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Chapter 7 Outline

• Microbial Physiology

– Introduction

– Microbial Nutritional Requirements

– Categorizing Microorganisms According to Their Energy and Carbon Sources

• Metabolic Enzymes

– Biologic Catalysts

– Factors That Affect the Efficiency of Enzymes

• Metabolism

– Catabolism

– Anabolism

• Bacterial Genetics

– Mutations

– Ways in Which Bacteria Acquire New Genetic Information

• Genetic Engineering

• Gene Therapy

Microbial PhysiologyIntroduction

• Physiology is the study of the vital life processes of organisms.

– Microbial physiology is very much chemical reactions (metabolism)

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Microbial PhysiologyNutritional Requirements

• All living protoplasm contains 6 major chemical elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur.

– Combinations of these and other elements make up vital macromolecules of life, including carbohydrates, lipids, proteins, and nucleic acids, vitamins, etc.

• Essential Nutrients:

• materials that organisms are unable to synthesize, but are required for building macromolecules and sustaining life,

• e.g., certain essential amino acids and essential fatty acids.

Categorizing Microorganisms by Energy and Carbon Sources

• Terms relating to an organism’s energy source.

– Phototrophs use light as an energy source.

– Chemotrophs use either inorganic or organic chemicals as an energy source.

• Chemolithotrophsuse inorganic chemicals as an energy source.

• Chemoorganotrophs use organic chemicals as an energy source.

organic

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Microbial PhysiologyCategorizing Microorganisms According to Their Energy and Carbon Sources, cont.

• Terms relating to an organism’s carbon source:

– Autotrophs use carbon dioxide (CO2) as their sole source of carbon.

– Heterotrophs use organic compounds other than CO2 as carbon sources.

• Terms that combine both energy and carbon source:

– Photoautotrophs use light as a carbon source and CO2 as an energy source.

– Chemoautotrophs use chemicals as a carbon source and CO2 as an energy source.

– Chemoheterotrophs use chemicals as a carbon source and organic compounds other than CO2 as an energy source.

Categorizing Microorganisms According to Their Energy and Carbon Sources, cont.

• Ecology is the study of the interactions between living organisms and the world around them.

• Ecosystem refers to the interactions between living organisms and their nonliving environment.

• Interrelationships among the different nutritional types are important in the functioning of the ecosystem.

– Example: Phototrophs, such as algae and plants, are the producers of food and oxygen for chemoheterotrophs, such as animals.

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Metabolic Enzymes

• Metabolism refers to all the chemical reactions that occur in a cell. The chemical reactions are referred to as metabolic reactions.

– Metabolic reactions are carried out by enzymes.

• Biologic Catalysts

– Enzymes are biologic catalysts; they are proteins that cause a particular chemical reaction to occur or accelerate it.

Metabolic EnzymesBiologic Catalysts, cont.

• Enzymes are specific, they only catalyze one particular chemical reaction.

• An enzyme only affects one particular substance, known as the substrate for that enzyme.

• The unique 3-dimensional shape of an enzyme enables it to fit the substrate like a key fits into a lock.

• http://youtu.be/PILzvT3spCQ

• An enzyme does not become altered during the chemical reaction it catalyzes. (They don’t last forever!)

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Factors That Affect the Efficiency of Enzymes

– pH - extreme acidity for example

– Temperature - heat can denature enzymes by breaking bonds

– Concentration of enzyme and/or substrate – may be too high or too low

– Inhibitors, for example heavy metals like lead, zinc, mercury and arsenic

Metabolism

• Metabolism refers to all of the chemical reactions within a cell

• A metabolite is any molecule that is a nutrient, an intermediary product, or an end product in a metabolic reaction.

• Metabolic reactions fall into 2 categories: catabolism and anabolism.

– Catabolism refers to all catabolic reactions in a cell.

– Anabolism refers to all anabolic reactions in a cell.

– http://youtu.be/v0OM-Qjdj88

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Metabolism, cont.

• Catabolic reactions involve the breaking down of larger molecules into smaller ones.

– Energy is released. Catabolic reactions are a cell’s major source of energy.

• Anabolic reactions involve the assembly of smaller molecules into larger molecules, requiring the formation of bonds. The bonds are stored energy.

• Much of the energy released during catabolic reactions is used to build molecules in anabolic reactions.

Metabolism, cont.

• Energy is temporarily stored in bonds in adenosine triphosphate (ATP).

• When ATP is used as an energy source, it is hydrolyzed (split) to adenosine diphosphate (ADP).

• ADP can be used as an energy source by hydrolysis to adenosine monophosphate(AMP).

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Interrelationships among ATP, ADP,

and AMP molecules.

Metabolism, cont.

Energy is required for metabolic pathways, growth, reproduction, sporulation, and movement of the organism, and active transport of substances across membranes.

a

Marine dinoflagellates use energy for bioluminescence.

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MetabolismCatabolism• Catabolic reactions release energy (by breaking bonds) and are a cell’s major source of energy.

– Some energy is lost as heat in catabolic reactions.

• Biochemical pathways are a series of linked biochemical reactions, with a starting chemical and an end product (chemical).

• Think of nutrients as energy sources for organisms and think of chemical bonds as stored energy.

• Glucose, for example, can be catabolizedby either aerobic respiration or fermentation.

• Glycolysis is shared by both: http://youtu.be/pnKih-4SRAE

A biochemical pathway with 4 steps. Compound A is

ultimately converted to compound E. Four enzymes are

required in this biochemical pathway. Compound A is the

substrate for Enzyme 1, Compound B for Enzyme 2, etc.

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MetabolismCatabolism, cont.

• Catabolism of glucose by aerobic respiration occurs in 3 phases (each is a biochemical pathway):

– Glycolysishttp://youtu.be/6JGXayUyNVw

– The Krebs cycle

– The electron transport chain

• The 1st phase (glycolysis) is anaerobic, but the other 2 phases are aerobic. So, the whole process is considered aerobic.

• Glycolysis is a 9-step biochemical pathway. Each step requires a specific enzyme.

Aerobic Respiration of

Glucose:

First Step = Glycolysis.

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CatabolismAerobic Respiration of Glucose, cont.

• The Krebs Cycle, aka citric acid cycle and TCA cycle:

– A biochemical pathway consisting of 8 separate reactions, each controlled by a different enzyme.

– Only 2 ATP molecules are produced, but NADH, H+, FADH2 are formed, which enter the electron transport chain.

• In eucaryotes, the Krebs/TCA cycle and the electron transport chain occur in mitochondria.

• In procaryotes, both occur at the inner surface of the cell membrane.

CatabolismAerobic Respiration of Glucose, cont.• The electron transport chain:

– A series of oxidation-reduction reactions, where energy is released as electrons which are transferred from one compound to another.

– Many enzymes are involved in the electron transport chain, including cytochrome oxidase,which transfers electrons to oxygen (the electron final acceptor).

– A large number of ATP molecules are produced by oxidative phosphorylation in the electron transport chain. http://youtu.be/DNReloT3QYU

• Aerobic respiration is very efficient!

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CatabolismFermentation of Glucose

• Fermentation reactions do not involve oxygen. They take place in anaerobic (no oxygen) environments.

– First step is glycolysis(anaerobic).

– The next step is conversion of pyruvic acid into an end product.

– The end product varies from one organism to another. Example: yeasts are used to make wine and beer; the end product is ethanol.

– Fermentation reactions produce very little energy, ~ 2 ATP molecules.

CatabolismOxidation-Reducton (Redox) Reactions• Oxidation-reduction reactions are paired reactions in which electrons are transferred from one compound to another.

• Oxidation occurs whenever an atom, ion, or molecule loses one or more electrons in a reaction; in which case, the molecule is said to be oxidized.

• The gain of one or more electrons by a molecule is called reduction and the molecule is said to be reduced.

• Within a cell, an oxidation reaction is always paired with a reduction reaction; hence the term, oxidation-reduction reaction.

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CatabolismOxidation-Reduction (Redox) Reactions, cont.

• In a redox reaction, the electron donor (compound A) is the reducing agent, and the electron acceptor (compound B) is the oxidizing agent.

• Many biologic oxidations are referred to as dehydrogenation reactionsbecause hydrogen ions, as well as electrons, are removed.

Anabolism

• Anabolic reactions require energy because chemical bonds are being formed. The energy that is used comes from catabolic reactions, which are occurring simultaneously.

• Biosynthesis of organic compounds requires energy. The energy may be obtained through photosynthesis (from light) or chemosynthesis (from chemicals).

– Photosynthetic reactions trap the radiant energy of light and convert it into chemical bond energy in ATP and carbohydrates (e.g., glucose).

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Bacterial Genetics

• Genetics = the study of heredity.

• An organism’s genotype is its complete collection of genes.

• An organism’s phenotype refers to its physical traits (e.g., includes hair and eye color in humans).

• An organism’s phenotype is the manifestation of that organism’s genotype because genes control all functions of the cell.

• Gene: a particular segment of the chromosome.

Bacterial GeneticsMutations

• A change in a DNA molecule (genetic alteration) that is transmissible to offspring is called a mutation.

– 3 categories of mutations:

• Beneficial mutations

• Harmful mutations (some are lethal mutations)

• Silent mutations

• Mutation rate (the rate at which mutations occur) can be increased by exposing cells to physical or chemical agents called mutagens.

• The organism containing the mutation is called a mutant.

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Bacterial GeneticsWays in Which Bacteria AcquireNew Genetic Information

• Ways in which bacteria acquire new genetic information (i.e., acquire new genes):

– Lysogenic Conversion

– Transduction

– Transformation

– Conjugation

• An extrachromosomal DNA molecule is called a plasmid. An organism that acquires a plasmid acquires new genes.

(A) A disrupted E. coli cell, in which the DNA has

spilled out. A plasmid can be seen slightly to the left

of top center (arrow). (B) Enlargement of plasmid.

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

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Ways in Which Bacteria Acquire New Genetic Information, cont.

• Lysogenic Conversion

– Temperate phages (or lysogenic phages) inject their DNA into a bacterial cell.

– The phage DNA integrates into the bacterial chromosome, but does not cause the lytic cycle to occur – this is known as lysogeny. This is the opposite of a lytic cycle, that causes the lytic cycle TO occur, resulting in the lysis (rupturing) of the host cell.

– A phage is called a prophage (early or first phage/virus)

when all that remains of it is its DNA.

– The bacterial cell containing the prophage is referred to as a lysogenic cell.

– The bacterial cell exhibits new properties, directed by the viral genes – this is referred to as lysogenic conversion.

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how Bacteria Acquire New Genetic Information, cont.

• Transduction (“to carry across”):

– Also involves bacteriophages.

– In transduction, bacterial genetic material is “carried across” from one bacterial cell to another by a bacterial virus; thus, in transduction, bacteria acquire new bacterial genes.

– Note how this differs from lysogenic conversion, wherein bacteria acquire new genetic information in the form of viral genes.

How Bacteria Acquire New Genetic Information, cont.

• Transformation

– A bacterial cell becomes genetically transformed following the uptake of DNA fragments (“naked DNA”) from its environment.

– The ability to absorb naked DNA into the cell is called competence and bacteria capable of absorbing naked DNA are said to be competent bacteria.

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How Bacteria Acquire New Genetic Information, cont.

• Conjugation

– Involves a specialized type of pilus called a sex pilus.

– A bacterial cell with a sex pilus (called the donor cell) attaches by means of the sex pilus to another bacterial cell (called the recipient cell).

– Some genetic material (usually a plasmid) is transferred through the hollow sex pilus from the donor cell to the recipient cell.

– A plasmid that contains multiple genes for antibiotic resistance is known as a resistance factor or R-factor. A bacterial cell that receives a R-factor becomes a“superbug.”

Conjugation in Escherichia coli.

Sex pilus

Copyright © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins

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Genetic Engineering

• Genetic engineering or recombinant DNA technology involves techniques to transfer eucaryotic genes (particularly human genes) into easily cultured cells to manufacture important gene products (mostly proteins).

• Plasmids are frequently used as vehicles for inserting genes into cells.

• There are many industrial and medical benefits from genetic engineering.

– Examples: synthesis of antibodies, antibiotics, drugs and vaccines; also, for synthesis of important enzymes and hormones for treatment of diseases.

Gene Therapy

• Gene therapy of human diseases involves the insertion of a normal gene into cells to correct a specific genetic disorder caused by a defective gene.

• Viral delivery is the most common method for inserting genes into cells; specific viruses are selected to target the DNA of specific cells.

• Genes may someday be regularly prescribed as “drugs” in the treatment of diseases (e.g., autoimmune diseases, sickle cell anemia, cancer, cystic fibrosis, heart disease, etc.)