: 

    • Thylakoid membranes contain several kinds of pigments, and chlorophyll is the main pigment, containing a porphyrin ring with a Mg++ in the center and a long hydrophobic side chain 

      • Chlorophyll a – absorbs light within the violet, blue and red wavelengths while mainly reflecting green 

      • Chlorophyll a initiates the light-dependent reaction (as primary electron donor in the electron transport chain and also transferring resonance energy in the antenna complex) 

      • Chlorophyll b – extends the absorption spectrum and acts as an accessory pigment that also participates in light absorption 

      • Carotenoids – another accessory pigment that absorb different wavelengths of light  

  • Pigments 

    • Stay at either ground state (lower energy) or excited state (higher energy) 

    • When a pigment absorbs a photon of light energy, one of its electrons becomes excited, meaning that the electron is boosted to a higher-energy orbital  

    • When the excited pigment returns to its ground state, its energy  

      • Is dissipated as heat or as an emission of fluorescence light 

      • Passes its excited electron to a neighboring receptor module 

  • Photosystem  

    • A light-harvesting unit of a chloroplast thylakoid membrane, containing a reaction center plus antenna complexes 

  • Reaction center  

    • Chlorophyll molecules in the thylakoid membrane are associated with chlorophyll-binding proteins and organized into units called antenna complexes (light-harvesting complex) 

    • Each antenna complex absorbs light energy and transfers it (resonance energy) to the reaction center 

    • The reaction center is a complex of chlorophyll molecules (chlorophyll a) and proteins including the primary electron acceptor, which participate directly in photosynthesis  

  • Two types of photosystems  

    • Photosystem I (PS I), also called P700 because the reaction center associated with PS I has an absorption peak at 700nm (red light) 

    • Photosystem II (PS II), called P680 made up of a reaction center with an absorption peak of about 680nm (a more orange shade of red) 

  • Function of photosystems: 

    • Absorption of light energy  

    • H2O splitting  

    • Release of O2 (PS II) 

    • Extraction of electrons 

    • Transfer electrons to primary electron acceptors in the electron transport chain  

 

Electron Transport 

  • The synthesis of ATP, and NADPH by the concerted action of photosystems II and I via noncyclic electron transport 

  • Electron transport chains 

    • Similar as in cellular respiration, consisting of a series of electron carrier molecules in the thylakoid membranes  

    • PS I 

      • Ferredoxin (Fd) 

      • NADP+ reductase etc 

    • PS II 

      • Plastoquinone (Q) 

      • Cytochrome complex (H+ pump) 

      • Plastocyanin (PC) etc. 

    • Electron transport chain through a noncyclic pathway caries the flow of electrons extracted from H20 to NADP+ 

  • When PS II (P680) is activated by absorbing protons, it (chlorophyll a) gives energized electrons to a primary electron acceptor, which are passed along the electron transport chain and eventually donated to PS I 

  • The PS II that has given up an electron is positively charged and functions as a strong oxidizing agent that is capable of pulling electron away from H2O 

    • A photolysis reaction probably catalyzed by a manganese (Mn in 4 oxidation states: Mn2+/3+/4+/5+) - containing enzyme with the release of O2 as a by-product 

  • Electrons transferred to PS I are "re-energized" by the absorption of additional light energy  

  • Re-energized electrons are passed along the electron transport chain  

  • The final electron acceptor is NADP+, (not O2), forming NADPH 

  • One-third of the energy of the photons absorbed by the two photosystems is used to transfer electrons from water to NADP+ 

  • Energy released during electron flow drives the transport of hydrogen ions across the thylakoid membrane. One-eighth of the light energy absorbed by the two photosystems is conserved by pumping protons into the lumen of the thylakoids via the cytochrome b6/f complex 

  • The high-energy molecule NADPH is released into the stroma and will be used in the reactions for carbon fixation 

  • The synthesis of ATP is driven by chemiosmosis (photophosphorylation) 

 

Chemiosmosis 

  • The production of ATP using the energy of H+ gradient across membranes to phosphorylate ADP, powers most ATP synthesis in cells 

  • Because the synthesis of ATP is coupled to the transport of electrons that have been energized by photons of light, the process is called phosphorylation 

    • The pigments and electron acceptors or carriers are embedded in the thylakoid membrane 

    • As electrons move down the electron transport chain, protons move from the stroma to the stroma to the thylakoid lumen 

    • A concentration gradient of protons is created between the thylakoid lumen and the stroma, reaching an approx. 1000-fold difference in proton concentration  

    • As the protons diffuse through an ATP synthase complex, this exergonic process of diffusion down a concentration gradient couples the endergonic process of phosphorylation of ADP to form ATP 

    • ATP is released into stroma 

  • Noncyclic electron flow involves both photosystems I and II and produces ATP and NADPH 

  • Cyclic electron flow uses only photosystem I and produces only ATP 

    • No H2O splitting occurs 

    • No NADPH is produced 

    • No O2 is generated  

    • ATP is formed by chemiosmosis 

  • Cyclic electron flow generates surplus ATP 

    • The process was used by ancient bacteria to produce ATP from light energy 

    • To satisfy the higher demand in the calvin cycle  

    • To drive other energy-requiring processes within the chloroplast 

 

Carbon Fixation 

  • The incorporation of carbon from atmospheric CO2 into the carbon in organic compounds 

  • During photosynthesis, in a C3 plants, carbon (CO2) is fixed into a three-carbon sugar (3-phosphoglycerate) as it enters the calvin cycle. In C3 and CAM (crassulacean acid metabolism) plants, carbon is fixed into a four-carbon sugar (oxaloacetate) 

  • In carbon fixation, the energy of ATP and NADPH during light reaction is used in formation of organic molecules from CO2 

  • the carbon fixation reactions could be summarized as follows: 


  • The second of two stages of photosynthesis; the calvin cycle is a cyclic series of chemical reactions that occur in the stroma of a chloroplast, using the carbon in CO2 and the ATP and NADPH produced by the light reactions to make the energy-rich sugar molecular glyceraldehyde 3-phosphate (G3P) 

  • Step 1 – carbon fixation 

    • CO2 is fixed to the energy-rich five-carbon compound ribulose 1, 5-bisphosphate (RuBP) 

    • This is catalyzed by Rubisco (ribulose 1, 5-biphosphate carboxylase/oxygenase), the most abundant protein in the chloroplast 

    • The product is two molecules of the three carbon compound 3-phosphoglycerate 

    • The product of the initial carbon fixation reaction is a three-carbon compound. Thus, the calvin cycle is also called C3 pathway 

  • Step 2 – energy consumption and carbon reduction 

    • The energy and reducing power from ATP and NADPH are used  

    • the PG molecule is phosphorylated by ATP and reduced by NADPH, resulting formation of glyceraldehyde 3-phosphate (G3P)  

    • Two molecules of ATP and two molecules of NADPH are consumed for each CO2 molecule fixation during this step 

    • Sugar release- an energy-rich molecule, glyceraldehydes-3-phosphate, might be removed from the cycle, and two molecules of G3P can lead to the formation of glucose of fructose in an exergonic reaction 

  • Step 3 –RuBP regeneration  

    • RuBP regeneration phase involves a complex series of ten reaction  

    • The intermediate ribulose 5-phosphate becomes phosphorylated in consumption of ATP to regenerate RuBP 

    • RuBP is ready to accept another CO2