Amino Acid


According to my immunology professor, the levo/dextro allergic reaction mentioned in the Mass Effect series is a mistake. Our immune system would simply pass over the “foreign” amino acid isomers without recognizing them as a threat. It’d still have no nutritional value though. (To keep it simple: eating turian/quarian food would be perfectly safe, but also totally useless for a human.)


Knowing the 20 Amino Acids is definitely a MUST for the 2015 MCAT 

Amino acids that are usually negative (i.e. de-protonated) at physiological pH:

- Glutamate (E) Glu, and Aspartate (D) Asp

Amino acids that are usually positive (i.e. protonated) at physiological pH:

- Lysine (K) Lye, Arginine ® Arg 

Histidine is sometimes charged at physiological pH. 

physiological pH = 7, Neutral 


28 July 2016, 13:00 || it’s just me, myself, and i, solo ride until i die || did lots of bio today! finished the entire unit of biochem, but i’m still in the process of rewriting my protein notes. these amino acids are going to be impossible to memorize :(

Chickens on an unsupplemented vegetarian diet typically fall short of an essential protein-based amino acid known as methionine, and without it, they fall ill. Worse, the birds will also turn on each other, pecking at each other in search of nutrients, and these incidents can escalate into a henhouse bloodbath, farmers say.

Which came first: The Thermophile or Halophile Environment? Or both?

Many scientists have believed that life originated from thermophile environments (environments with extremely high temperatures), such as deep ocean vents, where superheated water and mineral deposits are evacuated and met by cold water. Another leading theory says that RNA molecules were the first to emerge on the planet, probably also in high-temperature environments, which ultimately led to the first life forms on earth. This theory is widely believed within the scientific community because of the fact that all living cells contain RNA.

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A New Potential Cause for Alzheimer’s: Arginine Deprivation

Increasingly, evidence supports the idea that the immune system, which protects our bodies from foreign invaders, plays a part in Alzheimer’s disease. But the exact role of immunity in the disease is still a mystery.

(Image caption: In a mouse model of Alzheimer’s disease, immune cells called microglia (shown in the black stain) become active in areas of the brain involved in memory and consume an important amino acid, arginine. Credit: Carol Colton lab, Duke University)

A new Duke University study in mice suggests that in Alzheimer’s disease, certain immune cells that normally protect the brain begin to abnormally consume an important nutrient: arginine. Blocking this process with a small-molecule drug prevented the characteristic brain plaques and memory loss in a mouse model of the disease.

Published April 15 in the Journal of Neuroscience, the new research not only points to a new potential cause of Alzheimer’s but also may eventually lead to a new treatment strategy.

“If indeed arginine consumption is so important to the disease process, maybe we could block it and reverse the disease,” said senior author Carol Colton, professor of neurology at the Duke University School of Medicine, and a member of the Duke Institute for Brain Sciences.

The brains of people with Alzheimer’s disease show two hallmarks – ‘plaques’ and ‘tangles’ – that researchers have puzzled over for some time. Plaques are the build up of sticky proteins called beta amyloid, and tangles are twisted strands of a protein called tau.

In the study, the scientists used a type of mouse, called CVN-AD, that they had created several years ago by swapping out a handful of important genes to make the animal’s immune system more similar to a human’s.

Compared with other mice used in Alzheimer’s research, the CVN-AD mouse has it all: plaques and tangles, behavior changes, and neuron loss.

In addition, the gradual onset of these symptoms in the CVN-AD mouse gave researchers a chance to study its brain over time and to focus on how the disease begins, said the study’s first author Matthew Kan, an MD/PhD student in Colton’s lab.

Looking for immune abnormalities throughout the lifespan of the mice, the group found that most immune system components stayed the same in number, but a type of brain-resident immune cells called microglia that are known first responders to infection begin to divide and change early in the disease.

The microglia express a molecule, CD11c, on their surface. Isolating these cells and analyzing their patterns of gene activity, the scientists found heightened expression of genes associated with suppression of the immune system. They also found dampened expression of genes that work to ramp up the immune system.

“It’s surprising, because [suppression of the immune system is] not what the field has been thinking is happening in AD,” Kan said. Instead, scientists have previously assumed that the brain releases molecules involved in ramping up the immune system, that supposedly damage the brain.

The group did find CD11c microglia and arginase, an enzyme that breaks down arginine, are highly expressed in regions of the brain involved in memory, in the same regions where neurons had died.

Blocking arginase using the small drug difluoromethylornithine (DFMO) before the start of symptoms in the mice, the scientists saw fewer CD11c microglia and plaques develop in their brains. These mice performed better on memory tests.

“All of this suggests to us that if you can block this local process of amino acid deprivation, then you can protect – the mouse, at least – from Alzheimer’s disease,” Kan said.

DFMO is being investigated in human clinical trials to treat some types of cancer, but it hasn’t been tested as a potential therapy for Alzheimer’s. In the new study, Colton’s group administered it before the onset of symptoms; now they are investigating whether DFMO can treat features of Alzheimer’s after they appear.

Does the study suggest that people should eat more arginine or take dietary supplements? The answer is ‘no,’ Colton said, partly because a dense mesh of cells and blood vessels called the blood-brain barrier determines how much arginine will enter the brain. Eating more arginine may not help more get into the sites of the brain that need it. Besides, if the scientists’ theory is correct, then the enzyme arginase, unless it’s blocked, would still break down the arginine.

“We see this study opening the doors to thinking about Alzheimer’s in a completely different way, to break the stalemate of ideas in AD,“ Colton said. "The field has been driven by amyloid for the past 15, 20 years and we have to look at other things because we still do not understand the mechanism of disease or how to develop effective therapeutics.”


In solid phase peptide synthesis Kaiser Test is a quite important thing when you need to detect free N terminus at the end of your amino acid chain. The chain is linked via its C-terminus to the solid support, with the N-terminus extending off it. When that nitrogen is deprotected, a ninhydrin test yields blue. Amino-acid residues are attached with their N-terminus protected, so if the next residue has been successfully coupled onto the chain, the test gives a colorless or yellow result.

The only problem is when the ninhydrin solution accidentally goes through your gloves, gets on your skin and reacts with your amino acids, mainly with free N terminal of lysine (first pics) and turns your skin purple.

Also important that if the ninhydrin in at least 20 years old and it wasn’t stored properly it could decompose and could easily give fake results when using it for a Kaiser Test. To avoid this, we recrystallized a small sample of it (10g) and got those nice crystals as seen on the pics. Ninhydrin (2,2-Dihydroxyindane-1,3-dione) could be easily recrystallized from hot water with a small amount of decolonizing carbon to give pure samples. 

Life from the Ancient Soup: The Miller and Urey Experiment

Alright, so we know how eukaryotes came to be, but how did life arise in the first place? In the early 1950s, an experiment performed by a couple of guys at the University of Chicago gave us a pretty good idea.

Early in Earth’s history, the conditions of the planet were relatively hostile. Temperatures were high, lots of energy was running riot (such as lightning, volcanoes, and UV radiation), and the atmosphere was reducing rather than oxidising, meaning that it was devoid of gaseous oxygen, but had plenty of methane, hydrogen, carbon dioxide, water vapour and nitrogen.

Miller and Urey decided to simulate these early Earth conditions in the lab to see if they could produce some form of life. Basically, their aim was to find out whether these abiotic (lifeless) conditions were conducive to the rise of living organisms.

To do this, they sealed ammonia, methane, hydrogen and water into a closed, sterile system. Then they heated it to form water vapour, and passed electrical sparks through it to simulate lightning.

After a week or two of brewing time, they analysed their mixture and found that up to 15% of the carbon in their system had formed into organic molecules—most noticeably, amino acids. Amino acids are the building blocks of proteins, which are one of the three most important macromolecules of life.

(Image Source)

By themselves, amino acids are relatively small and simple, but together they join to build structures far bigger and grander than individual molecules: life.

So, Miller and Urey found that it’s a cinch to synthesise at least the building blocks of life out of some messy soup.

Further resources: Animation