Metabolic Pathways Overview of metabolism pathways - Catabolism - Anabolism - Bioenergetics - Important metabolic pathways - Catabolism: - Glucose catabolism - aerobic pathway - anaerobic pathway - Hydrocarbon - Nitrogen compounds - Anabolism: - Photosynthesis - Biosynthesis

Metabolic Pathways M : a complete set of chemical reactions that occur in living cells, allowing cells to grow and reproduce, maintain their structures, and respond to their environments. Major challenges in bioprocess development: To select an organism that can efficiently make a given product or digest wastes in the Environment. It is important to understand the metabolic pathways.

Metabolic Pathways - Overview of metabolism pathways Metabolism can be subdivided by - C : The intracellular process of degrading a compound into smaller and simpler products and generating energy. Glucose to CO2, and H2O, protein to amino acids. - A : the synthesis of more complex compounds and requires energy. Synthesis of small molecules (amino acids, nucleotides, fatty acids and sugars) and complex compounds (glycan (polysaccharide), DNA, RNA, and lipids.)

Major Metabolic Pathways in a Bacterial Cell (M.Shuler, 2002) End products are formed and released from the cells through these reactions, which are often valuable products for human or animal consumption. e.g. ethanol, amino acids, enzymes, fatty acids, antibodies.

Metabolic Pathways Bioenergetics Sunlight Photosynthesis by autotrophs : CO2 + H2O → carbohydrates Autotrophs or heterotrophs Catabolism generating energy, e.g ATP Anabolism requiring energy

Metabolic Pathways Bioenergetics - Energy is mainly stored or transferred by adenosine triphosphate (ATP). Other energy carrying compounds include GTP, UTP and CTP. Guanosine Triphospohate, Uridine triphosphate and cytidine triphosphate

Metabolic Pathways Bioenergetics - Reducing power: supply hydrogen atom in biosynthesis. Nicotinamide Adenine Dinucleotide (NADH) Flavin Adenine Dinucleotide (FADH2) NADH and FADH2 are major electron carriers in the oxidation of fuel molecules and for ATP generation. Nicotinamide Adenine Dinucleotide Phosphate (NADPH). major electron donor in reductive biosynthesis, e.g photosynthesis

Nicotinamide Adenine Dinucleotide (NAD+) 2e- , H+

Flavin Adenine Dinucleotide (FAD) 2 electrons Isoalloxazine ring

Nicotinamide Adenine Dinucleotide Phosphate (NADP+)

Review of Metabolism Pathways http://www. genome Review of Metabolism Pathways http://www.genome.jp/kegg/pathway/map/map01100.html Glucose metabolism is the centre of the cell metabolism pathways

Embden-Meyerhof-Parnas (EMP) Glucose Catabolism Glucose Glycolysis or Embden-Meyerhof-Parnas (EMP) Anaerobic metabolism Aerobic metabolism Fermentation: ethanol, acetic acid, lactate. Tricarboxylic acid (TCA) or (Krebs) or (Citric acid cycle) Oxidative phosphorylation

Glucose Catabolism Glycolysis http://www.science.smith.edu/departments/Biology/Bio231/glycolysis.html

Glucose Catabolism Glycolysis Glycolysis or Embden-Meyerhof-Parnas (EMP) Breakdown of a molecule of g to two pyruvate molecules. - Each pathway is catalyzed by particular enzyme(s) - Generating 2 ATP, 2 NADH and 2 pyruvate (Key Metabolite). - Taking place in cytoplasm

a-D-Glucose Pyruvate

Glycolysis (EPM) glycogen Amino acid Acetyl-CoA Ethanol Fatty acids control sites: feedback inhibition glycogen Amino acid Acetyl-CoA Ethanol Fatty acids

Glucose Catabolism Glycolysis The overall reaction in glycolysis is: Glucose + 2ADP + 2 NAD+ + 2 Pi →2 pyruvate + 2 ATP+ 2 (NADH + H+) Produce - e ; - Key metabolite: pyruvate

Embden-Meyerhof-Parnas (EMP) Glucose Catabolism Glucose Glycolysis or Embden-Meyerhof-Parnas (EMP) Anaerobic metabolism Aerobic metabolism Fermentation: ethanol, acetic acid, lactate. Tricarboxylic acid (TCA) or (Krebs) or (Citric acid cycle) Oxidative phosphorylation

Glucose Catabolism Krebs, Tricarboxylic Acid (TCA), or Citric Acid Cycle Under a conditions Taking place - in mitochondria in eucaryotes - associated with membrane-bound enzymes in procaryotes Pyruvate produced in glycolysis (EMP) pathway transfer its reducing power to NAD+. http://www.science.smith.edu/departments/Biology/Bio231/krebs.html

Citric Acid Cycle amino acid synthesis Control site by ATP NADH generated CO2 released FADH2 generated amino acid synthesis

Glucose Catabolism Citric Acid Cycle The overall reaction of TCA cycle: acetyl-CoA + 3 NAD + FAD + Pi + 2H2O → CoA + 3(NADH + H+) +FADH2+GTP+ 2CO2 Intermediate products such as oxylacetate and α–ketoglutarate are used as precursors for the synthesis of certain amino acids. The reducing power (NADH + H+ and FADH2) is used for biosynthesis pathway or for ATP generation through the electron transport chain.

Embden-Meyerhof-Parnas (EMP) Glucose Catabolism Glucose Glycolysis or Embden-Meyerhof-Parnas (EMP) Anaerobic metabolism Aerobic metabolism Fermentation: ethanol, acetic acid, lactate. Tricarboxylic acid (TCA) or (Krebs) or (Citric acid cycle) Respiratory chain: Oxidative phosphorylation

Glucose Catabolism Respiratory Chain-Oxidative Phosphorylation “Oxidative Phosphorylation is the electron transport chain that forms ATP as electrons are transferred from NADH or FADH2 to o by a series of electron carriers” (L. Stryer, 1988) - electron acceptor: oxygen (aerobic condition) - generate ATP, H2O - from NADH or FADH2 Taking place in mitochondria in eucaryotes or in cytoplasmic membrane in procaryotes http://www.brookscole.com/chemistry_d/templates/student_resources/shared_resources/animations/oxidative/oxidativephosphorylation.html

Glucose Catabolism Oxidative Phosphorylation In the process of Oxidative Phosphorylation In eucaryotes: NADH + H+ 3 ATP FADH2 2 ATP In procaryotes: NADH + H+ ≤2 ATP FADH2 ATP

Glucose Aerobic Catabolism Reaction Summary EMP (glycolysis) Glucose + 2ADP + 2 NAD+ + 2 Pi →2 pyruvate + 2 ATP+ 2 (NADH + H+) Entry of pyruvate 2pyruvate + 2NAD+ + 2CoA-SH →2 acetyl-CoA + 2CO2 + 2(NADH + H+) TCA cycle 2acetyl-CoA + 6 NAD + 2FAD + 2GDP+ 2Pi + 4H2O → 2CoA + 6(NADH + H+) +2FADH2+2GTP (~ATP) + 4CO2 Oxidative Phosphorylation In eucaryotes EMP: 2 NADH → 2 FADH2 → 4 ATP (glycerol phosphate shuttle) Entry of pyruvate and TCA: 8 NADH → 24 ATP TCA: 2FADH2 → 4 ATP The overall reaction: Glucose + 6O2 + 36ADP + 36 Pi → 6 CO2 + 6 H2O + 36 ATP

Embden-Meyerhof-Parnas (EMP) Glucose Catabolism Glucose Glycolysis or Embden-Meyerhof-Parnas (EMP) Anaerobic metabolism Aerobic metabolism Fermentation: ethanol, acetic acid, lactate. Tricarboxylic acid (TCA) or (Krebs) or (Citric acid cycle) Respiratory chain: Oxidative phosphorylation

Glucose Anaerobic Catabolism Glycolysis (EMP)

Hydrocarbon Catabolism Hydrocarbon: C & H - Aliaphatic hydrocarbon e.g. octane, C8H18 polyethylene –HC=CH- - Aromatic hydrocarbon naphthalene Metabolism of hydrocarbon - Requires oxygen - Hydrocarbons are converted to acetyl-CoA which is metabolized by TCA cycle. - Challenges : low solubility in aqueous solution. available microorganisms are limited Pseudomonas, Mycobacteria naphthalene

Nitrogen Compounds Catabolism Nitrogen compounds can be used for C, N and energy sources Proteins → peptides → amino acids → converted to other amino acids or organic acids and ammonia by deamination. - organic acids: acetyl-CoA into TCA cycle, lipids - amino acids: proteins, other amino acids or enter TCA cycle - ammonium: amino acid, protein, nucleic acids Nucleic acids → ribose/deoxyribose, phosphoric acid and purine/pyrimidine - sugar: glycolysis and TCA - Phosphoric acid: ATP, lipids, nucleic acids - bases: nucleic acids, urea, acetic acids

Photosynthesis Glycolysis and TCA

Overview of Biosynthesis Pentose-phosphate pathway (hexo-monophosphate pathway (HMP): convert glucose-6-phosphate into a carbon skeletons of C3 ~ C7 . Polysaccharides: glycan, glycogen gluconeogenesis Lipids Proteins Nucleic acids (DNAs, RNAs)

2 1 5 3 4 6

Summary of Metabolism Pathways - catabolism: ATP, C skeleton for further biosynthesis - anabolism: biosynthesis requiring energy Bioenergetics: - energy storage and carrier ATP - Reducing power carriers: NADH, NADPH, FADH

Summary of Metabolism Pathways Glucose catabolism: Glucose Anaerobic metabolism Tricarboxylic acid (TCA) or (Krebs) or (Citric acid cycle) Respiratory chain: Oxidative phosphorylation Glycolysis or Embden-Meyerhof-Parnas (EMP) Fermentation: ethanol, acetic acid, lactate. Aerobic metabolism

Summary of Metabolism Pathways Nitrogen compound catabolism Hydrocarbon catabolism Photosynthesis Biosynthesis