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Home , Protein catabolism

1/12/2016

Catabolic and Anabolic Reactions

Learninggj Objectives Invisible Invaders • Define and describe the Amazing Allies fundamental differences between and • Identify the role of ATP as an intermediate between catabolism and Chapter 5 anabolism Microbial Metabolism

Two types of chemical Metabolism – all reactions: chemical reactions and physical workings of a anabolism – biosynthesis; cell process that forms larger macromolecules from MtbliMetabolism is an smaller molecules; energy-balancing act requires energy input; since chemical dehydration synthesis reactions either (reactions release water) release or require catabolism –degradative; energy breaks the bonds of larger molllecules ffiorming smaller molecules; releases energy; hydrolytic reactions (water is used to break hydrogen bonds)

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Role of ATP in Coupling Anabolic and Enzymes Catabolic Reactions • Catabolic reactions provide Learning Objectives building blocks for anabolic reactions and furnish the • Identify the components of an enzyme energy needed to drive anabolic reactions • Describe the mechanism of enzymatic action • • List the factors that influence enzymatic (ATP) makes this coupling activity possible as it stores energy • Distinguish competitive and noncompetitive and releases it later to drive anabolism and to inhibition perform other cellular • Define ribozyme work. All of the cell’s metabolic pathways are determined by • Metabolic pathways are its enzymes, which in turn are determined by the cell’s determined by enzymes, which are encoded by genetic makeup. genes.

Collision Theory Collision Theory

Collision theory: all atoms, ions, and Reaction rate is the frequency of collisions molecules are continuously moving and with enough energy to bring about a reaction. colliding with one another. The energy Rate may be increased by increasing the transferred by the particles in the collision temperature, pressure, or concentration of disrupt their electron structure to break or reactants form chemical bonds. In living organisms, enzymes increase the AtitinActivation energy is the a mou nt o f en ergy reaction rate without raising the needed to disrupt electronic configurations temperature of any specific molecule; collision energy required for a chemical reaction

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Enzymes and Chemical Reactions Enzyme-Substrate Complex enables More Effective Collisions Lowering the Activation Energy Enzymes are biological catalysts that increase the rate of a chemical reaction by lowering the energy of activation without increasing the temperature of the living cell. Catalyst: a substance that speeds up a chemical reaction without being permanently altered in the reaction. Enzyme promotes 1. Substrate contacts the active site on a re action b y ser ving the enzyme as a physical site 2. Forms an enzyme-substrate complex for specific 3. Substrate is transformed into products substrate molecules to position. 4. Products are released 5. Enzyme is recovered unchanged

Enzyme Specificity and Efficiency Hexokinase

• The three-dimensional structure of an enzyme determines its substrate specificity • Unique structure enables each enzyme to find its substrate among diverse molecules in the cell. • Enzymes are very efficient

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Enzyme Specificity and Efficiency Enzyme Components

• Some enzymes are entirely • Under optimum conditions, they can • Most consist of catalyze a reaction up to - a protein part 10 billion times faster apoenzyme than without an enzyme - a non-protein part cofactor • The turnover number of substra te mo le cules is • Apoenzymes are inactive generally 1-10,000 without the cofactor molecules per second! • Holoenzyme –apoenzyme plus the cofactor

• Cofactors examples: ions Enzyme Components Mechanism of of iron, zinc, magnesium or Enzymatic Action calcium; form a bridge between enzyme and substrate, trace elements • Coenzyme is a cofactor that is organic in nature and assists the enzyme by accepting atoms removed

from the substrate or Enzyme: donating atoms required Sucrase for the substrate Products no longer fit • Coenzyme examples: vitamins, NAD, NADP, nicotinamide adenine dinucleotide (phosphate)

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Factors Influencing Enzymatic Activity Factors Influencing Enzyme Activity

• Temperature • pH • Substrate concentration • Inhibitors

Enzymes can be denatured by temperature and pH 3D-structure is lost

Factors Influencing Enzymatic Activity Substrate concentration Factors Influencing influences enzyme activity Enzymatic Activity a) Enzyme activity • Enzymes have a maximum rate at increases with which they can catalyze a increasing specific reaction. This occurs temperature until the when the concentration of enzyme, a protein, is substrate is high. saturation denatured by heat and • At a high level, the enzyme inactivated active site is always occupied and is saturated. b) Hydrogen ions compete • A further increase in with hyygdrogen and conce ntra tio n at this pintpoint w ill ionic bonds in an not increase the enzyme activity. enzyme and denature • Under normal cellular activity, the 3D structure. The enzymes are not saturated and enzyme illustrated is substrate levels influence most active at pH 5.0 enzyme activity.

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Enzymes Inhibitors: Feedback Inhibition Competitive and Noncompetitive An effective way to control bacterial growth is to • Non-competitive inhibitors inactivate enzymes. play a role in a type of Competitive inhibitors fill the active site and compete with subst rat e, does not undergo any reacti on, and is biochemical control called similar chemically to the substrate. feedback inhibition or end- Non-competitive inhibitors bind at a site other than the product inhibition active site and alters the structure of the enzyme so • that the substrate cannot bind. The mechanism stops the cell from making more of a substance that it needs and wasting chemical resources

• Prior to 1982, only Feedback Inhibition were believed to have Ribozymes enzymatic activity • Anabolic pathway – final end-product inhibits the • Ribozyme, an enzyme consisting of RNA, that activity of the first functions as a catalyst, has enzyme in the biochemical an active site that binds pathway substrate, and is not used up in a reaction. • Entire pathway shuts down and no new end-product is • Ribozyme acts on strands of RNA by removing made sections and splicing the pieces together again • When the end-product is used up, it no longer binds • Ribozymes are more the first enzyme and the restricted in diversity of substrates compared to pathway resumes activity protein enzymes.

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• molecules, like all molecules, have energy Energy Production associated with the electrons that form bonds between their atoms • Various reactions in catabolic pathways Learninggj Objectives concentrate the energy into bonds of ATP, which serves as a carrier of energy • Explain the term oxidation-reduction • ATP energy can be released easily and quickly due • List and provide examples of 3 type of to unstable bonds phosphorylation reactions that generate • ATP provides energy ATP for anabolic reactions • Explain the overall function of metabolic pathways

Oxidation-Reduction Reactions • Oxidation is the removal of electrons; a reaction that often produces energy • Reduction is the gain of electrons • Oxidation and reduction are always coupled • Pairing of these reactions is called oxidation- reduction or a redox reaction • Cells use redox reactions in catabolism to extract energy from

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• An organic molecule is oxidized by the loss of two • In biological systems, the electrons are hydrogen atoms and NAD+ is reduced. associated with hydrogen atoms. • NAD+ assists enzymes by accepting hydrogen ions • Biological oxidations are often from the substrate dehydrogenations due to the loss of • NADH is used to generate ATP in later reactions. hydrogen ion • Glucose contains many hydrogen atoms, are highly reduced, contains a large amount of potential energy, and is a valuable nutrient.

Generation of ATP Generation of ATP • Energy released during oxidation-reduction Organisms use 3 mechanisms of phosphorylation reactions is trapped within to generate ATP from ADP the cell in the form of ATP 1 – substrate level phosphorylation • Specifically, an inorganic phosphate group is added to 2 – oxidative phosphorylation ADP with the input of 3 - photophosphorylation energy or phosphorylation • When the third phosphate is removed (dephosphorylation) energy is released.

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Oxidative phosphorylation - energy released from the Three Mechanisms of Phosphorylation to transfer of electrons (oxidation) of one compound to an Generate ATP electron carrier, which then passes the electrons to a series of electron carriers (reduction) to molecules of oxygen or other oxidized molecules. Substrate level phosphorylation direct transfer of a high- Transfer of electrons is called an energy phosphate group from ET occurs in the one compound (substrate) to plasma membrane of ADP prokaryotes and the mitochondrial inner 1,3-diphosphoglyceric acid + ADP membrane of eukaryotes.  ATP + 3-phhlhosphoglyceric acid ATP synthase produces ATP via a process called chemiosmosis

Photophosphorylation - uses light energy to Metabolic Pathways of Energy Production phosphorylate ADP to ATP Organisms release and store energy from organic molecules by a series of controlled reactions rather than a single Occurs in photosynthetic burst. cells. If the energy were released as a single burst as heat, it could not be used to drive chemical reactions and it would Light causes chlorophyll damage the cell. to give up electrons. To extract energy from organic compounds and store it in Energy released from chemical form, organisms pass electrons from one compound to another via a series of oxidation-reduction the transfer of reactions. electrons (oxidation) of chlorophyll through A sequence of enzymatically catalyzed chemical a system of carrier reactions occurring in a molecules is used to cell is called a metabolic generate ATP. pathway.

9 1/12/2016

Carbohydrate Catabolism Catabolism: getting materials and energy

Learning Objectives • Glucose - most common energy • Describe the chemical reactions of source used by cells. • Iden tify the functi ons of the pent ose • Most common path way to break down gl ucos e phosphate and Entner-Doudoroff pathways is glycolysis • Explain the products of the Krebs cycle • is the breakdown • Describe the chemiosmotic model for ATP of carbohydrate molecules to produce generation energy. • Compare and contrast aerobic and anaerobic • Three major pathways respiration 1. Aerobic respiration • Describe the chemical reactions of, and list 2. some products of, 3. Fermentation

Respiration: series of reactions that convert

glucose to CO2 and allows the cell to recover significant amounts of energy Fermentation: when facultative and aerotolerant anaerobes use only the glycolysis scheme to incompletely oxidize glucose Aerobic respiration: When oxygen is used as the final electron acceptor at the end of the

respiration scheme to produce H2O. Anaerobic respiration: Does not use molecular oxygen as the final electron acceptor, but uses nitrogen or compounds of nitrogen or sulfur or compounds of sulfur, or other inorganic substances as the final electron acceptor.

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Aerobic Respiration Glycolysis (Embden-Meyerhof Pathway) - oxidation • Series of enzyme-catalyzed reactions of glucose to and is the first step in • Electrons are transferred from fuel molecules to oxygen as a final electron Two stages: acceptor 1. Preparative stage: 6-carbon glucose is • Principal energy-yielding scheme for phosphorylated, restructured, and split into two 3- most aerobic bacteria carbon compounds. Two ATP used. • Provides both ATP and metabolic 2. Energy conserving stage: two 3-carbon compounds are oxidized to 2 pyruvic acid. Two intermediates for many other NAD+ are reduced to 2 NADH and a net of 2 ATP pathways in the cell molecules are formed by substrate phosphorylation • Glucose is the starting compound Does not require oxygen • Glycolysis enzymatically converts Net gain of 2 ATP molecules for each molecule of glucose through several steps into glucose that is oxidized. pyruvic acid

Glycolysis Alternatives to Glycolysis

Preparative stage Many bacteria have another pathway in addition 2 ATP used to glycolysis for oxidation of glucose. • Pentose phosphate pathway operates simultaneously with glycolysis and provide a means for breakdown of 5-carbon compounds Energy-conserving as well as glucose stage • Produces important 5-carbon compounds used 2 ATP formed in the synthesis of nucleic acids, glucose from carbon diox ide in p hot osyn thes is, an d some amino acids. Net gain of 2 ATP for each molecule of • Net gain of 1 ATP molecule for each molecule glucose that is of glucose oxidized. oxidized

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Alternatives to Glycolysis Pentose Phosphate Entner-Doudoroff Pathway Pathway produces 2 NADPH molecules and 1 ATP for use in cellular biosynthetic reactions. • Bacteria can metabolize glucose without either glycolysis or the pentose phosphate pathway • Found only in bacteria and archaea • Pseudomonads are major genera that utilize this pathway, which is used to identify this bacterium. • Not generally found in Gram- positives

The Krebs Cycle: A Carbon and Energy Wheel • Pyruvic acid (from glycolysis) is oxidized and (loss

of CO2) occurs • The resulting two-carbon compound attaches to coenzyme A, forming acetyl CoA and NADH • Oxidation of acetyl-CoA produces

6 NADH and 2 FADH2, and 2 ATPs for each glucose molecule

• NADH and 2 FADH2 are the most important molecules generated as they contain most of the energy stored in glucose • Takes place in the cytoplasm of bacteria and in the mitochondrial matrix in eukaryotes

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Respiratory Chain: Electron Transport and Oxidative Phosphorylation Electron transport chain A series of redox reactions that transfer electrons from one compound to another that generates ATP by oxidative phosphorylation The major generator of ATP

NADH and FADH2 are main electron donors

Oxygen is the final electron acceptor

Chemiosmosis: a mechanism that uses a Potential Yield of ATPs from Oxidative proton gradient across a cytoplasmic membrane to generate ATP Phosphorylation

Electrons (from NADH) pass down the electron transport chain while protons are pumped across the membrane Establishes proton gradient (proton motive force)

Protons in higher concentration on one side of the membrane diffuse through ATP synthase EhEach NADH can be oxidi ididzed in the el ectron Releases energy to synthesize ATP transport chain to produce 3 molecules of ATP

Oxidative phosphorylation: synthesis Each FADH2 can produce 2 molecules of ATP of ATP coupled with electron transport

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Summary of Aerobic Respiration Anaerobic Respiration • Functions like the aerobic cytochrome Total possible yield of ATP is 40 system except it utilizes atoms or oxygen- - 4 from glycolysis containing ions NOT free oxygen as the - 2 from the Krebs cycle final electron acceptor - 34 from electron transport • Example - the nitrate and nitrite reduction But 2 ATPs are expended in early glycolysis, so a maximum yield of systems are best known, using the enzyme 38 ATPs for prokaryotes nitrate reductase NO - + 2H+ + 2e- → NO - + H O -6 CO2 molecules are produced 3 2 2 during the Krebs cycle • Essential for nitrogen and sulfur cycles in - 6 O2 molecules are consumed during electron transport the biosphere -6 H2O molecules are produced • ATP yield is lower than in aerobic in electron transport and 2 in respiration because only part of Krebs glycolysis; but 2 are used in cycle operates under anaerobic conditions Krebs cycle for a net of 6 (2-36 ATP)

Fermentation Defined Anaerobic Respiration A process that: 1. releases energy from sugars or other organic molecules Electron Acceptor Products 2. does not require oxygen – – NO3 NO2 , N2 + H2O 3. does not use the Krebs cycle or an electron transport chain SO – H S + H O 4 2 2 4. uses an organic molecule as the 2 – final electron acceptor CO3 CH4 + H2O 5. produces small amounts of ATP because much of the energy remains in the chemical bonds of the organic end-product, such as lactic acid or ethanol

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• Electrons are transferred (along Fermentation End Products of Various with protons) from reduced coenzymes (NADH, NADHP) to pyruvic acid or its derivatives. • Final electron acceptors are reduced to the end-products • An essential function of the second stage of fermentation is to ensure a steady supply of NAD+ and NADP+ so that glycolysis can continue. • ATP is generated only during glycolysis

Products of Fermentation in Microorganisms

• Pyruvic acid (2 molecules) is Products of Fermentation reduced by NADH to form 2 Alcoholic beverages molecules of lactic acid OiOrganic acids • LtLacticacid is the end pro duc t Dairy products and it does not undergo further Vitamins oxidation. Most of the energy remains in the lactic acid bonds. Antibiotics Hormones • Thus, incomplete oxidation of glucose results. Two general categories • Lactic acid fermentation can Alcoholic fermentation result in food spoilage Acidic fermentation • Or it can produce food products from milk

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Buttermilk Alcohol Fermentation Bacterial Ripened Lowfat milk- Lactobacillus and Cheeses • Pyruvic acid (2 molecules) is Streptococcus lactus Swiss cheese: holes converted to 2 molecules of Lactose fermented, milk clotted due to carbon dioxide acetaldehyde and two molecules due to low pH of carbon dioxide proddduced by bacter ia • The acetaldehyde is reduced by Cheddar Sour Cream 2 NADH to form 2 molecules of Parmesan Light cream with Lactobacillus and ethanol Streptococcus lactus • Again the energy contained in low pH the glucose molecule remains in the ethan ol , the end-pdtproduct • Yeast and a few bacteria Yogurtbulgaricus perform this Milk products with Lactobacillus thermophilus • and Streptococcus Ethanol used to make beverages • Carbon dioxide makes bread rise

Overview of Respiration and Fermentation

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Lipid and Protein Catabolism Catabolism • consist of fatty acids and glycerol Learninggj Objectives • Microbes produces enzymes lipases that break down fats Describe how lipids and proteins undergo into fatty acids and glycerol catabolism • Each component is metabolized separately

• Bac ter ia tha t can hyd ro lyze fatty acids can also degrade petroleum

• Beneficial for oil spills but not in a fuel storage tank

Protein Catabolism Catabolism of Various Organic Food Molecules

• Microbes produce extracellular and peptidases, enzymes that breakdown prote ins in to am ino ac ids, w hic h can cross the membrane. • Amino acids must be converted to other substances that enter the Krebs Cycle Deamination removes the amino group, which is converted to ammonium ion, which is excreted. Decarboxylation removes the carboxy group (-COOH)

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Biochemical Tests and Bacterial Catabolizing Enzymes Identification Bacteria are inoculated in tubes Learning Objectives containing glucose, a pH indicator, and a specific amino acid Acid produced from glucose Provide two examples of the use of fermentation activates the enzyme biochemical tests to identify bacteria in for the decarboxylation reaction. the laboratory - ) The pH indicator turns yellow when bacteria produce acid from glucose ______+ ) Alkaline products from Biochemical tests are designed to detect the decarboxlyation turn the indicator to presence of enzymes that are used to purple

identify bacteria Decarboxylation

Carbohydrate Fermentation

Test medium contains protein, a single carbohydrate, a pH indicator, Learning Objectives and an inverted Durham tube Bacteria use protein and • Compare and contrast cyclic and noncyclic carbohydrate as carbon and energy photophosphorylation source If they catabolize the carbohydrate • Compare and contrast the light-dependent and produce acid, the indicator and light-independent reactions of turns yellow photosynthesis Some microbes produce gas as well as • Compare and contrast oxidative acid and the Durham tube will phosphorylation and photophosphorylation capture gas.

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It All Starts with the Sun It All Starts with the Sun

Photosynthesis is the Takes place in two stages conversion of light energy Photophosphorylation Photophosphorylation Light-dependent from the sun into reactions: conversion of chemical energy Light Light energy light energy into chemical energy The chemical energy Water as Water as hydrogen Sugar energy (ATP and NADPH) hydrogen Sugar converts carbon dioxide donor donor Light-independent from the atmosphere into reactions: ATP and carbon compounds, Chemical NADPH are used to Chemical priilimarily sugars. energy energy reduce CO2 to sugar is the (carbon fixation) via the synthesis of sugars from Oxygen Carbon Calvin-Benson cycle Oxygen Carbon carbon dioxide released dioxide released dioxide fixation fixation

Light-Dependent Reactions Excited electrons jump from the chlorophyll to the first Solar energy is delivered in discrete energy packets called of a series of carrier photons molecules in an electron Photophosphorylation: Light energy is used to convert ADP transport system to ATP and NADP+ is reduced to NADPH Cyclic photophosphorylation: electrons released from Light is absorbed through photosynthetic pigments the chlorophyll eventually Electrons stay within the photosystem Chlorophylls (green) return to the chlorophyll. Carotenoids (yellow, orange, or red) Non-cyclic Phycobilins (red or blue-green) photophosphorylation: electrons released from chlorophyll do not return to Bacterial chlorophylls the chlorophyll but instead Contain a photocenter- a magnesium atom held in the become incorporated into center of a complex ringed molecule called a porphyrin NADPH. Electrons lost are replaced by electrons in Electrons lost are Harvest the energy of photons and converts it to replaced by water electron energy water.

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Light-Independent Reactions A Summary of Energy Production Mechanisms Use energy produced by the light phase to synthesize glucose by means of the Calvin cycle Learning Objectives

Write a sentence to summarize energy Ribulose diphosphate production in cells

In the living world, energy passes from one 2. Electrons are removed organism to another in from the energy source the form of potential and transferred to energy contained in the electron carriers. bonds of chemical Transfer is an compounds. oxidation-reduction Organisms obtain energy reaction. Some ATP is from oxidation produced reactions. 3. Electrons are 1. Toobtain energy in a transferred from the usable form, a cell must carriers to their final have an electron donor electron acceptors in (hydrogen), which serves further redox reactions. as an initial energy ATP is produced. source within the cell.

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Metabolic Diversity among Organisms Microbes are classified metabolically according to their nutritional Learning Objectives pattern In other words, their source of energy and Categorize the various nutritional patterns carbon. among organisms according to carbon source and mechanisms of carbohydrate Autotroph: organism that uses carbon dioxide as catabolism and ATP generation its main carbon source. HhHeterotroph: requires an organic carbon source Chemoheterotrophs are medically and economically important

Anabolism: Metabolic Pathways of Polysaccharide Biosynthesis Energy Use Intermediates to produce glucose are derived from Learning Objectives glycolysis. After synthesizing glucose, bacteria assemble it into more Describe the major types of anabolism and complex polysaccharides. their relationship to catabolism Glycogen is a multi-branched ______polysaccharide of glucose that Microbes use ATP: serves as a form of energy storage. to transport substances across the plasma membrane for flagellar rotation ADPG: adenosine dhdiphosph ogl ucose production of new compounds UDPG: uridine Autotrophs build organic compounds by fixing carbon diphosphoglucose dioxide UDPNAc: UDP-N- Heterotrophs must produce organic compounds from acetylglucosamine simpler molecules

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Lipids vary considerably and Lipid Biosynthesis Amino Acid and are synthesized by a variety of pathways. Amino acids are required for protein synthesis. Building units of fats and Some bacteria contain other lipids are linked via enzymes for the synthesis dehy dra tio n sy nthesis of all ami no acid s direct ly reactions and energy, not or indirectly from always in the form of ATP. intermediates of carbohydrate metabolism. Lipids are important Other microbe require that components of membranes. the environment provides Waxes are components of some amino acids. acid-fast bacteria. Amination: adding an amine group to an organic acid or Bacterial pigments and part of pyruvic acid chlorophyll are lipids Transamination: amine group Lipids also function in energy comes from a pre-existing storage. amino acid

Purine and Pyrimidine Biosynthesis Integration of Metabolism Repeating units of nucleotides make up DNA. Purine: adenine and guanine Learning Objectives PdPyrimidine: cytosine and thymine Define amphibolic pathways The 5-carbon sugar of nucleotides is derived from the pentose phosphate or Entner- Doudoroff pathways. Certain amino acids participate in synthesis of nucleotides and form the purine and pyrimidine rings.

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Biosynthesis and the Crossing Pathways of Metabolism Frugality of the Cell - Waste Not, Want Not Many pathways of metabolism are bi-directional or Most catabolic pathways contain strategic amphibolic. molllecular intermediates (bl)(metabolites) that Catabolic pathways contain molecular intermediates can be diverted into anabolic pathways (metabolites) that can be diverted into anabolic pathways. Amphibolic pathways: metabolic pathways - pyruvic acid can be converted into amino acids that function in both catabolic and anabolic through amination pathways to improve ce ll e ffici ency - amino acids can be converted into energy sources Principal sites of amphibolic interaction occur through deamination during glycolysis and the Krebs cycle - glyceraldehyde-3-phosphate can be converted into precursors for amino acids, and fats

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