Chemistry 203 Chapter 24 Biosynthetic Pathways Metabolism Catabolic reactions: Complex molecules Simple molecules + Energy Anabolic reactions: Biosynthetic reactions Simple molecules + Energy (in cell) Complex molecules Biosynthetic pathways Anabolic and catabolic reactions have different pathways. 1. Flexibility: if a normal biosynthetic pathway is blocked, the organism can often use the reverse of the catabolic pathway for synthesis. Catabolic Simple Molecules Complex Molecule Biosynthetic Biosynthetic pathways 2. Overcoming Le Chatelier’s principle: If a dynamic equilibrium is disturbed by changing the conditions, the position of equilibrium moves to counteract the change. (Glucose)n + Pi Glycogen phosphorylase (Glucos e)n-1 + Glu cose 1-ph osp hate Glycogen (one un it smaller) (Glucose)n-1 + UDP-glucose (Glucose)n + UDP Glycogen (one unit larger) Biosynthetic pathways Anabolic and catabolic reactions need different energy. Anabolic and catabolic reactions take place in different locations. Catabolic reactions Mitochondria Anabolic reactions Cytoplasm Biosynthetic pathways 1. Biosynthesis of Carbohydrates Biosynthesis of Fatty acids 2. Biosynthesis of Lipids Biosynthesis of Membrane Lipids 3. Biosynthesis of Amino acids Glycolysis Glucose is converted to two molecules of pyruvate. An anaerobic reaction in cytoplasm. 10 Reactions Glycolysis Steps [1] – [5] energy investment phase: 2 ATP molecules are hydrolyzed. The 6-carbon glucose molecule is converted into two 3-carbon segments. Glycolysis Steps [6] – [10] energy-generating phase: producing 1 NADH and 2 ATPs for each pyruvate formed. Glycolysis Enzymes: Glycolysis Step [1] begins with the phosphorylation of glucose into glucose 6-phosphate, using an ATP and a kinase enzyme. Glycolysis Step [2] isomerizes glucose 6-phosphate to fructose 6-phosphate with an isomerase enzyme. Glycolysis Step [3] is the phosphorylation of fructose 6-phosphate into fructose 1,6-bisphosphate with a kinase enzyme. Glycolysis Overall, the first three steps of glycolysis: 1. 2 phosphate groups is added. 2. A 6-membered glucose ring is isomerized into a 5-membered fructose ring. 3. The energy stored in 2 ATP molecules is utilized to modify the structure of glucose Glycolysis Step [4] cleaves the fructose ring into a dihydroxy-acetone phosphate and a glyceraldehyde 3-phosphate. Glycolysis Step [5] isomerizes the dihydroxyacetone phosphate into another glyceraldehyde 3-phosphate. Thus, the first phase of glycolysis converts glucose into 2 glyceraldehyde 3-phosphate units and 2 ATP is used. Glycolysis In step [6] the aldehyde end of the molecule is oxidized and phosphorylated by a dehydrogenase enzyme and NAD+; this produces 1,3-bisphospho-glycerate and NADH. Glycolysis In step [7], the phosphate group is transferred onto an ADP with a kinase enzyme, forming 3-phosphoglycerate and ATP. Glycolysis In step [8], the phosphate group is isomerized to a new position in 2-phosphoglycerate. Glycolysis In step [9], water is lost to form phosphoenol-pyruvate. Glycolysis In step [10], the phosphate is transferred to an ADP, yielding pyruvate and ATP with a kinase enzyme. Glycolysis The 2 glyceraldehyde 3-phosphate units are converted into 2 pyruvate units in phase two of glycolysis. Overall, the energy-generating phase forms 2 NADHs and 4 ATPs. Glycolysis 2 ATPs are used in phase one of glycolysis, and 4 ATPs are made in phase two of glycolysis. The net result is the synthesis of 2 ATPs from glycolysis. The 2 NADHs formed are made in the cytoplasm and must be transported to the mitochondria to join the electron transport chain and make ATP. Overall of glycolysis The fate of pyruvate under aerobic conditions under anaerobic conditions in fermentation by microorganisms Aerobic conditions Pyruvate must diffuse across the outer and inner membrane of mitochondria into the matrix. The NADH formed needs O2 to return to NAD+, so without O2 no additional pyruvate can be oxidized. Fermentation Fermentation is the anaerobic conversion of glucose to ethanol and CO2 by yeast and other microorganisms. 1. Biosynthesis of Carbohydrates In plants chloroph yll 6 H2 O 6 H O energy 6CO + + 2 2 (from sun) (from su n ligh t) Photosynthesis C6 H1 2 O6 + 6 H2 O Glu cose 1. Biosynthesis of Carbohydrates In animals When both glucose and stored glycogen are depleted, glucose can be synthesis by gluconeogenesis. (in liver) Intermediates of Glycolysis and Citric acid cycle are used to produce glucose. Gluconeogenesis is not the exact reversal of glycolysis: pyruvate to glucose does not occur by reversing the steps of glucose to pyruvate. 1. Biosynthesis of Carbohydrates Only four enzymes are unique. (compare to glycolysis) ATP is produced in glycolysis and used up in gluconeogenesis. Cori Cycle Lactate from glycolysis in muscle is transported to the liver, where gluconeogenesis converts it back to glucose. Gluconeogenesis Glucose is the main source of energy for cells and the only source of energy used by the brain. Gluconeogenesis is a mechanism that ensures that the brain has a supply of glucose when a diet is low in carbohydrates. Conversion of glucose to other Carbohydrates (in animals) Conversion of glucose to other hexoses (isomers) and synthesis of di- or polysaccharides. Activation of glucose by Uridine Triphosphate (UTP) to form UDP-glucose. (Similar to ATP) H CH 2 OH O H H OH HO H O H O O O-P-O-P-OCH2 O- OOH H HN O O H HO Uridine d iphosph ate glu cose (UD P-glucose) N H H OH Conversion of glucose to other Carbohydrates (in animals) Glycogenesis: conversion of glucose to glycogen. Exess glucose is stored in form of glycogen. Glu cose 1-ph osp hate + UTP (Glucose)n + UD P-glucose Glu cose 1-ph osp hate + UTP + O CH 2 OH CH 2 OH O O H HO HH H H HN HN O O O O H H OH OH Enzyme O N O- hate O-P-O-P-OCH O-P-O-P-OCH HO HO UD P-glucose 2N 2 pyrophosp + O O O OH O H OHH O OH H HH (Glucos e)n+1 + UDHP H H H OH OH HO HO CH 2 OH CH 2 OH O d iphosph ate glu cose Uridine O dUridine iphosph ate glu cose O H H (Glucose)nH H H(UDHP-glucose) HN (UD P-glucose) HN O O O O H H OH OH O O- hate O-P-O-P-OCH (Glucos P + pyrophosp HO e)n+1HO + UDO-P-O-P-OCH 2N 2 O O O OH O H OHH O OH H HH Same process to produce di- and H H H OH HO HO iphosph ate glu cose Uridine dUridine iphosphdate glu cose polysaccharides. (UD P-glucose) (UD P-glucose) O 2. Biosynthesis of Fatty acids Our body can produce all the fatty acids except essential fatty acids. Acetyl CoA They build up two C at a time. Fatty acids synthesis: in cytoplasm Degeradation of fatty acids: in mitochondria Excess food Acetyl CoA Fatty acids Lipid (fat) 2. Biosynthesis of Fatty acids Acyl Carrier Protein (ACP) ACP has a side chain that carries the growing fatty acid ACP rotates counterclockwise, and its side chain sweeps over the multienzyme system (empty spheres). At each enzyme, one reaction of chain is catalyzed. 2. Biosynthesis of Fatty acids Step 1: ACP picks up an acetyl group from acetyl CoA and delivers to the first enzyme: O CH3 C-SCoA + HS-ACP A cetyl-CoA O CH3 C-S-ACP + HS-CoA Acetyl-ACP O CH 3 C-S-ACP + HS-synth ase Acetyl-ACP O CH3 C-S-Synthas e + HS-ACP Acetyl-synthase O CH3 C-SCoA + HS-synth ase A cetyl-CoA O CH3 C-S-synthas e + HS-CoA Acetyl-synthase 2. Biosynthesis of Fatty acids Step 2: ACP-malonyltransferase reaction: O CH2 C-SCoA + HS-ACP COOMalonyl-CoA O CH2 C-S-ACP + HS-CoA COOMalonyl-ACP Step 3: condensation reaction: O O CH3 C-S-synth ase + CH2 C-A CP COOAcetyl-synthase Malonyl-ACP O O CH3 C-CH2 - C-S- A CP + CO 2 + HS-synth ase Acetoacetyl-ACP 2. Biosynthesis of Fatty acids Step 4: the first reduction: O O CH3 C-CH2 - C-S- A CP + N AD PH + H+ Acetoacetyl-ACP OH H H3 C C O CH2 -C- S- ACP + N AD P+ D--Hydroxybutyryl-ACP Step 5: dehydration: O C-S-A CP OH H H3 C C O CH2 -C- S- ACP D--Hydroxybutyryl-ACP H + H2 O C C H3 C H Crotonyl-ACP 2. Biosynthesis of Fatty acids Step 6: the second reduction: O C-S-A CP H C H3 C C H Crotonyl-ACP + N AD PH + H+ O CH3 -CH 2 - CH2 -C- S- ACP + N AD P+ Butyryl-ACP One cycle of merry-go-round. 2. Biosynthesis of Fatty acids Second cycle: O O CH 3 CH2 CH2 C-S- ACP + CH 2 C-S-A CP Butyryl-ACP CO 2 Malonyl-ACP 3. 4. 5. 6. condens ation reduction dehydration reduction O CH3 CH 2 CH2 CH2 CH 2 C- S- ACP Hexanoyl-ACP Maximum 16C (Palmitic acid). For 18C (Stearic acid) another system and enzyme. 3. Biosynthesis of Membrane Lipids 1- Glycerophospholipid 2- Cholesterol 3. Biosynthesis of Membrane Lipids Glycerol 1-phosphate, which is obtained by reduction of dihydroxyacetone phosphate (from glycolysis). CH2 -OH + NADH + H+ C=O 2CH2 -OPO3 D ihydroxyaceton e ph osp hate CH2 -OH + NAD+ HO CH 2CH2 -OPO3 Glycerol 1-p hosphate A vehicle for transporting electrons in and out of mitochondria. 3. Biosynthesis of Membrane Lipids Fatty acids are activated by CoA, forming Fatty Acyl CoA. CH2 -OH O + 2 RC-S-CoA HO CH CH2 -OPO3 2 Glycerol Acyl CoA 1-phosp hate O CH2 -OCR O + 2 CoA-SH RCO CH CH2 -OPO3 2 A phosp hatidate An amino alcohol is added to phosphate by phosphate ester bond. Is activated by CTP (like UTP but cytosine instead of uracil) 3. Biosynthesis of Membrane Lipids Cholesterol is made of acetyl CoA (all of the C atoms). In Liver First reaction of three acetyl CoA to form the six-carbon compound 3-hydroxy-3-methylglutaryl CoA (HMG-CoA). O 3 CH3 CSCoA Acetyl CoA O -2CoA-SH - O OH O SCoA 3-Hyd roxy-3methylglutaryl-CoA HMG-CoA reductase -1CoA-SH O - OH O OH Mevalonate 3. Biosynthesis of Membrane Lipids Mevalonate undergoes phosporylation and decarboxylation to give the C5 compound, isopentenyl pyrophosphate. O - OH O ATP ADP OH Mevalonate -CO2 OP2 O6 3 Isopen tenyl pyroph os phate Is op ren e Building block 3. Biosynthesis of Membrane Lipids Isopentenyl pyrophosphate (C5) is the building block for the synthesis of geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15). OP2 O6 3 Geranyl pyroph os phate OP2 O6 3 Farnesyl pyrophos ph ate 3. Biosynthesis of Membrane Lipids Two farnesyl pyrophosphate (C15) units are joined to form squalene (C30) and, in a series of at least 25 steps, squalene is converted to cholesterol (C27). Cholesterol HO 4. Biosynthesis of Amino Acids All 20 amino acids are found in a normal diet. Essential amino acids: cannot be synthesis in our body. Nonessential amino acids: can be synthesis in our body. 4. Biosynthesis of Amino Acids Most nonessential amino acids are synthesized from intermediates of either glycolysis or the citric acid cycle. N AD PH + H+ O O O- C- CH2 - CH 2 - C-COO - + N H4 + -Ketoglutarate N AD P+ + N H3 O O- C- CH2 - CH 2 - CH- COO Glutamate Amination and reduction Reverse of oxidative deamination reaction (degradation in catabolism). 4. Biosynthesis of Amino Acids Glutamate in turn serves as an intermediate in the synthesis of several amino acids by the transfer of its amino group by transamination. COOC= O CH3 COO+ CH- NH3 + CH2 CH2 COOPyruvate Glutamate COOCH- NH3 + + CH3 Alanine COOC= O CH2 CH2 COO-Ketoglutarate