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Microbiology Chapter 3 Microbial Metabolism > Microbial Metabolism > Flashcards

Microbial Metabolism Flashcards

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1
Q

Nutrients

A

-supply of monomers (or precursors of) required by cells for growth

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2
Q

Macronutrients

A

-nutrients required in large amounts

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3
Q

Micronutrients

A
  • nutrients required in minute
  • iron (Fe)
    • cellular respiration
  • trace metals (Table 3.1)
    • enzymes cofactors
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4
Q

Carbon, nitrogen, and other macronutrients

A

-required by ALL cells

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5
Q

Typical bacteria cell

A 
-(by dry weight)
~50% carbon
~20% oxygen
~14% nitrogen
~8% hydrogen
~3% phosphorus
~1% sulfur
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6
Q

Most microbes

A
  • heterotrophs

- use organic carbon

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7
Q

Autotrophs

A

-use carbon dioxide (CO2)

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8
Q

Nitrogen (N)

A
  • proteins, nucleic acids, and many more cell constituents
  • bulk of N in nature is ammonia (NH3), nitrate (NO3-), or nitrogen gas (N2)
  • nearly all microbes can use NH3
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9
Q

Form water

A

-oxygen (O)

hydrogen (H)

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10
Q

Phosphorus (P)

A

-nucleic acids and phospholipids

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11
Q

SUlfur (S)

A
  • sulfur-containing amino acids (cysteine and methionine)

- vitamins (e.g., thiamine, biotin, lipoid acid (sulfur containing cofactor))

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12
Q

Potassium (K)

A

-required for activity

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13
Q

Magnesium (Mg)

A
  • stabilizes ribosomes, membranes, and nucleic acids

- also required by many enzymes

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14
Q

Calcium (Ca) and Sodium (Na)

A

-required by some microbes (e.g., marine microbes)

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15
Q

Growth factors

A
  • organic compounds required in small amounts by certain organisms
    • examples: vitamins, amino acids, purines, pyrimidines
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16
Q

Vitamins

A
  • most frequently required growth factors

- most function as coenzymes

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17
Q

Active transport

A

-how cells accumulate solutes against concentration gradient

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18
Q

Transporters

A
  • three classes
    • simple transport: transmembrane transport protein
    • group translocation: series of proteins
    • ABC system: three components
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19
Q

Energy-driven processes

A

-proton motive force. ATP, or another energy-rich compound

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20
Q

Simple transport

A

-driven by proton (H+) motive force

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21
Q

Group translocation

A
  • substance transported is chemically modified
  • energy-rich organic compound (not proton-motive force) drives transport
  • best studied system
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22
Q

ABC system (ATP-binding cassette)

A
  • 200+ different systems identified in prokaryotes for organic and inorganic compounds
  • high substrate affinity
  • ATP drives uptake
  • requires transmembrane and ATP-hydrolyzing proteins plus:
  • gram-negative and gram-positive
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23
Q

Gram-negatives

A

-employ periplasmic binding proteins

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24
Q

Gram-positives and Archaea

A

-employ substrate-binding proteins on external surface of cytoplasmic membrane

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25
Q

Symport

A
  • solute and H+ co-transported in one direction

- E.coli lac permeate, phosphate, sulfate, other organics

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26
Q

Antiport

A

-solute and H+ transported in opposite directions

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27
Q

Phosphotransferase system in E. coli

A
  • best-studied group translocation system
  • glucose, fructose, and mannose
  • five proteins required
  • energy derived from phosphoenolpyruvate (form glycolysis
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28
Q

Metabolism

A

-sum of all chemical reactions that occur in a cell

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29
Q

Catabolism

A

-energy releasing metabolic reactions

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30
Q

Anabolism

A

-energy-requiring metabolic reactions

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31
Q

Microorganisms

A

-grouped into energy classes

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32
Q

Chemoorganotrophs

A

-obtain energy from organic chemicals

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33
Q

Chemolithrophs

A

-oxidize inorganic compounds (H2, H2S, NH4+) for energy

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34
Q

Phototrophs

A

-convert light energy in ATP

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35
Q

Heterotrophs

A

-obtain carbon from organics

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36
Q

Autotrophs

A

-obtain carbon from CO2

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37
Q

Principles of Bioenergetics

A
  • energy is measured in units of kilojoules (kJ0 of heat energy
  • in any chemical reaction, energy is either required or released
  • the change in energy during a reaction is referred to as ΔG0′
  • to calculate free-energy yield of a reaction, we need to know the free energy of formation
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38
Q

Standard conditions

A
  • 25 degrees C
    -atmospheric pressure (1 atm)
    -molar concentration
    pH 7
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39
Q

Free energy (G)

A
  • energy released that is available to do work

- free energy of elements is zero

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40
Q

Exergonic

A
  • reactions with –ΔG0′ release free energy

- only reactions to yield energy that can be conserved by the cell

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41
Q

Endergonic

A

-reaction with +ΔG0′ require energy

42
Q

Formation

A

-Gf0; the energy released or required during formation of a given molecule from the elements

43
Q

-ve

A

-values indicates most molecules can form spontaneously

44
Q

For the reaction A+B yield C+D

A
  • ΔG0′ = Gf0 [C + D] – Gf0[A + B] i.e. products - reactants
45
Q

ΔG0′

A
  • is not always a good estimate of actual free energy changes (artificial conditions)
46
Q

ΔG

A
  • free energy that occurs under actual conditions
    • ΔG = ΔG0′ + RT ln Keq
    • where R (gas constant) and T are physical constants and Keq is the equilibrium. constant for the reaction
47
Q

Catalysis and Enzymes

A
  • free energy calculations do not provide information on reaction rates i.e. theoretical
  • actual reaction rates might be very, very slow
48
Q

Activation energy

A

-minimum energy required to become reactive

49
Q

Catalyst

A
  • usually required to overcome activation energy barrier
  • substance that facilitates a reaction without being consumed
  • substance that lowers activation energy
  • substance that does not energetic or equilibrium of a reaction
  • substance that increases reaction rate
50
Q

Enzymes

A
  • biological catalysts
  • typically proteins (some RNAs (Ribozymes))
  • highly specific
  • active site
51
Q

Active site

A
  • region of enzymes that binds substrate

- many contain small non-protein, non-substrate molecules that participate in catalysis

52
Q

Prosthetic groups

A
  • tightly bound

- usually bind covalently and permanently (e.g., heme in cytochromes)

53
Q

Coenzymes

A
  • loosely bound

- most are derivatives of vitamins

54
Q

Enzyme catalysis

A
  • catalysis depends on substrate binding

- catalysis depends on position of substrate relative to catalytically active amino acids in active site

55
Q

Endergonic and Exergonic

A
  • reactions coupled
  • coupling energy requiring and energy producing reactions
    • example: ATP hydrolysis or proton motive force
56
Q

Reduction-oxidation

A
  • (redox) reactions is used in synthesis of energy-rich compounds (e.g. ATP)
  • redox reactions occur in pairs (two half reactions)
  • electron donor (reducing agent)
  • electron acceptor (oxidizing agent)
57
Q

Electron donor

A
  • reducing agent

- the substrate oxidized

58
Q

Electron acceptor

A
  • (oxidizing agent)

- the substrate reduced

59
Q

Redox couple

A

-substances can be either electron donors or electron acceptors under different circumstances

60
Q

Reduction potential

A
  • (E0′): tendency to donate electrons

- expressed as volts (V): potential difference

61
Q

Reduced substance

A

-of a redox couple with a more negative E0′ donates electrons to the oxidized substance of a redox couple with a more positive E0′

62
Q

Redox tower

A
  • represents the range of possible reduction potentials
  • substances towards the top (reduced) prefer to donate electrons
  • substances towards the bottom (oxidized) prefer to accept electrons
  • the further the electrons “drop” the grater the amount of the energy released (ΔE0′)
  • oxygen
  • ΔE0′ ∝ ΔG0′
63
Q

Oxygen (O2)

A

-strongest significant natural electron acceptor

64
Q

Electron donors and acceptors

A
  • NAD+ and NADH facilitate mainly catabolic redox reaction without being consumed; they are recycled
  • allow many different donors and acceptors to interact
  • coenzymes acts as intermediary
  • another example: NADP+/NADPH facilitate mainly anabolic (biosynthetic) redox reactions
65
Q

Energy-rich compounds

A
  • chemical energy released in redox reactions is primarily stored in certain phosphorylated compounds
  • ATP; the prime energy currency
  • phosphoenolpyruvate
  • chemical energy also soared in coenzymes A derivatives
66
Q

Long-term energy storage

A

-involves biosynthesis of insoluble polymers that can be oxidized to generate ATP

67
Q

Examples in prokaryotes

A
  • glycogen (polyglucose)
  • poly-β-hydroxybutyrate and other polyhydroxyalkanoates
  • elemental sulfur (S)
68
Q

Examples in eukaryotes

A
  • starch (also polyglucose)

- lipids (simple fats)

69
Q

Glycolysis and Fermentation

A

-two reaction series are liked to energy conservation in chemoorganotrophs: fermentation and respiration

70
Q

Fermentation

A

-anaerobic catabolism in which organic compounds donate and accept electrons

71
Q

Respiration

A

-aerobic or anaerobic catabolism in which a donor is oxidized with O2 (aerobic) or another compound (anaerobic) as an electron acceptor

72
Q

Glycolysis

A
  • embden-meyerhof-parnas pathway
  • a common pathway for catabolism of glucose that forms two ATP
  • glucose can be fermented or respired
  • ATP produced by substrate-level phosphorylation: energy-rich phosphate bond from organic compound is transferred to ADP, making ATP
73
Q

Glycolisis

A
  • three stages:
    • stage I: “preparatory,” form key intermediates
    • stage II: redox
    • stage III (fermentation): redox
    • net gain of two ATPs (4 made, 2 used
74
Q

Fermentative diversity

A
  • some fermentations allow additional ATP synthesis from substrate-level phosphorylation
  • involves coenzymes-A derivatives
  • some fermentations are beneficial for humans
  • fermentation-respiration switch is based on energetic benefit
75
Q

Respiration

A
  • citric acid and glyoxylate cycles
  • first catabolize glucose via glycolysis
  • pyruvate is fully oxidized to CO2 through citric acid and glyoxylate cycles
76
Q

Citric acid cycle (CAC)

A
  • pathway through which pyruvate is completely oxidized to CO2 much
  • much greater ATP yield than fermentation (38 vs. 2)
  • decarboxylation of pyruvate to CO2, NADH, and acetyl-CoA
  • Acetyl-CoA + oxaloacetate forms citric acid
  • 2 CO2, 3 NADH, 1 FADH2
  • oxaloacetate regenerated
  • per pyruvate, total= 3 CO2, 4 NADH, 1 FADH2
  • per glucose molecule, 6 CO2 molecules released and NADH and FASH2 generated
  • NADH and FADH2 oxidized in deletion transport chain: consumes electrons and produces ATP
77
Q

Biosynthesis

A
  • α-ketoglutarate and oxaloacetate (OAA): precursors of several among acids; OAA also converted to phosphoenolpyruvate
  • succiynl-CoA: required for synthesis of cytochromes, chlorophyll and other tetrapyrrole compounds (e.g., heme)
  • acetyl-CoA: necessary for fatty acid biosynthesis
78
Q

Glyoxylate cycle

A

-bacteria, archaea, protists, plants, and fungi
-C4-C6 citric cycle intermediates (e.g., citrate, malate, fumarate, and succinate) are common products and can be readily catabolized through the CAC
-catabolism of C2 (e.g., acetate) compounds catabolized through glyoxylate cycle
C3 compounds are carboxylated; glyoxylate cycle unnecessary

79
Q

Electron transport system

A
  • cytoplasmic membrane-associated
  • mediate transfer of electrons
  • conserve some energy released during transfer and use it to synthesize ATP
  • many oxidation-reduction enzymes involved in electron transport (e.g., NADH dehydrogenas, flavoproteins, iron-sulfur proteins, cytochromes)
  • also quinones: non-protein electron carriers
  • increasingly more positive reduction potential
80
Q

NADH dehydrogenases

A

-active sites bind NADH, accept two electrons and two protons that are transferred to flavoproteins, generate NAD+

81
Q

Flavoproteins

A

-contain flavin prosthetic group (e.g., FMN and FAD) that accepts two electrons and two protons but donates only electrons

82
Q

Cytochromes

A
  • iron-containing proteins
  • proteins that contain heme prosthetic groups
  • accept and donate a single electron via the iron atom in heme (Fe2+ and Fe3+)
  • sometimes form complexes (e.g., cytochrome bc1)
83
Q

Other iron proteins

A
  • non-heme iron
  • contain clusters of iron and sulfur (e.g., ferredoxin)
  • reduction potentials vary
  • only carry electrons
84
Q

Quinones

A
  • small hydrophobic non-protein redox molecules
  • can move within membrane
  • accept electrons and protons but transfer electrons only
  • accept: 2 e- + 2H+
  • transfer: 2e-
  • typically link iron-sulfur proteins and cytochromes
  • ubiquinone (coenzymes Q) and menaquinone most common
85
Q

Electron transport and the proton motive force

A
  • electron trasport system oriented in cytoplasmic membrane so that electrons are separated from protons
  • two electrons (2 e-) + two protons (2 H+) enter when NADH oxidized to NAD+ by NADH dehydrogenase
  • the final carrier in the chain donates the electrons and protons to the terminal electron acceptor
  • during electron transfer, protons are released on outside of the membrane
  • protons originate from 1) NADH and 2) dissociation of water
  • results in generation of pH gradient and an electrochemical potential across the membrane (the proton motive force)
  • the inside becomes electrically negative and alkaline (OH-)
  • the outside becomes electrically positive and acidic (H+)
86
Q

ATP synthase (ATPase)

A

-complex that converts proton motive force
into ATP; two components
-F1: multiprotein extra membrane complex extending into cytoplasm
-F0: membrane-integrated proton-translocating miltiprotein complex
-reversible catalysis of ADP +Pi to ATP
-consumes three to four H+ per ATP; these APT produced per two e-

87
Q

Options for energy conservation

A
  • microorganisms demonstrate a wide range of mechanisms for generating energy
  • anaerobic respiration
  • chemolithotrophy
  • phototrophy
88
Q

Anaerobi respiration

A

-use of electron acceptors other than oxygen
examples include nitrate (NO3-), ferric iron (Fe3+), sulfate (SO4 2-), carbon dioxide (CO2), and certain organic compounds (e.g., fumarate)
-less energy conserved compared to aerobic repiration

89
Q

Chemolithtrophy

A
  • uses inorganic chemicals as electron donors
  • examples: hydrogen sulfide (H2S), hydrogen gas (H2), ferrous iron (Fe2+), ammonium (NH4+)
  • many are waste products of chemotrophs
  • typically aerobic
  • begins with oxidation of inorganic electron donor
  • electron transport generate proton motive force
  • uses CO2 as carbon source an is thus an autotroph
90
Q

Phototrophy

A
  • uses light as energy source

- phosphorylation: light-mediated ATP synthesis

91
Q

Photoautotrophs

A

-use ATP + CO2 fro biosynthesis

92
Q

Photoheterotrophs

A
  • use ATP + organic carbon for biosynthesis
93
Q

Sugars and polysaccharides

A
  • prokaryotic polysaccharides are synthesized from activated glucose
  • major pathway for pentose production is the pentose phosphate pathway
  • major means for direct synthesis of NADH for deoxyribosenucleotide and fatty acid biosynthesis
94
Q

Urine diphosphoglucose (UDPG)

A

-precursor of some glucose derivatives needed for biosynthesis of important polysaccharides (e.g., N-acetylglucosamine and N-acetylmuramic acid)

95
Q

Adenosime diphosphoglucose (ADPG)

A

-precursor for glycogen biosynthesis

96
Q

Gluconeogenesis

A

-synthesis of glucose from phosphiemolpyruvate (from oxaloacetate)

97
Q

Pentoses

A
  • C5 sugars
  • formed by the removal of one carbon atom from a hexose
  • required for the synthesis of nucleic acids
98
Q

Amino acids and nucleotides

A
  • biosynthesis often involves long, multistep pathways
  • amino acid biosynthesis
  • carbon Skeltons came from intermediates of glycolysis or citric acid cycle
  • ammonia is incorporated by glutamine dehydrogenase or glutamine syntheses
  • amino group transferred by transaminase and amino transferase/synthase
99
Q

Purines

A
  • biosynthesis are complex

- inosinic acid precursor to adenine and guanine

100
Q

Pyrimidines

A
  • biosynthesis are complex

- orotic acid precursors to thymine, cytosine, and uracil

101
Q

Fatty acids

A
  • biosynthesized two carbons at a time
  • acyl carrier protein (ACP) holds the growing fatty acid as it is being synthesized
  • varies between species and at different temperatures
  • lower temps: shorter, more unsaturated
  • higer temps: longer, more saturated
102
Q

Fatty acids and lipids

A
  • in Bacteria and Eukarya, assembly of lipids involves addition of fatty acids to glycerol
  • in Archaea, ;lipids contain phytanyl side chains instead of fatty acids
  • in all three kingdoms, polar groups necessary for canonical membrane architecture (hydrophobic interior, hydrophilic surface)

Microbiology Chapter 3 Microbial Metabolism (2 decks)

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