Aufbau Principle

Wow, it's been a while since I posted anything on this site... Earlier today, I was helping my little brother with some high school chemistry and I started filling up orbital diagrams with electrons in a wanton fashion before I realized that I was forgetting something. "Wait a minute... Aufbau." I said, before correcting my work.
In case you don't remember (and there's no shame in that--I clearly can't remember this stuff) Aufbau is German for "building up". Basically, it states that lower energy orbitals are filled before the higher energy ones are. 1s before 2s, 3p, before 4p, 4s before 3d, etc.
Let's review. In groups one and two we have the S orbitals. Two electrons, s1 and s2. Hydrogen, for example is 1s1, being in period one with one S electron. Calcium, for example is 4s2, being in the fourth period with 2 S electrons.
The metals, groups 3-12, are in the d orbitals, while the non-metals in groups 13-18 are in the p orbitals. Lanthanides and actinides fill the f orbitals. Orbitals are ordered by energy, which corresponds to the period with the exception of the d and f orbitals. D orbitals are n-1, such that they are 3d, 4d, 5d, 6d, even though they are in periods 4-7. F orbitals are n-2.

O2 binding curve of Hemoglobin

It seems I've been slacking on Science for Slackers lately, but I supose that's to be expected given the name of the blog. I've spent the last month doing a wilderness EMT course in the mountains. During that time we talked a lot about breathing and although we never touched on the subject I couldn't help but think a bit about the factors that effect hemoglobin's ability to bind oxygen.

As we all remember, hemoglobin is a tetrameric (four part) protein of erythrocytes (red blood cells) and is primarily responsible for delivering oxygen to the body's tissues and removing the CO2 that they have built up by carrying it back to the lungs.

The above chart gives a nice basic summary of some of the major factors that effect the oxygen saturation of hemoglobing. As shown on the chart a decrease in pH, an increase in temperature, or the precense of the coenzyme 2,3-DPG (2,3-diphosphoglycerate, also know as 2,3-bisphosphoglycerate or 2,3-BPG) can all shift the curve to the right. This means that hemoglobin does not bind oxygen as well, but it binds CO2 better. The opposite can happen as well.

In general, both of these processes will take place congruently in the body. For example, lung tissue generally has a higher pH than muscle tissue and therefore binds O2 better and releases CO2 more easily, but when the same erythrocytes reach slightly more acidic muscle tissues, the curve shifts to the left and they release O2 in favor of binding CO2.

Electromagnetic Spectrum

I was just refreshing my memory with some details of the electromagnetic spectrum. In case you need a refresher too, here it is:

Image source

Mars rover still rockin'!

The Mars rover, Spirit, has been exploring Mars since 2004. Since May 1st it has been stuck in a sandy area, which consists mostly of ferric sulfate, Fe2(SO4)3. The soil where Spirit currently rests has little cohesion and the rover has been unable to move. Scientists have been attempting to figure out the best way to free the rover. Luckily, the spot where the rover currently resides is apparently quite geologically interesting and the rover has been busy examining the layers of sediment in the area, which are like compacted sand. Each layer is a different color and one hypothesis suggests that liquid water may have caused the cementing action that resulted in these layers!

Finals Week and Graduation

Sorry for the lack of posts recently. It's been a hectic end to the quarter and this week is finals week, so it won't be much better. Coming up though, I've got an interesting article on the Hubble and also a bit of an exploration of clean coal. Hopefully by midweek, finals stress should calm down enough for me to finish those articles.

Wolfram|Alpha a new way to search?

Sorry for the slow posting this week, I've been busy trying to graduate in two weeks and taking advantage of the great weather to do some climbing.

A new search engine Wolfram Alpha launched last week. Although it currently is configured for technology, science and math searches more than normal searches, it has the potential to be revolutionary. Unlike google, the search engine is semantic. It answers questions rather than giving results based on keywords. It's probably not something you want to start using on a day to day basis, but this has the potential to really change the way we search.

It also has a lot of data readily available. For example, you can type in a chemical compound and it will give you all the physical and chemical properties. You can even do side by side comparisons.
Typing in a math equation results in plots of the equations, derivatives and integrals, local minimums and maximus...etc.

There really is a ton of information here and you don't have to visit a bunch of websites to find it all, it just loads up in the same page. Check it out: http://www.wolframalpha.com/

Hubble Telescope

A few weeks ago, on May 11, NASA space shuttle Atlantis blasted off on the fifth and final mission to service the productive space telescope known as the Hubble.
The Hubble telescope was launched in April 1990 and has taken some amazing pictures over the last nineteen years. One reason the Hubble has been so productive over the last two decades is that it is the only space telescope that has been designed to be serviced in space. There have been five service missions to the Hubble. The last mission, which occurred last month, fixed a few of the failed instruments and NASA hopes that it will extend the life of the Hubble until 2014.
The Hubble currently has six imaging instruments on board and can detect visible, infared and UV light.
In 2014 a new space telescope, called the James Webb Space Telescope, will be launched to replace the Hubble. The JWST will not be able to detect visible or UV light like the hubble, but it is much more sensitive to infrared radiation and will hopefully be able to detect light from stars that are extremely far away. Since it can see light that is so far away, the light that is detected is also from events a very long time ago. Hopefully this telescope will allow us to learn a bit about how stars and galaxies are formed.

Sun Protective Clothing

I work at an outdoor store part time and I've been seeing more and more sun protective clothing on our racks. The promotion of UPF rated clothing seems to be following the trend of greater awareness of the dangers of sunburns and many people come looking specifically for UPF rated clothing, but what does UPF mean and how does it work?
Well, there is some good information on this outdoor retailer's website, but here's what it boils down to.

UPF means 'ultraviolet protection factor', which is similar to an SPF rating (sun protection factor) that you might see on a bottle of sunscreen, except that SPF usually only protects against UVB rays not UVA. Remember that sun light reaching the ground includes both UVA and UVB type rays and that UVB rays are generally more damaging due to their shorter wavelenth and greater energy, but both UVA and UVB can cause sunburns.

Sunscreen generally contains a mixture of organic molecules that happen to absorb UV light at the specific wavelenths that can cause sunburns. UPF clothing however does not necessarily use chemical treatments to protect us form UV light, so what are the major ways that the clothing can protect us?
Let's start with the obvious:
1. Thick or densely woven fabric. This makes intuitive sense, if the fabric is thick or tightly woven, light rays, even high energy UV light rays, won't be able to penetrate it. For example, even though your jeans are not UPF rated, you probably have never been sunburned through them, because they are thick and densely woven, but a thin loosely woven linen shirt wouldn't protect you for a minute.
2. Dyes. Various dyes, and the concentration that they are used to color the fabric can dramatically increase the sun protection of even thin or relatively loosely woven fabrics. This is similar to the sunscreen idea. The dyes help absorb UV light because of their chemical structure. Note: this does not have to do with the color of the garment, rather the chemical structure and concentration of the dye in the fabric.
3. Chemical treatment. Further chemical treatments, which operate like sunscreen, can be used to increase the UPF rating of various fabrics in addition to the dye.
4. Materials. The choice of material which the fabric is woven from makes a big difference. For example, polyester, which has a chemical structure ready to absorb UV light is quite good at protecting you. Nylon, wool and silk in descending order follow behind polyester, while cotton and hemp type fabrics usually aren't very good.
Most UPF rated garments use a mixture of these qualities to protect you from the sun. For example, a tightly woven polyester shirt can be dyed with a UV absorbing dye and subjected to further chemical treatment for optimal UV protection.

Remember, all clothing is going to give you some UV protection, simply because it is a physical barrier between you and the photons coming from the sun, but the ratings displayed on some clothing items are intended to quantify that protection.
The rating displayed is usually representative of the fraction of UV light that the fabric will allow through. For example, a 25 UPF shirt will allow 1/25th of the UV light that hits it through (4% UV light transmission) and a 50 UPF pair of pants will allow 1/50th of the UV light through (2% t).

That's the basics of UPF clothing. I'll try to get into a bit more of the chemistry behind it later this week.

ATP Synthase is similar to a combustion engine

After seeing this gif (created by John Walker's lab at MRC) in biochem class the other day, I couldn't help but notice that the gamma subunit of ATP synthase serves a strikingly similar purpose to a camshaft on most modern combustion engines.

Just think of that central blue colored gamma unit, which is slightly bent, as a camshaft shifting the yellow beta units and catalyzing the ATP synthesis reaction, ADP+P-->ATP. You can see the similarities below on the two camshafts of this internal combustion engine animation, which operate intake and outtake valves rather than catalytic proteins.


The ATP Synthase can make up to 150 revolutions per second. That would be 9,000 rpms in automobile jargon--a speed that most car engines cannot manage!

Invisibility Cloak? Not just yet.

Scientists at Lawrence Berkley National Laboratory and Cornell University have jointly developed what they call an invisibility cloak. Before you get any images of futuristic jungle wars against invisible aliens in your head (just think Arnold Schwarzenegger in 'Predator'), let's examine some of their claims.

My roommate showed me this article the other day. He was really excited about the prospect of invisibility being commercially available. As I read the article, my science radar--that skeptical voice in the back of my head--kept going off. The device works by allowing light to flow around an object like water around a rock. Except in this case, the object they were cloaking was a 1 micron bump (see image). Did your science radar go off when you read that? It should have. One micrometer (0.001 mm) is not big enough to see with the naked eye. In fact according to my biology text, the unaided eye can usually only see things as small as 90 micrometers. In fact, one micron is smaller than most Eukaryotic cells, and even on the small side for a bacterial cells.

The article goes on to say that previous cloaks have only worked in the radio and in microwave spectrums, but this one is barely within the visible spectrum. It works by placing silicon nanoparticles at varying densities over the bump they are trying to conceal so that the light reflects off of it as if it were a flat surface. The labs say they will soon be able to scale it up in size and shift it to cloak in the visible spectrum. Certainly looks promising, but don't expect any disappearing acts soon.


Source

What are viruses anyway?

Continuing my discussion of viruses, I'm probably becoming part of the frothy mouthed, virus-frenzied media I mentioned the other day. However, Swine flu is still being discussed and I'm still curious to explore some basic virology. So today's question is: What are viruses anyway? To answer this question, I dusted off (literally) my trusty Biology text (1).

The first thing we need to do when discussing viruses is try to get a sense of the scale of a virus. Viruses can range anywhere form 20-250nm. A nanometer is 0.000000001 meters. To give that a little more context most plant and animal cells are 10-100um. (A micro meter is 0.000001 meters) Which means that the average virus is 1000 times smaller than most cells.

Viruses are extremely varied in that their genomes can be constituted by a variety of nucleic acid types. Some viruses are based on DNA and some use RNA, some are double stranded and some are single stranded. Regardless of the type of nucleic acids that make up a virus' genome, no virus can replicate its own genes and must infect a host organism to do so.

Most viruses have a protein shell called a capsid that protects the viral genome. These capsids have a variety of shapes and are made of a variety of proteins. The surface proteins of the capsid are generally what produce a specific antibody reaction of the immune system in an infected organism. There are a variety of shapes of virus capsids.

Image source.

As mentioned above, viruses consist of a protein shell containing some form of nucleic acid genome and lack the cellular machinery necessary to replicate their own genetic material. To overcome this disadvantage viruses infect host organisms and take advantage of the hosts ability to copy its genome. The basic scheme goes like this:
A virus enters the cell and its capsid is dissolved releasing the virus' genetic material within the cell. The host cell replicates the genetic material and produces more of the capsid proteins and several new viruses are reassembled. These viruses leave the cell and each go on to infect a new host cell. This process is called the Lytic cycle (see image below).

Of course, this is an extremely basic understanding of how viruses operate and it should be noted that many viruses can incorporate their genes into the DNA of a host and remain dormant for some time, waiting for favorable cellular conditions before replicating. This process is called the Lysogenic cycle (see image below).




1. Campbell; Reece. Biology. 7th Ed. 2005.

Naming Virus Strains: The Meaning of H1N1

With all the talk about swine flu lately the term H1N1 has been thrown around a lot. Hearing it repeatedly, I became curious how viruses are named, so here's a brief explanation:

Influenza causing viruses come from a family of viruses called Orthomyxoviridae. Orthos is Greek for "straight" and myxa is Greek for "mucus" (1). While there are actually five subcategories or genera of Orthomyxoviridae, only three infect humans. Those are the influenza causing viruses termed Influenza A, B and C. The terms A, B and C come from the type of antibody response generated by a body infected with the particular strain of virus. Although humans can be infected with all three types, influenza A is the most serious and is the cause of most major outbreaks.

After the genera of the virus has been determined, the subtype of the virus must be named. This is based on the type of surface proteins on the virus. There are usually two classes of proteins, hemagglutinin (HA) or neuraminidase (NA). Sixteen types of hemagglutinins and nine types of neuraminidases are known to scientists. These recieve the designations H1-H16 and N1-N9. All possible combinations of HA and NA porteins do exist, but only a few of them are known to infect humans. The current swine flu virus is titled Influenza A (H1N1).


Image source. Note the HA and NA surface proteins that elicit the immune response of antibodies.

There is, however, one more complication to the naming of viruses. Viruses can mutate very quickly. This means that there are many strains that are similar but slightly different. This makes viruses difficult to inoculate against and also difficult to name. Scientists have taken to naming viruses according to the procedure described above, but they also get more specific. Scientists sometimes further identify the specific strain of virus by noting some or all of the following descriptors: the animal it was isolated from, the year, the location and possibly the lab which grew the culture. For example, here are more than 100 different gene sequences for the current A(H1N1) strain isolated in the last two weeks. Each one is named like this: (A/Arizona/01/2009(H1N1)) or (A/Valencia/GP4/2009(H1N1)) noting first the genera (A), then the location, the specific culture, the year and finally the subtype.

For more about influenza check out my main source.