MCB100 Introductory Microbiology February 18, 2019 Chapter 5 - Microbial Metabolism

1. MCB100 Introductory Microbiology February 18, 2019 Chapter 5 - Microbial Metabolism

2. Metabolism: the sum of all the chemical reactions that go in an organism (and there are a few thousand different chemical reactions going on in a typical cell) • Anabolic reactions • - involved in the building up of biological molecules • (DNA, proteins, lipids, polysaccharides, and precursor molecules) • - produce the complex molecules that cytoplasm is made of • associated with growth • - consume energy in the form of ATP • Catabolic reactions • - release energy that is used to produce ATP • - involved in the breaking downof complex molecules to yield • simple moleculesthat the cell can use as synthetic raw material • See "Catabolism and Anabolism" on pages 125-126 and figure 5.1 on page 126.

3. Metabolic Pathways and Metabolic Intermediates A metabolic pathway is a conceptual tool to help visualize relationships between some of the biochemical reactions that go on in a cell. Many biosynthetic reactions (and biodegradations too) require two or more steps to get from the starting materials to the final products. When a biochemist writes down the steps that a cell carries out to synthesize or degrade some compound, the resulting series of chemical reactions is called a metabolic pathway.There is no physical track in the cytoplasm that acts as a road for the movement of metabolic intermediates. Synthesis of methionine from aspartate is an example of a metabolic pathway. The pathway for converting the amino acid aspartate to methionine involves six steps. Each reaction is catalyzed by a specific enzyme. A metabolic intermediate is a transitory product that is made from the starting material and is quickly converted to the next product.

5. Enzymes An enzyme is a biological catalyst. Most enzymes are proteins but there are some RNA molecules with catalytic activity. Enzymes are made by living cells and are absolutely required for growth. Impairment of enzymes (sometimes just one) can cause death of a cell (or a drastic change in its activity). A catalyst is a substance that helps a chemical reaction occur faster. A catalyst cannot make an unfavorable chemical reaction occur. Catalysts accelerate chemical reactions by reducing the activation energy barrier. Reactant molecules bind to the surface of a catalyst and are converted to products. An enzyme destabilizes chemical bonds in the substrates (reactants) and promotes formation of the activated complex, a state that is in-between the substrates and the products. Catalysts are not consumed by chemical reaction that they accelerate. A typical enzyme can make a reaction go 100 million times faster. Typical cells have about 2000 – 3000 different enzymes.

6. Bacterial Enzymes Enzymes of Excreted Hydrolytic EnzymesLipase: an exoenzyme for digesting fatsAmylase: an exoenzyme for digesting starchGelatinase: an exoenzyme for digesting protein

7. The 3 General Areas in or Around a Cell Where Enzymes are Found - outside of the cell, in the culture media,excreted enzymes, (exoenzymes) Some exoenzymes help to digest large molecules such as starch to release smallermolecules like sugars that can be absorbed by the cell. Other exoenzymes may be toxins that cause disease in the host animal, example: Streptococcus pyogenes excretes an exoenzyme called hemolysin whichbreaks open red blood cells. This releases nutrients for the bacteria. - embedded within the cytoplasmic membrane Some important enzymes involved in respiration are found in the cytoplasmic membrane. Some of these enzymes pump ions across the membrane. Other enzymes that are embedded within the cytoplasmic membrane include those that actively pump nutrients into the cell and waste products out. Some membrane bound enzymes cause metabolic changes within the cell in response to external signals. - in the cytoplasm of the bacterial cell There are more than 1000 different enzymes at work in the cytoplasm. Some of themsynthesize amino acids, proteins, nucleotides, nucleic acids, sugars etc. Others breakdown nutrients to simple compounds while producing energy in the form of ATP.

8. See table 5.1 on page 128

9. Enzyme Classes Hydrolase Isomerase Ligase (polymerase)

10. Enzyme Classes Lyase Oxidoreductase Transferase

11. Enzymes and Metabolism – 1 Which one of the following statements about enzymes and metabolism is TRUE? A. The synthesis of methionine from aspartic acid is an example of a catabolic metabolic pathway. B. In most bacteria the enzymes involved in making methionine from aspartic acid are exoenzymes. C. Most metabolic pathways that are anabolic in nature consume more ATP than they produce. D. Enzymes make chemical reactions go faster by changing the free energy of the reaction.

12. Enzymes and Metabolism – 1 Which one of the following statements about enzymes and metabolism is TRUE? A. The synthesis of methionine from aspartic acid is an example of a catabolic metabolic pathway. B. In most bacteria the enzymes involved in making methionine from aspartic acid are exoenzymes. C. Most metabolic pathways that are anabolic in nature consume more ATP than they produce. D. Enzymes make chemical reactions go faster by changing the free energy of the reaction.

14. ENZYMES – The ACTIVE SITE The active site of an enzyme is the catalytic site. The active site is usually a pocket or cleft where the substrates bind. Functional groups on amino acids that surround the active site bind to the substrate molecules, create stress on the old chemical bonds and encourage formation of new chemical bonds leading to formation of the product. Some enzymes convert a single substrate to a single product but many enzymes use two or more substrates and produce two or more products. For example: the glycolysis enzyme fructose 1,6-bisphosphate aldolase converts one substrate, fructose 1,6-bisphosphate into two products: glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP). The glycolysis enzyme triose phosphate isomerase converts one substrate, DHAP to one product: G3P. Triose phosphate isomerase

15. The General Steps of an Enzyme Catalyzed Biochemical Reaction 1) substrate(s) bind to the enzyme at the active site 2) flexing of the enzyme produces a strain or distortion of some of the chemical bonds that are found in the substrate molecules 3) substrates are chemically changed into products 4) product is released 5) the enzyme emerges from the reaction unchanged and ready to bind and change another molecule of substrate See figure 5.7 on page 131 of the textbook

17. Enzymes and Metabolism 2 Which one of these enzymes is a transferase? A. Lipase - an enzyme that helps degrade fats by breaking ester bonds: triglyceride +3H2O  glycerol + 3 fatty acids B. Succinate dehydrogenase – a Krebs cycle enzyme that converts succinate to fumarate: C4O4H6 + FAD  C4O4H4 + FADH2 C. Citrate synthase – an enzyme that converts: acetyl-CoA + oxaloacetic acid  citric acid + CoA CoA-COCH3 + C4H4O5 + H2O  C6H8O7 + CoA-H D. Phosphoglycerate Mutase – an enzyme that converts 3-phosphoglycerate  2-phosphoglycerate C3H7O7P C3H7O7P

18. Enzymes and Metabolism 2 Which one of these enzymes is a transferase? A. Lipase - an enzyme that helps degrade fats by breaking ester bonds: triglyceride +3H2O  glycerol + 3 fatty acidsLipaseis a hydrolase. B. Succinate dehydrogenase – a Krebs cycle enzyme that converts succinate to fumarate: SD is an oxidoreductase. C4O4H6 + FAD  C4O4H4 + FADH2 C. Citrate synthase – an enzyme that converts: acetyl-CoA + oxaloacetic acid  citric acid + CoA CoA-COCH3 + C4H4O5 + H2O  C6H8O7 + CoA-H D. Phosphoglycerate Mutase – an enzyme that converts 3-phosphoglycerate  2-phosphoglycerate C3H7O7P C3H7O7P PgM is an isomerase.

19. The lock and key model for enzyme activity refers to the need for structural compatibility between the substrate and the enzyme. Enzymes are very specific catalysts. A given enzyme will recognize only one type of substrate molecule and convert it to only one particular type of product. The shape of the active site of an enzyme is complementary to the shape of the substrate. The enzyme that attaches alanine to a tRNA needs a pocket where alanine can bind, but the enzyme that attaches lysine to a tRNA needs a bigger pocket.

21. SIMPLE PROTEINS AND CONJUGATED PROTEINS A simple protein is just a chain of amino acids. A conjugated enzyme consists of protein plus additional organic or inorganic molecules that are closely associated with the protein. Succinate dehydrogenase is an example of a conjugated enzyme. The role of succinate dehydrogenase is to remove two hydrogen atoms from succinate to produce fumarate.  This reaction is a part of the tricarboxylic acid cycle, or Kreb's cycle. An apoenzyme is the protein portion of a conjugated enzyme without any cofactors. The apoenzyme of succinate dehydrogenase consists of two peptide chains or subunits.A cofactor is a small molecule that binds to an enzyme and helps to produce the catalytic activity. An enzyme cofactor is called a coenzyme if it is an organic molecule.

23. Succinate dehydrogenase requires several cofactors. Succinate dehydrogenase uses a coenzyme, flavone adenine dinucleotide (FAD), as the acceptor of the two hydrogens.Metal ions are another important group of enzyme cofactors and succinate dehydrogenase requires several iron ions, in what are called iron-sulfur clusters.Succinate dehydrogenase reaction Succinate dehydrogenase structure