Biotechnology, General Chemistry MDeLosReyes

AMAZING MICROBES!!! (How Do They Do That)

Be amazed on how microorganisms function in many different ways and how we can use their properties in a variety of innovative applications. Realize the importance of chemical bonds and chemical reactions. These articles demonstrate how microbiology and biochemistry are so interconnected!

1. Bacteria color your poop to diagnose what ails you

By Garth Hogan, posted January 29, 2012
http://www.microbeworld.org/index.php?option=com_jlibrary&view=article&id=8218

What if diagnosing salmonella or colorectal cancer was as easy as looking in the toilet? Scientists and designers are collaborating to create a new type of bacteria that beautifies your fecal matter while diagnosing your illness. We mentioned E. chromi, the color-coded designer bacteria made from E. coli, back in June. When brought to genetically engineered life, the bacteria will have a number of uses, including testing groundwater and as a chemical-free food coloring. But none of them hit my juvenile funny bone while making me pray this becomes a reality quite like the poop-coloring possibilities. The idea is that, someday soon, you'll be able to drink a probiotic shake filled with E. chromi. The modified E. coli contain genes capable of producing color. When the bacteria react with certain enzymes, proteins, and chemicals in your gastrointestinal tract, they will produce certain colors, making diagnosis as simple as reading a color chart.

2. Hot! Hot! Hot! But How?

By administrator, posted January 14, 2009
http://www.microbeworld.org/index.php?option=com_content&view=article&id=164:hot-hothot-but-how&catid=43:everyday-roles&Itemid=80

Ever been outside on a day so hot, you said to your friends, "I feel like Im melting"? Well, of course you were exaggerating. But there are microbes called thermophiles <thermo-files>, or heat-lovers, that live in temperatures so hot, the microbes could actually melt if they hadnt developed tricks and tools to handle such extreme heat.

General Chemistry, MDeLosReyes

Special Enzymes
Thermophiles have certain proteins, or enzymes, that are specially geared to working in high temperatures even as hot at 284 F (140 C). Keep in mind that water boils at 212 F (100 C). The normal-temperature proteins and enzymes in your body would start unfolding and breaking apart long before it got as hot as 284 F. You see, proteins are strings of molecules called amino <ah-mee-no> acids (imagine a string of pearls with each pearl representing an amino acid). But for proteins to work right, their amino acid strings cant just stretch out in a line. They have to be twisted and folded in just the right threedimensional patterns (imagine bunching that pearl necklace up in your hand). High heat can cause these 3-D structures to unfold and the links holding the pattern together to break. And when they unfold, enzymes no longer work right. Enzymes in thermophiles are called extremozymes <ex-treem-oh-zimes>. One thing that these extremozymes do to hold their 3-D shapes together in high heat is folding themselves tighter than normal temperature enzymes do. As you know, a tight knot in your shoelace is harder to get out than a loose one. Also, lots of chemical bonds formed between amino acids on the outer surfaces of extremozymes help keep these proteins intact and folded just right. These bonds act as fasteners holding together the shape of the enzymes. Another trick is having a smaller amount of the amino acid glycine <gly-seen> than normal-temperature proteins have. Of the 20 different amino acids that make proteins, glycine is the second most commonly found in regular proteins. It helps them be flexible and bend a bit. Having less glycine makes extremozymes more rigid and sturdier. One really cool tool hyperthermophiles use to keep their enzymes working right is a special type of fix-it protein called "chaperonin" <shap-er-oh-nin>. These chaperonin proteins fix enzymes beginning to fall apart by latching onto them and refolding them back into their active patternssort of like a microscopic back doctor except that chaperonins put the kinks back in instead of taking them out.

3. Beat that Cold

By administrator, posted January 14, 2009
http://www.microbeworld.org/index.php?option=com_content&view=article&id=163:beat-thatcold&catid=43:everyday-roles&Itemid=81

General Chemistry, MDeLosReyes In recent years, scientists have turned up microbes living in the frigid waters of Antarctic lakes that are permanently covered with snow and a thick layer of ice. Scientists have found microbes thriving in the wind-blasted rocks and soil atop high mountain summits and in polar snow. Now maybe all this doesnt seem quite so amazing at first: after all, penguins waddle across the Antarctic ice floes and polar bears and walruses meander the Arctic tundra and even we humans can trek to the poles given enough layers of down, fleece and wool. But how in the world do microbes do it without the aid of blubber, fur or other obvious insulating protection? After all, cold kills or at least slows down lots of microbesthats why we put our food in refrigerators to keep it fresh longer. Scientists studying microbes that thrive in the cold (which go by the fancy name of psychrophiles <sigh-crow-files>) have not yet discovered all the secrets to these microbes amazing cold-loving abilities. However, they have learned a couple of neat things. Cold-loving microbes may not have fur or down-filled coats, but they do have special proteins or enzymes that help them shrug off the frigid chill. What are enzymes, you say? These are proteins that help make lots of chemical reactions take place inside cells and basically help cells do all the things they need to do to stay alive. So, psychrophilic <sigh-crow-fill-ick> enzymes are similar to the enzymes in microbes that live at normal temperatures, but the psychrophilic enzymes continue to function at temperatures below which normal enzymes get sluggish or stop working. How? It appears that enzymes in cold-adapted microbes have a little more flexibility in them because theyve lost a few of the fastener molecules that keep these protein folded rigidly into a specific threedimensional shape. (Proteins bunch up into 3-D shapes that are very important to how well they work.) Since these enzymes can flex a bit, they dont need as much energy to do their thing, which is good in an environment where you cant count on heat for energy. Another way cold-loving microbes thrive in their chilly environments is keeping the membranes of their cells loose with molecules called fatty acids. Membranes are like plastic sacks with holes that surround the goopy fluid and all the parts inside of cells. A fatty acid is a long chain of carbon atoms strung together. Having a lot of these fatty acids keeps membranes fluid in low temperatures so they can continue to easily take in and release molecules "food" and "wastes" basicallythrough their cells. Theres a lot still to learn about how microbes live comfortably in super-cold temperatures. These are just a couple of the microbial tricks for beating the cold. Scientists are studying ways that we humans could put these psychrophilic enzymes to

General Chemistry, MDeLosReyes work for us, say in preserving foods without freezer burn, improving microbial clean up of pollution, and making new medicines.

4. How "Conan the Bacterium "Survives Lethal Radiation Blasts

By administrator, posted January 14, 2009
http://www.microbeworld.org/index.php?option=com_content&view=article&id=162:surviveradiation&catid=43:everyday-roles&Itemid=82

When you go to the dentist to have your jaws X-rayed, youll notice that you have to wear a heavy lead apronand the person who takes the X-ray leaves the room to do it. X-rays are safe, but these precautions give you some sense of how careful we have to be around even relatively harmless levels of radiation. The problem is that unsafe levels of radiation can mess with the cells and molecules in our body, warping them and even breaking them apart. It does the same thing to microbial cells. But theres one bacterium called Deinococcus radiodurans <dieno-cah-cuss radio-dur-anz> that can live through blasts of radiation thousands of times greater than the level that would kill a human being. Radiation is measured in units called rads. A dose of 500 to 1,000 rads is enough to kill a person. D. radiodurans thrives even after being hit by up to 1,500,000 radsyikes! The bacteriums Latin name means "strange berry that withstands radiation." Scientists who study D. radiodurans have nicknamed it "Conan the Bacterium." The Guinness Book of World Records dubbed it the worlds toughest bacterium. So how does D. radiodurans manage to live through such intense blasts of radiation? If youve read other pages on this site, you may have learned that some bacteria form protective spores to survive through drought, heat and radiation (see How Microbes Form Spores). So could it be that D. radiodurans forms extra tough spores? Actually no, its not a spore-former. Anyway, while bacterial spores can endure radiation, none can take nearly as much as D. radiodurans can. So, without any special protective coating, what then does D. radiodurans do to withstand all that radiation? Lets first take a quick look at what radiation does to a living thing. When a creature gets hit by a high dose of radiation, the intense energy causes the large DNA molecule in each cellthe collection of all the genes that make a living thing what it is to fall apart. No creature can survive without its genes in working order. Most microbes have tools they use to repair occasional damage to their DNA. For example, when a break happens in the DNA of an E. coli bacterium (one of the common bacteria living in your gut), the bug can usually repair it and get on with daily life.

General Chemistry, MDeLosReyes However, E. coli usually cant survive more than two or three major breaks in its DNA. D. radiodurans, on the other hand, can stitch back together DNA shattered to bits by radiation within a matter of a few hours. One reason is that it has lots of extra copies of its genes. D. radiodurans cells have four to ten copies of their DNA molecule. Most bacteria have only one copy. These copies serve as back-ups, kind of like the back-up copies you make of your important computer files in case one day your computer crashes. So when radiation hits and D. radiodurans DNA gets busted up, the microbe has lots more chances of finding an intact copy of each gene to use as it stitches its DNA back together. A special protein called RecA does the stitching. Also, it appears that D. radiodurans may have more of the cell repair tools that most bugs have. Still, scientists arent entirely clear exactly how and why D. radiodurans is so much more radiation-resistant than other microbes. After all, other microbes have many of the same tools, although not in as high numbers and variety as D. radiodurans does. And some other bacteria have more than one copy of their genes, although none have quite as many copies as D. radiodurans. Scientists are sifting through the genes of D. radiodurans, trying to figure out if the bacterium has any unique tools or genes that give it extra radiation protection. Theyre also trying to figure out why D. radiodurans evolved this super radiationresistance in the first place. After all, there arent any places on the planet where the microbe would have been exposed naturally to such incredibly high radiation blasts. It turns out that D. radiodurans is also amazingly able to live through long periods with absolutely no water without turning into a tiny dried-out husk. Some researchers think that the bacteriums radiation resistance is a lucky side effect of the ability the bug evolved to withstand long periods without watera common natural occurrence. This is because dehydration causes the same kinds of breaks in DNA as radiation does and requires the same patching process to fix these breaks. However it does what it does, D. radiodurans is indeed the toughest of the tough in the microbial world.

5. Repair DNA
By Chris Condayan, posted February 04, 2009
http://www.microbeworld.org/index.php?option=com_content&view=article&id=235:repairdna&catid=43:everyday-roles&Itemid=83

Developing tricks and tools to keep their enzymes in order is one way thermophiles survive. They also use techniques to keep their DNA from falling apart under intense

General Chemistry, MDeLosReyes heat. Like proteins, the parts of the long, spiral ladder-shaped DNA molecule start to unravel and break apart under high heat. One way thermophiles keep that from happening is with a helper enzyme called "reverse DNA gyrase" <jeye-race>. This enzyme makes DNA coil up and twist upon itself in a certain way that makes the DNA more stable in high heat. (If youve ever seen a telephone handset cord that gets twisted and bunched up on itself, then you know what DNA coiling is like, only coiled up DNA is thousands of times more tightly twisted and bunched.) Microbes that live at normal temperatures have regular "DNA gyrase" instead, which also makes their DNA coil up, but in a different, looser way. Thermophiles also have lots of DNA binding proteins. These binding proteins do just what their name suggests, running around gluing the pieces and parts of the DNA molecule back together when they start to come undone, much like the chaperonin proteins discussed above. Holding it All Together Of course, tools that keep the enzymes, DNA and other inside parts of the cell from breaking up will do no good if the outside or surface of the cell is falling apart. So these heat-loving creatures have cell membranesthe rubbery lining just inside the cell wall that surrounds the cell fluidthat are formed differently than those of microbes living at normal temperatures. Normal temperature microbes have membranes that are formed by two layers of molecules called lipids which join together to create whats called a bilayer. In thermophiles, the parts of each lipid layer that point inward are chemically glued together so that instead of a bilayer that could be pulled apart in intense heat, thermophiles have a thick single or monolayer. Theres a lot that scientists still are learning about how these amazing heat-loving microbes live happily at such high temperatures. They may well have other tools and tricks that we dont know about yet. The more we learn, the better for us because some of these techniques and tools could become useful products for us. For example, an extremozyme called Taq <tack> from one thermophilic bacterium is what makes DNA testing and DNA fingerprinting possible. Thanks in part to Taq, scientists have been able to sequence the entire human genomeeverything on the whole humongous human DNA moleculeand the genomes of lots of microbes and other living things, too.

6. Microbial Spore Formation

By administrator, posted January 14, 2009
http://www.microbeworld.org/index.php?option=com_content&view=article&id=160:microbialspore-formation&catid=43:everyday-roles&Itemid=84

General Chemistry, MDeLosReyes You may have read elsewhere in this site that bacteria sometimes form protective spores to help them survive through tough times. Some other kinds of microbes do, too. Here's how that transformation takes place. First off, you might think of a bacterial spore roughly as a mummified bacterium. The spore has a hard protective coating that encases the key parts of the bacteriumthink of this coating as the sarcophagus that protects a mummy. The spore also has layers of protective membranes, sort of like the wrappings around a mummy. Within these membranes and the hard coating, the dormant bacterium is able to survive for weeks, even years, through drought, heat and even radiation. When conditions become more favorable againwhen theres more water or more food availablethe bacterium "comes to life" again, transforming from a spore back to a cell. Some bacterial spores have possibly been revived after they lay underground for more than 250 million years! Ok, so how do bacteria turn themselves into spores? First, the bacterium senses that its home or habitat is turning bad: food is becoming scarce or water is disappearing or the temperature is rising to uncomfortable levels. So it makes a copy of its chromosome, the string of DNA that carries all its genes.

Then, the rubbery cell membrane that surrounds the bacterial cell fluid begins pinching inward around this chromosome copy, until theres a little cell within the larger b acterial cell. This little cell is called the "daughter cell" and the bigger, original one, what starts out as the "vegetative cell" in this illustration, is now called the "mother cell." Next, the membrane of the mother cell surrounds and swallows up the smaller cell, so that now two membrane layers surround the daughter cell. Between these two membranes a thick wall forms made out of stuff called peptidoglycan <pep-tid-oh-gly-can>, the same stuff found in bacterias rigid cell walls. Finally, a tough outer coating made up of a bunch of proteins forms around all this, closing off the entire daughter cell, which is now a spore. As the mother cell withers away or gets blasted by all kinds of environmental damage, the spore lies dormant, enduring it all, just waiting for things to get better.

General Chemistry, MDeLosReyes Not all bacteria can form spores. But several types that live in the soil can. Bacteria in the Bacillus <buh-sill-us> and Clostridium <clah-strih-dee-um> groups are spore-formers. Their spores are called endospores. Another group of bacteria called Methylosinus <meth-ill-oh-sigh-nus> produces spores called exospores. The difference between endospores and exospores is mainly in how they form. Endospores form inside the original bacterial cell, as described above. Exospores form outside by growing or budding out from one end of the cell. Exospores also dont have all the same building blocks as endospores, but theyre similarly durable. Members of the Azotobacter <ay-zoh-toe-back-ter>, Bdellovibrio <dell-oh-vih-bree-oh>, Myxococcus <mix-oh-cah-cuss> and Cyanobacteria <sigh-an-oh-back-teer-ee-uh> groups form protective structures called cysts <cists>. Cysts are thick-walled structures that, like spores, protect bacteria from harm, but theyre somewhat less durable than endospores and exospores. Bacteria arent the only microbes that can form protective spores, however. Some protists can, too. For example, a group of parasitic protozoa called Microsporidia <mike-rowspore-ih-dee-uh> encase themselves in protective spores when they infect their hosts. Microsporidia are found mainly in the guts of insects and the skin and muscles of fish, although a few species can cause illness in people. Microsporidia spores are usually round, oval or rod-shaped, although many species have elaborately shaped spores that may help hide them from their host immune systems. The spores help the protozoa survive while outside of a hosts body. Typically, hosts are infected when they swallow Microsporidia spores. Once the spores reach the gut, they poke a tube through their spore coats. This tube stabs through the hosts gut wall and other tissues. Then the Microsporidia cell fluid and nucleusa cell's central command centermove through the hollow tube from the spore into the host cells. As Microsporidia reproduce in the host cells, new spores are formed that are typically passed out of the body with feces. Note: The spores were talking about on this page are protective spores. A group of bacteria called Actinomycetes <ack-tin-oh-my-see-tees> and many kinds of fungi produce seed-like structures during reproduction that are also called spores. If youve ever stomped on a puffball mushroom, the brown cloud that jets out is a cloud of these reproductive spores. Like seeds, reproductive spores have tough outer coatings on them, but they arent as durable as protective spores or cysts.

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