AP Biology class blog for discussing current research in Biology

Tag: enzyme

The Future of CRISPR

CRISPR is starting to become more and more of a reality as Harvard professor David Liu continues to work on it. Liu was the person who originally developed CRISPR first base editor which allowed for single letter changes in the genetic code. Liu has come up with two new features to CRISPR-Cas9.

The first is called cellular detective or CAMERA(CRISPR-mediated analog multievent recording apparatus systems). What this function does is it finds the genetic problem that is responsible for the disease someone is experiencing. Cas9 will record all the cell data and piece info together, which overall will provide more information about cancer, stem cells, aging, and overall disease.

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The second finding is referred to as sharp scissors which is a CRISPR enzyme. Sharp scissors are way more precise and accurate than the old enzyme making is much safer. The scissors depend on specific DNA to find the region where it is supposed to cut or edit. CRISPR is progressing and as more research is being done could be used on humans in the future.


New Enzyme Reducing Off-Target DNA Editing

A new enzyme named xCas9 allows researchers to target more sites in the genome than with traditional CRISPR-Cas9 editing, while also reducing off-target effects. The technique was reported earlier this year (February 28) by a biologist David Liu and his colleagues.

CRISPR-Cas9 has become the gene-editing tool of choice in many labs due to the effectiveness and convenience. But CRISPR-Cas9 has limitations like the necessity of targeting a particular sequence called a PAM near the gene to be modified, which limits researchers’ ability to make specific genetic changes.

“Relief from the PAM restriction is quite important,” Albert Jeltsch of the University of Stuttgart in Germany. “Some of these elements are quite small, and then the restriction can be quite relevant.”

Liu and his colleagues used a laboratory technique to evolve an enzyme that could recognize a broader range of PAM sequences, enabling more sites in the genome to be targeted. It just so happens that xCas9 also turned out to be more specific to the targeted sites, with fewer off-target effects. xCas9 will allow gene therapy to have higher success rates.

Chemical Changes Triggering Allergic Reactions

A research team at Oxford University recently conducted a study to determine what conditions are more likely to trigger an allergic reaction to nuts in mice. The team used roasted peanuts and raw (regular) peanuts, purifying the proteins from both and then introducing the 2 types of peanut proteins multiple ways.

The response was shocking: the mice who were exposed to dry roasted peanut proteins had many more immune responses than the mice exposed to raw peanut proteins. This “immune response” closely resembles a human allergic reaction.

8483070167_1a90af12df_zThe actual act of roasting peanuts seems like it wouldn’t change much other than taste, but the science of the act shows that with heat, the proteins are chemically modified. The common concept of enzyme performance being altered by changing the temperature or pH applied in this experience. Peanuts contain the enzyme Cyp11a1,  a recurring link in allergic reactions. When heat was applied to the protein of a peanut, the enzyme’s shape changed and therefore the active site was altered and the enzyme was unable to perform its function. Therefore, an allergic reaction to the heat-modified (roasted) nuts was more easily triggered.

Being someone who suffers from a nut allergy (I know, I’m missing out on Nutella), I found this article very interesting because I’ve experienced certain situation with inconsistent reaction triggers, and I’m curious as to what they might be. I also found the geographical link regarding the allergy outstanding – the Western population of nut allergies is reportedly much higher than that of the Eastern population, but in the article, the distinction is made that as Westerners, we tend to eat our peanuts roasted/dry-roasted, whereas the Eastern population is likely to eat their food raw.

Photo by: Daniella Segura ; Some Rights Reserved


Study Shows Link Between Enzyme and Spread of Breast Cancer


 “40,000 women in America will die of breast cancer in 2014.” This is a truly terrifying projection. Breast Cancer is an extremely deadly, and extremely prevalent cancer that affects the lives of millions each year. In my personal experience, I have many friends and family members that have battled against this cancer. So many are affected, and there is still no concrete cure. There is no cure, however, researchers at the University of California, San Diego School of Medicine have identified an enzyme that is closely related to the metastasis of breast cancer cells. This is great news, for it suggests the possibility of further research using this finding to end breast cancer for good. Xuefeng Wu, a lead scientist involved with this research, has stated that the team has been able to “target breast cancer metastasis through a pathway regulated by an enzyme“. This enzyme is called UBC13 and it regulates the activity of a protein called p38.

This p38 protein, when not in use, prevents metastasis. By identifying the enzyme that prevents the use of p38, researchers have come one step closer to preventing the spread of breast cancer in the body, and therefore defeating it. With the use of a lentivirus injected into the mammary tissues of mice, the scientists were able to suppress the functions of both UBC13 and protein p38. The mice grew primary tumors, as was expected, however the primary tumors did not metastasize and spread breast cancer cells throughout the bodies, which means the cancer was stopped from spreading throughout the body. This prohibition of the cancer cells to spread is a major breakthrough in breast cancer research and will without a doubt contribute greatly to the ending of breast cancer.

The Perfect “Enzyme Cocktail”



Photo taken by Vincecate

There is currently a great desire worldwide to create fuels from plants (that are abundant and not eaten).  For background on this topic, click here.  This process is possible, but making the fuel is expensive, time consuming, and difficult.  However, chemists at the Department of Energy’s Pacific Northwest National Laboratory have done research to develop a new, highly improved method for procuring economical, more realistic biofuels.

The most crucial step in the biofuel production process (making fuel from plants such as corn stalks and switchgrass) is the break down of sugar polymers into monomers, which can then be made into fuel compounds.  Plants contain energy, which they store in their carbon bonds.  This energy can be converted to fuel if these bonds are broken.  However, lignocellulose, which holds the plants together structurally, is difficult to break apart.

Finding a more efficient way to break down the sugars in plants would greatly lower the cost of biofuel production.  Trichoderma reesei is a fungus that can “churn out enzymes that chew through molecules like complex sugars”.  Thus, the fungus produces many enzymes that can help to procure fuel from plants.  New research is being done to find which of these enzymes (called glycoside hydrolase) work most efficiently together and individually at different temperatures, pressures, and pH levels in an effort to reach maximum efficiency in the process.  Chemist Aaron Wright said, “Identifying exactly which enzymes are doing most of the work you need done is crucial for making this an economical process.”

This procedure of tracking each enzyme through each stage of a complicated process would normally take months to complete with regular enzyme testing (perhaps like the testing we did in class, but much more complex!).  However, Wright’s team created a chemical probe that allows intense testing to be accomplished in only a few days.

As the price and sources of gas are such common concerns today, I am curious to see if this experiment will come to fruition to produce an environmentally friendly, sustainable, efficient, and economical source of fuel.

Original Article

Hearing Loss Clue Uncovered

In the United States, approximately forty-eight million (twenty percent) of men and women suffer some degree of hearing loss, as it is the third most common physical condition after arthritis and heart disease. While it is most often associated with the population sixty-five and
older, hearing loss effects all ages, as thirty school children per out one-thousand are afflicted in some varying degree. An individual is able to hear sound involving the ear’s main structures. In age-related hearing loss, one or more of these structures is damaged: the external ear canal, the middle ear, and the inner ear. External ear canal impairment is related exclusively to conducive hearing loss. The middle ear, which is separated from the ear canal by the eardrum may be caused by sensorineural hearing loss. Lastly, the inner ear, which contains the cochlea, the main sensory organ of hearing. When the vibrations from the middle ear enter the cochlea it causes the fluid to move and the sensory hair cells pick up this movement. In response to the movement of the fluid the hair cells send an electrical signal up the auditory nerve to the brain where it’s recognized as sound.


Now, how do these different internal departments of the human ear gradually induce hearing loss? While we get older, some may develop presbycusis, which causes the tiny hair-like cells in the cochlea to deteriorate over time. Clarity of sound decreases, as the hairs are unable to vibrate as effectively in response to sound. Recently, otolaryngologists have discovered new evidence that human hearing loss relates to a certain genetic mutations. A study at the University of Melbourne revealed “a novel genetic mutation was first identified in 2010 as causing hearing loss in humans… now discovered that this mutation induces malfunction of an inhibitor of an enzyme commonly found in our body that destroys proteins – known scientifically as SERPINB6. Individuals who lacked both copies of this “good gene” were shown to have lost their hearing by twenty years of age.


Although this discovery is changing the way scientists previously viewed hearing loss, the answer to why this mutation, SERPINB6, is a catalysts for such loss, is inconclusive. However, this mutative gene has created a revelation for many: it is now not unusual to show gradual signs of hearing loss under the age of sixty years.


To better understand the effects of the mutant gene, mice were used in order to imitate the condition from youth to adulthood. At only three weeks of age, mice with SERPINB6 had begun to lose hearing – three weeks is equivalent to pubescent or teenage years in humans. And as we could have predicted, the mice continued to show a decrease in hearing ability, much the same as humans. Researchers examined the mice’s inner ear, which revealed the cells responsible for interpreting sound (sensory hair cells) had died.


Fortunately, this new discovery of a mutant gene in human sensory cells has created new attention to better understand the case of those who are effected by the condition. 



Protein Might Help Fight Deadly Diseases

The enzyme “Cholesterol-25-Hydroxylase,” or CH25H, might help fight against human viruses such as Rift Valley Fever, Niphah and HIV. CH25H converts cholesterol to an oxysterol called 25HC, which can permeate a cell’s wall to prevent a virus from getting in. The CH25H enzyme is activated by interferon, an anti-viral cell signaling protein produced in the body.  Researchers have known that interferon has been part of the body’s defense mechanism against viruses, though it does not have any antiviral properties itself.

This discovery is revolutionary because other antiviral genes have not been able to be used for treatment of viruses in humans. According to Yang Lui, a student at the David Geffen School of Medicine at UCLA, most antiviral genes are difficult to use in therapy because the genes are difficult for cells to express. However, CH25H is different because it is naturally synthesized.

HIV Replication within a cell

The discovery of CH25H is relevant to the efforts to develop broad antivirals against an increase of emerging pathogens. In a collaboration with Dr. Lee, another UCLA professor, it was discovered that the 25HC produced from CH25H can inhibit HIV growth in vivo. The researchers initially found that 25HC inhibited HIV growth in cultures. When implanted mice with human tissues, the 25HC reduced the HIV in within 7 days and reversed T-Cell depletion caused by the HIV. It was also discovered that 25HC inhibited the growth of other diseases such as Rift Valley Fever Virus and Ebola.

There are still some weaknesses with the study. It’s difficult to deliver 25HC in the large doses needed to fight viruses. Researchers also need to compare 25HC to other antiviral HIV treatments.

Amino Acids and Autism

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According to a recent study, an amino acid deficiency may be to blame for a rare form of hereditary autism. As stated in the Nature magazine article, genome sequencing in six children with Middle Eastern backgrounds uncovered “mutations in a gene that stops several essential amino acids being depleted” (Callaway). These mutations inactivate the enzyme BCKD-kinase. As we discussed in class, an enzyme increases the rate of a chemical reaction. However, why the lack of this enzyme would cause autism is still unknown.

Joseph Gleeson, a child neurologist who headed the study, suggests that low levels of branched amino acids to the brain, high levels of larger amino acids , or both might be behind autism symptoms.

Mice who also lacked BCKD-kinase exhibited tremors and epileptic seizures common to autism. However, when given dietary supplements of the branched amino acids, the chemical imbalance was treated and their symptoms disappeared.

Supplements given to the autistic children normalized their blood levels of amino acids. The patients’ conditions did not worsen, however, there was no real evidence that symptoms were reduced. Consequently, Gleeson hopes to conduct a clinical trial testing the effectiveness of dietary supplements in mitigating symptoms of autism and further identify children with the gene mutations for BCKD-kinase.

Matthew Anderson states that Gleeson’s study will “encourage other researchers to explore metabolic pathways as causes of autism.”

The amino acid deficiency may only compose a small percentage of all autism cases, but this is still a large step. The results of further study may present us with the “first treatable form of autism” (Gleeson).

Comments welcome!


Gamers solve some of biology’s most difficult riddles?

Who is solving some of biology’s most difficult puzzles and riddles? Obviously scientists, right? Think again. It’s the gamers.

An article recently reported that a revolutionary online game called Foldit, allows anyone, from gamers to students, to help predict the foldings and structures of  various proteins by playing competitively online. Protein folding is one of biology’s most difficult and costly problems, and is even a troublesome task for the most capable computers. A game such as Foldit requires much insight and an intuitive understanding to fold the proteins, allowing human intuition to triumph over a computer’s calculations. As we have learned in class, proteins are very prevalent in the human body. Hormones, enzymes, and antibodies are all examples of proteins, but many proteins are also associated with strands of viruses and diseases.

This is where you, as the gamers, come into the picture.

Since proteins play a large role in the functions of viruses and diseases, gamers playing Foldit can help design new proteins to help treat or provide a cure for the condition. The article reported that gamers have most recently solved the structure of an enzyme crucial for the reproduction of the AIDS virus. Knowing the structure, scientists are now able to find certain drugs to neutralize the enzyme and stop the reproduction of AIDS virus.

In class, we have learned that there is basically an infinite amount of combinations of proteins; there are 20 amino acids and can be combined to form chains of various lengths. We have also learned that the structure of a protein is also correlated with its function. The bonds present in the primary, secondary, tertiary, and quaternary structures of proteins are an important part to the shape and folds of a protein, giving the protein certain properties due to its shape. All of the information we have learned about proteins in our AP Biology class, can be seen and easily applied to the game, Foldit.

Now since we know the vital importance of proteins, do you want contribute to the next cure for a virus or disease? Get your game on and try Foldit out and see what you can do to solve some of biology’s most difficult riddles!




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