MCB100 Introductory Microbiology October 3, 2018 Chapter 5 - Microbial Metabolism

1. MCB100 Introductory Microbiology October 3, 2018 Chapter 5 - Microbial Metabolism

2. 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

3. 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.

5. 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.

7. Succinate dehydrogenase requires several cofactors. Succinate dehydrogenase uses a coenzyme flavone adenine dinucleotide (FAD), as the acceptor of the two hydrogens.Metal ions are the other 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

8. ENZYMES - WHAT THEY CAN AND CANNOT DO Enzymes make biochemical reactions go faster by reducing the activation energy barrier by stabilizing the transition state. Enzymes do not change the nature of the reactants or products. Enzymes do not change the chemical potential energy of substances. Enzymes do not change the Free Energy of a Reaction. Enzymes do not make unfavorable reactions favorable.

9. ATP – The Energy Molecule of Cells ATP stands for adenosine triphosphate, it has 3 phosphate groups on adenosine. Bonds between phosphates are unstable & have high chemical potential energy. Adenosine diphosphate or ADP has 2 phosphate groups, so it has 1 less "high energy" bond. Energy is released when ATP looses a phosphate to form ADP + free phosphate. Energy from a catabolic reaction can be trapped by the celland used to attach a phosphate to ADP to make ATP. This is how a cell stores energy for a short while. The structure of ATP is shown in your textbook on page 52-53 and figure 2.27.

10. Cells use ATP as an energy source to drive unfavorable biosynthetic reactions.

13. What are some of the ways that a cell uses ATP? Substrate Activation - For glucose to be broken down it must be activated by the attachment of two phosphates. The cell converts glucose to glucose-1, 6-bisphosphate, which can then be broken down to yield energy and form ATP. - ATP and similar nucleotide triphosphates are the activated building blocks of nucleic acid biosynthesis. - Energy from ATP is used to attach amino acids to tRNA molecules. This is a key energy consuming step in protein biosynthesis. Power Cellular Motion - Energy from ATP is used to make flagella rotate and muscle fibers contract. - Energy from the hydrolysis of a similar compound, GTP, is used to make a ribosome move along a strand of mRNA in a specific direction. Energy from ATP can be used to make GTP. Pump ions or other molecules across a membrane - Active transport, to take in nutrients or excrete wastes

14. ATP and Enzymes Select the FALSE statement about ATP and enzymes. A. All types of cells must have some way to make or acquire ATP. B. All enzymes that catalyze an unfavorable chemical reaction use hydrolysis of ATP to supply energy that is needed to make the reaction go forwards. C. Molecules of UTP, CTP and GTP have two high-energy phosphoanhydride bonds that are similar to those seen in a molecule of ATP. D. ATP is one of the starting materials required for synthesis of RNA.

15. Enzymes The chemical nature of a typical enzyme is mostly: A. one or more chains of amino acids. B. a double stranded chain of deoxynucleotides. C. a complex branching chain of sugars. D. a net-like bag composed of long sugar chains cross-linked by peptide bridges. E. glycerol molecules that are attached to fatty acids and phosphate groups

16. Conditions that affect the activity of an enzyme - Protein denaturation - Temperature - pH - Substrate concentration - Presence of competitive inhibitors - Allosteric inhibitors or activators - Feedback inhibition (regulation of activity) Denaturation loss of functional globular structure

17. The Folding of a Protein to Its Final Shape Primary Structure: - The sequence of amino acids in the chain - Determined by the genetic information encoded in the mRNA - Determines the final shape and function of the protein Secondary Structure: - Local folding of a protein chain - Alpha helix and Beta sheet are common motifs - Stabilized by interactions between backbone groups that are fairly close to each other in the primary sequence Tertiary Structure: - Final folding of a single protein chain to its globular form - Stabilized by interactions between groups on side chains that may be far apart in the primary sequence but close together in the final 3-D shape Quaternary Structure: - The noncovalent attraction of two or more separate protein chains to form a functional unit - Stabilized by interactions between groups on side chains that may be far apart in the primary sequence but close together in the final 3-D shape

18. HEAT

24. Enzyme Activity Choose the response that is FALSE. A. Enzymes from a thermophillic bacterial strain have to be stable at the high temperature the bacteria grows at. B. Enzymes can be inactivated by an excessively high or low pH. Bacterial cells can be killed by substances that change their intracellular pH. C. Once an enzyme is made by a cell it is always active. Enzymes catalyze chemical reactions at full speed all of the time. D. Most poisons and medicinal drugs are enzyme inhibitors in one way or another.

25. Conditions that can affect the activity of an enzyme - Temperature (warmer = faster, up to a point, too hot is bad) - pH (too high or too low is bad)

26. Conditions that can affect the activity of an enzyme - Substrate concentration - Presence of competitive inhibitors