Microbial Metabolism Flashcards
Nutrients
-supply of monomers (or precursors of) required by cells for growth
Macronutrients
-nutrients required in large amounts
Micronutrients
- nutrients required in minute
- iron (Fe)
- cellular respiration
- trace metals (Table 3.1)
- enzymes cofactors
Carbon, nitrogen, and other macronutrients
-required by ALL cells
Typical bacteria cell
-(by dry weight) ~50% carbon ~20% oxygen ~14% nitrogen ~8% hydrogen ~3% phosphorus ~1% sulfur
Most microbes
- heterotrophs
- use organic carbon
Autotrophs
-use carbon dioxide (CO2)
Nitrogen (N)
- 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
Form water
-oxygen (O)
hydrogen (H)
Phosphorus (P)
-nucleic acids and phospholipids
SUlfur (S)
- sulfur-containing amino acids (cysteine and methionine)
- vitamins (e.g., thiamine, biotin, lipoid acid (sulfur containing cofactor))
Potassium (K)
-required for activity
Magnesium (Mg)
- stabilizes ribosomes, membranes, and nucleic acids
- also required by many enzymes
Calcium (Ca) and Sodium (Na)
-required by some microbes (e.g., marine microbes)
Growth factors
- organic compounds required in small amounts by certain organisms
- examples: vitamins, amino acids, purines, pyrimidines
Vitamins
- most frequently required growth factors
- most function as coenzymes
Active transport
-how cells accumulate solutes against concentration gradient
Transporters
- three classes
- simple transport: transmembrane transport protein
- group translocation: series of proteins
- ABC system: three components
Energy-driven processes
-proton motive force. ATP, or another energy-rich compound
Simple transport
-driven by proton (H+) motive force
Group translocation
- substance transported is chemically modified
- energy-rich organic compound (not proton-motive force) drives transport
- best studied system
ABC system (ATP-binding cassette)
- 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
Gram-negatives
-employ periplasmic binding proteins
Gram-positives and Archaea
-employ substrate-binding proteins on external surface of cytoplasmic membrane
Symport
- solute and H+ co-transported in one direction
- E.coli lac permeate, phosphate, sulfate, other organics
Antiport
-solute and H+ transported in opposite directions
Phosphotransferase system in E. coli
- best-studied group translocation system
- glucose, fructose, and mannose
- five proteins required
- energy derived from phosphoenolpyruvate (form glycolysis
Metabolism
-sum of all chemical reactions that occur in a cell
Catabolism
-energy releasing metabolic reactions
Anabolism
-energy-requiring metabolic reactions
Microorganisms
-grouped into energy classes
Chemoorganotrophs
-obtain energy from organic chemicals
Chemolithrophs
-oxidize inorganic compounds (H2, H2S, NH4+) for energy
Phototrophs
-convert light energy in ATP
Heterotrophs
-obtain carbon from organics
Autotrophs
-obtain carbon from CO2
Principles of Bioenergetics
- 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
Standard conditions
- 25 degrees C
-atmospheric pressure (1 atm)
-molar concentration
pH 7
Free energy (G)
- energy released that is available to do work
- free energy of elements is zero
Exergonic
- reactions with –ΔG0′ release free energy
- only reactions to yield energy that can be conserved by the cell
Endergonic
-reaction with +ΔG0′ require energy
Formation
-Gf0; the energy released or required during formation of a given molecule from the elements
-ve
-values indicates most molecules can form spontaneously
For the reaction A+B yield C+D
- ΔG0′ = Gf0 [C + D] – Gf0[A + B] i.e. products - reactants
ΔG0′
- is not always a good estimate of actual free energy changes (artificial conditions)
ΔG
- 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
Catalysis and Enzymes
- free energy calculations do not provide information on reaction rates i.e. theoretical
- actual reaction rates might be very, very slow
Activation energy
-minimum energy required to become reactive
Catalyst
- 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
Enzymes
- biological catalysts
- typically proteins (some RNAs (Ribozymes))
- highly specific
- active site
Active site
- region of enzymes that binds substrate
- many contain small non-protein, non-substrate molecules that participate in catalysis
Prosthetic groups
- tightly bound
- usually bind covalently and permanently (e.g., heme in cytochromes)
Coenzymes
- loosely bound
- most are derivatives of vitamins
Enzyme catalysis
- catalysis depends on substrate binding
- catalysis depends on position of substrate relative to catalytically active amino acids in active site
Endergonic and Exergonic
- reactions coupled
- coupling energy requiring and energy producing reactions
- example: ATP hydrolysis or proton motive force
Reduction-oxidation
- (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)
Electron donor
- reducing agent
- the substrate oxidized
Electron acceptor
- (oxidizing agent)
- the substrate reduced
Redox couple
-substances can be either electron donors or electron acceptors under different circumstances
Reduction potential
- (E0′): tendency to donate electrons
- expressed as volts (V): potential difference
Reduced substance
-of a redox couple with a more negative E0′ donates electrons to the oxidized substance of a redox couple with a more positive E0′
Redox tower
- 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′
Oxygen (O2)
-strongest significant natural electron acceptor
Electron donors and acceptors
- 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
Energy-rich compounds
- 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
Long-term energy storage
-involves biosynthesis of insoluble polymers that can be oxidized to generate ATP
Examples in prokaryotes
- glycogen (polyglucose)
- poly-β-hydroxybutyrate and other polyhydroxyalkanoates
- elemental sulfur (S)
Examples in eukaryotes
- starch (also polyglucose)
- lipids (simple fats)
Glycolysis and Fermentation
-two reaction series are liked to energy conservation in chemoorganotrophs: fermentation and respiration
Fermentation
-anaerobic catabolism in which organic compounds donate and accept electrons
Respiration
-aerobic or anaerobic catabolism in which a donor is oxidized with O2 (aerobic) or another compound (anaerobic) as an electron acceptor
Glycolysis
- 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
Glycolisis
- three stages:
- stage I: “preparatory,” form key intermediates
- stage II: redox
- stage III (fermentation): redox
- net gain of two ATPs (4 made, 2 used
Fermentative diversity
- 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
Respiration
- citric acid and glyoxylate cycles
- first catabolize glucose via glycolysis
- pyruvate is fully oxidized to CO2 through citric acid and glyoxylate cycles
Citric acid cycle (CAC)
- 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
Biosynthesis
- 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
Glyoxylate cycle
-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
Electron transport system
- 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
NADH dehydrogenases
-active sites bind NADH, accept two electrons and two protons that are transferred to flavoproteins, generate NAD+
Flavoproteins
-contain flavin prosthetic group (e.g., FMN and FAD) that accepts two electrons and two protons but donates only electrons
Cytochromes
- 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)
Other iron proteins
- non-heme iron
- contain clusters of iron and sulfur (e.g., ferredoxin)
- reduction potentials vary
- only carry electrons
Quinones
- 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
Electron transport and the proton motive force
- 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+)
ATP synthase (ATPase)
-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-
Options for energy conservation
- microorganisms demonstrate a wide range of mechanisms for generating energy
- anaerobic respiration
- chemolithotrophy
- phototrophy
Anaerobi respiration
-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
Chemolithtrophy
- 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
Phototrophy
- uses light as energy source
- phosphorylation: light-mediated ATP synthesis
Photoautotrophs
-use ATP + CO2 fro biosynthesis
Photoheterotrophs
- use ATP + organic carbon for biosynthesis
Sugars and polysaccharides
- 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
Urine diphosphoglucose (UDPG)
-precursor of some glucose derivatives needed for biosynthesis of important polysaccharides (e.g., N-acetylglucosamine and N-acetylmuramic acid)
Adenosime diphosphoglucose (ADPG)
-precursor for glycogen biosynthesis
Gluconeogenesis
-synthesis of glucose from phosphiemolpyruvate (from oxaloacetate)
Pentoses
- C5 sugars
- formed by the removal of one carbon atom from a hexose
- required for the synthesis of nucleic acids
Amino acids and nucleotides
- 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
Purines
- biosynthesis are complex
- inosinic acid precursor to adenine and guanine
Pyrimidines
- biosynthesis are complex
- orotic acid precursors to thymine, cytosine, and uracil
Fatty acids
- 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
Fatty acids and lipids
- 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)
