Exam 1 Flashcards

Question

Theme 2 of metabolism

Answer 1

Cellular redox reactions require electron carriers * NAD+ is a diffusible electron shuttle in the cytoplasm * Quinones are a diffusible electron shuttle in membranes * Iron-sulfur clusters, heme and flavins are incorporated into proteins (so not diffusible unless the protein diffuses).

Answer 2

Energy is captured in two ways * Ion gradient across a membrane (e.g., proton motive force) * “High energy bonds” as in ATP These can be used directly but are also interconvertible

Answer 3

Products are more stable than reactants (ATP) giving them a much lower energy and resulting in a large release of energy Ex: NAD+ is a key electron carrier in metabolism NAD+ has more resonance stabilization that NADH Therefore, it is “hard” to put electrons into NAD+, but once they are there it is “easy” for NADH to donate those electrons to something else, like an electron transport chain. One can say NADH is a carrier of “high energy electrons”

Answer 4

Two mechanisms of ATP synthesis ➢ Substrate level phosphorylation ➢ Harnessing a proton motive force (PMF)

Answer 5

converts glucose to pyruvate while producing a little ATP and a little NADH.

Answer 6

mbden-Meyerhof Pathway (EMP) the most common pathway for converting glucose to pyruvate.

Answer 7

-Phosphorylate glucose twice and isomerize it to fructose -Split it down the middle to produce triose phosphates -Oxidize the triose phosphates with concomitant formation of high-energy phosphate bonds -Harvest ATP from the doubly phosphorylated triose phosphates

Answer 8

1. Recovery of NAD+ that was reduced elsewhere in pathway 2. Stepwise reduction of carbonyl groups to alcohols 3. Sometimes generate an ATP if possible, usually via a CoA intermediate (SLP)

Answer 9

Conserved features of these pathways are * Redox balance * Carbon redox patterns (e.g., acid to aldehyde to alcohol) * A site for energy conservation by substrate level phosphorylation * Variable features of these pathways are the specific substrates, intermediates and end products

Answer 10

(fermentation of amino acids by some Clostridia) Ferment amino acid pairs One acts as the e- donor, the other as the e- acceptor Alanine/glycine pair is textbook exampleAlanine oxidized to acetate + C02 Glycine reduced to acetate Themes: recovery of NAD+, R-CoA intermediate allows synthesis of ATP by SLP.

Answer 11

NADH needs to be regenerated

Answer 12

1. Pyruvate from glycolysis converted to acetyl-CoA and fed into TCA cycle 2. Two carbons will be lost as CO2 as the cycle turns 3. Two turns per glucose 4. Direct synthesis of ATP (via Succinyl-CoA intermediate and GTP) 5. Generate 1 FADH2 6. Generate 3 NADH + H+ Each FADH2 will make 2 ATP in the ETC, while each NADH will make 3

Answer 13

O2, SO4, CO2, NADP

Answer 14

Two ATP are invested at the start of the pathway, so the net gain is 2 ATP.

Answer 15

Which of the following produces CO2? Glycolysis -NO TCA Cycle-YES ETC with O2 as final electron acceptor - NO Lactic acid fermentation – NO Stickland fermentation of an alanine-glycine pair - YES

Answer 16

Yes, such a mutant can grow by glucose fermentation. As noted in one of the slides, E. coli carries out the mixed acid fermentation, but the question did not specify that you include the name of the pathway.

Answer 17

H2 is the donor and its redox state is 0 at the start, +1 at the end. O2 is the acceptor and its redox state is 0 at the start, -2 at the end.

Answer 18

C. difficile→ No, it requires an electron acceptor such as glycine to ferment alanine. E. coli → Yes, alanine gets deaminated to pyruvate (look at the C. dif pathway I presented in class), and pyruvate can enter the TCA cycle.

Answer 19

O2 is preferred because the energy drop is larger. The E0’ for the Nitrate/nitrite couple is +0.42 but for the O2/H20 couple it is +0.82.

Answer 20

Some of the ATP from fermentation is hydrolyzed by the F1F0 ATP “synthase” to generate a PMF. In other words, the F1F0 ATP synthase runs backwards.

Answer 21

2 CO2, 3 NADH and 1 FAD

Answer 22

ΔG°‘ = -nFΔE0‘ = -2 x 96.48 kJ/V x 1.24 V = -239 kJ

Answer 23

The cutoff for growth is about -30 kJ/mol

Answer 24

Superheated water (350°C) comes up from the mantle carrying dissolved minerals. The minerals ppt when the hot water mixes with cold sea water (2°C), creating black “smoke”. Sea water has lots of oxygen, allowing for bacteria to respire the reduced compounds emerging from the smoker. Sulfide oxidation is most important. The bacteria also fix CO2

Answer 25

Symbiosis with sulfur-oxidizing bacteria. The tubeworms have an internal organ called the “trophosome” that houses vast numbers of sulfur-oxidizing bacteria

Answer 26

* CO2, O2 and H2S absorbed into blood in brachial plume; blood delivers these inorganic compounds to bacteria in trophosome (shown in blue) * Bacteria oxide H2S to produce ATP (an example of aerobic respiration). * The ATP (and reductant) are used to fix CO2 * Major N source is nitrate (NO3-), which the bacteria reduce to ammonia (NH3) and incorporate into amino acids. * Some of the organic molecules made by the bacteria pass into the blood; the tubeworm uses these for energy and biosynthesis

Answer 27

100-150 Liters 39°C pH 5.5-7 Anaerobic Well-mixed Typical cow rumen contains ~400 bacterial species at ~1010 bacteria per ml.

Answer 28

cellulose is converted to glucose using cellulase from bacteria. Feremnting bacteria then turn glucose into volatile fatty acids which go into the cows blood stream as energy. Methanogenic archaea take the leftover CO2 and H to make methane

Answer 29

Without methanogens the pathway grinds to a halt and the ruminant starves because the build up of H2 prevents fermentation. The H2 is an electron sink that the fermenters need to recover their NAD+.

Answer 30

Neutrophils migrate into the lumen of the intestine, where they release reactive oxygen species (ROS) * ROS oxidizes thiosulfate to tetrathionate Bottom line: Salmonella provokes host inflammation to create its own private electron acceptor, thereby gaining a huge growth advantage over the “healthy” gut bacteria!

Answer 31

VFA = volatile fatty acids. Short-chain compounds like acetate, propionate, butyrate. They are produced by bacteria that ferment sugars released from cellulose and other complex carbohydrates derived from plant material. The VFAs diffuse across the rumen wall and enter the cow’s blood stream, ultimately to become a major source of energy for the cow which would otherwise be unable to digest cellulose.

Answer 32

Cellulose degrading microbes convert cellulose to free sugars, which are then taken up and fermented to VFAs by fermenting bacteria. The VFAs provide energy to the cow, as described above (ultimately they enter the TCA cycle).

Answer 33

Producer = autotroph. Lithoautotrophic bacteria like the one that lives in Riftia trophosomes and gets energy by oxidizing sulfide to sulfate is an example. Primary consumer = an organism that eats the producers. Sea vent crabs eat bacteria. Secondary consumer = an organism that eats the primary consumers. An octopus that eats the crabs is an example.

Answer 34

H2S, O2, CO2 and NO3- are taken up by the worm in the gill plume, which is highly vascularized and exposed to sea water. These chemicals are abundant in the vicinity of deep sea hydrothermal vents because they are dissolved in superheated water that comes up from magma below. (Except for O2, which dissolves into sea water at the ocean surface.) The chemicals are of no use to the tube worm (except for O2—the tube worm is an aerobe with a metabolism like ours). The worm’s circulatory system transports the chemicals to the trophosome, where they diffuse into cells called bacteriocytes. Bacteriocytes are packed with symbiotic Proteobacteria that get their energy by oxidizing H2S with O2 as terminal electron acceptor. While most of the electrons liberated from H2S are used to make a PMF and thus ATP, some are diverted to biosynthesis, such as reduction of CO2 to make sugars. This is possible because the bacteria are autotrophs and have a Calvin Cycle like plants do. Meanwhile, the bacteria also reduce nitrate to ammonia, which they incorporate into glutamate and glutamine. From there the N can be transferred to various other N-containing molecules. Some of the carbon compounds and amino acids are exported to the Riftia. In summary, Riftia “feeds” the bacteria small molecules (H2S, O2, CO2 and NO3-). The bacteria are amazing biochemists who can turn these simple compounds into all the complex molecules that make up their cells. In return the bacteria “feed” their host sugars and amino acids.

Answer 35

* Energy source = H2S, the preferred electron donor * C source = CO2 because the organism is an autotroph and fixes CO2 using the Calvin Cycle like plants do. So, would not add glucose (or the like) to the plates! * Incubate aerobically because O2 is the terminal electron acceptor for sulfide oxidation. Contrary to popular belief, there is plenty of O2 in seawater. Our lungs are not designed to extract dissolved O2, so we can’t breathe under water, but the O2 is there.

Answer 36

Anaerobic bacteria in the lumen of the small intestine make sulfide, H2S, as a byproduct of their metabolism. Because sulfide is toxic, our cells oxidize it to the harmless form thiosulfate,S2O32-. In response to a Salmonella infection our body mobilizes neutrophils, which transmigrate across the intestinal epithelium and release “reactive oxygen species” (ROS) in the lumen of the small intestine. The ROS is intended to kill invading pathogens, but some of it reacts with thiosulfate, converting it to tetrathionate, S4O62-.

Answer 37

he ttrA mutant Salmonella probably can’t colonize the gut because this mutant would not be able to use tetrathionate as terminal electron acceptor. Salmonella can grow by fermentation, but it is not very competitive against the dedicated fermenters (mostly Bacteroides and Clostridia) that make up our normal intestinal microbiota.