CHEM 106

Coming across one of the blog entries on rainbows, I immediately thought of the time when I saw the Northern Lights while on holiday. Till date, it is one of the most spectacular and breathtaking phenomenon I have ever seen! The multitude of colors intermingling with each other across the night sky, it is a truly gorgeous sight. Our discussion on light motivated me to read more about how this phenomenon occurs.

The Northern Lights or the aurora borealis are nothing more than a sight caused by the interaction of charged electrons and magnetic poles of the earth. Solar winds stream away from the sun at speeds of about 1 million miles per hour. When they reach the earth, some 40 hours after leaving the sun, they follow the lines of magnetic force generated by the earth’s core and flow through the magnetosphere, a teardrop-shaped area of highly charged electrical and magnetic fields.

­As the electrons enter the earth’s upper atmosphere, they will encounter atoms of oxygen and nitrogen at altitudes from 20 to 200 miles above the earth’s surface. The color of the aurora depends on which atom is struck, and the altitude of the meeting. We see green when the electrons encounter oxygen upto 150 miles in altitude, red when electrons interact with oxygen above 150 miles, blue when they interact with nitrogen upto 60 miles and purple when they encounter nitrogen beyond 60 miles.

But then how do we see the lights dance? All these magnetic and electrical forces constantly react with each other in changing combinations and this causes the auroras to dance! Also more pertinent to what we learnt in class, green, red, blue and purple aren’t the only colors we can see in an aurora borealis. These different colors all blend together due to the constantly shifting magnetic and electric forces and we see a plethora of different colors based on which colors combine and in what ratio!

I am intrigued to be introduced to new concepts related to light so that I can continue to explore such similar topics that I am curious to learn about. 

https://www.youtube.com/watch?v=fVsONlc3OUY

Sound waves are a vibration (disturbance of air) that travels through a medium (air, water, a solid, etc.). The vibrations are different in size and shape, which is what produces different sounds. Sound waves can not exist in a vacuum (because inside there is no air to vibrate) but lightwaves can exist in a vacuum. Light is a wave of vibrating electric and magnetic fields. Both sound waves and lightwaves have the same shape for the most part. They are very similar forms of moving energy.

Synesthesia is a sensory disease in which “stimulation of one sensory or cognitive pathway leads to automatic, involuntary experiences in a second sensory or cognitive pathway.” Some synthesthetes associate colors with numbers, but another type of synesthesia is one in which sound is highly associated with different colors. Many master musicians have synesthesia when it comes to sound, and understand sound as a color. It helps them learn and makes them fascinated in the music. I wonder if synesthetes are somehow sensing something about the wave formation similarity between lightwaves and sound waves. It does not seem shocking to me that people associate sound and color in this way because of their similarity.

The experience of synesthesia is unique and hard for people without to understand. But similarly people with synesthesia have trouble understanding what it is like to not have synesthesia. Famous Hungarian conductor and piano virtuouso, Franz Listz, notoriously demanded to his orchestra: “O please, gentlemen, a little bluer, if you please! This tone type requires it!” and “That is a deep violet, please, depend on it! Not so rose!” Many synesthetes are highly successful creative people because of their cognitive differences. 

http://www.classicfm.com/discover/music/synesthesia-gallery/#P5AXSIqw3yw6yIXK.99

https://van.physics.illinois.edu/qa/listing.php?id=2048

http://en.wikipedia.org/wiki/Synesthesia

This week in class, we learned about the speed of light and how light can travel through objects like air and water, but can also travel through nothing in a vacuum. As I looked up more information about the speed of light and its properties, I learned that light actually travels at different speeds depending on what it is traveling through. The fastest that light can travel, and the fastest that anything can travel according to the laws of physics is nearly 3×10^8 m/s . This speed is called c. Light travels through objects like air and glass at a speed less than c. The ratio between c and the speed v at which light travels in a material is called the refractive index n of the material (n = c / v). The refractive index of glass is typically around 1.5, meaning that light in glass travels at c / 1.5 ≈ 200000 km/s and the refractive index of air is about 1.0003, so the speed of light in air is about 299700 km/s. Regardless of what it is traveling through, light is extremely fast.

In watching Ron Hipschman’s talk about light and its properties such as speed, wavelength, and other relative measures, I was inspired to understand how this transmission of light and sound can be applied in everyday life.  First and foremost, he describes Galileo’s speed of light experiment.  In this experiment, Galileo and a friend stood very far apart from one another, each holding up a lantern, and planned that as soon as the first light could be seen from the other side, the second person would turn theirs on as well.  They deduced that this light travel was almost instantaneous.  As Ron Hipschman confirmed, the speed of light is indeed very fast; however, he notes that during the first trip to the moon there were lags in the audio communication due to the sheer distance that the radio waves (acting as sound waves) were transmitted.

               As aforementioned, this example made me question whether or not this delay in travel effects more central to our lives, primarily regarding television functionalities.  While it is widespread knowledge that shows airing ‘live’ have a slight lag time of a few seconds, what I mean by this inquiry is whether or not audio and visual television waves must be sent at the same time or at a slight lag, because intuitively, if both of these waves must be sent first through a satellite, it would make sense for there to be an approximate 3 seconds between the release of the showing and the deliverance to our individual televisions.  While this makes sense because as I mentioned before in regards to the space flight, radio waves travel with the same characteristics as light, I was unable to find any information confirming or disassociating the speed of sound nor light and television difficulties.

In doing some of this week’s readings, I came across some information on the formation of rainbows. Since I was little, I have long been obsessed with the idea of a rainbow and all of its psychedelic colors. I thought I understood the basic concepts of a rainbow (that it was formed when white sunlight strikes water, and so on); but it turns out that there is so much more to the beautiful arcs in the sky than I thought!

In reading Our World of Light and Color, part of this week’s assigned lectures, I was fascinated by the introduction which describes how rainbows are formed.

It turns out that rainbows aren’t even arcs! They’re actually circles but only half of the circle is reflected in the sky! Therefore we’re only ever seeing half of a rainbow! (However, from an airplane you can sometimes see the full circle.)

Additionally, the separation of colors results from the refraction of sunlight at a 42 degree angle from within the water droplet. If two people are viewing the same rainbow from slightly different angles, they will actually being viewing two entirely different rainbows.

I thought all of this additional information about rainbows was very fascinating and can’t wait to learn more about how the human eye perceives color.

One unique characteristic of prion diseases is that they tend to be extraordinarily resistant to extreme conditions. This, added with both the facts that they have fatal effects and they tend to have long incubation times, marks them as very daunting diseases. Because these diseases are so scary, it is obviously important to find ways to prevent them- specifically before the infectious agents are able to enter bodies and cause the diseases.

I read about how the environment can neutralize prion proteins, the infectious agents of prion diseases in a recent article published on February 23rd. Prions can enter the environment- in particular into the soil- through various ways such as waste, saliva, blood, and the decomposition of the proteins’ hosts. After entering the soil, they can remain there for years and then, through acts of inhalation or ingestion, enter into new hosts. Scientists have found that the environment has a natural and common way of combatting this process: rain and sun.

Scientists from Colorado State University, Creighton University, and UNL found that through the procedure of watering and drying soil, they were able to weaken the brutal effects of prion proteins on brain tissue. In fact, even by only repeating the procedure ten times, they noticed a negative effect on the prion protein capabilities.

The scientists know that rain and sun can change the properties of soil, and that drying can affect the structure of proteins. However, the scientists are still unsure as to how exactly the wetting and drying negatively affects the prion proteins’ process- it could be simply the effects on the soil, simply the effects on the prions, or a combination of the two effects. The experimental results demonstrated that the composition of soil influences its ability to affect the prion process, as some soil types better protected the prions. This suggests that some soils might be more likely to retain prions, and thus animals exposed to those soils might be more likely to contract prion diseases. Further, the experimental results suggest that some types of prions are affected more than others by the watering and drying process.

http://medicalxpress.com/news/2015-02-environment-neutralize-lethal-proteins.html

In the reading, E. Coli was used to isolate the PrP. It was difficult at first because of the instability and solubility level of the protein (PrP). There were also problems in the combination of E. Coli and PrP because of the disulphide bonds, which were essential for the proper folding structure of the protein. The cytoplasm of E. Coli “in vivo” were therefore, not effective.

I found this part of the reading a bit difficult, so I looked up some background information on E. Coli that I thought I would share.

E. Coli or escherichia coli, is a species of bacteria that live in the intestines of most healthy people and organisms. Most E. coli does not result in any significant illness.  But there are particular substrains of E. coli that can cause severe digestive illness.

Dangerous strains of E. coli come from food (and sometimes even water) that have been infected with the bacteria. Foods that are particularly at risk of having E. coli is raw vegetables, unpasteurized milk, and undercooked beef. Most people, even when infected with a dangerous strain of E. coli can recover. But children and elderly people, or people with other complicating diseases, can become so sick from E. coli that they need to be hospitalized. The most serious complication that can result from E. coli is hemolytic uremic syndrome, which can be a fatal type of kidney failure.

The Center for Disease Control (CDC) is in charge of tracking potentially contaminated food stocks and tracking the spread of the disease. Most E. coli outbreaks happen between June and September, though it is unclear why. (Maybe because people are eating more raw vegetables and hamburger in the summer??). The last multi-state outbreak of E. coli happened in late July. Nineteen people in six states were affected. 44% were hospitalized. No fatalities.

This research showed me the importance of the government in tracking the epidemiology of diseases and keeping the public safe.

Transmissible Spongiform Encephalopathies, or prion diseases are the result of proteins trying to fold properly but getting it wrong. When proteins get it wrong in mammals it can lead to horrible diseases such as Kuru which causes people to slowly loose motor function and die while completely aware in their minds.

What’s interesting about infectious prion proteins that we have not already talked about is that they can sometimes be beneficial. For example cells containing yeast prions when exposed to certain unsavory conditions can actually fare better than their prion-free siblings. This suggests that the ability to adopt an advantageous prion form may result from positive evolutionary selection in fungi.

Good for you fungi!

Too bad when prions fold improperly in humans they cause the protein to go berserk and kill the host.

I have always known that protein is necessary for the human body to function. We ingest meat, fish, cheese, tofu, beans, eggs, yogurt/milk, soy, and nuts (the top 10 most protein-rich foods) to give our bodies energy. But how exactly does it work?

After learning in class this week about how amino acid chains are put together and broken down, I did some research on how exactly the human body uses protein that it ingests. It turns out that humans need nine amino acids. We cannot produce these essential amino acids on our own, so we need to eat them. They are:

1. histidine
2. isoleucine
3. leucine
4. lysine
5. methionine
6. phenylalanine
7. threonine
8. tryptophan
9. valine

When we eat foods that contain these proteins, they are broken down by our stomach and intestines until the amino acids are just peptides, or a chain of two or three amino acids. Next, the peptides are absorbed into the bloodstream and delivered all over the body. Many go to the liver, where new proteins are synthesized and others are processed into energy. Amino acids are constantly broken down and put back together, so the same pieces are being reattached and detached all the time.

As we looked at the models of proteins in our last class, I was very interested in the model that represented the protein that allows certain jellyfish to glow-in-the-dark. The green fluorescent protein is made of 238 amino acids. Green fluorescent proteins have a beta barrel structure made of 11 B-strands. Scientists first isolated the protein from a specific kind of jellyfish called Aequorea Victoria. Some jellyfish use their luminescence as a defense system if they are attacked by a predator. Once they are attacked, they begin t glow to confuse their attacker and hopefully get away.

Scientists have been able to use this protein as a reporter gene in their experiments. Scientists introduce the fluorescent gene to a bacteria or animal in order to indicate if a certain gene is present. This is helpful because no invasive test is needed to determine if the gene is present. Scientists simply shine a light on the bacteria and if if glows, then the gene is present.