Hydrophobic interaction and cell design

One concept that students usually find hard to understand is the concept of hydrophobic interaction and its role in cell design.

The fact that the term itself is really a misnomer probably contributes to this difficulty.

Why a misnomer? Well, the energy that is used during the interaction between hydrophobic molecules actually comes from the hydrophilic molecules. Huh? Ok, let’s put it this way.

Some molecules are hydrophilic or “water loving”. “Hydro-“ means water and “philia” means love. Other molecules like oil on the other hand are hydrophobic or “water fearing”. “Phobia” means fear. However, these terms can be misleading because the molecules do not really fear water. What happens is ... in the presence of water, these molecules tend to join together. Why?

Well, water molecules actually have a greater affinity or greater attraction for each other as compared with any attraction between water and other molecules like oil. Thus, when we place drops of oil in water, the water molecules tend to go together and push or squeeze the oil droplets as far away from the water molecules as possible. This therefore results in the oil droplets joining together to form a bigger drop of oil. This joining together of oil droplets in the presence of water is what is called hydrophobic interaction. This is the reason why oil and water do not mix.

So what is the importance of hydrophobic interaction in cell design?

Let’s go back to what cells are made of. Cells consist primarily of water, proteins, lipids, carbohydrates, nucleic acids and traces of some minerals. Cells are separated from their environment by membranes that are basically phospholipid in nature. Because phospholipids have hydrophobic ends and hydrophilic ends, through hydrophobic interaction they therefore naturally form a double membrane in the presence of water.

Thus we can see that hydrophobic interaction contributes very much to the design of cells. Without membranes, we will never have cells.

The picture I used for my banner in this blog is actually a picture of oil droplets in water. Notice how the droplets naturally form "cell membranes".

Junctional complex – all together now

Source of image: http://www.nature.com/nrm/journal/v2/n4/images/nrm0401_285a_f1.gif
A.Diagrammatic representation of junctional complex in intestinal cells
B.Electron micrograph of of actual intestinal cells

Let’s put together all the components of our junctional complex.

In epithelial cells lining the small intestine for example, the components of the junctional complex are usually arranged in the following sequence, starting from the free surface or exposed surface:
• Tight junction http://acellstoryaday.blogspot.com/2009/02/tight-junction-holding-on-tight.html
• Adhesive junction http://acellstoryaday.blogspot.com/2009/02/adhesive-junction-lets-stick-together.html
• Gap junction http://acellstoryaday.blogspot.com/2008/11/intercellular-communication.html

The adhesive or adherens junction that is labelled in the image above is what we mentioned last time as the belt desmosome while the one labelled as desmosome is what we called as spot desmosome.

There is logic to this kind of arrangement based on the nature and function of the components of the junctional complex.

The tight junction is always at the topmost or most exposed part of the cells because it is supposed to prevent any entrance or exit of materials between cells. The scientific term for tight junction is actually zonula occludens, meaning ring-like occlusion.

The adhesive junctions are usually located below the tight junction because they glue cells together and provide mechanical support to the tight junction.

Finally, gap junctions are at the lowermost part or the least exposed part of the cells. There is actually some space between cells here such that there is rapid exchange of information between cells.

By the way, there may be a 3rd kind of desmosome, the hemidesmosome. As the name implies, it is half of a desmosome. This kind of adhesive junction usually glues epithelial cells to the basal lamina which is in contact with the connective tissues underneath epithelial tissues.

Why do cells put on "kinky" membranes when it's cold?

Remember, I mentioned in one of my earliest posts that cell membranes are my favourite part of the cell (Nov 1, my favourite part of the cell)? Today, I’d like to go back to cell membranes. Why? Well, the cold weather reminded me about what cells do to their membranes when their surroundings get cold.

As you probably know, cell membranes are basically made up of phospholipid bilayers. Then proteins are inserted into this phospholipid bilayer either half-way through or all the way through (please the diagrams above).

Most of the time, the phospholipid molecules in the membrane are fully saturated, so their “tails” appear straight as shown in diagram A. When the temperature gets cold however, the cells replace the saturated phospholipid molecules with unsaturated ones. The unsaturation or addition of double bonds in these molecules produce “kinks” in their “tails” (please see diagram B).

So what is the significance of these “kinks” in the phospholipid molecules? Well, because of the kinks, the molecules become harder to compress and therefore also harder to crystallize. Molecules have to be close together in order to crystallize them. If they are far apart, they cannot be crystallized. This process thus protects the cells because their membrane remains fluid and substances can still go in or out of cells. The same thing is impossible if the molecules are crystallized.

So when it’s cold, cells put on “kinky” membranes in order to survive. Isn’t that cool? (pun intentional)

Ghost cells, are they true?

Are there really ghost cells? Do they say “boo!”?

I know it’s a long way to Halloween but I thought that today would be as good as any other(day) to introduce a new cell, the “ghost cell”.

Well, “ghost cell” was originally used to describe a red blood cell that has lost its haemoglobin because of hemolysis. Since a human red blood cell has no nucleus, once it loses its haemoglobin, it appears like a “ghost” because only the cell membrane remains. So it appears just like a transparent circle, a ghost.

Lately however, the term “ghost cell” is also used to refer to any cell without any nucleus or cytoplasmic structures such that only the outline of the cell is visible.

One form of cancer, ameloblastoma, a cancer of the jaw and tooth related structures, is characterized by the presence of ghost cell tumor.

So ghost cells are really dead cells!Let's just hope they don't go a-haunting.

one more from Lewis Thomas

I mentioned in one of my earlier post (Nov 1) that my favorite part of the cell is the cell membrane. Well, I was happy to rediscover this paragraph while I was rereading Lewis Thomas' "Lives of a Cell" the other day...

"It takes a membrane to make sense out of disorder in biology. You have to be able to catch energy and hold it, storing precisely the needed amount and releasing it in measured shares. A cell does this, and so do the organelles inside. Each assemblage is poised in the flow of solar energy, tapping off energy from metabolic surrogates of the sun. To stay alive, you have to be able to hold out against equilibrium, maintain imbalance, bank against entropy, and you can only transact this business with membranes in our kind of world".

All I can say is "Amen" to this. Lewis Thomas speaks exactly what I think about cell membranes. What do you think?

Complementarity between structure and function at the cellular level

One recurring theme in biology is the complementarity between structure and function. This can be observed starting from the subcellular level up to the organismic level. Since my blog is about cells, I’ll focus first on the cellular level. Then in a future post, I will talk about this on the subcellular level.
Since you have already seen how a nerve cell and an intestinal cell look like (Nov 20and 22), I’ll just focus on these two first.

A nerve cell’s function is communication, so its many processes are arranged in such a way that it can receive as well as send as much information as possible. The dendrites, the receiving ends, are highly branched, while the axon, the sending end, reaches out as far as possible.

An intestinal cell on the other hand is mainly absorptive in its function. Thus the “frills” or microvilli that I mentioned before are designed to increase the absorptive surface of this cell.

We can look other cells in a future post or you can start looking at other cells in your books and try to see if you can determine the function of the cell based on its structure.

display, tell and kiss

A cell usually has many things on display at its surface. Most of these are receptors. Having receptors is a way by which cells communicate with other cells (see Nov 4 post “cells talk”). However, there are some cells that are “professional display artists.” These cells “make a living” by displaying bits and pieces of foreign antigen on there cell surface. I’m talking here about the “antigen presenting cells” or APCs.

APCs “eat” foreign antigens and process these in their lysosomes (see Nov 19 post “phagocytosis”). Then they display bits and pieces of these foreign antigens on their cell surface so they can attract circulating T lymphocytes. It’s their way of telling the T lymphocytes that a foreign substance is present in the body. When the two meet, they then “kiss” through the displayed antigen and the T lymphocyte receptor. After the “kiss” the T lymphocyte becomes activated and then sets the immune response rolling. The continuation of this story will be the subject of another post.

So in the cellular world, display, tell and kiss (not display, kiss and tell) is the way to go to get things moving.

cell design 101.4

Question – “How would you design a cell that has very limited space but needs lots of free surface for interaction?”
Answer – Add frills to its free surface. And that’s exactly how intestinal cells are designed.
Intestinal cells are involved in absorption so they need lots of surface where absorption takes place. However, they must also be attached closely and strongly with other intestinal cells. They cannot allow food substances to pass between them. Whatever food we eat, these have to pass through, not between the intestinal cells. Not only that, these cells must also be anchored close to blood vessels so that whatever food they absorb, these can be transferred right away to the blood and then distributed to the rest of our body. So imagine that – the intestinal cell design has so many constraints: anchored at one end, attached to the sides and large free surface area.

Well, good news, - our intestinal cells are designed exactly that way, as shown in the illustration above.

phagocytosis

Phagocytosis or “cell eating” is a way of getting large matter inside the cell. During this process, the cells form “pseudopods” or special folds of their cell membrane and entrap or enclose food particles, small organisms, and other particulate matter. The folds then fuse and form a vacuole that pinches off from the membrane. Once inside the cytoplasm, the vacuole is now called a phagosome and it fuses with a lysosome. Lysosomal enzymes then digest the particle and release the digested material to the cytoplasm where it is used by the cell for various purposes. Phagocytosis is how the Amoeba obtains its food from the environment.

In animals, some cells act as “professional” phagocytes. Among these are the neutrophils and macrophages. These cells act like roving guards. They move around in the body eating or phagocytizing any particulate material that they encounter. The particulate material can include foreign invaders, dead or damaged cells, and cellular debris. So in these cells, phagocytosis is more of a clean up process rather than an eating process.

In the bone, a special phagocyte, the osteoclast, “eats” old cartilage and bone tissue and partners with the osteoblast, a “bone builder”, in bone formation, reconstruction and repair.

While the “eating habits” of our phagocytes are meant to protect us, sometimes, some enterprising microorganism can take advantage of this activity. Mycobacterium tuberculosis, the tuberculosis-causing bacterium for example, is one such enterprising organism. Once taken inside the cell through phagocytosis, the bacterium secretes an enzyme that prevents fusion of the phagosome with the lysosome. Thus, lysosomal enzymes cannot digest the bacterium and it then can multiply inside the cell and infect other cells too.

So, cells just like organisms should also watch what they are eating or suffer the consequences.

active transport

Cells keep various molecules at specific concentrations. For example, Potassium ions (K+) are kept high inside cells but Sodium ions (Na+) are kept low. Whereas outside of cells, concentration of K+ is low while that of Na+ is high. There is thus a concentration gradient created across the cell membrane. How does the cell maintain this concentration difference? Through active transport, that’s how.

Active transport moves substances against their concentration gradients and thus requires the expenditure of metabolic energy, usually ATP. The transporters are called pumps so there is a Na+/K+ pump for example. This pump transports Na+ out of the cell and transports K+ back into the cell. This way, the concentration difference across the cell membrane is maintained.

What is the importance of active transport in biological systems? Well, for one, it is responsible for enabling us to absorb more food from our intestines. If there is no active transport, then most of the food that we eat will be wasted. If absorption only depends on diffusion, then once the concentration of food in and out of the intestinal cells becomes the same, then absorption will stop. But as we have experienced, we can have 2nd helpings or even 3rds of some of our favorite food. So we have active transport to thank (blame?)for that.

Second, active transport is responsible for selective reabsorption of substances in the kidneys. There is a Na pump in kidney cells that pumps back Na into the intercellular space. Through osmosis, water then naturally follows the solutes. This is how we are able to reabsorb some water.

Third, cells have proton pumps that pump hydrogen ions during energy generation. These pumps are also used to maintain intracellular pH.

Active transport is also used by plants in absorbing minerals from the soil. While animal cells use Calcium pumps to maintain intracellular Calcium (Ca++) levels. After every muscle contraction for example, Ca ions (Ca++) are pumped back into storage so that muscles can relax. When a person dies, the cells lack ATP and active transport of Ca++ cannot occur. Thus, the muscle cells remain contracted and the dead person exhibits rigor mortis.

ion channels

Ions are charged molecules and cannot easily pass through the cell membrane. As we know, cell membranes are basically made up of a double layer of phospholipids. By their nature, ions cannot therefore pass through these membranes. That’s why ions can only get in and out of cells through ion channels.

These channels are protein molecules inserted through the membranes. They have an inner core that is hydrophilic through which the ions can pass and an outer hydrophobic region that interacts with the phospholipid membrane.

There are two major kinds of ion channels: leaky channels and gated channels. As the name implies, leaky channels are open all the time and ions can leak through if there is a concentration difference across the membrane. However, there are only few leaky channels. The gated channels are more numerous and different factors can swing open or close their gates.

For example, some gated channels swing open or close depending on changes in voltage across the cell membrane. These voltage-gated channels usually participate in conducting electrical signals.

Other gated channels swing or close when specific molecules bind to receptors associated with them. They are therefore called ligand-gated channels.

There are also volume-gated channels that swing or close when there are changes in the volume in and around cells. And mechanical-gated channels like those associated with touch receptors, swing or close when there is mechanical change around them.

Opening and closing of these gated channels usually produce specific physiological changes in the cell. Changes in ion concentrations inside cells are signals for specific physiological activity. Examples of physiological activity are: nerve impulse conduction, beating of the heart, activation of visual receptors, touch receptors and other sensory receptors and many more.

Many disorders are associated with ion channel malfunction. Many toxins produce their effct by blocking ion channels. For example, the reason why red tide can poison people is due to blockage in sodium channels.

osmosis

One of the most common misconceptions I usually encounter in biology textbooks is about osmosis. The following is a direct quotation from one of these textbooks. “Osmosis is the diffusion of water through a selectively permeable membrane from a greater concentration of water molecules to a lesser concentration of water molecules.”

Do you see anything wrong with that statement? I hope you do. It’s the phrase “concentration of water molecules.” Water is not concentrated, it’s the solution that is concentrated. A solution may contain more water molecules or less water molecules. The former is a diluted solution while the latter is concentrated. So it’s the solution that is either concentrated or diluted, not the water.

During osmosis, water moves through a differentially permeable membrane towards an area that has more solute molecules. Wherever the solutes are, that is where water will move to. Thus, for solutions that are separated by a differentially permeable membrane, water will always move from where there is more water molecules (the diluted solution) to where there is less water molecules (the concentrated solution). Please remember, water is not concentrated!

Cells touch

Touch is a very important form of communication. We touch somebody when we want to show love or sorrow, joy or approval. We touch babies and they smile. Research shows that babies who do not receive a loving touch usually develop abnormally. In the same manner, cells that do not receive the touch of other cells do not develop at all into specialized, functional cells. Why?

Remember we started as a single, fertilized cell? Well after fertilization, this single cell divided and divided until there were so many small cells that are literally clones – no different from each other. However, after they reached a certain number, they started communicating with each other through touch (through receptors on their membranes) and exchange of molecules. When the cells were dividing and dividing, there was not much communication going on. However, when they stopped dividing and started communicating with each other, something beautiful happened. The cells began to develop their own identities (in the language of developmental biology, this is called differentiation).

Some of the cells later started moving together until they reached a certain destination. There they establish their territory and develop into an intricately designed organ like the heart or the brain. Others formed the stomach or the lungs and all our other beautifully formed organs(in the language of developmental biology, again, this is called organogenesis).

It is amazing how a touch can change a clone-like cell to a beautiful beating heart cell or a fiery nerve cell.

cell design 101.3

After incorporating two major variations (internal membrane system and cell wall) to the basic cell design, all further variations are what I call “icing on the cake.”

So what can we consider as “icing on the cake” variations? Well, in animal cells, further variations include changes in size, shape, structure, etc. Some cells stretched out, flattened, became spherical, developed processes, merged, branched, and exhibited other changes. With every change emerge a new cell. Thus we have so many different kinds of animal cells like: muscle cell, nerve cell, lung cell, red blood cell, liver cell, bone cell, egg cell, sperm cell, etc. In the human body for example, there are more than 200 different cell types.

What about plant cells, what kind of “icing on the cake” variations occurred? Well, because of their cell wall, plants cells cannot change shape or stretch out or flatten. So how do plant cells vary? Well, their variations are mostly in their cell walls. Some have very thick or very thin cell walls, while others have added new substances, or even spaces to their cell walls. Thus, we recognize plant cells as: collenchyma, parenchyma, or sclerenchyma. Their main differences are simply in their cell wall. Of course plant cells also differ from animal cells by having chloroplasts and a large vacuole in their cytoplasm.

Cells talk

Do you know that cells talk non-stop? Huh? Yes they do. This is accomplished through receptors that are found mostly on their cell membrane. Some receptors however are found in their cytoplasm and in their nucleus.

Cells keep a variety of receptors on their membrane. These receptors respond to specific information produced by other cells and their surroundings. For example, neurons send information (neurotransmitters) to other cells adjacent to them while endocrine glands send information (hormones) to other cells that are far from them.

Anyway, these information molecules bind with specific receptors on the membranes of their target cells. Once binding occurs, a series of signals are set in motion and the target cell responds. The response depends on the information received. If the information for example is a neurotransmitter, and the target cell is another neuron, then this target neuron may be excited or inhibited. If on the other hand the information is a hormone like insulin, then the target cell starts absorbing glucose and using this for its metabolic needs.

Thus, a cell maintains a diversity of receptors so they can receive constant information from other cells and from their surroundings. They have to keep on talking with these other cells and their surroundings. The talk is essential for their survival.

Do you know that if cells can’t talk, they will die? This will be the subject of a future post.

My favorite part of the cell

My favorite part of the cell is the cell membrane. Why? Because so many interesting things happen on and in the cell membrane.

Just think - what is the first thing that happens when a sperm meets an egg during fertilization? - cell membrane interaction of course. What is involved when a neuron gets excited and fires a nerve impulse? - cell membrane transport changes, that's what happens. When the environment gets freezing cold, what do cells do? - put on "kinky" cell membranes.

I could go on and on about cell membranes but I think you get what I mean. There is so much going on and in cell membranes. I can actually use up one whole class period just talking about cell membranes but this is not a class but a blog. So this is where I stop today. But I hope I got you thinking about cell membranes.

cell design 101

“If you were to design a cell, what would be your basic requirements or design?” This is the very first question I always ask my students about cells. Their answers always include: “nucleus, cytoplasm, cell membrane, organelles, etc.” When they answer this way, I then ask – “Is the bacterium a cell?” Of course they will answer “yes.” This answer is then perfect for my next question: “But the bacterium does not have a nucleus, so why did you list it as a basic requirement for your cell design?” I always follow this up with more questions and answers that eventually make students think really hard of what are the basic requirements of cells. This then sets the stage for my first lesson on “cell design 101” – wherein we will eventually agree that the basic requirements for cell design are simply: cell membrane, genetic material and biosynthetic machinery.

You can click on any of the links above and they will bring you to related post about these basic requirements for cell design.