Introduction to Biology - Molecules and Cells

Introduction to Biology

Molecules and Cells

Chapter 9 - Respiration Processes

Hey, Isn't That Just Breathing Oxygen?

As you've probably guessed - no, no it isn't. Respiration is a process that can happen many ways: any process that breaks down existing molecules for the energy needed for metabolism is a type of respiration. Since all living things have energetic metabolisms, they all respire. Some use oxygen in the process and are called aerobic respirers; some don't use oxygen and are called anaerobic respirers.
Some organisms can take molecules from the environment that can't be used for energy and use environmental energy to form bonds between them, producing fuel molecules that they use and pass along up the food chain. The most common way this happens is through photosynthesis (covered at more length in the next chapter), which uses light energy to produce bonds between carbons and make glucose. In some ecosystems, chemosynthesis happens at the bottom of the food chain: this uses the energy of heat-boosted molecules to make sugars. This can be found at hydrothermal vents, cracks in the Earth's crusts on the ocean floors, where heated organic molecules that might date back to the formation of the planet mix out of lava into superheated ocean water. We've talked about fuel makers as producers; they are also called autotrophs, "self-feeders," and the rest of the food chain are heterotrophs, "other feeders."	Chemosynthesis, plus links to all thing vent-y. Basics of hydrothermal vents. Autotrophs and heterotrophs.
Most forms of respiration use sugar as a basic fuel, pulling the carbons apart and moving that bond energy into more easily-used molecules like ATP. Anaerobic respiration, done without oxygen, is done many ways, all less efficient than aerobic respiration, but enough for the cells that use it. In some cases, anaerobic respirers can't even be active around oxygen, which poisons them. We depend upon anaerobic respiration for a number of things. First, our own aerobic respiration starts with an anaerobic step, so we couldn't exist without it. However, we use many anaerobes commercially. Some anaerobes produce ethyl alcohol, a 2-carbon molecule, as an end product of fermentation. Uses for that range from the obvious, in beer, wine, and liquor, to the unexpected, in baker's yeast, which produces some ethanol and a lot of carbon dioxide gas to make dough rise. Some anaerobes produce various small carbon-based acids, and are involved in the making of cheeses (and in making your milk go bad). Our colons, a very low-oxygen environment, are full of anaerobic bacteria, most of which do useful jobs for us. Some anaerobes affect us in bad ways: the bacteria that produce botulism, or tetanus, are anaerobic.	Functions of anaerobes. Production of ethyl alcohol (scroll down to biological production). Effects of diet on colon symbionts. Yeast used to make mead.
The basic process of aerobic respiration can be written - C₆H₁₂O₆ + 6 O₂ ----------------> 6 CO₂ + 6 H₂O \------- Energy to ATP Aerobic respiration has three major steps. The first step is anaerobic and happens in the cytoplasm of cells; the aerobic steps happen in mitochondria. In the first step, glycolysis, the 6-carbon glucose molecule is destabilized with phosphates (2 from ATP, 2 free phosphates brought in), broken roughly in half, and used to make 4 ATP molecules. For every glucose molecule, 2 ATPs are invested and 4 are made, so there is a small gain for the cell. The second step is called the Krebs cycle (also called the citric acid cycle). It releases carbon dioxide and produces a couple of ATPs and a lot of energy-carrying molecules that feed into the third step, the electron-transport chain, that uses the oxygen (hydrogens are attached to make the water) and produces many ATPs. These last two steps produce from 32-34 ATPs, depending upon how you estimate, so the aerobic stage is much better at getting and moving the glucose energy then the aerobic stage. Anaerobes generally get less energy from fuel than aerobes, but their processes may work better than our glycolysis.	The steps of the steps. Glycolysis: the molecules and changes. The aerobic steps, with more detail on how and where. The Krebs Cycle. The Electron Transport Chain. More on ATP Yield.
In some cells, if activity is required but the supply of oxygen can't keep up, the cell may go into oxygen debt: it keeps doing glycolysis, building up lactic acid as a "holding" product, to get a bit of ATP even without oxygen. This happens in the muscle cells of animals that must run or fight for their lives, cells that need all of the energy they can get even if their oxygen supply can't keep up. If they survive, the lactic acid must be processed through the aerobic steps, "paying off" the debt in oxygen.	More on oxygen debt.
The Krebs cycle can also be "fed" molecular bits from molecules other than carbohydrates. The fatty acid chains in lipids hold a lot of energy for ATP production. Proteins can be broken down to amino acids (and there are many of those in any protein), and once the nitrogen piece is removed, what's left can be fed into the Krebs cycle for its energy. This also produces toxic nitrogenous wastes, which must be removed and/or processed into a nontoxic form. Ammonia is one such waste, and the urea that we make is processed to be less toxic. Calories are used to measure the amount of available energy in the foods we eat. A calorie (little "c") is a measure of energy, technically of heat, and our Calorie (capital "C") is 1000 of those. Notice that this should be a measure of usable energy: it should represent materials we can break down, absorb, and use, which is not the easiest thing to measure. You should understand why digestible starches and fats are so high in calories, though.	How various molecules feed respiration. Different nitrogenous wastes. The Calorie Counter - but which "calories" are they talking about?

So Where Did All of This Stuff Come From?

We wouldn't be human beings is we didn't wonder how everything began. There are, of course, many religious explanations for where it all came from; science tends to shy away from these not because scientists are non-religious, but because those supernatural explanations can really be tested in any way, while scientific explanations can be. Scientists also aren't that interested in a concept called panspermia: this is the idea that the earliest life began someplace other than Earth and was somehow carried here. Also not very testable (although some researchers believe that viable bacteria have been found sealed in meteors). We can't travel backward in time, but we can make predictions based upon hypotheses and test the predictions.

When scientists first began to think about how Life on Earth began, they looked at how Life worked around them, and everything depended upon fuel from plants to exist. The process of photosynthesis is very complex, and its appearance as a first step would have required some sort of supernatural intervention: this was known as the photosynthesis or plant problem.

It took better knowledge of how the Earth formed, and the chemistry of the early Earth, to solve that problem. The space dust that would have been coalesced to form the Earth, it turns out, has a decent proportion of organic molecules already in it. What emerged from that discovery was the Heterotroph Hypothesis, based on the idea of a Primordial Soup, a planet-covering solution of simple organic molecules, exposed to many types of energy, from lava heat to ultra-violet light to lightning in an extremely active atmosphere (it's still pretty active today, with an estimated 100 bolts per second planet-wide). The question was, could small organics, given such conditions, form larger organic molecules, and larger yet, until they became cooperative systems, able to self-organize, reproduce, and evolve? This is still an open question, but many small predictions based upon the hypothesis have been confirmed.

Some discoveries: RNA was found to have enzyme properties, providing a first possible living-system molecule that could have led to protein chemistry and DNA coding; some components of stardust were found to be lipids, critical in the formation of cell-like membranes; hydrothermal vents, with a fairly stable supply of raw materials and energy, and ecosystems based upon relatively simple chemosynthesis, were found; a primitive form of photosynthesis was found in bacteria near hydrothermal vents; a layer of rust in the fossil record indicated a rough date for the appearance of widespread release of oxygen from photosynthesis, after indications that life already had existed for some time; chemistry very much like the hypothesized primordial soup can be found elsewhere in the solar system, such as the moons of Jupiter and Saturn.

Unless we find a world in the early stages of developing its own living systems (which might be happening deep in those moons), we can't be too sure that it works the way the hypothesis says, but the evidence slowly mounts.

A broad assortment of creation stories.

More on panspermia.

Some more on Primordial Soup.

How'd it get to be RNA?

"Soup" from volcano.

More on that primitive photosynthesis.

Extraterrestrial conditions and chemistry.

And could it produce a type of Life?

Go On to Next Chapter - Photosynthesis

Introduction to Biology - Molecules & Cells.
For SC-135.

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