NUTRITION, CULTURE & METABOLISM OF MICROORGANISM Flashcards by Secret acc

______
– The sum total of all chemical reactions that occur in a cell

Metabolism

How well did you know this?

Not at all

Perfectly

______
– Energy-releasing metabolic reactions

Catabolic reactions (catabolism)

How well did you know this?

Not at all

Perfectly

______
– Energy-requiring metabolic reactions

Anabolic reactions (anabolism)

How well did you know this?

Not at all

Perfectly

Most knowledge of microbial metabolism is based on study of ______

laboratory cultures

How well did you know this?

Not at all

Perfectly

______
– Supply of monomers (or precursors of) required by cells for growth

Nutrients

How well did you know this?

Not at all

Perfectly

______
– Nutrients required in large amounts

Macronutrients

How well did you know this?

Not at all

Perfectly

______
– Nutrients required in trace amount

Micronutrients

How well did you know this?

Not at all

Perfectly

______
– Required by all cells

Carbon

How well did you know this?

Not at all

Perfectly

Carbon
– Typical bacterial cell ~______% carbon (by ______)

50, dry weight

How well did you know this?

Not at all

Perfectly

______
– Major element in all classes of macromolecules

Carbon

How well did you know this?

Not at all

Perfectly

Carbon
– ______ use organic carbon

Heterotrophs

How well did you know this?

Not at all

Perfectly

Carbon
– ______ use inorganic carbon

Autotrophs

How well did you know this?

Not at all

Perfectly

Nitrogen
– Typical bacterial cell ~______% nitrogen (by ______)

12, dry weight

How well did you know this?

Not at all

Perfectly

______
– Key element in proteins, nucleic acids, and many more cell constituents

Nitrogen

How well did you know this?

Not at all

Perfectly

Macronutrients:

Phosphorus (P)
Sulfur (S)
Potassium (K)
Magnesium (Mg)
Calcium (Ca)
Sodium (Na)

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Synthesis of nucleic acids and phospholipids

Phosphorus (P)

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Sulfur-containing amino acids (______ and ______)

Sulfur (S), cysteine, methionine

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Vitamins (e.g., thiamine, biotin, lipoic acid) and coenzyme A

Sulfur (S)

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Required by enzymes for activity

Potassium (K)

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Stabilizes ribosomes, membranes, and nucleic acids

Magnesium (Mg)

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Also required for many enzymes

Magnesium (Mg)

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Helps stabilize cell walls in microbes

Calcium (Ca)

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Plays key role in heat stability of endospores

Calcium (Ca)

How well did you know this?

Not at all

Perfectly

Macronutrients

______
– Required by some microbes (e.g., marine microbes)

Sodium (Na)

How well did you know this?

Not at all

Perfectly

Micronutrients:

Iron Growth Factors Vitamins

Micronutrients ______ – Key component of cytochromes and FeS proteins involved in electron transport

Iron

Micronutrients Iron – Under anoxic conditions, generally ______ (______) form; ______

ferrous, Fe2+, soluble

Micronutrients Iron – Under oxic conditions: generally ______ (______) form; exists as ______ minerals

ferric, Fe3+, insoluble

Micronutrients Iron – Cells produce ______ (iron-binding agents) to obtain iron from insoluble mineral form

siderophores

Micronutrients ______ – Organic compounds required in small amounts by certain organisms

Growth Factors

Micronutrients Growth Factors – Examples:

vitamins, amino acids, purines, pyrimidines

Micronutrients ______ – Most commonly required growth factors

Vitamins

Micronutrients ______ – Most function as coenyzmes

Vitamins

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Autoinducer for quorum sensing in bacteria; also found in some polyketide antibiotics

Boron (B)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Possible but not proven component for glucose metabolism (necessary in mammals)

Chromium (Cr)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Vitamin B12; transcarboxylase (only in proprionic acid bacteria)

Cobalt (Co)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: In respiration, cytochrome c oxidase; in photosynthesis, plastocyanin, some superoxide dismutases

Copper (Cu)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Cytochromes; catalases; peroxidases; iron-sulfur proteins; oxygenases; all nitrogenases

Iron (Fe)^b

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Activator of many enzymes; component of certain superoxide dismutases and of the water-splitting enzyme in oxygenic phototrophs (photosystem II)

Manganese (Mn)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Certain flavin-containing enzymes; some nitrogenases, nitrate reductases, sulfite oxidases, DMSO-TMAO reductases; some formate dehydrogenases

Molybdenum (Mo)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Most hydrogenases; coenzyme F430 of methanogens; carbon monoxide dehydrogenase; urease

Nickel (Ni)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Formate dehydrogenase; some hydrogenases; the amino acid selenocysteine

Selenium (Se)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Some formate dehydrogenases; oxotransferases of hyperthermophiles

Tungsten (W)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Vanadium nitrogenase; bromoperoxidase

Vanadium (V)

Micronutrients (trace elements) needed by microorganisms Element: ______ Cellular function or molecule of which a part: Carbonic anhydrase; alcohol dehydrogenase; RNA and DNA polymerases; and many DNA-binding proteins

Zinc (Zn)

______ – Nutrient solutions used to grow microbes in the laboratory

Culture Media

Two broad classes of Culture Media:

Defined media Complex media

Two broad classes of Culture Media ______: precise chemical composition in known

Defined media

Two broad classes of Culture Media ______: composed of digests of chemically undefined substances (e.g., yeast and meat extracts)

Complex media

Culture Media ______ – Contains compounds that selectively inhibit growth of some microbes but not others

Selective Media

Culture Media ______ – Contains an indicator, usually a dye, that detects particular chemical reactions occurring during growth

Differential Media

Culture Media For successful cultivation of a microbe, it is important to know the ______ and supply them in proper ______ and ______ in a culture medium

nutritional requirements, form, proportions

Laboratory Culture ______: culture containing only a single kind of microbe

Pure culture

Laboratory Culture ______: unwanted organisms in a culture

Contaminants

Laboratory Culture Cells can be grown in ______ or ______ culture media

liquid, solid

Laboratory Culture Cells can be grown in liquid or solid culture media – Solid media are prepared by addition of a ______ (______ or ______)

gelling agent, agar, gelatin

Laboratory Culture Cells can be grown in liquid or solid culture media – When grown on solid media, cells form ______ (______)

isolated masses, colonies

Laboratory Culture Microbes are everywhere – ______ of media is critical – ______ should be followed

Sterilization, Aseptic technique

Laboratory Culture Pure culture technique – ______ – ______ – ______

Streak plate, Pour plate, Spread plate

Bioenergetics Energy is defined in units of ______, a measure of ______ energy

kilojoules (kJ), heat

Bioenergetics In any chemical reaction, some energy is lost as ______

heat

Bioenergetics ______: energy released that is available to do work

Free energy (G)

Bioenergetics The change in free energy during a reaction is referred to as ______

🔺G0′

Bioenergetics 🔺G0′: under standard conditions; ______ M, pH ______, ______oC, ______ atm

1, 7, 25, 1

Bioenergetics Reactions with a negative 🔺G0′ ______ free energy (______)

release, exergonic

Bioenergetics Reactions with a positive 🔺G0′ ______ free energy (______)

require, endergonic

Bioenergetics To calculate free-energy yield of a reaction, we need to know the ______ (Gf0; the energy released or required during formation of a given molecule from the elements)

free energy of formation

Catalysis and Enzymes • ______ calculations do not provide information on reaction rates

Free-energy

Catalysis and Enzymes • ______: energy required to bring all molecules in a chemical reaction into the reactive state

Activation energy

Catalysis and Enzymes Activation energy A ______ is usually required to breach activation energy barrier

catalysis

Catalysis and Enzymes • Even chemical reactions that ______ energy may not proceed spontaneously, because the reactants must first be ______. • Once they are activated, the reaction proceeds ______. • ______ such as enzymes ______ the required activation energy.

release, activated, spontaneously, Catalysts, lower

Catalysis and Enzymes Catalyst: substance that – Lowers the ______ of a reaction – Increases ______ – Does not affect ______ or ______ of a reaction

activation energy, reaction rate, energetics, equilibrium

Catalysis and Enzymes ______ – Biological catalysts

Enzymes

Catalysis and Enzymes Enzymes – Typically ______ (some ______)

proteins, RNAs

Catalysis and Enzymes Enzymes – Highly ______

specific

Catalysis and Enzymes Enzymes – Generally ______ than substrate

larger

Catalysis and Enzymes Enzymes – Typically rely on ______ • Examples: hydrogen bonds, van der Waals forces, hydrophobic interactions

weak bonds

Catalysis and Enzymes ______: region of enzyme that binds substrate

Active site

Catalysis and Enzymes Enzymes – Increase the rate of chemical reactions by ______ to ______ times the spontaneous rate

108, 1020

Catalysis and Enzymes Enzymes Catalysis dependent on • Substrate ______ • ______ of substrate relative to catalytically active amino acids in active site

binding, Position

Catalysis and Enzymes Many enzymes contain small ______ molecules that participate in ______ but are not ______

nonprotein, catalysis, substrates

Catalysis and Enzymes Many enzymes contain small nonprotein molecules that participate in catalysis but are not substrates • ______ – Bind tightly to enzymes

Prosthetic groups

Catalysis and Enzymes Many enzymes contain small nonprotein molecules that participate in catalysis but are not substrates • Prosthetic groups – Usually bind ______ and ______ (e.g., heme group in cytochromes)

covalently, permanently

Catalysis and Enzymes Many enzymes contain small nonprotein molecules that participate in catalysis but are not substrates • ______ – Loosely bound to enzymes

Coenzymes

Catalysis and Enzymes Many enzymes contain small nonprotein molecules that participate in catalysis but are not substrates • Coenzymes – Most are derivatives of ______ (e.g., NAD+/NADH)

vitamins

Electron Donors and Electron Acceptors • Energy from oxidation–reduction (______) reactions is used in synthesis of ______ compounds (e.g., ATP)

redox, energy-rich

Electron Donors and Electron Acceptors Redox reactions occur in pairs (two half reactions):

Electron donor Electron acceptor

Electron Donors and Electron Acceptors Redox reactions occur in pairs: ______: the substance oxidized in a redox reaction

Electron donor

Electron Donors and Electron Acceptors Redox reactions occur in pairs: ______: the substance reduced in a redox reaction

Electron acceptor

Electron Donors and Electron Acceptors ______: tendency to donate electrons

Reduction potential (E0')

Electron Donors and Electron Acceptors Reduction potential (E0') – Expressed as ______

volts (V)

Electron Donors and Electron Acceptors Substances can be either electron ______ or ______ under different circumstances (______)

donors, acceptors, redox couple

Electron Donors and Electron Acceptors Reduced substance of a redox couple with a more ______ donates electrons to the oxidized substance of a redox couple with a more ______

negative E0′, positive E0′

Electron Donors and Electron Acceptors The ______ represents the range of possible reduction potentials

redox tower

Electron Donors and Electron Acceptors The ______ substance at the top of the tower ______ electrons

reduced, donates

Electron Donors and Electron Acceptors The ______ substance at the bottom of the tower ______ electrons

oxidized, accepts

Electron Donors and Electron Acceptors The farther the electrons “______,” the greater the amount of energy ______

drop, released

Electron Donors and Electron Acceptors Redox reactions usually involve reactions between intermediates (______)

carriers

Electron Donors and Electron Acceptors Electron carriers are divided into two classes:

Prosthetic groups Coenzymes

Electron Donors and Electron Acceptors Electron carriers are divided into two classes: ______ (attached to enzymes)

Prosthetic groups

Electron Donors and Electron Acceptors Electron carriers are divided into two classes: ______ (diffusible)

Coenzymes

Electron Donors and Electron Acceptors ______ and ______ facilitate redox reactions without being consumed; they are ______

NAD+, NADH, recycled

Energy-Rich Compounds and Energy Storage Chemical energy released in redox reactions is primarily stored in certain ______ compounds

phosphorylated

Energy-Rich Compounds and Energy Storage Chemical energy released in redox reactions is primarily stored in certain phosphorylated compounds –______ –______ –______

ATP; the prime energy currency Phosphoenolpyruvate Glucose 6-phosphate

Energy-Rich Compounds and Energy Storage Chemical energy also stored in ______

coenzyme A

Energy-Rich Compounds and Energy Storage Long-term energy storage involves ______ polymers that can be ______ to generate ______

insoluble, oxidized, ATP

Energy-Rich Compounds and Energy Storage Long-term energy storage involves insoluble polymers that can be oxidized to generate ATP –Examples in prokaryotes:

•Glycogen •Poly--hydroxybutyrate and other polyhydroxyalkanoates •Elemental sulfur

Energy-Rich Compounds and Energy Storage Long-term energy storage involves insoluble polymers that can be oxidized to generate ATP –Examples in eukaryotes:

•Starch •Lipids (simple fats)

Glycolysis Two reaction series are linked to energy conservation in chemoorganotrophs: ______ and ______

fermentation, respiration

Glycolysis Two reaction series are linked to energy conservation in chemoorganotrophs Differ in mechanism of ATP synthesis –______: substrate-level phosphorylation; ATP directly synthesized from an energy-rich intermediate

Fermentation

Glycolysis Two reaction series are linked to energy conservation in chemoorganotrophs Differ in mechanism of ATP synthesis –______: oxidative phosphorylation; ATP produced from proton motive force formed by transport of electrons

Respiration

Glycolysis – ______ consumed – Two ______ produced – ______ products generated • Some harnessed by humans for ______

Glucose, ATPs, Fermentation, consumption

Respiration and Electron Carriers ______ – Oxidation using O2 as the terminal electron acceptor

Aerobic Respiration

Respiration and Electron Carriers Aerobic Respiration – ______ ATP yield than fermentations • ATP produced at the expense of the ______, which is generated by electron transport

Higher, proton motive force

Respiration and Electron Carriers Electron Transport Systems – ______ associated

Membrane

Respiration and Electron Carriers ______ – Mediate transfer of electrons

Electron Transport Systems

Respiration and Electron Carriers ______ – Conserve some of the energy released during transfer and use it to synthesize ATP

Electron Transport Systems

Respiration and Electron Carriers Electron Transport Systems – Many ______ enzymes are involved in electron transport (e.g., NADH dehydrogenases, flavoproteins, iron–sulfur proteins, cytochromes)

oxidation–reduction

The Proton Motive Force Electron transport system oriented in ______ so that electrons are separated from ______

cytoplasmic membrane, protons

The Proton Motive Force Electron carriers arranged in membrane in order of their ______

reduction potential

The Proton Motive Force The ______ carrier in the chain donates the electrons and protons to the ______

final, terminal electron acceptor

The Proton Motive Force During electron transfer, several protons are ______ on outside of the membrane – Protons originate from ______ and the dissociation of ______

released, NADH, water

The Proton Motive Force Results in generation of ______ and an ______ across the membrane (the proton motive force)

pH gradient, electrochemical potential

The Proton Motive Force Results in generation of pH gradient and an electrochemical potential across the membrane (the proton motive force) – The inside becomes electrically ______ and ______ – The outside becomes electrically ______ and ______

negative, alkaline positive, acidic

______: pathway through which pyruvate is completely oxidized to CO2

Citric acid cycle (CAC)

The Citric Acid Cycle – Initial steps (______ to ______) same as glycolysis – Per glucose molecule, 6 ______ molecules released and ______ and ______ generated – Plays a key role in ______ and ______

glucose, pyruvate CO2, NADH, FADH catabolism, biosynthesis

The Citric Acid Cycle Energetics advantage to ______

aerobic respiration

Catabolic Diversity Microorganisms demonstrate a wide range of mechanisms for generating energy:

–Fermentation –Aerobic respiration –Anaerobic respiration –Chemolithotrophy –Phototrophy

Catabolic Diversity ______ – The use of electron acceptors other than oxygen

Anaerobic Respiration

Catabolic Diversity Anaerobic Respiration – ______ energy released compared to aerobic respiration

Less

Catabolic Diversity ______ – Dependent on electron transport, generation of a proton motive force, and ATPase activity

Anaerobic Respiration

Catabolic Diversity ______ – Uses inorganic chemicals as electron donors •Examples include hydrogen sulfide (H2S), hydrogen gas (H2), ferrous iron (Fe2+), ammonia (NH3)

Chemolithotrophy

Catabolic Diversity Chemolithotrophy – Typically ______

aerobic

Catabolic Diversity ______ – Begins with oxidation of inorganic electron donor

Chemolithotrophy

Catabolic Diversity Chemolithotrophy – Uses ______ and ______

electron transport chain, proton motive force

Catabolic Diversity ______ – Autotrophic; uses CO2 as carbon source

Chemolithotrophy

Catabolic Diversity ______: uses light as energy source

Phototrophy

Catabolic Diversity ______: light-mediated ATP synthesis

Photophosphorylation

Catabolic Diversity ______: use ATP for assimilation of CO2 for biosynthesis

Photoautotrophs

Catabolic Diversity ______: use ATP for assimilation of organic carbon for biosynthesis

Photoheterotrophs

Regulating the Activity of Biosynthetic Enzymes Two major modes of enzyme regulation:

Amount Activity

Regulating the Activity of Biosynthetic Enzymes Two major modes of enzyme regulation: ______ • Regulation at the gene level

Amount

Regulating the Activity of Biosynthetic Enzymes Two major modes of enzyme regulation: ______ • Temporary inactivation of the protein through changes in enzyme structure

Activity

Regulating the Activity of Biosynthetic Enzymes ______: mechanism for turning off the reactions in a biosynthetic pathway

Feedback Inhibition

Regulating the Activity of Biosynthetic Enzymes Feedback Inhibition – End product of the pathway binds to the first ______ in the pathway, thus ______ its activity

enzyme, inhibiting

Regulating the Activity of Biosynthetic Enzymes Feedback Inhibition – The inhibited enzyme is an ______ enzyme

allosteric

Regulating the Activity of Biosynthetic Enzymes Feedback Inhibition Two binding sites: ______ and ______

active, allosteric

Regulating the Activity of Biosynthetic Enzymes Feedback Inhibition – ______ reaction

Reversible