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Two main methods have evolved for energy coupling:
#1) (Which we learned on Friday)
#2) The other method of energy coupling used by living things..
In this method, energy from some sets of energy-releasing processes (This seems like a very odd method, but it is very efficient)
Bacteria use their plasma membranes for this purpose
Mitochondria use the inner of their two membranes,
A few one-celled animals just don't have mitochondria: Chloroplasts have 3 sets of membranes, and use the inner-most of the 3 to pump hydrogen ions INWARD across; so these ions leak back out, and drive the ATP synthase on their way back outward.
NOTE: Many scientists call hydrogen ions "protons", because
a lone hydrogen without an electron would indeed be a proton.
In mitochondria, these H+ gradients are generated by energy from those other energy carrying chemicals NADH and FADH2.
Incidentally, back in the 1960s a major argument against the chemiosmosis theory was that the NADH exchange rate was
But really, these rates are only approximate!!
Mitochondrial membrane proteins lets NADH become NAD The H+ ions then leak back, driving ROTATION of an enzyme named ATP Synthase, that makes ATP from ADP + P as it spins! By the way, this rotation was proven by Japanese experiments in which fluorescent actin assembled into fibers long enough to see by DIC microscopy, & the fibers rotated like a second hand on a clock!
Animal cells get their energy from oxidizing sugars and fats (mostly) Much more energy can be gotten from oxidation of the lactic acid in chemical reactions that occur in mitochondria.
These chemical reactions are collectively called "the Krebs Cycle"
These reactions take acetic acid (in the form of acetyl CoenzymeA)
Acetic acid is a two-carbon chemical;
Other enzymes then oxidize citric acid a little bit,
Next, further oxidation results in release of another CO2
Next, further oxidation results in release of another CO2
So this happens over and over What did Krebs himself actually discover, and how?
Before Krebs, lots of other researchers had isolated all the enzymes needed to oxidize acetic acid to carbon dioxide.
Other researchers then found that the reactions could be made to go
Because adding them would allow the reactions to go forever, Krebs figured out the real explanation. Questions that you should be able to answer: 1) What are the two main kinds of energy coupling? 2) Why does one of them require intact membrane sacks? 3) What was my joke about nearly all eucaryotes having "pet" procaryotes in their cytoplasm? Why do plants have 2 kinds? 4) Which membrane of mitochondria is equivalent to the plasma membrane of its procaryote ancestor? 5) Across which membranes do chloroplasts pump hydrogen ions?
**6) In what sense can one call hydrogen ions "protons"? 7) What is meant by chemiosmosis? Which 3 kinds of membranes have chemiosmotic coupling of ATP synthesis? *8) Figure out some of the kinds of experimental observations that supported the chemiosmosis theory? hint: changes in acidity around isolated mitochondria; failure to make ATP in mitochondria etc. whose membranes had been broken; what else?
*9) As mentioned in a previous lecture, bacterial "flagella" are stiff coils that rotate (instead of bending because of dynein etc.). 10) How many sets of membranes do chloroplasts have (like Russian dolls, one inside the next)? Which of these contains the ATP synthase? **11) Can you invent any possible reasons why chloroplast chemiosmosis uses different membranes than the mitochondrial form? (hint: think about changes in cytoplasmic acidity) 12) How are NADH and FADH2 related to chemiosmosis? **13) Why did it seem to disprove chemiosmotic coupling that the ratio of ATPs made to NADHs oxidized seemed to be exactly 3? 14) What was the eventual solution to this apparent "disproof"? 15) What is meant by fermentation? 16) Name at least two alternative chemicals sometimes produced by fermentation. (**If you want meat to taste like yogurt, what should be done to the cow just before slaughter?) 17) Which captures more chemical energy: fermentation or the oxidation of fermentation products by mitochondria? 18) Would you expect that yeasts or other organisms could survive if they somehow lost all their mitochondria, or the mitochondria stopped functioning? 19) How would your answer to the preceding question be related to whether the organism in question can survive without oxygen? 20) What's another name for the citric acid cycle? *21) Was it named in honor of Sir Hans Citric-Acid? 22) Two carbons plus four carbons equals how many carbons? **23) Six carbons minus CO2 equals one NADH plus what? ***24) Can you figure out why release of the second carbon in the Krebs cycle results in GDP -> GTP, instead of ADP->ATP? I can't! 25) Why will the Krebs cycle not work without starting with at least some of the chemical intermediates, like citric acid or succinic acid, even if all the enzymes are present and there is plenty of acetic acid? 26) How can adding some of these chemicals speed up the reaction, more or less permanently, until the acetic acid runs out? hint: are these chemicals really acting as co-enzymes enzymes? *27) Could these reactions go if there were no NAD, FAD and GDP? **What about if there were no coenzymeA? **28) At the time of Krebs' breakthrough idea, radioactive carbon and other tracers were not yet available (as they would be after the war thanks to certain other refugees from Germany); but if C14 labeling HAD been possible, can you figure out how they could have been used to test whether succinic acid etc. were themselves being oxidized, in contrast to acting as coenzymes? **29) For those who know some Organic Chemistry: Can you see why oxaloacetic acid either ought to be called alpha-keto-succinic acid, or alternatively alpha-keto-glutaric acid ought to be called propionoacetic acid? Just to be consistent! And what might have been be called alpha-hydroxy-beta-carboxy-glutarate? *30) Drawing chemical structures, imagine the sequence of chemicals by which acetate could have been directly oxidized all the way to carbon dioxide and water (if it were done directly, instead of by binding the acetates to a 4-carbon compound. **31) Another one for the Organic Chemistry fanatics: What similarities can you find between aldol condensations, or any other common organic reactions, and the reactions of the Krebs cycle? *32) If a given species of bacterium normally lives in environments with low acidity, or in which the acidity varies with location, then why would it be better off to use sodium ions for chemiosmotic synthesis of ATP? 33) Suppose a certain kind of bacterium lives along the boundary between an environment having a high acidity, and one having a low acidity: if these bacteria can swim back and forth, then how could they use the acidity difference as an energy source in making ATP?
*34) If you look at a periodic table of the elements, you will see that arsenic is right below phosphorous. In fact, these elements form rather similar ions, with arsenate being very similar to phosphate.
35) Suppose that an enzyme uses energy from ATP to drive polymerization of some monomers X to form XXXXXX: 36) Why would it harm a cell to contain an enzyme that can catalyse release of phosphate from this X, even when not forming XXX polymer? *37) If mitochondria were deprived of either phosphate ions or of Adenosine monophosphate, then why might their internal acidity become much lower than usual? *38) Suppose that the ratio of concentrations of ATP to ADP in the cytoplasm of a cell became much lower than usual, how might that be related to differences in acidity between the inside of mitochondria and the surrounding cytoplasm? *39) Dinitrophenol is a poison that can bind reversibly to hydrogen ions and can diffuse through membranes whether or not it is currently bound to a hydrogen ions; in the 1930s, it was sometimes prescribed by physicians to patients who were trying to lose weight, but didn't want to exercise. It was very effective for this purpose, but sometimes fatal. Can you figure out how it works? **40) Newborn babies and some kinds of animals that need to keep warm have special "brown fat" cells, within which the mitochondria have unusually permeable inner membranes: can you figure out how these cells produce rapid heating, without shivering?
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