Microbiology: A Systems Approach, 2nd ed.

Chapter 8: Microbial Metabolism- the Chemical Crossroads of Life

8.1 The Metabolism of Microbes• Metabolism: All chemical reactions and physical workings

of the cell• Anabolism: also called biosynthesis- any process that

results in synthesis of cell molecules and structures (usually requires energy input)

• Catabolism: the breakdown of bonds of larger molecules into smaller molecules (often release energy)

• Functions of metabolism– Assembles smaller molecules into larger macromolecules

needed for the cell– Degrades macromolecules into smaller molecules and yields

energy– Energy is conserved in the form of ATP or heat

Figure 8.1

Enzymes

• Catalyze the chemical reactions of life• Enzymes: an example of catalysts, chemicals that

increase the rate of a chemical reaction without becoming part of the products or being consumed in the reaction

How do Enzymes Work?

• Energy of activation: the amount of energy which must be overcome for a reaction to proceed. Can be achieved by:– Increasing thermal energy to increase molecular velocity– Increasing the concentration of reactants to increase the

rate of molecular collisions– Adding a catalyst

• An enzyme promotes a reaction by serving as a physical site upon which the reactant molecules (substrates) can be positioned for various interactions

Enzyme Structure

• Most- protein• Can be classified as simple or conjugated

– Simple enzymes consist of protein alone– Conjugated enzymes contain protein and non-

protein molecules• A conjugated enzyme (haloenzyme) is a combination of

a protein (now called the apoenzyme) and one or more cofactors

• Cofactors are either organic molecules (coenzymes) or inorganic elements (metal ions)

Figure 8.3

Figure 8.2

Apoenzymes: Specificity and the Active Site

• Exhibits levels of molecular complexity called the primary, secondary, tertiary, and quaternary organization

• The actual site where the substrate binds is a crevice or groove called the active site or catalytic site

Enzyme-Substrate Interactions

• For a reaction to take place, a temporary enzyme-substrate union must occur at the active site. (Called an enzyme-substrate complex.)

• “Lock-and-key” fit• The bonds are weak and easily reversible

Figure 8.4

Cofactors: Supporting the Work of Enzymes

• Metallic cofactors– Include Fe, Cu, Mg, Mn, Zn, Co, Se– Metals activate enzymes, help bring the active site and

substrate close together, and participate directly in chemical reactions with the enzyme-substrate complex

• Coenzymes– Organic compounds that work in conjunction with an

apoenzyme to perform a necessary alteration of a substrate

– Removes a chemical group from one substrate molecule and adds it to another substrate

– Vitamins: one of the most important components of coenzymes

Classification of Enzyme Functions

• Site of action• Type of action• Substrate

Location and Regularity of Enzyme Action

• Either inside or outside of the cell• Exoenzymes break down molecules outside of

the cell• Endoenzymes break down molecules inside of

the cell

Figure 8.5

Synthesis and Hydrolysis Reactions

Figure 8.7

Transfer Reactions by Enzymes• Oxidation-reduction reactions

– A compound loses electrons (oxidized)– A compound receives electrons (reduced)– Common in the cell– Important components- oxidoreductases

• Other enzymes that play a role in necessary molecular conversions by directing the transfer of functional groups:– Aminotransferases– Phosphotransferases– Methyltranferases– Decarboxylases

The Role of Microbial Enzymes in Disease

• Many pathogens secrete unique exoenzymes• Help them avoid host defenses or promote

multiplication in tissues• These exoenzymes are called virulence factors

or toxins

The Sensitivity of Enzymes to Their Environment

• Enzyme activity is highly influenced by the cell’s environment

• Enzymes generally operate only under the natural temperature, pH, and osmotic pressure of an organism’s habitat

• When enzymes are subjected to changes in normal conditions, they become chemically unstable (labile)

• Denaturation: the weak bonds that maintain the native shape of the apoenzyme are broken

Regulation of Enzymatic Activity and Metabolic Pathways

• Metabolic Pathways– Metabolic reactions usually occur in a multiseries

step or pathway– Each step is catalyzed by an enzyme– Every pathway has one or more enzyme

pacemakers that set the rate of a pathway’s progression

Figure 8.8

Rate of Enzyme Production

• Enzymes are not all produced in the cell in equal amounts or at equal rates– Constitutive enzymes: production is continuous

and in relatively constant amounts– Regulated enzymes: production is either induced

or repressed in response to a change in concentration of the substrate

Control of Enzyme Activity

• Direct control of enzyme activity (constitutive enzymes)

• Regulation of enzyme synthesis (regulated enzymes)

Direct Controls on the Action of Enzymes

• Competitive inhibition: The cell supplies a molecule that resembles the enzyme’s normal substrate, which then occupies and blocks the enzyme’s active site

• Noncompetitive inhibition: The enzyme has two binding sites- the active site and the regulatory site; a regulator molecule binds to the regulatory site providing a negative feedback mechanism

Figure 8.9

Controls on Enzyme Synthesis

• Enzymes eventually must be replaced• Enzyme repression: stops further synthesis of

an enzyme somewhere along its pathway• Enzyme induction: The inverse of enzyme

repression

Regulated Enzymes

• Inducible enzymes- break down complex substrates into simpler products; eg. lactose to glucose; enzymes are only synthesized (induced) when excess substrate is present. Otherwise the enzymes are not synthesized.

• Repressible enzymes- synthesize products such as tryptophan when the product is not available in nutrient sources. Presence of excess product represses enzyme production.

Figure 8.6

Figure 8.10

8.2 The Pursuit and Utilization of Energy

• Energy in Cells– Exergonic reaction: a reaction that releases

energy as it goes forward– Endergonic reaction: a reaction that is driven

forward with the addition of energy

Figure 8.11

A Closer Look at Biological Oxidation and Reduction

• Biological systems often extract energy through redox reactions

• Redox reactions always occur in pairs– An electron donor and electron acceptor– Redox pair

• Electron donor (reduced) + electron acceptor (oxidized) Electron donor (oxidized) + electron acceptor (reduced)

• This process leaves the previously reduced compound with less energy than the now oxidized one

• The energy in the electron acceptor can be captured to phosphorylate to ADP or some other compound, storing the energy in a high-energy molecule like ATP

Electron Carriers: Molecular Shuttles

• Electron carriers repeatedly accept and release electrons and hydrogens

• Facilitate the transfer of redox energy• Most carriers are coenzymes that transfer

both electrons and hydrogens• Some transfer electrns only• Most common carrier- NAD

Figure 8.12

Adenosine Triphosphate: Metabolic Money

• ATP• Can be earned, banked, saved, spent, and exchanged• A temporary energy repository• The Molecular Structure of ATP

– Three-part molecule• Nitrogen base (adenine)• 5-carbon sugar (ribose)• Chain of three phosphate groups

– The high energy originates in the orientation of the phosphate groups

– Breaking the bonds between two successive phosphates of ATP yields ADP

– ADP can then be converted to AMP

Figure 8.13

The Metabolic Role of ATP• Primary energy currency of the cell• When used in a chemical reaction, must be replaced• Ongoing cycle• Adding a phosphate to ADP replenishes ATP but it

requires an input of energy• In heterotrophs, this energy comes from certain steps

of catabolic pathways• Some ATP molecules are formed through substrate-

level phosphorylation – ATP is formed by a transfer of a phosphate group from a

phosphorylated compound (substrate) directly to ADP

Figure 8.14

Phosphorylation

• Oxidative phosphorylation– Series of redox reactions occurring during the final

phase of the respiratory pathway

• Photophosphorylation– ATP is formed through a series of sunlight-driven

reactions in phototrophic organisms

8.3 The Pathways• Pathway- a series of biochemical reactions• Metabolism uses enzymes to catalyze reactions

that break down (catabolize) organic molecules to materials (precursor molecules) that cells can then use to build (anabolize) larger, more complex molecules that are particularly suited to them.

• Reducing power and energy are needed in large quantities for the anabolic parts of metabolism; they are produced during the catabolic part of metabolism.

Catabolism: Getting Materials and Energy

• Frequently the nutrient needed is glucose• Most common pathway to break down glucose is glycolysis• Three major pathways

– 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 and the final electron acceptor.

Figure 8.15

Aerobic Respiration• Series of enzyme-catalyzed reactions• Electrons are transferred from fuel molecules to

oxygen as a final electron acceptor• Principal energy-yielding scheme for aerobic

heterotrophs• Provides both ATP and metabolic intermediates

for many other pathways in the cell• Glucose is the starting compound• Glycolysis enzymatically converts glucose through

several steps into pyruvic acid

Figure 8.16

Pyruvic Acid- A Central Metabolite

• Pyruvic acid from glycolysis serves an important position in several pathways

• Different organisms handle it in different ways• In strictly aerobic organisms and some

anaerobes, pyruvic acid enters the Krebs cycle

Figure 8.17

The Krebs Cycle: A Carbon and Energy Wheel

• Pyruvic acid is energy-rich, but its hydrogens need to be transferred to oxygen

• Takes place in the cytoplasm of bacteria and in the mitochondrial matrix in eukaryotes

• Produces reduced coenzymes NADH and FADH2, 2 ATPs for each glucose molecule

Insight 8.3

The Respiratory Chain: Electron Transport and Oxidative

Phosphorylation• The final “processing mill” for electrons and

hydrogen ions• The major generator of ATP• A chain of special redox carriers that receives

electrons from reduced carriers (NADH and FADH2) and passes them in a sequential and orderly fashion from one redox molecule to the next

Figure 8.18

Figure 8.19

Potential Yield of ATPs from Oxidative Phosphorylation

• Five NADHs (four from Krebs cycle and one from glycolysis) can be used to synthesize:– 3 ATP’s per electron pair from NADH– 15 ATPs for ETS (5 X 3 per electron pair)– 15 X 2 = 30 ATPs per glucose

• The single FADH produced during the Krebs cycle results in– 2 ATPs per electron pair– 2 X 2 = 4 ATPs per glucose

Summary of Aerobic Respiration• The total possible yield of ATP is 40

– 4 from glycolysis– 2 from the Krebs cycle– 34 from electron transport

• But 2 ATPs are expended in early glycolysis, so a maximum yield of 38 ATPs for prokaryotes

• 6 CO2 molecules are generated during the Krebs cycle• 6 O2 molecules are consumed during electron

transport• 6 H2O molecules are produced in electron transport

and 2 in glycolysis; but 2 are used in Krebs cycle for a net number of 6

The Terminal Step

• Oxygen accepts the electrons• Catalyzed by cytochrome aa3 (cytochrome

oxidase)• 2 H+ + 2 e- + 1/2O2 H2O• Most eukaryotic aerobes have a fully

functioning cytochrome system• Bacteria exhibit wide-ranging variations which

can be used to differentiate among certain genera of bacteria

Anaerobic Respiration

• Functions like the aerobic cytochrome system except it utilizes atoms or oxygen-containing ions rather than free oxygen as the final electron acceptor

• The nitrate and nitrite reduction systems are best known, using the enzyme nitrate reductase

• Denitrification: when enzymes can further reduce nitrite to nitric oxide, nitrous oxide, and nitrogen gas- important in recycling nitrogen in the biosphere

Fermentation

• The incomplete oxidation of glucose or other carbohydrates in the absence of oxygen

• Uses organic compounds as the terminal electron acceptors and yields a small amount of ATP

• Many bacteria can grow as fast using fermentation as they would in the presence of oxygen– This is made possible by an increase in the rate of

glycolysis– Permits independence from molecular oxygen

Products of Fermentation in Microorganisms

• Products of Fermentation in Microorganisms– Alcoholic beverages– Organic acids– Dairy products– Vitamins, antibiotics, and even hormones– Two general categories

• Alcoholic fermentation• Acidic fermentation

Alcoholic Fermentation Products

• Occurs in yeast or bacterial species that have metabolic pathways for converting pyruvic acid to ethanol

• Products: ethanol and CO2

Figure 8.20

Acidic Fermentation Products

• Extremely varied pathways• Lactic acid bacteria ferment pyruvate and reduce

it to lactic acid• Heterolactic fermentation- when glucose is

fermented to a mixture of lactic acid, acetic acid, and carbon dioxide

• Mixed acid fermentation- produces a combination of acetic, lactic, succinic, and formic acids and lowers the pH of a medium to about 4.0

Catabolism of Noncarboyhdrate Compounds

• Polysaccharides can easily be broken down into their component sugars which can enter glycolysis

• Microbes can break down lipids and proteins to produce precursor metabolites and energy– Lipases break apart fats into fatty acids and glycerol

• The glycerol is then converted to DHAP• DHAP can enter step 4 of glycolysis• The fatty acid component goes through beta oxidation• Can yield a large amount of energy (oxidation of a 6-carbon fatty acid

yields 50 ATPs)– Proteases break proteins down to their amino acid components

• Amino groups are then removed by deamination• Results in a carbon compound which can be converted to one of

several intermediates of either glycolysis or the Krebs cycle

Figure 8.21

8.4 Biosynthesis and the Crossing Pathways of Metabolism

• The Frugality of the Cell- Waste Not, Want Not– Most catabolic pathways contain strategic

molecular intermediates (metabolites) that can be diverted into anabolic pathways

– Amphibolism: the property of a system to integrate catabolic and anabolic pathways to improve cell efficiency

– Principal sites of amphibolic interaction occur during glycolysis and the Krebs cycle

Figure 8.22

Amphibolic Sources of Cellular Building Blocks

• Glyceraldehyde-3-phosphate can be diverted away from glycolysis and converted into precursors for amino acid, carbohydrate, and triglyceride synthesis

• Pyruvate also provides intermediates for amino acids and can serve as the starting point in glucose synthesis from metabolic intermediates (gluconeogenesis)

• The acetyl group that starts the Krebs cycle can be fed into a number of synthetic pathways

• Fats can be degraded to acetyl through beta oxidation• Two metabolites of carbohydrate catabolism that the Krebs cycle

produces are essential intermediates in the synthesis of amino acids– Oxaloacetic acid– Α-ketoglutaric acid– Occurs through amination

• Amino acids and carbohydrates can be interchanged through transanimation

Figure 8.23

Anabolism: Formation of Macromolecules

• Monosaccharides, amino acids, fatty acids, nitrogen bases, and vitamins come from two possible sources– Enter the cell from outside as nutrients– Can be synthesized through various cellular pathways

• Carbohydrate Biosynthesis– Several alternative pathways

• Amino Acids, Protein Synthesis, and Nucleic Acid Synthesis– Some organisms can synthesize all 20 amino acids– Other organisms (especially animals) must acquire the

essential ones from their diets

Assembly of the Cell

• When anabolism produces enough macromolecules to serve two cells

• When DNA replication produces duplicate copies of the cell’s genetic material

• Then the cell undergoes binary fission

8.5 It All Starts with the Sun

• Photosynthesis– Proceeds in two phases

• Light-dependent reactions• Light-independent reactions

Light-Dependent Reactions• Solar energy delivered in discrete energy packets called photons• Light strikes photosynthetic pigments

– Some wavelengths are absorbed– Some pass through– Some are reflected

• Light is absorbed through photosynthetic pigments– Chlorophylls (green)– Carotenoids (yellow, orange, or red)– Phycobilinss (red or blue-green)

• Bacterial chlorophylls– Contain a photocenter- a magnesium atom held in the center of a complex

ringed molecule called a porphyrin– Harvest the energy of photons and converts it to electron energy

• Accessory photosynthetic pigments trap light energy and shuttle it to chlorophyll

Figure 8.24

Figure 8.25

Light-Independent Reactions

• Occur in the chloroplast stroma or the cytoplasm of cyanobacteria

• Use energy produced by the light phase to synthesize glucose by means of the Calvin cycle

Figure 8.26

Other Mechanisms of Photosynthesis

• Oxygenic (oxygen-releasing) photosynthesis that occurs in plants, algae, and cyanobacteria – the dominant type of photosynthesis on earth

• Other photosynthesizers such as green and purple bacteria – Possess bacteriochlorophyll– More versatile in capturing light– Only have a cyclic photosystem I– These bacteria use H2, H2S, or elemental sulfur rather than

H2O as a source of electrons and reducing power– They are anoxygenic (non-oxygen-producing); many are

strict anaerobes