Overview Of Metabolism PDF

Overview of Metabolism  BYU22201 Integration/overview of metabolism Recognizing reduced and oxidised metabolites Metabolism simplified in carbon units Key functional groups explain metabolism Compartmentation and metabolism Irreversible steps are important in metabolism...

Overview of Metabolism  BYU22201 Integration/overview of metabolism Recognizing reduced and oxidised metabolites Metabolism simplified in carbon units Key functional groups explain metabolism Compartmentation and metabolism Irreversible steps are important in metabolism Energetics and surface area and the origin of eukaryotes  Simplifying principle of catabolism Breakdown of polymers to monomer:glucose/amono acids/fatty acids. Essentially this is an oxidation reduction reaction: carbohydrate is oxidised to CO2 and oxygen is reduced to Water. This process involves stripping out the hydrogens and electrons and storing them in thermodynamically molecules that act as cellular currencies: reduced forms NADH/NADPH etc Subsequent transfer of these electrons to oxygen to generate ATP by oxidative phosphorylation A universal form of biological chemistry  Carbon oxidation states: relevance to metabolism Energy yielding reaction in this direction Reduced Oxidised O C O Methane Methanol Formaldehye Formic acid Carbon Dioxide Oxidation: loss of pair of electrons Two electron oxidation/reduction at each step reduction: loss of pair of electrons Energy-yielding metabolites are typically organic molecules that are in reduced states. State of reduction corresponds to no of H around C atom For example methane is eight electron reduced compared to Carbon dioxide  Carbon oxidation states: at 2 carbon level Reduced Oxidised Ethane Ethanol Acetaldehyde Acetic acid why are fatty acids better form of energy storage than polymers of glucose? The deeper state of reduction of fatty acids compared to glucose (C-H bonds v C-OH bonds) means that when cells store energy, fatty acids are more efficient storage molecules carbon per carbon than glycogen or starch. Carbon flow & the Glucose central role of the TCA cycle Fatty acids/Lipid Glycolysis Fatty acid Gluconeogenesis oxidation Acetyl CoA Fatty acid synthesis TCA cycle Transamination CO2 Reducing equivalence Proteins & Amino Acids Amino acid NADH/FADH break down ATP and H2O  The flow of Carbon 1 carbon 6 carbon C6-C3: DNA 2ADP → 2ATP FAT & 5 carbon 2NAD – 2 NADH RNA 3 carbon Carbon N x 2 Carbon Rearrangements 2 carbon 1 carbon Amino C6-C1 4 carbon 6 carbon acids 10 NAD → 10NADH 2FAD → 2FADH2 5 carbon 1 carbon 1 carbon Amino 30 ATP acids key functional groups in metabolism, the arrangement of carbon , hydrogen and oxygen Alcohol: reduced form of O in Carbohydrates Glucose etc Ketone and aldehydes: a ketone is an organic compound where the carbonyl group is attached to two carbon atoms. Note this differs from an aldehyde group The carboxyl group has two components: a carbonyl group and a hydroxyl group  A Key compounds that are central in metabolism: ketoacids Two COOH groups Keto group 2-oxoglutarate (or a-ketoglutarate) A 5 carbon keto-acid and intermediate of the TCA cycle. Extremely important compound in amino acid metabolism. Functional group notes: contains 2 carboxyl acid groups (COOH)and a Keto group. R1 Key feature of keto acids: they can undergo decarboxylation this is an energy yielding reaction The carboxyl group adjacent to the carbonyl group in CO2 a keto acid is easy to release as CO2: this generally thorough oxidative decarboxylation. This is a recurring theme in metabolism a-ketoglutarate Undergoes decarboxylation to succinate (via succinyl CoA in the TCA cycle). Energetically very favourable reaction CO2 Pryuvate: undergoes oxidative decarboxylation to acetyl CoA Catalysed by pryuvate dehydrogenase An irreversible step in most cells, which cannot add 1 carbon to a 2-carbon acceptor In addition this reaction yield a thermodynamically activated but kinetically stable acetyl (2 carbon) group. This is why fatty acid metabolism revolves around C2 unirs  Glycolysis C6 Keto acids are key intermediates and link major metabolic pathways Note change in length of Co enzyme A carbon skeleton arising PDH through decarboxylation (loss CO2 of CO2) Pyruvate C3 Acetyl-CoA; C2 CS Citrate C6 CO2 TCA Amino acids CYCLE Oxaloacetate C4 Fatty Acids Acetoacetate 2-oxoglutarate C5 CO2 Oxaloacetate can also undergo decarboxylation To produce the three carbon intermediate of glycolysis: Phosphoenolpyruvate.  The remarkable TCA cycle The TCA cycle is an 8 step cycle that achieves the efficient and complete oxidation of a single 2C acetyl unit. This complex piece of chemistry is achieved efficiently and under mild conditions. only 4 of steps are oxidative (2 of which are decarboxylating) the other 4 steps are rearrangements to facilitate these steps but also to regenerate the cycling C4 subunit substrate: oxaloacetate You need to full turns of the cycle to oxidise the acetyl group and you produce 3 NADH and 1 FADH2 molecules each transferring a pair of electrons to the mitochondrial electron transport chain The cycle is amphibolic: it can work in a catabolic direction but also in a biosynthetic direction, depending on the energy /neutrition status of the cell It can be modified operate fully as a cycle or as partial cycle in certain types of cells: e.g. activated immune cells What about Glycolysis: why split C6 to C3 and how is this achieved. Position of the carbonyl group is important β- Cleavage and aldolase Glucose (aldehyde) and Fructose (Keto): interconversion is isomerisation Cleavage of the β-carbon bond Why is G-6-P converted to F-6-P in second step of glycolysis The β-cleavage: the bond indicated is easier to break Here we slpit into the ketol 3 –carbon triose (DHAP in glycolysis) and the aldehyde triose GAP in glycolysis. Why 3 C units: because these can be used to produce ATP directly by substrate level phosphorylation and to produce a 3C molecule (Pyruvate). Oxidation and decarboxylation of pyruvate is energetically very favourable and also produces an energetically activated 2 carbon acetyl group (acetyl CoA)  Compartmentation is important Cytoplasm : Glycolysis , Hexose monophosphate shut (HMP) or pentose phosphate pathway), Fatty acid Biosynthesis, Gluconeogensis (making glucose) , amino acid breakdown general biosynthesis Mitochondrion: the TCA cycle, b- oxidation of fatty acids; oxidative phosphorylation, some amino acid metabolism, transmination : topping up intermediates of the TCA cycle , such as 2-oxoglutrate (a- ketoglutarate)and oxaloacetate First steps of gluconeogenesis Transport steps across the mitochondrial Other compartments: Peroxisomes: inner membrane are important: often driven oxidative degradation of very long by the proton electrochemical gradient: e.g uptake of pyruvate with H+ chain and methyl branched fatty acids.  Mitochondrial Transporter and implications for metabolism ATP/ADP ratio in cytoplasm and mitochondrial matrix are different. The ATP/ADP ratio is higher in the cytoplasm that the matrix This is achieved by the ATP/ADP translocator. The driving for for the exchange is the mitochondrial membrane potential. Mitochondrial oxidative metabolism results in a low NAD+/NADH matrix ratio of ~ 7–8 compared with the cytosolic redox ratio of Note the multiplicity of transporters and up to 700 exchangers But No transporters for NADH, Acetyl-CoA or Cytoplasm higher relative levels oxaloacetate. of NAD (more oxidising) Mitochondrial Transport of NADH (reducing equivalence) across oxidative the inner membrane: important for the Practical metabolism results in a low NAD+/NADH matrix ratio of ~ 7– 8 (more reducing) compared cASAT mASAT with the cytosolic redox ratio of up to 700 Matrix Cytoplasm higher Inter membrane Matrix Inner relative levels of space membrane NAD (more The cytoplasmic and matrix pools of NAD/NADH are separated by the mitochondrial oxidising) inner membrane Matrix has higher NADH is transferred across the mtochondrial inner membrane by the shuttle relative levels of involving glutamate and malate: the malate-aspartate shuttle. NADH NADH is transferred effectively in the form of malate Note the role of c & mASAT: cytoplasmic and mitochondrial forms of aspartate amino transferase and malate dehydrogenase. Note aspartate transported with a net negative charge, To transport NADH into isolated mitochondria in practical you have to add glutamate is Glutamate and Malate co-transported with a proton, making the aspartate/glutamate Key Point: separate pools of NADH/NAD in transport electrogenic: exchange involves cytoplasm and Mitochondrial matrix movement of a negative charge out of matrix NADH is transferred into matrix as malate  Mitochondrial inner membrane is impermeable to acetyl CoA Why: because this separates the pathways for fatty acid oxidation (matrix) from the pathways for Fatty acid synthesis Acetyl units (C2) are moved out of the matrix as citrate Converted in cytoplasm to oxaloacetate (OAA) and Acetyl CoA OAA is converted to malate (Via NADH) and enters matrix  Irreversible steps are important: Pyruvate kinase and Pyruvate dehydrogenase NADH Cytoplasm Co-enzyme A (CoA) CO2 NAD ADP ATP PEP, PK Phosphoenolpyruvate Pyruvate Pyruvate Kinase Dehydrogenase PDH PK: very large negative ΔG ~ -62.0 kJ/mol Mitiochondrial Matrix PDH: key point: nature has not devised a way to add a single Carbon unit (CO2) to a Two carbon unit, say acetate.  Glucose Reversal of pyruvate kinase: generate a four carbon unit and decarboxylate to make glucose GDP + CO2 Phosphoenolpyruvate (PEP) PEP carboxykinase Pyruvate GTP cytoplasm Malate oxaloacetate oxaloacetate Pyruvate carboxylase + CO2 Malate ATP Mitochondrial matrix ADP Reversal of the pyruvate dehydrogenase step, cells cannot add a C1 unit to a C2 NADH Co-enzyme A (CoA) CO2 NAD You cannot make glucose from Fat! The metabolic fate of acetyl CoA is either oxidation via the TCA cycle or synthesis of fatty acids. Pyruvate Pyruvate Dehydrogenase PDH Fat burns in the fire of carbohydrate! To oxidise acetyl CoA you need a TCA cycle, specifically you need Oxaloacetate (C4) to start the cycle to generate citrate (C6) from Acetyl CoA (C2). But Oxaloacetate can only be generated using carbon from glucose or amino acids.  Why are Bacteria small and structurally limited, while eukaryotes are large and structurally complex? Bioenergtics has an answer The answer may be the area available to energy transducing membranes and proton gradients: Perhaps this pressure drove the origin of eukaryotes and fusion of an archaeal host and a bacterial endosymbiont On average Bacteria are ~ 30 smaller (diameter) than typical eurkaryote Expand a bacteria cells to size of eukaryote is a problem 4 Volume (as a sphere) difference is huge (𝑉 = 𝜋𝑟 3 ), increases by 27,000 times but surface 3 2 area (𝐴 = 4𝜋𝑟 ) increases only 900 times. This is important Why? The cell has increase 27,00 time but surface for ATP production only 900  Consider the surface area of energy transducing membranes e.g. those with proton gradients? To a first approximation for cell energy production is a function of the surface area of energy transducing membranes (where Ox Phos occurs as this produces ~90% of ATP). In bacteria, Ox Phos occurs across the surface membrane: this becomes limiting as increasing size cell size outstrips the capacity to produce ATP. Expand bacteria to eukaryote size volume increases 29,000 times but ability to produce ATP only 90 times: effectively a 30-fold drop relative to cell size The emergence of eukaryotes solved this problem: the surface membrane is not longer engaged in energy transduction (ATP synthesis) : instead hundreds of mitochondria with highly folded inner membranes; an enormous surface area available for ATP synthesis. Also this membrane has a higher density of proteins devoted to Ox Phos that possible if in a surface membrane as in bacteria which has to accommodate many additional proteins required to interact with external world Eukaryotic cell produces 5000 times more energy per cell compared to Liver cells ~ 1000-2000 mito per prokaryote: Even allowing for a bigger genome have ~ 1500 times more cell energy per gene to express these genes The total surface area of the inner membrane is far larger than the RESULT: COMPLEXITY surface area of a liver cell.