Biochemistry - The Science Behind Crying

Crying

A Topic We are All Quite Familiar with After Taking Honors Chemistry

Those of you who know me well will understand just how fitting this topic is for me because I tend to cry... like a lot. I can rarely ever control my emotions, whether they be anxiety, sadness, happiness, or frustration, and I often end up in tears. But emotions aren't the only thing that cause tears. In fact, there are three different kinds of tears; basal tears, reflex tears, and emotional tears. The circumstance and mechanism surrounding each tear determines the chemical makeup which can tell a lot about its biological function. You probably don't know it, but your body is constantly producing basal tears. And by constantly I mean 1.2 ml of tears a day. Basal tears consist of three layers and their main objective is to keep dirt and debris away from your eyes. The first layer, the mucus layer, keeps the whole thing fastened to the eye. The second layer, the aqueous layer, keeps the eye hydrated, repels invasive bacteria, and protects the cornea from damage. The third layer, the lipid layer, is an oily outer film that keeps the surface smooth for the eye to see through and also keeps the other layers from evaporating. The lacrimal glands make basal tears constantly, which contain water, mucin, lipids, lysozyme, lactoferrin, lipocalin, lacitin, immunoglobulins, glucose, urea, sodium, and potassium. The lacrimal puncta drains the old tears away through a complex tube system.

Reflex tears are the kind that collect in your eyes when something is irritating them. These tears contain a high concentration of antibodies to stop microorganisms from damaging your eyes. When a foreign substance is detected by the sensory nerves in your cornea, they communicate this irritation to your brian stem, which then sends hormones to the glands in the eyelids. These hormones cause the eyes to produce tears. Some examples of substances that would trigger reflex tears are tear gas, pepper spray, or onion vapors. When an onion is cut a chemical reaction happens to convert sulfoxides into sulfenic acid, which then becomes Syn-propanediol A-oxide (RS(O)CH₂CH₂R → RSOH + CH₂=CHR). The gas stings the eye and reflex tears kick in to wash away harmful substances.

To your body, strong emotions such as stress, frustration, sadness and happiness feel like a loss of control which can be dangerous. First emotions are registered in the temporal lobe of the cerebrum. Then the endocrine system is triggered to release hormones to the ocular area, which causes tears to form. Emotional tears are sent in to stabilize the mood as quickly as possible, much like an increased heart rate and slow breathing. Emotional tears are produced in such large quantity that they overflow and overwhelm the nasal canal of the tear ducts and flow down our cheeks. Humans are the only species that cry emotional tears and the purpose of these tears is still being determined. Some theories suggest emotional tears work as a social mechanism to elicit sympathy or show submission. While reflex tears are 98% water, emotional tears contain high levels of stress hormones, such as prolactin, Adrenocorticotropic hormones (which indicate high-stress levels), and enkephalin (an endorphin that reduces pain). It seems as if the body is getting rid of these chemicals through tears. This suggests emotional tears directly calm down emotions as well as signal emotional state to others, which makes for easier communication.

Biochemistry in Animal Testing

Biochemistry in Animal Testing

What is animal testing?

Animal testing occurs when scientists use animals to test certain products or perform experiments as a substitute for humans. By using animals in experiments, scientists can avoid the possibility of the death or injury of humans.

How does it relate to Biochemistry?

Animal testing relates to biochemistry in many different ways. Scientists must have a very in-depth knowledge of the animal that they are testing, including an understanding of the overall body structure, and the specific chemical processes that occur within it. As well as this, scientists have to use animals that share similar characteristics with humans in order to be sure that the product or experiment will not behave differently once used in the real world. This requires intensive knowledge of the specific chemical processes, enzymes, proteins, and DNA within both the test animal, and humans.

Example of Human Chromosomes

Through animal testing, scientists have also been able to make many new advancements in the biochemistry realm, with opportunities to learn more about the bodily functions that occur within living organisms, the DNA in living organisms, and other specific chemical reactions that can occur within living organisms.

What kind of animals are used in animal testing?

The most common animals that are used in experimentation and testing include mice, rabbits, guinea pigs, and monkeys. Because these animals are mammals, they tend to replicate common human behavior, and genetic characteristics. As well as this, animals like mice, rabbits, and guinea pigs are small, easy to handle, and inexpensive. The genomes of mice and humans are 85% identical, and mice and humans have nearly the same number of chromosomes. As well as this, the mouse was the first mammal to have its entire genome sequenced (excluding humans).

Comparison of Mice and Human Chromosomes

What are the benefits of animal testing?

Although many people feel strongly that animal testing is cruel and inhumane, the use of animals in testing and experimentation has provided many opportunities for scientific advancement and has allowed for the protection of human lives that might be affected at a greater cost. Many beauty products that women use daily are tested on animals to ensure their safety, and nearly every new medical advancement in the 20th century resulted from the use of animals testing.

What are the disadvantages of animal testing?

Although many important medical advancements and scientific developments have been made through the use of animal testing, many disadvantages also exist. In some instances, the scientific results from animal testing were completely inapplicable to the human test subjects, resulting in death or serious injury. Although the DNA and the bodily structures of the animals used for experimentation may be relatively similar to that of humans, one small difference in DNA (because of its ability to replicate itself) can have a major effect on the entire system, resulting in completely ineffective results.

Alternative Options:

• Computer models: Advanced technology allows scientists to use computer models to simulate chemical processes and predict the outcomes of certain chemical reactions
• Patient simulators: Many medical schools make use of patient simulators, teaching their students to respond to a medical situation correctly without having to harm any animals
• Midcrodosing: Test subjects are given very small dosages of the test product and they are closely monitored and screened, allowing the scientists to understand the behavior of the drug

Works Cited:

• https://www.crueltyfreeinternational.org/why-we-do-it/what-animal-testing
• http://www.peta.org/issues/animals-used-for-experimentation/alternatives-animal-testing/
• http://www.peta.org/issues/animals-used-for-experimentation/

Biochemistry - Spider Silk

The Spider: Scientist and Spinster

     Spider silk can be stronger than steel while still being a fraction if its weight, and in some cases, proving to be antimicrobial and anti-fungal, which have advantageous applications to use in medicine and surgery. While people have been trying to utilize silk for several years now, but progress has been slow due to the inability to identify and characterize the spider silk genes. However, recently, the Perelman School of Medicine at Pennsylvania State University have announced advancements in this field of study. The scientists and their team at Penn state were able to sequence the full genome of the golden orb-weaver spider, one of the most active silk-spinning spider species. This particular species of spider produces 28 different kinds of silk proteins. These scientists were able to to find new patterns within the genes that may be able to explain the different unique properties of different types of silk. These new DNA sequences hint at possible relation to silk strength, toughness, stretchiness and other properties, such as silk proteins being made in venom glands instead of silk glands. The pursuit for this miracle fiber has been in the works for over 50 years. Scientists hope to be able to extract these genes or decode them in order to understand how we could synthetically bioengineer a material similar to it, manipulating all the possible variations in order to create the "perfect material". Just to illustrate the complexity of this daunting task, the team at Penn was able to identify more than 14,000 likely genes: 28 hat encode spider silk proteins (spidroins), 400 short sequences that they believe relate to silk properties (high-tensile strength, flexibility, stickiness, etc) and 649 non-spidroin genes that control the production of silk, such as conversion of liquid silk from spider cells into workable fibers, a process that many biotech engineers are just beginning to find success in.

     Spider silk is a highly complex biomaterial that has fascinated humanity for centuries, for many reasons: it has tensile strength (resistance to breakage under tension) comparable to steel, elasticity comparable to rubber and toughness that is two to three times that of Kevlar or Nylon. It's antimicrobial, anti-fungal, hypoallergenic and biodegradability also make it extremely versatile and useful. Spiders have  an arsenal of different silks that they use to hunt, capture prey, spin webs, spin cocoons for their eggs and even make draglines (like a safety line that they use to escape from predators). Other than the obvious use of biochemistry to produce such intricate materials, spiders also use intermolecular forces. Not all spiders can spin an adhesive silk, instead using their cribellate silk to act as an "adhesive". A cribellate silk is a wooly, textured silk that is just normal silk that has been combed out to have a texture by the cribella, the spider's hind legs. It exhibits adhesive properties much like a gecko's nano-hair coated feet, through van-der-Waal forces, the spider utilizes the intermolecular attraction between molecules to become "sticky". However, this method of silk spinning is extremely time and energy consuming, which is why ecribellate spiders evolved.

     Ecribellate spiders are able to spin a silk that is sticky through adhesion rather than using the adhesive properties of the nano-hairs. This sticky silk is coated in organic molecules, salts, fatty acids and small glycoproteins (protein strand with attached sugar); many scientists also propose that this silk may also be coated in small peptides, which act as metal chelators (meaning they attract metal ions and attach to them, which is why spider silk can be anti-microbial).

     All these different types of silks and their different applications, but what are spider silks made of? What gives them such useful properties? Spider silk is mainly composed of large amounts of nonpolar, hydrophobic amino acids glycine and alanine but not tryptophan. The spider silk proteins are made up of repeating amino acid sequences (too complex for a sophomore chemistry student to describe or explain). It also has crystalline structures within the silk, beta sheets of nanofibers; the mixture of crystalline and elastic, semi-amorphous materials is what gives the silk such durability and strength, while still retaining flexibility and stretch/contract properties. Along with being thread, it has also been found that in vitro (prior to spinning) the silk protein can be transformed into a multitude of possible shapes: a thread, film, hydrogel, nano-fibril, capsule and a sphere.

     Other than just the complexity of the silk's buildup and the genomes that code it, the actual mechanisms of spinning the silk are also hard for human bioengineers to mimic. Methods of syringe needle, microfluidics and electrospinning have experienced varying degrees of success, often lacking cost efficiency, consistent results or a product that is on par with the natural, spider spun silk. The spider itself has 5 different organs that have evolved over centuries to specialize in spinning its silk; so far, they have been able to genetically modify goats to produce milk that contains silk protein and can be drawn out, but this process is costly in regards to finances and time, while producing thread that is thicker and heavier than natural spider silk while also being less strong. The current largest piece of spider silk is a gold tinted cape made from the silk of golden orb spiders; this 11-by-4-foot cape took 83 people over a year to collect 1 million spiders and extract their silk. Scientists can only hope that with these new genetic sequencing advancements in spider research, we will be able to genetically modify other animals to produce spider silk at a much more efficient and expedited rate, or at least identify the technique of the spider and the make up of their silk, as scientists still have many theories about the spider that remain unstudied and untested.

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658765/ 
2. https://www.sciencedaily.com/releases/2017/05/170501112627.htm  
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658765/figure/F1/

Biochemistry in the ALS ice bucket challenge [Fight or flight reflex]

            Chemistry of the ice bucket challenge

            It seems that every year there is a new internet challenge going around which goads unsuspecting children into doing something stupid. Whether it is the 'cinnamon challenge' or the 'light yourself on fire challenge'. However, in 2015 a new challenge appeared known as the 'ALS ice bucket challenge'. This challenge stormed the internet and participants would have to dump a bucket of ice water on their heads. Although this challenge raised awareness for ALS, many people were injured in many different ways. However, we are not gathered here today to talk about the finer details of the challenge. We are here today to talk about how the ice bucket challenge and the affects it has on the human body is more complicated than what meets the eye. We are here to talk about the chemistry involved in whats known as the 'fight or flight' reflex.

            Basics of the fight or flight reflex

            The 'fight or flight' reflex is a survival instinct that lies within everyone's subconscious. It is thought to have first manifested in humans at a very early time in our history as a species and has been passed on through generations ever since. The fight or flight reflex is a psychological that is designed to ensure the preservation of your mental and physical health. On the outside it seems to be very simple; when faced with what you perceive as a threatening situation you will either "fight" and face the situation head on, or you will "flight" and run away from your problem. However, sometimes this reflex can fail to work as designed and will cause you to freeze and not do anything.

The parts involved

(Taken from www.chemistryislife.com/the-chemistry-of-fight-or-flight)

• Brain
• Hypothalamus
• Cerebral cortex
• Amygdala
• Catecholamines
• Norepinephrine/nor-adrenaline (C8H11NO3)
• Epinephrine/adrenaline (C9H13NO3)
• Hormones
• Hypothalamic pituitary adrenal system
• Estrogen (C18H24O2)
• Testosterone (C19H28O2)
• Cortisol (C21H30O5)
• Neurotransmitters
• Dopamine (C8H11NO2)
• Serotonin (C10H12N2O)
• Autonomic nervous system
• Sympathetic nervous system
• Muscles
• Eyes
• Respiratory system
• Cardiovascular system

The 2 most important parts involved in the fight or flight reflex are the Autonomic Nervous System (ANS), and catecholamines. The ANS is the system that deals with all body functions that don't require specific thought. So moving your arm is not controlled by ANS but your heart is, and since no one chooses to activate their fight or flight reflex the ANS is heavily involved in doing so. Once you perceive a threat with any of your five senses, in the case of the ice bucket challenge it would be feeling the threat, then the ANS takes over, activates the reflex, and spreads the message to the rest of your body to get ready to fight or flight in order to survive. In order to do this the ANS releases epinephrine and norepinephrine. These chemicals are released from your adrenal glands and prime the body for fight or flight. Epinephrine makes the body stronger and faster, while norepinephrine increases vigilance.

The role of the chemicals

  Norepinephrine is a chemical released in the brain and affects attention and responding actions by increasing alertness, focuses attention, enhances formation, and the ability to retrieve memories. Each cell is then prompted to either shut down, slow down, restrict, or speed up according to the situation. On the other hand, epinephrine is released directly into the bloodstream from your adrenal glands and is carried to different locations in your body. This is so that energy can be provided to all the different muscle groups so that the body can physically respond to the threat.

Relating it back to the ice bucket challenge

            
             Now you might be wondering how all this intense chemistry relates back to something as trivial as the ice bucket challenge. Well basically it goes something like this. The ice water is very cold so that is what triggers the fight or flight reflex. The chemicals previously mentioned synthesizes and is released into your body. This is why people have the reactions they have when doing the ice bucket challenge. Some people run, but a lot of people freeze up because their fight or flight reflex has failed them. 

Sources:

http://www.chemistryislife.com/the-chemistry-of-fight-or-flight

https://en.wikipedia.org/wiki/Fight-or-flight_response

http://www.psychologistworld.com/stress/fightflight.php

https://anxietyboss.com/what-are-the-two-components-of-the-fight-or-flight-response/

(Nucler chemistry) Space Exploration

Chemistry in Improving Conditions for Space Travel

As technology advances and the urge to discover the Universe and search for other civilizations becomes more and more pertinent, researchers have been discovering ways to improve conditions for space travel so that astronauts are accessible to travel further in a smaller amount of time.  Scientists think that Nuclear Rockets could be a reality to utilize for space exploration. NASA is investigating and researching many technologies for nuclear rocket propulsion and nuclear power for bases on the Moon and Mars. The nuclear rocket system will use electricity generated by a nuclear reactor to power an electric ion drive system. The new generation of space-craft will be capable of taking man to the outer reaches of the solar system that no one has explored before. The concept of nuclear rockets is, in fact, 50 years old.  Between 1957 and 1972 several nuclear rocket designs were proposed, but only a few were partially tested.  A major problem with the chemical rocket systems is weight. Chemical fuels are heavy and add much weight to the launch vehicle.  In addition to electricity and thrust, the early designs exhibited a couple of design flaws that were never fully resolved by the program for Chemical Rockets’ end. They mostly rattled and vibrated enough to crack the fuel bundles, making the rockets useless. The rockets also became so hot that the heated  hydrogen steam eroded the walls of the reactor.

In 1998, NASA launched Deep Space 1 and Deep Space 2, and they successfully demonstrated that an electrostatic ion engine could propel a spacecraft. Both spacecrafts were able to successfully follow comets and report back photographs. Deep Space 2 successfully reached Mars but the surface probes failed to function. In both cases, the electrostatic ion engines performed better than expected.  The way the engine works is that it is bombarding a gas with a beam of electrons. This action knocks electrons off the atoms of the gas and creates a positively charged ion. There are high voltage metal grids at the back of the engine chamber which accelerate the positive ions toward the grid. As the ions pass the grid, they reach speeds of over 30 km/s and are focused into an ion beam before being exhausted out the back of the engine. Lastly, a neutralizer collects excess electrons and injects them into the ion beam to prevent a build-up of negative charge on the spacecraft, which could have a negative effect on the spacecraft and result in failure.  Plutonium-238 is a valuable commodity for deep space exploration where insufficient amounts of sunlight render solar panels useless. NASA's radioisotope thermoelectric generators (RTG) that most of power these missions instead run on a nugget of Pu-238. While plutonium is a poor conductor of electricity, its emission of alpha particles as part of its decay process generates a terrific amount of heat to run the RTGs.

Works Cited:

http://teachnuclear.ca/all-things-nuclear/other-nuclear-applications/space-exploration/

http://gizmodo.com/5992441/how-nasas-nuclear-rockets-will-take-us-way-beyond-mars

The Chemical Art of Color (Biochemistry)

The Chemical Art of Color

Many tools are used by artists to create a whimsical image visibly appealing to the eye. Some examples include ink, dye, and paint or pigments. All of these unique instruments have one main characteristic in common: chemistry!

Dyes, for example, are colored substances that add to or change the color of whatever they are added to. They are ionizing, organic compounds that use chromophores (atoms responsible for the color of a compound) as the major component. The process of textile dyeing (with materials such as leather, fabric, fiber, and yarn) encompasses many well-known chemicals such as acetic acid, sodium hydroxide, and sodium chloride.

Pigments, on the other hand, appear colorful because they reflect and absorb specific types of visible light, depending on the source of light. They are insoluble products that can be either natural or synthetic. Some organic pigments include indigo and Indian yellow, while there are biological pigments such as chlorophyll found in plants, as well as myoglobin, which is found in muscle cells.

Ink substances are unique in that they can consist of solvents, pigments, dyes, surfactants, and other materials. The solvents are what makes ink a liquid. The two most popular kind of inks are pad printing inks (found in pens) and screen printing inks (like the ink jet cartridges bought at office supply stores). The difference between the two is that pad printing inks are formulated for the purpose of rapid evaporation, while screen printing inks are designed to resist evaporation so that they don't dry inside the screen.

There are a wide variety of jobs that use chemical analysis of paint every day. Chemists who work with these materials in their labs and experiments have developed new formulations of these chemicals that are less expensive to make and have a better color quality. They also are developing products with greater stability and better interactions with the material that they so often come into contact with. Museum workers also use chemistry to analyze the pigments and dyes in historical paintings and artifacts to determine their age and place of origin. They can use this information to preserve and restore these artifacts. Finally, forensic chemists analyze evidence like this for criminal court cases, such as car paint or cosmetics remainders.

Sources:

https://www.slideshare.net/bejoybj/chemistry-of-inks-dyes-and-pigments

https://www.acs.org/content/acs/en/careers/college-to-career/chemistry-careers/dyes-pigments-ink.html

Particle Acceleration

  

     Particle Acceleration were invented during the 1930's to provide energetic particles in order to investigate the nucleus of atoms. However, these machines have evolved and are now in use to investigate many aspects of particle physics. A particle accelerator is used to speed up or increase the energy of particles within a beam by creating electric fields that accelerate them. There are two types of accelerators: a linear accelerator and a circular accelerator. In a linear accelerator the beam travels in a straight line, while in a circular the beam travels on a curve forming a complete circle.
     The particle will vary based upon the purpose of the experiment, however atoms can be combined to form new elements in the case of elements 116-118 all being classified as man-made. The way to accomplish this is by using a hydrogen atom and then using these incredible speeds to shed the electron forming just one proton and neutron moving at high speeds gaining kinetic energy. This is done by switching electric field from positive to negative forcing the proton to tear apart from the electron and then providing energy. Radio-frequency can also be used because as each time the particle passes through the radio waves are supplying energy to the particle and moving it forward. This method is much more common in circular accelerators since they can pass in a ring and the revolutions pick up each time leading to an increase in energy eventually reaching the speed required. Then the high-energy particle is smashed into another nucleus causing both to completely disassemble and then reassemble almost instantly. This means that elements can be created using one hydrogen atom and an atom of another substance. However, this does not mean that this transmutation is stable by nature the half-life of element 118 is 0.89 milliseconds. This is a type of fusion that can be controlled by humans.
    While of course we can manipulate this beam and control it to produce energy theoretically, the energy required to reach these speeds are enormous, so that's why the most common form of particle accelerator is seen in the sun, where the heat and the temperature causes this phenomenon to combine two hydrogen atoms into one helium atom. Humans have to input large amount of energy to match this kinetic energy done and is why this method is only done for research and not commercial use. Another reason is that every part of the collision has to be very precise to avoid the copper magnets melting, and this is due to the fact that the cavities that are receive the frequency flip are heating up as well as the particle gaining energy, this means that it must be controlled to make sure that the copper does not melt and require replacement.
   So what is the point? This allows scientist to analyze a different type of physics all together and take some aspects of alchemy and apply it to real life, Theoretically this information and experimentation could be used to create energy, but this is also developing very slowly due to the size of the LHC, or large hardron collider, being 27km long and using superconducting magnets to somewhat limit the amount of energy required to do particle acceleration experiments. However, these nucleus fusions are still very very inefficient and will require much more time to accomplish this feat. Until then, particle acceleration will only be used to find new elements that meet the criteria, and study how particles act, something that completely changes the realm of physics as we know it.


https://home.cern/about/how-accelerator-works
https://www.sciencelearn.org.nz/videos/1047-what-is-a-particle-accelerator
http://www.economist.com/news/science-and-technology/21588048-fundamental-physics-seems-have-insatiable-appetite-bigger-more