Cell Bio 102: What Makes The Cell (Fried Chicken) – Part 1

You may or may not have read the last post, and if you’ve had high school Biology, there is no compulsion on you to read this one as well. In the last post, I talked fleetingly about the cell and its components: the cell membrane, mitochondria, nucleus, DNA, RNA, proteins, enzymes (which were also proteins), and the Central Dogma. This time, I want to talk about what makes a cell.

In this post, I would be covering carbohydrates, lipids (in the context of lipid bilayers), proteins, and nucleic acids (collective term for DNA and RNA).

Basically, I want to talk about Fried Chicken.

One bite of this includes carbohydrates from the crisp, proteins from all the muscle inside, nucleic acids because you’re consuming the nuclei (singular: nucleus), and lipids (as fats) because well.. they’re fried.^[1]

(note: by the time I hit 1,500 words, I felt like this post should be chopped into two parts. Hence, the first part covers carbohydrates and lipids. The second would cover proteins, and the nucleic acids)

Carbohydrates

Carbo- comes from the word for coal in Latin, hydr- comes from the word for water (hudōr) in Greek, and -ate comes from the word for multiple oxygen atoms in Chemistry. So, carbohydrates are wet coal brimming with oxygens! Well.. almost.

Carbohydrates are called carbohydrates because they’re made up from carbon, hydrogen and oxygen atoms, and vary in many, many forms. In the simplest form, carbohydrates are found as monosaccharides (single sugars). You’ve probably heard of glucose-that’s one of them. Fructose, galactose and ribose are other examples of monosaccharaarsdsise monosaccharides (you don’t have to get the proper spelling on the first try, don’t worry). When two monosaccharides join together- we get a disaccharide (two sugars, you can probably see a pattern now). Cane sugar (or just.. sugar in English) is made from glucose and fructose linked together. Lactose (the thing you find in milk that makes Asians and old people sick)^[2] is made from glucose and galactose linked together. Starch and fiber are polysaccharides and made of many such monosaccharides linked together. 

Carbohydrates are the energy sources of life. You get yours from animals who get theirs from plants (or you can cut the middleman and grab it directly from plants). Plants, however, through science(!!!) and magic, MAKE their carbs from air, water, and SUNLIGHT (this is beyond cool). Carbohydrates are what make your food taste so good (hint: pizza, french fries, biryani, pad thai, muffins, cakes, donuts, chocolates, ice cream, and the list goes on endlessly), probably because you’ve evolved to like them. Carbs are broken down inside your stomach into simple sugars (monosaccharides), and then these simple sugars are further broken down in your mitochondria to release tremendous amounts of energy that you use to breathe, think, pump blood, digest, move, run, fight, talk, grow, repair, and basically do everything that makes you, you. This is achieved through a process called cellular respiration, which is beyond the scope of this blog (this is one of the things that I would not be excited to explain. Here’s a confession- I love Chemistry and Virology, NOT Biology).

Lipids

Lipids root from the Greek word for fat (lipos), however, lipids are NOT fats. Fats ARE lipids (bear with me, it’ll get clarified in a few).

Defining a lipid is much more harder than I anticipated. It turns out that there isn’t any well-defined concept of what a lipid is. Generally, they are small hydrophobic (this word means that they do NOT dissolve in water) molecules whose functions include energy storing, chemical signalling (means through which your cells talk to one another), and acting as structural components of the cell membrane (as lipid bilayers). They include fatty acids, fats, fat-soluble vitamins (A, D, E, K), waxes, phospholipids, steroids (like cholesterol) and much more. Fats are a subset of lipids- similar to how all trees are plants, yet not all plants are trees.

A few examples of lipids

Fatty acids, even according to Wikipedia, are not to be confused with fats. They’re the building blocks of fats. A fatty acid is a carboxylic acid with a long (10+) aliphatic chain. Aliphatic compounds, opposed to aromatic compounds, are.. compounds that are not aromatic compounds. (Sorry for the circular loop, but I’d be more than willing to explain what they mean if you coerce me into doing so). They’re basically (I’m lying, but it’s fine for now) carbon atoms that are linked to other carbon atoms in a straight chain, without making a ring. The effect is shown below. The compound on the left is an aliphatic hexa-triene, and the one on the right is an aromatic cyclohexa-triene (also known as Mercedes Benzene).

When three fatty acids get linked to a glycerol molecule (shown on the left), you get a triglyceride. This is also a lipid, and a triglyceride in English is what we call ‘fat’. This is oil, butter, obesity, and whatever name you give to fat.

When two fatty acids and a phosphate group get linked to a glycerol molecule, you get a phospholipid. This is what forms the cell membrane (and the envelopes of viruses and organelles).

The parts of a phospholipid molecule. This example is phosphatidylcholine, represented (A) schematically, (B) by a formula, (C) as a space-filling model, and (D) as a symbol.

I get excited when Chemistry intersects with literally anything- so bear with me if I come off as too nerdy. Phospholipids are ‘amphiphilic’- meaning they have a hydrophobic and hydrophilic (water-loving) properties.

—- Start Of A Short Chemistry Lesson —-

If you’ve ever seen a cat scream while its in water- you can conclude the cat is hydrophobic. It doesn’t dissolve in water.

The properties of hydrophilicity and hydrophobicity arise because of an awesome property of Chemical bonds that we call polarity. To best explain the idea of polarity, I ask you to imagine a tug-of-war competition featuring a team of fifteen year-old students versus clones of Arnold Schwarzenegger. The rope would be lying unevenly, most of it towards team Arnold Schwarzenegger- and that situation is similar to how chemical bonds are made.

A chemical bond is made when atoms share electrons between themselves to fill valence shells (read: to complete each other- very, very romantic).^[3] Some atoms, with a stronger force from the nucleus (the positive region), pull on those electrons (the rope) strongly compared to the other atom in the bond. The atoms who like pulling electrons (Team Arnold Schwarzenegger) are what we refer to as more electronegative atoms (because.. they like to be negatively charged). Then, there are atoms who like giving away those shared electrons (Team fifteen year-old), and we call them less electronegative. This creates a disparity across the chemical bond- and one side becomes slightly/partially (symbolized as δ-) negative, and the other side becomes slightly/partially (symbolized as δ+) positive.If the force is strong enough, the electrons in the bond can be completely stripped off from one atom, and we call that an ionic bond.

This disparity in charge is called polarity, and it gives rise to hydrophobicity and hydrophilicity. In short, polar molecules tend to be hydrophilic. They love water so much that they’d rather dissolve in it (like table salt, alcohol, tea etc.). Less polar molecules (these arise when there isn’t a significant electronegativity difference between the atoms that form the bond, like a carbon-hydrogen bond)  tend to be hydrophobic. They would rather dissolve in lipids instead of water (much like how cooking oil tends to float and form separate patches of oil on the surface of water- yet canola and olive oil mix together leaving no trace of such patches). Hydrophilicity and Hydrophobicity are very very important concepts in Biology, and they help explain key concepts like chemical reactivity, enzyme specificity (that’ll be covered later in Part 2), and even transport through the..

PHOSPHOLIPID BILAYER!! (I can finally call the cell membrane as a phospholipid bilayer without people having to cringe at the name)

—- End Of A Short Chemistry Lesson —-

Lets return to the part where I said phospholipids are amphiphilic. The phospholipids have a hydrophilic head (of the phosphate group and glycerol), and a hydrophobic tail (of the two fatty acid chains). Now, you have to understand that opposites attract even in chemistry. The δ+ side prefers to face a δ- side if possible. However, hydrophilic (or polar) molecules prefer hydrophilic molecules and hydrophobic (or non-polar) molecules prefer hydrophobic molecules (in terms of what dissolves in what). This is NOT going against the opposites rule- so don’t be confused. This just means that when polar molecules are next to each other, they would reorient themselves such that the δ- side is paired against δ+ side and so on (dragging each other closer because they are then attracted). Similarly, if you put together a polar molecule against a non-polar molecule, the δ+/δ- side (of the polar molecule) has nothing on the other molecule (the non-polar molecule) to attract to. Through an oversimplification, this allows hydrophilic molecules to dissolve in water (a polar ‘solvent’) whereas hydrophobic molecules do not dissolve in water, and are soluble in fats and other non-polar solvents.

Imagine how you can make an infinitely long chain as long as you have enough hooks that are willing to go into loops- and loops that are willing to accommodate hooks (similar to how δ+ can link up with δ- infinitely). You can’t, however, fit the hook into anything that isn’t a loop (lets say, you can’t hook and attach a wall to the chain). Illustrated below, this phenomenon of polar molecules attracting each other (such as water molecules and acetone on the left) to form a compact shape is visible. In the case of 2-methyl propanone, it is non-polar, and it (although similar in size) occupies a larger space. This non-compatibility results in 2-methyl propanone being insoluble in water (or other polar solvents), and hence, hydrophobic.

 Anyways, moving away form the digressions, there is a certain property that arises because of the amphiphilicity and shape of the phospholipids, causes them to either form a or spherical micelle or a bilayer.^[4] In each case, the polar side of the phospholipid is in contact with water, and the hydrophobic side is facing other hydrophobic sides of the same structure. Similarly, the nature of a bilayer restricts it to have any ‘free-edges’ that are exposed to water, and causes the bilayer to fold onto itself in a compartment. This very nature of the phospholipid bilayer gives the cell a shape. Otherwise, they’d probably look like sunny-side up eggs.

(A) Wedge-shaped lipid molecules (above) form micelles, whereas cylinder-shaped phospholipid molecules (below) form bilayers. (B) A micelle and a bilayer seen in cross section.

This formation of the cell membrane causes it to be semi-permeable. The lipid bilayer is permeable to both small and non-polar substances to pass. Ions (charged particles), and large polar molecules cannot pass through the membrane without assistance. This assistance is provided by cell-surface (or transmembrane) receptors on the cell, which regulate the transport of many biochemicals in and out of the cell.

Here, I think we should stop. Initially I was planning to go through proteins and nucleic acids in the same post, but I think things were getting dense. So, all of that would be lumped in the second part of this post.

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1. Although Fried Chicken is extremely delicious, the author is not, in any way at all, encouraging you to consume Fried Chicken as a well-rounded diet.
2. This was meant to be taken in light humor. I fully recognize that race has no basis in biology- however- statistics do show few trends that are retained genetically through races (or at least geographical distributions). Furthermore, this was meant to be taken as a stereotype since people of Jewish, African, and Native American descent have similar rates of lactose intolerant people as of East Asian descent. Anywho- since majority of the world’s adult population is lactose intolerant- it really can’t be lumped to any race. So yes, it makes East Asians sick, but it also makes everybody else sick (they’re just famous for it).
3. I have made vast assumptions regarding background knowledge of valence shells, atoms, protons, electrons, and bonding. You can go here to understand covalent bonding. If you do not know what are atoms and sub-atomic particles (protons and electrons), feel free to contact me. I cannot make it simpler for the purpose of this blog, so I’d be more than willing to explain separately!
4. This property is free energy minimization. Exposing the polar side to water allows energetically favorable bonds to form (releasing energy). Exposing the non-polar side to water causes water to form a cage-like structure (as shown in the picture) which is a more ‘orderly’ state for these water molecules (lowering entropy). Hence, free energy is minimized when the polar ends are exposed to water and the non-polar sides are away from water as much as possible. This is why the phosphate heads point away, and the fatty acid chains are facing each other.

For further reading:

Carbohydrates: Wikipedia, Simplified.

Cellular Respiration: Wikipedia, Simplified, SparkNotes, VERY Detailed.

Lipids: Wikipedia, Simplified, Detailed.

Covalent Bonding: Wikipedia, Sufficient (I love UCDavis), Detailed.

Polarity: Wikipedia, Sufficient.

Transport Across Phospholipid Bilayer: Wikipedia, Detailed.

Cell Biology 101

Initially, I was going to write a post about the virus replication cycle, of how it invades a cell through the surface receptor, affixes itself into DNA, makes proteins and all that stuff and I realized I wouldn’t be doing justice to a fifteen year-old. Hence, behold. Cell Biology 101.

Hear this: Every living thing on this Big Bang given (or God-given, depending on your affiliations) world can be reduced to this thing in biology we call a cell.

Yes, you can reduce it further and strip the cell down into individual chemicals, and those into atoms and so forth, but in that process you would lose the living aspect. And this statement would serve to satisfy a very good friend of mine, but, in doing so (the process of reduction), you would enter the realm of Physics- not Biology. So, what exactly is a cell?

For the purpose of this post, I would be talking only about human cells.^[1] There are blatant exceptions to what I’m about to say, and they are found in blood cells, plant cells, in bacteria, and in archaea. For now, don’t worry about them.

There is a world inside you, and a cell is the simplest living occupant of that world. Invisible to the naked eye, it’s a building block of everything. Of your bones, your skin, your muscles and everything that is inside you. And everything inside everyone other living thing. The wood in your wooden chair is made of cells. The cotton in your clothes is made of cells. That annoying nerd in high-school (probably me), the first crush from primary school, kings, janitors, presidents, parents, and everyone imaginable is made from these cells. If God were physically tangible, you’d find cells inside there.

There are some living-beings (organisms) that are made from only one cell (called unicellular organisms), and you’ve heard of a few unicellular organisms like germs and bacteria. The people you see, however, are made of a LOT of cells. We are multicellular organisms (so are plants and animals!). Multi stands for more than one, so I don’t think that does justice to the term multicellular. Having more than 10,000,000,000,000 cells, I say we are tonne-load-cellular organisms, and, to the left, are some of mine. Yes, they look like sunny-side up eggs.

The easiest way to imagine these sunny-side up eggs is to think of them like small, self-sustaining, yet interconnected towns. Inside individual towns, you have farmers, blacksmiths, cattle-herders, bankers, and, if you’re lucky, some fellows wishing to talk to you about Jesus Christ.

The point is, there are many units contributing to that town’s well-being, and these units (blacksmith, farms, banks, restaurants) can be categorized by their functions. These individual structures responsible for specific functions inside your cells are organelles. An organelle, by definition, needs to be enveloped by a lipid bilayer, a fancy term we use for a fatty envelope. A cell marks it boundary by a semi-permeable plasma membrane (meaning it allows some things to pass, not all. Much like an angry interviewer when you apply for a visa abroad) which is also a lipid bilayer. Everything inside that plasma membrane, including the organelles, are suspended in cytoplasm (cyto is a prefix that refers to cells and you would see it in many places, for e.g. cytokines, cytokinesis, cytotoxicity). This cytoplasm is the gooey-goodness that keeps everything inside the cell intact and gives the cell a shape- much like how you need to add air or water inside a balloon to make it blow up.

A cut-open image of an animal cell. Inside, the various organelles (most of which are pretty irrelevant for now) are shown.

For the purpose of this blog, you need to know about two organelles: mitochondrion and the nucleus. Along with those, you need to know about the DNA, mRNA, ribosomes, enzymes, and surface receptors. Grab your chisels and stone tablets, this could get very confusing very fast.

The Organelles

The kidney-shaped mitochondrion (plural: mitochondria) is the powerhouse of the cell. The food you eat is chopped and diced, smashed and squeezed, until it releases energy (which you read as calories on nutritional labels) inside your mitochondria. This energy is used to do everything your cells need to do to allow you to do what you need to do. Fun fact: Cyanide, commonly found in apple seeds and CIA assassination plots, targets the mitochondria. Your heart doesn’t receive the energy it needs to pump blood, causing you to die. Hence, an apple a day keeps the doctor away, as long as you stay away from the goddamn seeds.^[2]

The nucleus is like the brain of a cell. It contains blueprints and all the necessary information needed for the cell to survive. It’s that secret diary you used to write in middle school that had all the information of your life. Similarly, even the cell wouldn’t want to give its secret diary away (especially to another virus). This diary contains information in the form of DNA (Deoxyribonucleic acid), which dictates what exactly the cell needs to make, and where the products need to be transported. The DNA is responsible for the way you look- from your eye color to your very bones- and is passed down to your children.
All of this is dictated thanks to the way these base pairs (shown on the left) are arranged. Like the alphabet and how their many arrangements make separate words and words make sentences- The arrangements of these base pairs code for separate amino acids (whose arrangement code for separate proteins). What you need to know about amino acids is that they make up proteins. And proteins have many functions. They can form structures like your nails and hair, they form receptors and sensors, they digest your food and even allocate where energy should be stored. What you need to know about proteins is that some of them are enzymes. Enzymes are like individual workers inside the town, and strive mainly to synthesize other proteins, move around other proteins, start and stop reactions, and basically carry out processes inside your cell.

Think of it like this. If you need to build a house in that town, you probably need cement and wood, both of which are proteins in this analogy. However, you need a blueprint that plans out the house (the DNA), and workers (enzymes, which are also proteins) who would gladly knock together the raw material (cement and wood) proteins to make the house you need (which is the product, COULD be a protein, but it could be anything else as well, like, your eye).

However, these base pairs and their arrangements inside the DNA need to be read first. This blueprint needs to be read by an architect who understands the language. This architect, when he sees that an electric socket needs to be repaired, refers to the chapter on electric wiring and sockets inside the house, and does not need to demolish and rebuild the whole house to fix that single problem. Similarly, your DNA has localized chapters of information that we call genes.

Each gene codes for a protein..

.. and you have genes that code for proteins responsible for your height, weight, shape of your eyes, hair color, insulin, cancer, prevention of cancer, and even for transporting and storing other proteins.

Following the analogy, this gene is first transcribed (a photocopy is made, so you don’t end up ruining the original blueprint) into an mRNA (messenger Ribonucleic acid) with the help of an enzyme called mRNA polymerase (here is a recurring theme of enzymes, they’re named after their functions and end with a suffix ‘ase’. In this case, mRNA polymerase forms a polymer strand of RNA after reading the DNA). The message inside the gene is now carried by the mRNA (without losing the original message in the DNA), and this mRNA is transported towards a ribosome where it is translated into the protein the original gene was coding for. Hence, the mRNA being rightly called the messenger RNA as it transports the original information the DNA had.^[3]

A gene, coding for a protein, is transcribed into an mRNA. This mRNA, taken to a ribosome, is translated into the protein. This is referred to as the central dogma of molecular biology: DNA begets RNA, and RNA begets protein.

Are we done? Almost.

The last thing you need to know about is the cell-surface receptor. These are proteins that stick through the plasma membrane, having exposed sides both inside and outside the cell. Following the town analogy, although the town is self-sufficient, communication and trade between neighboring towns is always helpful. And THIS is exactly what the cell-surface (or also called transmembrane because they stick through the plasma membrane) receptors do. They communicate between the outside world and the cell they’re a part of. There exist specific sites on these proteins on which if something (anything that can fit really, we call this a ligand) attaches, it triggers the protein to relay the information to the inside of the cell and a response is generated that could manifest in many separate ways.

We’re done! Here’s the takeaway message:

Your cells are very, very complex machines that don’t have a brain of their own. They NEED the DNA’s information to be precise and perfect to carry out their functions. They NEED the energy from the mitochondria to carry out these functions. Most of these functions are carried out with the help of enzymes, and they NEED the enzymes to be working normally. There is no policing and mRNA polymerase transcribes the DNA as it sees it, and if there is a change in that DNA, your mRNA cannot recognize it and just transcribes it anyway. For ANY foreign particle to be imported into the cell, it must pass the plasma membrane, and this can also be done by attaching to the transmembrane receptor. If it fits there, it can possibly get inside from there (the receptor). And if it slips inside your cell and messes with your DNA, mRNA polymerase will see this change as a piece of DNA that needs to be transcribed and translated. This can interrupt the normal processing of your cell if the imported particle is not your cell’s daily cup of tea.

If you managed to understand the paragraph above- you’re capable to understand basic virology. Congratulations!

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1. If you embark on further reading, you would realize that there are eukaryotic and prokaryotic cells. You can go here to understand the difference between the two. In a very simplified view, you just need to understand animal cells (eukaryotic) for the purposes of this blog since I would be talking about viral infections pertaining to animals. IF I do delve into bacterial pathology, I would be talking about prokaryotic cells and would give a slight background.
2. Yes, apple seeds (and many other seeds) contain cyanide. Cyanide works by inhibiting cytochrome oxidase, a very vital complex in the electron-transport-chain that is responsible for generating energy inside a mitochondrion. The dosage in seeds from a single apple isn’t enough to kill you. An average human being needs around 1.5mg/kg of body weight for cyanide to be fatal, and a kilogram of appleseeds has 700mg of cyanide. You need 100 grams of apple seeds to dispatch someone you don’t like (and you need a LOT of apples for that many seeds). The only point I wanted to make with that statement is that not everything natural is healthy. Poison is a function of dosage and is not an innate property.
3. I skipped many details about the nature of DNA and RNA (single or double stranded, positive or negative sense etc.) and their composition. Here’s some extra reading for the curious minds detailing the difference in the two. I wouldn’t be going into more details regarding DNA when I talk about viral infections, but it is important you know the nature of DNA and RNA in an understandable depth.

For further reading:

Cells: Wikipedia, Simplified, Detailed

Mitochondria: Wikipedia, Simplified, Detailed.

DNA and RNA: Just take this one.

Central Dogma: Wikipedia, Simplified.

Lipid Bilayer: Wikipedia, Simplified, Detailed.

Transmembrane Receptors: Wikipedia, Detailed.