MICR 301 Exam 3

heterotrophic metabolism

process where bacteria break down/oxidize organic carbon compounds (glucose, amino acids, fatty acids) to extract ATP and carbon building blocks for biosynthesis

respiration

high-yield energy process that couples the oxidation of organic donors with the membrane’s ETC, generating PMF and producing ATP via oxidative phosphorylation

aerobic respiration

respiration in which oxygen (O2) is the final election acceptor

anerobic respiration

respiration in which a molecule other than oxygen (such as nitrate, sulfate, ferric ion or organic fumarate) is the final electron acceptor

fermentation

a low yield catabolic process that does not use the ETC, and generates small amounts of ATP exclusively through substrate-level phosphorylation

substrate level phosphorylation

The direct enzymatic transfer of a high-energy phosphate group from a metabolic intermediate (e.g., phosphoenolpyruvate) onto ADP to form ATP

oxidative phosphorylation

indirect synthesis of ATP where electron transfer through a membrane-bound ETC pumps protons across the membrane to generate PMF, which powers ATP synthase

redox potential

A measure (in mV) of a molecule's tendency to donate or accept electrons

electron sink

An internal organic molecule (such as pyruvate or acetaldehyde) reduced during fermentation to accept electrons from NADH and regenerate NAD+, allowing glycolysis to continue

EMP/glycolysis

Primary catabolic (and amphibolic) pathway in both prokaryotes and eukaryotes to break down glucose for ATP synthesis, reducing power, and central precursor metabolites

ED pathway

alternative glucose breakdown pathway that requires lower enzymatic load and fewer ATP initial inputs than EMP, critical for obligate aerobes that lack phosphfructokinase

pentose phosphate pathway PPP

Anabolic pathway that generates NADPH and ribose-5-phosphate, a precursor sugar for the synthesis of RNA, DNA, and aromatic amino acids

TCA cycle

Central cyclic pathway for complete oxidation of acetyl groups to CO2, harvesting high amounts of reducing power to drive the ETC for respiration, while providing essential biosynthetic precursors (α-ketoglutarate, oxaloacetate, succinyl-CoA)

glyoxylate cycle

anabolic bypass of the TCA cycle that skips the two CO2-releasing decarboxylation steps, preserving carbon to allow growth on non-glucose 2-carbon sources (like fatty acids and acetate) to make glucose via gluconeogenesis

beta oxidation pathway

Cyclic catabolic breakdown of long-chain fatty acids (LCFAs) into 2-carbon Acetyl-CoA units to yield energy. High LCFA concentrations also bind the FadR repressor, signaling that the bacterium has entered a host and should increase virulence

FadR

binds to the Fad operator in the absence of fatty acids; when fatty acids are present, they bind to it and release it from the operon to induce transcription of fad genes

replicative phase

in legionella, this phase occurs inside the legionella-containing vacuole, where amino acids are abundant (and preferred over sugars as carbon and energy sources)

transmissive phase

in legionella, this phase is triggered when amino acids become limiting. Cell division stops, the bacterium aquires a flagella, and glucose is catabolized through the ED pathway to build a large carbon reserve of poly-3-hydroxybutyrate for starvation survival

the stringent response

this signaling pathway drives the switch from replicative → transmissive phase in legionella, triggered by low amino acids. Stress sigma factor RpoS is activated

AnkB

anchors to the the legionella-containing vacuole surface to recruit host machinery and increase host protein degradation to release amino acids into the cytoplasm and feed replicating bacteria

catabolic

If a pathway produced ATP, it is _____

deamination

the removal of the first amino group (-NH2) from an amino acid, always the first step in amino acid catabolism

nutritional virulence

the ability of pathogens to manipulate host metabolic processes to acquire nutrients and override host attempts at nutrient starvation

NADH

electron donors made in glycolysis/EMP?

2, 4, 2

ATP in glycolysis/EMP: invested, generated, yield

1, 2, 1

ATP in Entner-Doudoroff (ED): invested, generated, yield

NADH, NADPH

electron donors made in ED pathway?

NADPH

electron donors made in pentose phosphate pathway?

0, 2, 2

ATP in TCA Cycle: invested, generated, yield

NADH, FADH2, NADPH

electron donors made in TCA cycle?

A pathway in which intermediates serve as starting materials for other structures

amphibolic

NADH, FADH2

electron donors made in glyoxylate cycle?

assimilatory

pathways in which inorganic compounds are reduced and incorporated into organic cellular biomass (e.g. proteins, nucleic acids)

fixation

pathways in which an inorganic gas is converted into an organic or usable cellular form for assimilation

dissimilatory pathways

pathways in which inorganic compounds are used as terminal electron acceptors during anaerobic respiration, and the reduced product is excreted as waste instead of being incorporated into biomass

oxidative pathways

pathways in which organic compounds are electron donors (energy sources) and are oxidized through an ETC to generate ATP

consume energy; biosynthesis

energy outcome and purpose of assimilatory pathways

consume energy; biosynthesis

energy outcome and purpose of fixation pathways

generate energy; respiration

energy outcome and purpose of dissimilatory pathways

generate energy; chemolithotrophy

energy outcome and purpose of oxidative pathways

chemoorganotrophs

organisms that derive energy (source their electrons) from oxidizing organic compounds, and use heterotrophic metabolism

chemolithotrophs

organisms that derive energy (source their electrons) from the oxidation of inorganic compounds (may derive carbon from organic or inorganic sources)

chemolithoautotrophs

organisms that derive their energy/electrons AND carbon from inorganic compounds

nitrate

NO3-

nitrite

NO2-

ammonium

NH4+

8

how many electrons are required for the reduction of nitrogen and sulfur?

glutamine

nitrogen containing biomolecules: purines, pyrimadines, amino sugars, some amino acids

glutamate

nitrogen containing biomolecules: many amino acids

sulfate

SO4²-

nitrogenase enzyme complex

oxygen-sensitive, 2-protein enzyme complex that can fix N2 to NH3 at the cost of 16 ATP and 8 electrons per N2 molecule

dinitrogenase reductase Fe protein

part of the nitrogenase enzyme complex; dimer containing a 4Fe-FS cluster that binds and hydrolyzes 2ATP per electron to drive electron transfer to the MoFe protein

dinitrogenase MoFe protein

part of the nitrogenase enzyme complex; tetramer of nitrogenase containing P-clusters and the FeMo-cofactor. This is the catalytic active site where N2 binds and is reduced to 2 NH3

H2

obligate byproduct of nitrogenase

heterocyst

specialized, thick-walled, non-dividing cyanobacterial cells dedicated exclusively to N2 fixation

nitrification

strictly aerobic, oxidative process in the nitrogen cycle that converts ammonia to nitrate in two steps carried out by two distinct bacterial groups NH3 → NO2- → NO3-

AOB

chemolithoautotrophs that oxidize ammonia to nitrite using ammonia monooxygenase and hydroxylamine oxidoreductase

NOB

chemolithoautotrophs that oxidize nitrite to nitrate using nitrite oxidoreductase

reverse electron transport

process where chemolithotrophs use energy from the proton motive force to force electrons uphill backward through the respiratory chain to reduce NAD+ → NADH

nitrification

aerobic process in which nitrogen compounds are the electron donors, performed by chemolithotrophs

denitrification

anaerobic process (generates PMF and ATP) where nitrogen compounds are the terminal electron acceptors and will be excreted as waste products; performed by chemoheterotrophs

paracoccus denitrificans

representative organism for denitrification

sulfate reducing microbes

anaerobic microbes that use sulfate SO4²- as a terminal electron acceptor, reducing it to hydrogen sulfide which is excreted as waste

SRB habitats

oxygen depleted sediments, mud, aquatic environments, human/animal GI tract

desulfivibrio

representative sulfate-reducing microbe; uses H2 as its electron donor

sulfur oxidizing bacteria

chemolithotrophs (or phototrophs) that oxidize reduced sulfur compounds (H2S, elemental sulfur, thiosulfate) to sulfate, channeling electrons into an aerobic ETC