Ch 8: An Intro to Metabolism 2016

Chapter 8: Metabolism From Topic 8.1 Understandings: • Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism. From Topic 2.5 Essential idea: Enzymes control the metabolism of the cell. Nature of science: Experimental design—accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability. (3.2) • Enzymes have an active site to which specific substrates bind. • Enzyme catalysis involves molecular motion and the collision of substrates with the active site. • Temperature, pH and substrate concentration affect the rate of activity of enzymes. • Enzymes can be denatured. • Immobilized enzymes are widely used in industry. Applications and skills: • Application: Methods of production of lactose-free milk and its advantages. • Skill: Design of experiments to test the effect of temperature, pH and substrate concentration on the activity of enzymes. • Skill: Experimental investigation of a factor affecting enzyme activity (Practical 3). Guidance: • Lactase can be immobilized in alginate beads and experiments can then be carried out in which the lactose in milk is hydrolysed. • Students should be able to sketch graphs to show the expected effects of temperature, pH and substrate concentration on the activity of enzymes. They should be able to explain the patterns or trends apparent in these graphs. Utilization: • Enzymes are extensively used in industry for the production of items from fruit juice to washing powder. From Topic 8.1 Understandings: • Enzymes lower the activation energy of the chemical reactions that they catalyse. • Enzyme inhibitors can be competitive or non-competitive. • Metabolic pathways can be controlled by end-product inhibition. • Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions. Applications and skills: • Application: Use of databases to identify potential new anti-malarial drugs. • Application: End-product inhibition of the pathway that converts threonine to isoleucine. • Skill: Calculating and plotting rates of reaction from raw experimental results. • Skill: Distinguishing different types of inhibition from graphs at specified substrate concentration. Guidance: • Enzyme inhibition should be studied using one specific example for competitive and non-competitive inhibition. Utilization: • Many enzyme inhibitors have been used in medicine. For example ethanol has been used to act as a competitive inhibitor for antifreeze poisoning. • Fomepizole, which is an inhibitor of alcohol dehydrogenase, has also been used for antifreeze poisoning. Aims: • Aim 6: Experiments on enzyme inhibition can be performed. • Aim 7: Computer simulations on enzyme action including metabolic inhibition are available.

Chapter 8: Metabolism From Topic 6.1 (further discussed in Digestion Mini-Unit of HL 1) Understandings: • The contraction of circular and longitudinal muscle of the small intestine mixes the food with enzymes and moves it along the gut. • The pancreas secretes enzymes into the lumen of the small intestine. • Enzymes digest most macromolecules in food into monomers in the small intestine. Utilization: • Some hydrolytic enzymes have economic importance, for example amylase in production of sugars from starch and in the brewing of beer. Guidance: • Students should know that amylase, lipase and an endopeptidase are secreted by the pancreas. The name trypsin and the method used to activate it are not required.

Free Energy (G) Unstable systems have a lot free energy (G) and have a tendency to change spontaneously to a more stable state. Cells can then use this release of energy for cellular work.

Free Energy (G) Exergonic Endergonic

Activation Energy EA Enzyme help lower the Activation Energy of chemical reaction; thus speeding the process - Energy of activation (activation energy or EA)= amount of energy that reactant molecules need to absorb to start a reaction. http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html

EA – Reaching the Transition State In order for reactants A+B and C+D to be converted to products, they must absorb enough energy from their surroundings (pass the EA) to reach the unstable transition state, where bonds can become unstable and can reform. Q: Based on this graph, is it an exergonic or endergonic reaction?

Catalysts Catalyst: chemical agent that accelerates a reaction without being permanently changed in the process. Enzymes: are biological catalysts. - Are proteins. - Lower activation energy. - Do not change the nature of the reaction but only speed it up. - Are very selective - Can continue their function after a reaction.

Enzymes Enzymes are substrate specific. Substrate: the substance an enzyme acts on. Place where enzyme binds to substrate is called the active site. Usually a pocket or groove on protein’s surface. Formed with only a few of the enzymes amino acids (charged etc…) Determines specificity. Changes shape in response to substrate.

How Enzymes lower EA Active site hold two or more reactants in proper position. Induced fit may distort bonds making it easier. Active site provides proper microenvironment. Amino acids may play a direct role in reaction.

Enzyme Function, pg153

Induced Fit

Rates of Reaction The higher the substrate concentration the higher the rate of reaction up to a certain point. Enzymes become saturated at a point. Then it depends on how fast the reaction happens. The rate of reaction can increase if more enzyme is added up to a point.

Environmental Factors Temperature: each has an optimal temperature. (Mostly between 35-40⁰C). Enzymatic activity increases with temp up to a certain point. 2) Ph: amount of charge (H+) in the environment. 3) Salt Concentration: Na+ and Cl- (charged ions)

Environmental Factors Cont. Changes in temperature, pH, and salt concentration can lead to an enzyme losing its confirmation (shape) leading to denaturation. - too hot breaks the bonds within a protein - charges in H+, Na+, or Cl- can disrupt the bonds within the protein

Factors affecting Enzymes Graphs Effect of Temperature

Factors affecting Enzymes Graphs Effect of pH

Factors affecting Enzymes Graphs Effect of Substrate Concentration

Designing an Experiment

Designing an Experiment

Designing an Experiment

Designing an Experiment

Designing an Experiment

Enzyme Inhibitors Can be reversible or irreversible. Competitive inhibitors: compete for active site. Ex. Sulpha drugs. Non-competitive inhibitors : don’t bind to active site. Ex: Metals, antibiotics, DDT or another molecule in the metabolic pathway. http://www.wiley.com/college/pratt/0471393878/student/animations/enzyme_inhibition/ Sulpha Drugs: Sulfa drugs are a class of synthetic drugs that all have a sulfonamide chemical group. These drugs have many different uses, but in this lesson we will focus on the ones that are antibacterial. They are often used to treat bladder infections because they reach high concentrations in the urine. Sulfa antibiotics inhibit the pathway that bacteria use to synthesize folic acid, which is an important metabolite, or substance formed by metabolism for all cells. Bacteria have to make folic acid on their own. This is the pathway that leads to folic acid synthesis in bacteria. You can see the enzymes involved and the metabolites that are made along the way. Drugs that inhibit folic acid synthesis are bacteriostatic because the bacteria can't reproduce if they don't have enough folic acid to make new DNA, RNA and proteins. They are also broad-spectrum drugs - they are effective against many types of bacteria. Sulfa drugs like Sulfamethoxazole inhibit the enzyme that catalyzes the first step of this pathway. Sulfa drugs are competitive inhibitors of this enzyme, meaning that they compete with the real substrate of the enzyme, which is para-aminobenzoic acid and is called PABA for short. If we compare the structures of PABA and a sulfa drug, we can easily see how these drugs can be competitive inhibitors. They look a lot alike to us - and to the enzyme too. If most of the copies of this enzyme in the bacterial cell are busy binding to sulfa drugs instead of to PABA, not much of the next metabolite in the pathway can be produced. However, some of the next metabolite could be made, because chances are at least some of the enzymes will bind to PABA instead of the sulfa drug. That means that some folic acid could still be produced.

Competitive Inhibition Example Sulpha drugs contain sulfonamide group. Act as an competitive inhibitor to DHPS, which is an enzyme responsible for folic acid biosynthesis. Folic acid is a vitamin needed to make nucleotides and amino acids. Sulpha drugs are used as antibiotics to inhibit bacteria’s ability to make DNA/RNA and amino acids. Deoxyhypusine synthase = DHPS Dihydrofolate reductase = DHFR

Noncompetitive Inhibition Example Isoleucine an amino acid that acts as a noncompetitive inhibitor to threonine deaminase. Stopping its own metabolic pathway.

Inhibition Graphs

Controlling Metabolism w/ Enzymes Allosteric regulation: activation, inhibition, or cooperativity. Allosteric site: specific site on enzyme other than active site. Allosteric regulator: bind to allosteric site and can either activate or inhibit the enzyme activity. Activation: turns on the enzyme Inhibition: turns off the enzyme Cooperativity- a type of activation; binding of the substrate may enhance the enzymes function. Feedback inhibition: a metabolic pathway in which it is turned off with its own end-product; the product attaches to an enzyme in an earlier reaction http://bcs.whfreeman.com/thelifewire/content/chp06/0602002.html http://programs.northlandcollege.edu/biology/Biology1111/animations/enzyme.html

Allosteric Control http://content.bfwpub.com/webroot_pubcontent/Content/BCS_4/Hillis1e/Animated%20Tutorials/at0303/pol_0303.swf

Feedback Inhibition: Noncompetitive http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter2/animation__feedback_inhibition_of_biochemical_pathways.html