The Endosymbiont Theory, pac-man style

Pac-man style


First Artificial Enzyme Created by Evolution in a Test Tube>>> Moving Forward with ENZYMES

IWANTTOGOHOMESeelig created the fledgling enzyme by using directed evolution in the laboratory. Working with colleague Gianluigi Veglia, graduate student Fa-An Chao, and other team members, he subsequently determined its structure, which made its debut December 9 as an advance online publication in Nature Chemical Biology. Lab tests show that the enzyme (a type of RNA ligase, which connects two RNA molecules) functions like natural enzymes although its structure looks very different and it is flexible rather than rigid. Seelig speculates the new protein resembles primordial enzymes, before their current structures evolved.

Seelig and Veglia are professors in the College of Biological Sciences, where Fa-An Chao is a graduate student. Both faculty members have appointments in the Department of Biochemistry, Molecular Biology and Biophysics and Seelig is member of the BioTechnology Institute. Veglia also has an appointment in the Department of Chemistry in the university’s College of Science and Engineering.

While a handful of groups worldwide are developing artificial enzymes, they use rational design to construct the proteins on computers. Instead, the Seelig lab employs directed evolution. “To my knowledge, our enzyme is the only entirely artificial enzyme created in a test tube by simply following the principles of natural selection and evolution,” he says.

Rational enzyme design relies on preconceived notions of what a new enzyme should look like and how it should function. In contrast, directed evolution involves producing a large quantity of candidate proteins and screening several generations to produce one with the desired function. With this approach, the outcome isn’t limited by current knowledge of enzyme structure.

“Just as in nature, only the fittest survive after each successive generation,” Seelig explains. The process continues until it produces an enzyme that efficiently catalyzes a desired biochemical reaction. In this case, the new enzyme joins two pieces of RNA together.

“It’s kind of like giving typewriters to monkeys,” he says. “One monkey and one typewriter won’t produce anything clever. But if you have enough monkeys and typewriters, eventually one of them will write ‘to be or not to be’.” The lottery provides another analogy. “If you buy more tickets, you’re more likely to win,” Seelig says.

Like all proteins, the new RNA ligase enzyme is a chain of amino acids folded into a 3D structure, but the resemblance stops there. Natural enzymes, like all proteins, are made from alpha helices and beta strands. Seelig’s artificial enzyme lacks those structures. Instead, it forms around two metal ions and is not rigid. “Compared to enzymes we know from nature, the artificial enzyme has a rather unusual structure and dynamics,” Seelig says.

For decades, naturally occurring enzymes have been tweaked by industry to make industrial processes and products more effective. The ability to create enzymes from scratch using a natural process opens the door to a vast array of new products that provide business opportunities and improve quality of life without harmful environmental effects.

Going forward, Seelig plans to create enzymes with useful applications while he continues to explore the underlying basic science of enzyme structure and function, aiming to learn more about the origin of enzymes and how proteins evolve.


Referenced: Science Daily.2013.First Artificial Enzyme Created by Evolution in a Test Tube.

Mayo Clinic Researchers Identify New Enzyme To Fight Alzheimer’s Disease

An enzyme that could represent a powerful new tool for combating Alzheimer’s disease has been discovered by researchers at Mayo Clinic in Florida. The enzyme — known as Beta-secretase 2( BACE2 )— destroys beta-amyloid, a toxic protein fragment that litters the brains of patients who have the disease.

Alzheimer’s disease is the most common memory disorder. It affects more that 5.5 million people in the United States. Despite the disorder’s enormous financial and personal toll, effective treatments have not yet been found.

The Mayo research team, led by Malcolm A. Leissring, Ph.D., aneuroscientist at Mayo Clinic in Florida, made the discovery by testing hundreds of enzymes for the ability to lower beta-amyloid levels. BACE2 was found to lower beta-amyloid more effectively than all other enzymes tested. The discovery is interesting because BACE2 is closely related to another enzyme, known as BACE1, involved in producing beta-amyloid.


“Despite their close similarity, the two enzymes have completely opposite effects on beta-amyloid — BACE1 giveth, while BACE2 taketh away,” Dr. Leissring says.

Beta-amyloid is a fragment of a larger protein, known as APP, and is produced by enzymes that cut APP at two places. BACE1 is the enzyme responsible for making the first cut that generates beta-amyloid. The research showed that BACE2 cuts beta-amyloid into smaller pieces, thereby destroying it, instead. Although other enzymes are known to break down beta-amyloid, BACE2 is particularly efficient at this function, the study found.

Previous work had shown that BACE2 can also lower beta-amyloid levels by a second mechanism: by cutting APP at a different spot from BACE1. BACE2 cuts in the middle of the beta-amyloid portion, which prevents beta-amyloid production.

“The fact that BACE2 can lower beta-amyloid by two distinct mechanisms makes this enzyme an especially attractive candidate for gene therapy to treat Alzheimer’s disease,” says first author Samer Abdul-Hay, Ph.D., a neuroscientist at Mayo Clinic in Florida.

The discovery suggests that impairments in BACE2 might increase the risk of Alzheimer’s disease. This is important because certain drugs in clinical use — for example, antiviral drugs used to treat human immunodeficiency virus (HIV) — work by inhibiting enzymes similar to BACE2.

Although BACE2 can lower beta-amyloid by two distinct mechanisms, only the newly discovered mechanism — beta-amyloid destruction — is likely relevant to the disease, the researchers note. This is because the second mechanism, which involves BACE2 cutting APP, does not occur in the brain. The researchers have obtained a grant from the National Institutes of Health to study whether blocking beta-amyloid destruction by BACE2 can increase the risk for Alzheimer’s disease in a mouse model of the disease.


Reference: Mayo clinic.2012.Mayo Clinic Researchers Identify New Enzyme To Fight Alzheimer’s Disease.

My second video review


When an apple is cut (or bruised), oxygen is introduced into the injured plant tissue. When oxygen is present in cells, polyphenol oxidase (PPO) enzymes in the chloroplasts rapidly oxidize phenolic compounds naturally present in the apple tissues to o-quinones, colorless precursors to brown-colored secondary products. O-quinones then produce the well documented brown color by reacting to form compounds with amino acids or proteins, or they self-assemble to make polymers. One question that often accompanies yours is, “Why do some apples seem to brown faster than others?” Well, nearly all plant tissues contain PPO, however, the level of PPO activity and concentration of substrate can vary between varieties of fruits. In addition, a tissue’s PPO level can vary depending on growing conditions and fruit maturity. One approach the food industry employs to prevent enzymatic browning is to select fruit varieties that are less susceptible to discoloration; either due to lower PPO activity or lower substrate concentration. This approach, however, may not be practical for the home “culinary scientist.” In the home kitchen enzymatic browning can be prevented by either reducing PPO oxidation activity or lowering the amount of substrate to which the enzyme can bind. Coating freshly cut apples in sugar or syrup can reduce oxygen diffusion and thus slow the browning reaction. Lemon or pineapple juices, both of which naturally contain antioxidants, can be used to coat apple slices and slow enzymatic browning. In addition, both fruit juices are acidic and the lower pH that they bring about causes PPO to become less active. Heating can also be used to inactivate PPO enzymes; apples can be blanched in boiling water for four to five minutes to nearly eliminate PPO activity. Enzymatic browning is not unique to apples. PPO,a mixture of monophenol oxidase and catechol oxidase enzymes is present in nearly all plant tissues and can also be found in bacteria, animals and fungi. In fact, browning by PPO is not always an undesirable reaction; the familiar brown color of tea, coffee and cocoa is developed by PPO enzymatic browning during product processing.

Various aspects were left out in the video so i added the missing substantial information. However the video answered some interesting questions about the browning of apples, a case where many people do not really understand. The video could improve vastly b including structural formula and equations to validate the information being given. I have finally learned why my fruits turn brown when i leave it exposed for a while. The video was quite nice and provided some relevant information  but as mentioned before, as a biochemistry student, i would have liked to see the reactions,structural formula and equations of the various components.




“Oxidation in apples,” YouTube Video, 4:12, posted by “DNA Geek,” April 12, 2011,

Scientific American.2007.Why do apple slices turn brown after being cut?

The universe is full of life! Discoveries Suggest Icy Cosmic Start for Amino Acids and DNA Ingredients


Using new technology at the telescope and in laboratories, researchers have discovered an important pair of prebiotic molecules in interstellar space. The discoveries indicate that some basic chemicals that are key steps on the way to life may have formed on dusty ice grains floating between the stars. The scientists used the National Science Foundation’s Green Bank Telescope (GBT) in West Virginia to study a giant cloud of gas some 25,000 light-years from Earth, near the center of our Milky Way Galaxy. The chemicals they found in that cloud include a molecule thought to be a precursor to a key component of DNA and another that may have a role in the formation of the amino acid alanine.One of the newly-discovered molecules, called cyanomethanimine, is one step in the process that chemists believe produces adenine, one of the four nucleobases that form the “rungs” in the ladder-like structure of DNA.


The other molecule, called ethanamine, is thought to play a role in forming alanine, one of the twenty amino acids in the genetic code. “Finding these molecules in an interstellar gas cloud means that important building blocks for DNA and amino acids can ‘seed’ newly-formed planets with the chemical precursors for life,” said Anthony Remijan, of the National Radio Astronomy Observatory (NRAO).In each case, the newly-discovered interstellar molecules are intermediate stages in multi-step chemical processes leading to the final biological molecule. Details of the processes remain unclear, but the discoveries give new insight on where these processes occur.Previously, scientists thought such processes took place in the very tenuous gas between the stars. The new discoveries, however, suggest that the chemical formation sequences for these molecules occurred not in gas, but on the surfaces of ice grains in interstellar space. “We need to do further experiments to better understand how these reactions work, but it could be that some of the first key steps toward biological chemicals occurred on tiny ice grains,” Remijan said.The discoveries were made possible by new technology that speeds the process of identifying the “fingerprints” of cosmic chemicals. Each molecule has a specific set of rotational states that it can assume. When it changes from one state to another, a specific amount of energy is either emitted or absorbed, often as radio waves at specific frequencies that can be observed with the GBT.New laboratory techniques have allowed astrochemists to measure the characteristic patterns of such radio frequencies for specific molecules. Armed with that information, they then can match that pattern with the data received by the telescope. Laboratories at the University of Virginia and the Harvard-Smithsonian Center for Astrophysics measured radio emission from cyanomethanimine and ethanamine, and the frequency patterns from those molecules then were matched to publicly-available data produced by a survey done with the GBT from 2008 to 2011.A team of undergraduate students participating in a special summer research program for minority students at the University of Virginia (U.Va.) conducted some of the experiments leading to the discovery of cyanomethanimine. The students worked under U.Va. professors Brooks Pate and Ed Murphy, and Remijan. The program, funded by the National Science Foundation, brought students from four universities for summer research experiences. They worked in Pate’s astrochemistry laboratory, as well as with the GBT data.”This is a pretty special discovery and proves that early-career students can do remarkable research,” Pate said.The researchers are reporting their findings in the Astrophysical Journal Letters. News from: The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.

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Good News. 2013. The universe is full of life! Discoveries Suggest Icy Cosmic Start for Amino Acids and DNA Ingredients.

21st Century Amino Acids

Biological Wires Carry Electricity Thanks to Special Amino Acids




In nature, the bacterium Geobacter sulfurreducens uses these nanowires, called pili, to transport electrons to remote iron particles or other microbes, but the benefits of these wires can also be harnessed by humans for use in fuel cells or bioelectronics. The study in mBio® reveals that a core of aromatic amino acids are required to turn these hair-like appendages into functioning electron-carrying biological wires.

“It’s the aromatic amino acids that make it a wire,” says lead author Derek Lovley of the University of Massachusetts, Amherst. Lovley and his colleagues removed the pivotal amino acids from the pili and replaced them with smaller, non-aromatic amino acids. Without these key components, Lovley says, the pili are nothing more than protein strings. “We showed it’s not good enough to just make the string — you’ve got to make a wire,” says Lovley.

G. sulfurreducens “breathes” by removing electrons from organic materials and funneling them to iron oxides or to other microorganisms, much the way humans pull electrons out of organic molecules in food and dump them on oxygen. The bacteria use their pili to reach out to iron oxides or other microbes, transferring the “waste” electrons along the structure to the destination. Geobacter‘s pili are only 3-5 nanometers wide, but they can be 20 micrometers long, many times longer than the cell itself.

Trafficking in electrons is how all living things breathe, but it is normally carried out by discrete proteins or other molecules that act like containers for shuttling electrons from one place to another. Lovley says earlier results showed the pili in G. sulfurreducens possess metallic-like conductivity, the ability to carry electrons along a continuous structure, a controversial finding in biology.

To investigate how pili accomplish this singular feat, Lovley says they looked to non-biological organic materials that can conduct electricity. “In those synthetic materials, it’s aromatic compounds that are responsible for the conductivity. We hypothesized that maybe it’s similar in the Geobacter pili. In this case, it would be aromatic amino acids.” Aromatic compounds have a highly stable ring-shaped structure made of carbon atoms.

Turning to the pili, Lovley says his group looked for aromatic amino acids in the parts of the pili proteins that would most likely contribute to the conductivity. Using genetic techniques, they developed a strain of Geobacter that makes pili that lack aromatic amino acids in these key regions, then they tested whether these pili could still conduct electricity. They could not. Removing the aromatic amino acids was a bit like taking the copper out of a plastic-covered electrical wire: no copper means no current, and all you’re left with is a string.


Removing aromatic amino acids from the pili prevents the bacteria from reducing iron, too, says Lovley, an important point because it adds further proof that Geobacter uses its pili as nanowires for carrying electrons to support respiration.

Metal reducers like Geobacter show a lot of promise for use in fuel cells, says Lovley, and by feeding electrons to the microbes that produce the methane, they’re an important component of anaerobic digesters that produce methane gas from waste products. Understanding how they shuttle their electrons around and how to optimize the way the pili function could lead to better technologies.



Science Daily.2013.Biological Wires Carry Electricity Thanks to Special Amino Acids.

Here’s your lucky day to find out how Jell-O is formed

What is Jell-O? How does it turn from a liquid to a solid when it cools?


David J. McClements, an assistant professor in the Biopolymers and Colloids Research Laboratory at the University of Massachusetts at Amherst, provides this more extensive overview of dessert science:


“The principal component responsible for the transition from a liquid to a semisolid gel on cooling is gelatin. Gelatin is a protein derived from collagen, the major component of the connective tissue of animals. Jell-O and other, similar products consist of powdered gelatin mixed with sweeteners, flavorings and coloring agents.

“In its natural state, collagen exists as fibers that contain three polypeptide chains entwined into a helical structure. Collagen is converted to gelatin by heating it in the presence of water. This procedure breaks down the relatively weak (noncovalent) bonds holding the three polypeptides together, as well as some of the stronger, covalent bonds, and produces a solution in which the polypeptides are arranged into a predominantly amorphous structure.

“When the solution of gelatin cools below a certain temperature, the molecules tend to associate with one another in order to regain some of their original helical structure. In this way, junction zones are formed. The junction zones mark a local return of the original form: three polypeptide chains in a helical formation. If there is enough gelatin present, a gel will form. The gel consists of a three-dimensional network of gelatin molecules linked by these junction zones, which is capable of en-training large amounts of water through capillary forces. This gel has solid-like characteristics, although it is really a viscoelastic material.

“Gelatin is a thermoreversible, cold-setting polymer: if the gel is reheated, it will convert back to a liquid because the forces favoring the amorphous state (mainly configurational entropy) outweigh those favoring the aggregated state (mainly hydrogen bonds). For this reason, gelatin cannot be used in ‘cook and serve’ products such as puddings that are supposed to form gels when heated. These products must incorporate a heat-setting polymer, such as starch.”


Reference: Scientific American.2000.What is Jell-O?How does it turn from a liqiud to a solid  when it cools?


Image kidnapped from;

Die protein…….Die…….

So i have been learning about protein and amino acids and i came across this interesting topic:


Cooked Protein Vs. Raw Protein

Do you think that cooking food has any effect on its protein content in terms of its quality and availability to the cells of our body? For some, this question may have never crossed your mind, especially if you’re new to the idea of a raw foods diet.

How Does Heat Effect Protein?

Most people are unaware that cooking food drastically changes the chemical composition of those foods, including the extreme molecular change to protein. The fact that cooking food destroys protein is not news.“Essentials to Human Anatomy & Physiology”, Elaine N. Marieb writes:

“The fibrous structural proteins are exceptionally stable; the globular functional proteins are quite the opposite. Hydrogen bonds are critically important in maintaining their structure, but hydrogen bonds are fragile and are easily broken by heat and excesses of pH. When their three-dimensional structure are destroyed, the proteins are said to be denatured and can no longer perform their physiological roles.”


Cooked Proteins Become Substantially Useless to Our Bodies

When we apply high heat to food, over 115 degrees Fahrenheit,the hydrogen bonds are destroyed and the amino acids fuse together with enzyme-resistant bonds that preclude them from being fully broken down by the body, creating coagulated proteins. This changes the particular structure of proteins, which are three-dimensional. Their particular functions depend on their specific structure, rendering them unable to ‘fit’ and interact with other molecules of complementary shape, ultimately becoming useless to the body. For example, the protein molecule hemoglobin can then no longer fit with and transport oxygen and is useless to perform its specific function.According to the Max Planck Institute, cooking foods coagulates at least 50% of the protein, making them less bio-available to the body.

Cooked Proteins & Toxicity

Now we have these newly created molecules – from cooked proteins, which the body absolutely can’t recognize as ‘food’. Now these partially broken down proteins, called polypeptides, are targeted as ‘foreign invaders’ and it becomes a toxic substance that the body needs to work extremely hard to remove. This causes the immune system has to focus energy on protecting the body from something that was eaten, instead of focusing on other areas of the body that may need immune support, causing the entire system to work and perform extremely inefficiently. This is one of the reasons why there is such a dramatic increase in white blood cell count (the immune system’s army) after cooked food is eaten.

Proteins, in order to be usable by the body need to be broken down into amino acids. Digestive enzymes can’t easily break down these ‘fused’ together proteins into simple amino acids because they’ve coagulated, putting extra strain on the digestive system and the pancreas.

To top it all off, undigested proteins are one of the main culprits for allergies, arthritis, leaky gut and auto immune diseases. Eating proteins in their raw state does not have this same effect at all, and are actually more bio-available (usable) by our bodies.

It seems quite obvious, once explained, that the body would recognize these mutant protein molecules as ‘foreign’ and not as food as this is not what’s found in nature – one of the most intuitive explanations supporting the consumption of a primarily raw foods diet.


This information was obtained from:

Sacred Source Nutrition.2013. Cooked Protein vs Raw Protein.

Image obtained from: