CHAPTER 5: MAJOR METABOLIC PATHWAYS Shuler, M. L. and Kargi. (2002). Bioprocess Engineering: Basic Concept. 2 nd Ed. Upper Saddle River, NJ: Prentice Hall PTR PTT203: BIOCHEMICAL ENGINEERING SEMESTER 1 (2014/2015) By: Puan Nurul Ain Harmiza 1
COURSE OUTCOME 2: Ability to ANALYZE the types of metabolic pathways in microorganisms and their growth kinetics. By: Puan Nurul Ain Harmiza 2
CONTENT 5.1 Introduction 5.2 Bioenergetics 5.3 Glucose Metabolism 5.4 Respiration 5.5 Control Sites in Aerobic Glucose Metabolism 5.6 Metabolism of Nitrogenous Compounds 5.7 Nitrogen Fixation 5.8 Metabolism of Hydrocarbons 5.9 Overview of Biosynthesis 5.10 Overview of Anaerobic Metabolism 5.11 Overview of Autotrophic Metabolism 5.12 Summary
This course will only cover the red-colored topics. The blue- colored topics have been taught in PTT103 5.1 Introduction 5.2 Bioenergetics 5.3 Glucose Metabolism 5.4 Respiration 5.5 Control Sites in Aerobic Glucose Metabolism 5.6 Metabolism of Nitrogenous Compounds 5.7 Nitrogen Fixation 5.8 Metabolism of Hydrocarbons 5.9 Overview of Biosynthesis 5.10 Overview of Anaerobic Metabolism 5.11 Overview of Autotrophic Metabolism 5.12 Summary
5.1 INTRODUCTION • Metabolism is the collection of amylase enzyme catalyzed reactions that Starch smaller glucose convert substrates that are internal external external to the cell into various internal products. • Metabolic pathways are series of chemical reactions (metabolism) occurring within a cell. • Genetic Engineering allows for the alteration of metabolism by insertion or deletion of selected genes in a predetermined manner ( Metabolic Engineering ). • An understanding of metabolic pathways in the organism of interest is of primary importance in bioprocess development . Why we need to learn the metabolic pathways?
Characteristics of Metabolism • Varies from organisms to organism. • Many common characteristics. • Affected by environmental conditions. – O2 availability: Saccharomyces cerevisiae • Aerobic growth on glucose → more cells • Anaerobic growth on glucose → ethanol Is S.cerevisiae a obligate anaerobes or facultative anaerobes?
Types of Metabolism Which one is EXERGONIC and which • Catabolism one is ENDERGONIC ? – Metabolic reactions in the cell that degrade a substrate into smaller / simpler products . • Glucose → CO 2 + H 2 O – Produces energy. • Anabolism – Metabolic reactions that result in the synthesis of larger / more complex molecules. • Glucose → glycogen – Requires energy.
5.2 BIOENERGETICS • It is the quantitative study of the energy relationships and energy conversions in biological systems . • It concerned with the energy involved in making and breaking of chemical bonds in the molecules found in biological organisms. • All organisms need free energy to keep themselves alive and functioning. • The Sun is the ultimate energy source for the life processes on earth. • The source of energy is just one; solar energy. Only plants use that energy directly. What the organisms use is the chemical energy in the form of foods. The very first conversion of solar energy into a chemical energy is the sugar molecule. • On one side the conversion of solar energy into chemical energy with the help of photosynthesis happens, and on the other hand this photosynthesis makes it possible with the passage of time on earth to accumulate free oxygen in the earth's atmosphere making possible the evolution of respiration. Respiration is important for bioenergetics as it stores the energy to form a molecule ATP; adenosine triphosphate. This molecule is a link between catabolism and anabolisms. The process of photosynthesis is helpful in understanding the principles of energy conversion i.e. bioenergetics. What is bioenergetics ?
Plants make their own food by photosynthesis. Carbon dioxide and water react together in the presence of light and chlorophyll to make glucose and oxygen. The glucose is converted into starch, fats and oils for storage. It is used to make cellulose for cell walls, and proteins for growth and repair. It is also used by the plant to release energy by respiration. Respiration and photosynthesis are the main processes dealing with bioenergetics
Metabolic Reactions • Can be classified into 3 major categories ( refer to figure 5.1 pg 135 ): 1. Degradatation of nutrients 2. Biosynthesis of small molecules (amino acid, nucleotides) 3. Biosynthesis of large molecules This reaction takes place in the cell simultaneously.
Figure 5.1: Classes of Reactions (Pg. 135) Which Class is CATABOLISM and which is ANABOLISM? Energetics of bacterial growth: balance of anabolic and catabolic reactions.
Figure 5.1: Classes of Reactions (Pg. 135) Energetics of bacterial growth: balance of anabolic and catabolic reactions.
ATP : Metabolic Energy • Adenosine triphosphate (ATP) stored and transports ENERGY in cells. • It is the energy currency of life. • It is used by the cell as ‘money’ . – Some activities such as breaking down glucose produce ATP (money) others such as making DNA consume ATP ATP • It contains high-energy phosphate bonds . • The energy in ATP is obtained from the breakdown of foods .
ATP : Metabolic Energy • ATP: Adenosine triphosphate and ADP: Adenosine diphosphate. • So when a phosphate is lost, energy is released. • Technically speaking, the whole enchilada from a biological perspective is thus: – ADP is the end-product that results when ATP loses one of its phosphate groups located at the end of the molecule. The conversion of these two molecules plays a critical role in supplying energy for many processes of life. – The deletion of one of ATP’s phosphorus bonds generates approximately 7.3 kilocalories per Mole of ATP. – ADP can be converted, or powered back to ATP through the process of releasing the chemical energy available in food; in humans this is constantly performed via aerobic respiration in the mitochondria. ”
ATP : Metabolic Energy
ATP : Metabolic Energy • Analog compounds of ATP (GTP, UTP and CTP) also store and transfer high- energy phosphate bonds but not to the extent of ATP. • High-energy phosphate compounds (phosphoenol pyruvate and 1,3- diphosphoglycerate) produced during metabolism, transfer their ~P group into ATP. • Energy stored in ATP is later transferred to lower-energy phosphate compounds (glucose -6-phosphate and glycerol-3-phosphate) – refer Figure 5.2 pg 135.
GLUCOSE METABOLISM This topic has been thought in PTT103 BIOCHEMISTRY by Pn. Khadijah Hanim. Please refer these three previous slides for your additional references.
5.5 CONTROL SITES IN AEROBIC GLUCOSE METABOLISM
Control in Glycolysis: Feedback Inhibition • The major control site in glycolysis is the phosphorylation of fructose-6- phsophate by phosphofructokinase : fructose-6-phosphate + ATP fructose-1,6-diphosphate + ADP • Phosphofructokinase (PFK) catalyzes the rate-limiting step in glycolysis and is the most important control point. • The enzyme phosphofructokinase is an allosteric enzyme activated by ADP and P i but inactivated by ATP . Explain HOW is the mechanism? ATP phosphofructokinase (active) phosphofructokinase (inactive) ADP When ATP levels are high in the cell, the cell no longer needs metabolic energy production to occur. In this case, PFK's activity is inhibited by allosteric regulation by ATP itself, closing the valve on the flow of carbohydrates through glycolysis. Recall that allosteric regulators bind to a different site on the enzyme than the active (catalytic) site. Thus ATP binds in two places on PFK: in the active site as a substrate and in the regulatory site as a negative modulator. ATP bound in the regulatory site acts as a modulator by lowering the affinity of PFK for its other substrate, fructose-6-phosphate.
Rate-limiting enzyme for glycolysis is phosphofructokinase The phosphorylation of fructose 6-phosphate is highly exergonic and irreversible, and phosphofructokinase, the enzyme that catalyzes it, is the key enzyme in glycolysis. Glycolysis
Control in Glycolysis: Pasteur Effect – The Pasteur effect is an inhibiting effect of oxygen on the fermentation process (Louis Pasteur, 1857). – The rate of glycolysis under anaerobic conditions is higher than that under aerobic conditions. – In the presence of O 2 , ATP yield is high since the TCA cycle and ETC are operating. – So, ADP and Pi become limiting and phosphofructokinase becomes inhibited. – A high NADH/NAD+ ratio also reduces the glycolysis rate.
Control in TCA Cycle: Feedback Inhibition • Certain enzymes of the Krebs cycle are also regulated by feedback inhibition . • Pyruvate dehydrogenase is inhibited by ATP, NADH, and Acetyl CoA and activated by ADP, AMP, and NAD+. • Citrate synthase is inhibited by NAD+. • In general, high ATP/ADP and NADH/NAD+ ratios reduce the processing rate of the TCA cycle. Explain HOW?
Citric acid cycle
5.6 METABOLISM OF NITROGENOUS COMPOUNDS • Most organic nitrogen compounds have an oxidation level between carbohydrates and lipids. • Nitrogeneous compounds can be used as nitrogen, carbon, and energy source. • Proteins are hydrolyzed to peptides and further to amino acids by proteases. • Amino acids are first converted to organic acids by deamination (removal of amino group).
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