The Hardware of the Cell

This blog post is a bit of a 2 for 1 sale on learning. You’ll learn about the hardware parts that make up your computer (you can go into any Apple store and intimidate the employees), and you’ll also learn about the various organelles that make up eukaryotic cells. So whether you’re learning about what CPU means, or what cilia are you’ll be entertained.

When you walk into Best Buy, the Windows store, etc. you are first struck by the visual similarities and difference between one computer and another. Some are gray and shiny, others black and matte, most have an emblem of some sort whether that be fruit, a cartoon alien, or simply the brand name. Computers also vary significantly by size. The largest computer ever built is the Sunway TaihuLight which has the average computing power of 93 petaflops (yeah, that’s a measurement), check out this video below to have your mind blown. The smallest computer is the Michigan Micro Mote, at one millimeter cubed it’s the smallest autonomous computer in the world.

Similarly, the outsides of eukaryotic cells come in many shapes, colors, sizes, and textures. Some have flagellum or cilia (bacterial cells), others have a rigid structure (plants cells), and others are amorphous (animal). Members of the Ostreococcus genus rank as the smallest eukaryote. They have an average size of 0.8 µm, a genome 13 Mb long, and contain only four organelles: a nucleus, a single chloroplast, a single mitochondrion, and a single Golgi body. (Fun fact, their genome is still 13 Mb which four times the size of smallest recorded genome of 2.9 Mb). The largest eukaryotic cell (sorry slime molds, I’m disqualifying you) are neuron cells found in particularly large animals. A  published in Progress in Neurobiology found some neuron cells in the blue whale to be 10 cm long!

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Laptops have varying degrees of protection and rigidity. The kind used by the military (you know, the ones Samuel L. Jackson is usually holding in movies) are water and shock absorbent and are extremely rigid. On the other hand, companies are actively working on creating computers with flexible displays. Cells are also highly variant in these qualities with plant cells being very rigid and highly structured, and animal cells being shapeless and fluid. This difference is due to the cell wall/membrane. In plant cells, the cell wall is made of sugars (cellulose and chitin) and can range in thickness from 0.1 to 10 µm. Animal cells have a cell membrane made of fats (phospholipids) which make the cell have more of a flexible form.

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Both types of cells have what is called a cytoplasm. The cytoplasm is mostly made of water and nutrients and fills the cell in and gives it its shape (picture the water in a water balloon). It helps the organelles stay in place and allows proteins, chemicals, etc. to move around the cell. Much like the cytoplasm, every good computer needs a cooling system to circulate through the entire computer to ensure all of the parts do not overheat and fail. There are two main cooling systems for computers, either air (usually made by installing fans, this is the noise you hear when your computer is working hard), or the riskier option for hardcore gamers: water.

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The cytoskeleton is usually referred to as the skeletal structure of the cell, it’s all of the proteins that maintain the cell structure and organelle organization. The motherboard doesn’t actually do anything, it relies on the processor to give the machine power, relies on the RAM to store memory, but it is the circuit board of the computer that ensures all of the electrical signals from the various parts of the computer go in the most efficient and correct direction.

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The endoplasmic reticulum is the highway of the cell, a network of membranes that is connected to the nucleus, to the golgi apparatus, etc. It comes in two flavors, smooth and rough.The smooth ER contains various enzymes to aid in creating lipids, detoxifying noxious chemicals to make the soluble in water, and stores ions the cell may need later for energy. The rough ER is covered in ribosomes (hence its name) and is essential to the synthesis and packaging of proteins. The ribosomes are the organelles specifically responsible for creating polypeptides out of amino acids. When the ribosomes are finished synthesizing the leave the ER and move to the golgi apparatus. A major component of computers is wiring. Wires that connect the motherboard, the case, the power source, the fan, etc. all together, there really is a ton of wires… Much like the ER which is responsible for shuttling genetic information through the central dogma process, the wires in a computer are essential in sending data and electrons throughout the machine making all of the independent pieces work together.

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The golgi apparatus takes the proteins and lipids made by the ribosomes in and determines and directs where the proteins should be sent. The golgi puts the components in a vesicle that will be able to get around the cell or through the cell wall without being damaged or degraded. This is very similar to what a hard drive does. The hard drive is where data is stored and retrieved in a computer, data is placed on the hard drive via electrical currents on a bit as a 1 or a 0, and the these 1’s and 0’s are read, converted back into electrical currents and the data is retrieved. The number of bits used is dependent on how complicated the data is. For example, an average photo is made of millions of bits. Hard drives keep getting smaller and smaller as more bits can be placed on smaller surfaces. See here for some helpful visualizations. The golgi and the hard drive both act as temporary storage and go-betweens in shuttling data (in the case of the cell, genetic data) around the cell/computer.

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Lysosomes attach to old organelles such as mitochondria, or to foreign particles, and break them down so it is easily digested by the cell. The cache acts as temporary storage, the data stored on the cache is usually old or duplicated data which is kept in order to faster serve future requests by the user, however, when the computer is turned off this data is completely erased.

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The nucleus is the most familiar organelle, it’s usually referred to as the brain of cell. It is where all of the genetic material is kept. When an environmental factor outside of the cell is sensed (most likely a change in chemistry) by the nucleus and the nucleus directs the organelles to respond to the stimulus appropriately. DNA is relaxed from it’s normal compressed form and various proteins flow into the nucleus to transcribe the code and take it for translation into proteins. The nucleus decides when the cell divides, when and what proteins are made, and even when the cell should self-destruct. The nucleus is a lot like the processor of a computer. The processor receives input data (the click of a mouse of instance), processes this data, and provides output data (opens an application). Without the processor, the computer could not be able to respond to stimulus which would make it useless, much like a cell without a nucleus.

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The phase “Mitochondria are the power house of cell” is so common and lame that it makes my skin crawl, but it is true. The mitochondria supplies the cell with energy in the form of ATP by breaking down nutrients and utilizing the electrons. ATP is then released into the cytoplasm so the other organelles can perform essential functions. The process is much more complicated than that, so I will bore you with it another time. This is a lot like how the computer uses the PSU (power supply unit). The PSU converts the alternating current power supply you get from sockets into the low-voltage direct current power the computer needs to run, much like how the mitochondria converts nutrients into ATP.

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I have no clever conclusion, my computer and I are both very tired.

Dalton’s Atomic Legos

John Dalton… oh he was one crazy cat. A colorblind chemist quaker, what could be cooler than that? He’s most famous for his atomic theory, though he also studied colorblindness (pretty selfish really), the nature of gasses (don’t giggle, it’s rude), and he even recorded the daily weather for 57 years straight (https://cdn.meme.am/instances/19233870.jpg).

You’ve probably heard his name before. Most likely in the very first session of an introductory chemistry course. You know, when you’re still excited about the semester, you’re actually still taking notes, and you have the naivety to think, ‘I can totally handle this class, no problem!’.

The reason why Dalton’s Atomic Theory is such a big deal is because it was the postulate that really got the field of nuclear chemistry going. Sure, Democritus came up with a half-assed theory in 400 something BC, but by the time Dalton was recording rainfall 2,300 years later, the concept of the atom had mostly been forgotten.

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Democritus was sassy af

After Dalton’s theory, hundreds of scientists proceeded to play with cathode tubes (they didn’t have Netflix back then), JJ Thomson discovered electrons (fun fact, he originally named them corpuscles, I think it’s cooler, but whatever) and created the plum pudding model of the atom (plum pudding has no plums in it, btw). Rutherford then serendipitously discovered protons and the nucleus, and Bohr postulated that electrons move around the nucleus in a circular fashion. And then quantum theory. Okay, yeah, I skipped some stuff there, but we’re talking about Dalton here.

And then quantum theory. Okay, yeah, I skipped some stuff there, but we’re talking about Dalton here.

Okay, yeah, I skipped some stuff there, but we’re talking about Dalton here.

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But seriously, someone name their band The Corpuscles.

Keep in mind that John Dalton essentially pulled this theory out of his ass, with very little experimental context compared to today’s standards. And yet, almost all of it still holds true.

Here is his theory in a plum shell (no it’s not an expression, but it is now):

1) All matter is made of atoms. Atoms are indivisible and indestructible.

2) All atoms of a given element are identical in mass and properties.

3) Compounds are formed by a combination of two or more different kinds of atoms.

4) A chemical reaction is a rearrangement of atoms.

Now let’s break this down with legos. Here is our little lego John Dalton. I know, I couldn’t get the hair just right, but everything else is spot on.

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1) All matter is made of atoms. Atoms are indivisible and indestructible.

The greeks actually came up with the concept of the atom, or “atomos” (the prefix “a” means “not” and the word “tomos” means cut), with a simple thought experiment. You cut an apple in half. You then cut the half in half. So on and so on, until you can cut no more, this uncuttable unit would be the atom. This apple analogy actually works well to understand this part of the theory (assuming it’s granny smith, if it’s red delicious it falls apart).

Imagine you are playing with Lego Dalton (I have every confidence that this sentence has never been used in all of human history). You take apart his lower body, his upper body, his head and his hair, you now have four parts, you cannot take apart Dalton any further. Unless you pull out a hammer, in this analogy, that would an atomic bomb. Which is why this part of the theory isn’t entirely true anymore.

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But look how cool lego Batman looks in front of explosions.

2) All atoms of a given element are identical in mass and properties.

An element is an object made entirely of the same atoms. So in this case, lego Dalton, is not an element (for spoilers scroll down). However, three lower body lego pieces are an element, three upper body pieces, and so on.

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3) Compounds are formed by a combination of two or more different kinds of atoms.

The opposite of an element is a compound. This is an object made of different types of atoms, lego Dalton is a compound. So is random chemistry mermaid!

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The funny thing is, when people immediately thing of element, they may think of water, fire, air, and earth. However, these are not elements, they’re compounds! Water is a mixture of oxygen atoms and hydrogen atoms. Fire is oxygen, nitrogen, carbon. Air is mostly nitrogen and oxygen. And earth? Oxygen, aluminum, calcium, magnesium, potassium, and sodium atoms just to name a few.

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LIES, ALL LIES!

4) A chemical reaction is a rearrangement of atoms.

Let’s say we wanted to make a chemical reaction between John Dalton and chemistry mermaid (okay folks, let’s keep this PG). Each compound is made of four atoms (hair, head, upper body, and lower body). When these atoms are exchanged, moved, and rearranged a chemical reaction has occurred.

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Chemical rxn #1

In this case, the chemical reaction has had no net change as there are still four elements on the left and four on the right.

However, you could take two head atoms and stack them, making an element, and take the remaining hair (x2), lower body (x2), and upper body (x2) atoms and create a compound. This chemical reaction (chemical rxn #2) would result in a compound (made up of multiple atom types) and an element (made up of 2 head atoms).

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Chemical rxn #2

Another chemical reaction could give you two compounds but in a different arrangement. With one compound containing one head atom and one hair atom, and the other compound with the remaining head (x1), hair (x1), upper body (x2), and lower body (x2).

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Chemical rxn #3

As you can probably tell there are endless combinations of chemical reactions. Actually, there are 40,320 to be exact.

See parents? Everything makes more sense with legos. Go buy your children hundreds of dollars of them if you want them to pass chemistry.

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Bonus:

Dalton’s super secret diary in which he drew his postulations about atoms… and where he wrote his vampire romance novel.640px-Daltons_symbols.gif

Saturday Science Musings: Genealogy of Scientists

“Science is a co-operative enterprise, spanning the generations. It’s the passing of a torch from teacher to student to teacher. A community of minds reaching back from antiquity and forward to the stars.”
-Neil deGrasse Tyson, Cosmos
I’ve been thinking about this quote in the context of my own scientific career. Not only do mentor/mentee relationships increase the connectiveness of the scientific community, it connects individuals that may never met before. Though the technology we use and the questions we ask may change through out the years; the tips, the tricks, the passion, and the core concepts of the scientific theory are preserved through out time through these connections/relationships.
I can’t wait to meet my future mentors and mentees. We’re going to have a lot of fun.
Also, a series of manatees… because I hope my weirdness lives on too.musings
I’m not the first person to think about this, in fact there are genealogies made for entire fields (http://academictree.org/)…
In fact, I was able to find some of my mentors on this site, some of which I was able to trace back their mentors, their mentor’s mentors, etc.
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Though it’s fairly creepy that mentors and mentees are referred to as parents and children, it’s not entirely inaccurate. Much like parents, not every mentor is exemplary or effective, and not all mentees continue their predecessors work.