A Cell Story A Day

Surprising Discovery - Mitochodrial DNA Exhibits Great Diversity

2010-03-04T09:48:00.001+08:00

New Finding! - A recent article said that mitochondrial DNA exhibits great diversity even in the same individual. This is a big surprise and has great significance in making of genetic markers as well as in the field of forensics.

The article says that different tissues are observed to have different mitochondrial DNA. They are not sure yet when this diversity become manifest.

Here is the link to this article.
http://www.the-scientist.com/blog/display/57199/

2009-12-22T11:25:00.001+08:00

Dear Everyone,
May you have a blessed Christmas and may the New Year bring you joy and peace!
Love you!

Teaching Teachers About Cells

2009-12-03T08:54:00.005+08:00

Two weeks ago I taught a group of high school teachers from Caloocan (a city here in Metro Manila). Our topics were Cell Biology and Cell Reproduction. I truly enjoyed my 2 hour session with them and I hope they did too.
I always enjoy teaching about cells. Cells really inspire me and I never run out of stories to tell about them. Sometimes it's so frustrating though to discover that there are so many misconceptions about cells written in textbooks. I always try my best to point out and correct these misconceptions.

I have talked about some of these misconceptions in some of my earliest post in this blog. Do check them out. Here are some of them: http://acellstoryaday.blogspot.com/search/label/misconception

My 100th post!

2009-09-17T17:30:00.003+08:00

Sorry, I have not updated this blog for a long time. I have not been receiving feedback or comments so I thought that nobody is interested. Well, I was wrong. Just today, I received some comments in one of my post. So, some people are actually reading this! Imagine!

Ok, so what can I say about cells today just to celebrate my 100th post?

I think I will repeat here what I said before about cells - "God put life in a little cell to remind us that big things come from little ones".

I was inspired to write that line after I got to know more and more about cells especially when I started teaching Cell Biology.

Mother's Day

2009-05-10T18:18:00.002+08:00

I know it's been a while since I last posted in this blog. However, I wish to greet all the mothers in the world today with a card I specially made for you. I hope you like it.

Easter Greetings

2009-04-12T11:40:00.000+08:00

Hello Everyone,

May the miracle of Easter bring you blessings and happiness!

Happy Easter!

Hydrophobic interaction and cell design

2009-04-08T16:20:00.004+08:00

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".

a day with some high school teachers

2009-04-06T09:27:00.002+08:00

Last Wednesday, I was a facilitator at a teacher-training project for a group of high school teachers. The project was arranged by some of their alumni.

Anyway, my topics were "cell biology" and "animal anatomy-physiology" - my favorite topics for teacher training.

It was fun to interact with teachers again. It was very satisfying to update them as well as correct some existing misconceptions.

Anyway, I also directed them to this blog for more cell stories.

Hello, I'm back

2009-03-29T20:05:00.002+08:00

Hello, I'm back. I have made some changes in this blog. I added "labels" so you can easily navigate by clicking on a word and find what you are looking for. I also added a few more gadgets like the "encyclopedia" and "endangered animal for the day". I hope that you like and enjoy these changes. Please write me if you have other suggestions to make this blog enjoyable to visit. Thank you.

taking a break

2009-02-21T10:13:00.001+08:00

I am taking a break from this blog for a while. I am still trying to consolidate the feedback I got.

I'll be back soon.

Why the cell membrane model is called “fluid mosaic model”

2009-02-08T19:17:00.008+08:00

Yeah, why “fluid”, why “mosaic”?

Let’s look at our model of the membrane again. The basic membrane is the double phospholipid layer and the proteins and carbohydrates are just add-ons.

So what makes this a fluid mosaic model?

Well, the fluid that is being referred to is the fluidity of the phospholipid bilayer. Each of the phospholipid molecule here can change places with each other side to side. Sometimes, they can even change places in to out or vice versa.

Because of the fluidity of the phospholipid bilayer, the proteins embedded in them can also change places. They can be clumped in one section or they can be spread out in another. Since the membrane is very dynamic, there is constant motion of molecules making it up. Thus, the membrane that one sees at one time is not exactly the same membrane at another time. This is the reason why the membrane is “mosaic”.

So the “fluidity” of the membrane is due to the phospholipid molecules while the “mosaicity” is due to the proteins.

the genetic alphabet - A,T or U, C and G

2009-02-07T22:10:00.004+08:00

Can we write instructions with only 4 (or 5) letters?

The answer to that is “yes”! Our cells’ genetic instructions are written using only the letters A, C, T or U and G. Can you believe that?

If that is the case, how come there are so many different cells? How come we are different from each other?

Well, these letters vary in number as well as in their sequence in every cell. Also, sometimes not all the sequences of these letters are active at the same time. If for example we designate numbers to the various sequence of these letters in a cell, it’s possible that only sequences 1, 2, and 3 are active in one cell while it can be sequences 1, 5, and 8 in another cell.

So if you think about it, just varying the number of A, T, C and G as well as their sequence in a cell are enough to produce almost limitless variety of combinations.

By the way, in the genetic alphabet, A always pairs with T or U and C always pairs with G. So that actually limits the combinations because there will always be the same number of A and T or U and equal number of C and G. Still even with this constraint, the possibilities are almost limitless.

Why do eukaryotic cells keep their genetic material inside a nuclear membrane?

2009-02-05T19:40:00.004+08:00

If you recall, the major difference between eukaryotic and prokaryotic cells is the presence of an internal membrane system in the former (Nov 3, cell design 101.1).

This internal membrane system encloses the various metabolic centers and separates them into organelles. It also encloses the genetic material and we now recognize a nucleus in eukaryotic cells.

So, what is the advantage of this kind of design?

Well, as Sherlock Holmes would say, “elementary my dear Watson, elementary”. Just think about it, the genetic material contains the ‘blueprint’ of the cell’s life. So it’s but natural to ensure its safety, right?

The cell cannot leave its 'blueprint' lying around, exposed to all the enzymes and activities going on in the various metabolic centers. What if an enzyme will act on it and split it into pieces? What if it suddenly gets entangled in all the activities going on? The information in the blueprint might be destroyed or lost.

Now, do you wonder why prokaryotic cells mutate so fast? Their genetic material is not protected like that of eukaryotic cells.

Junctional complex – all together now

2009-02-03T19:35:00.014+08:00

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.

Carbon fixation - why plants need carbon dioxide

2009-02-02T10:54:00.007+08:00

In my Jan 23 post, ‘why is it better to water plants in the morning”, we talked about the first phase of photosynthesis or the light dependent phase. Today, we will talk about the second phase of photosynthesis or the light-independent phase, also known as carbon fixation.

If sunlight and water are needed in the 1st phase, carbon dioxide and the energy produced from the 1st phase are the ones needed in this 2nd phase.

The end result of this carbon fixation phase is the formation of organic molecules especially carbohydrates.

Different plants use different ways of fixing carbon dioxide into organic molecules. The difference is dictated by the surrounding temperature.

Plants found in temperate regions or what are called C3 plants, generally use a 3-Carbon compound as their first molecule in the process. This process is also called Calvin cycle.

Plants in tropical regions on the other hand, use a preliminary 4-Carbon compound before it proceeds to the Calvin cycle. Plants using this process are therefore called C4 plants.

Finally, plants in desert areas cannot open their stomata (passage way for carbon dioxide) during daytime because they will lose too much water this way. They can thus take in carbon dioxide only at night. They store the carbon dioxide in organic acids at night and just transform these acids into carbohydrates during daytime. Plants belonging to this group include various cacti (singular, cactus) and are called CAM plants or Crassulacean Acid Metabolism plants.

Anyway, whichever process is used by plants to fix carbon dioxide, they still end up making organic compounds especially carbohydrates. These compounds are what we use as food.

So this gives us more reasons to thank green plants. Don’t you agree?

Adhesive junction – let’s stick together

2009-02-01T22:44:00.006+08:00

As the name implies, adhesive junction glues adjacent cells together. There are two kinds of adhesive junction in cells: the belt desmosome and the spot desmosome.

Both belt and spot desmosomes are made up of adhesion proteins that form a kind of bridge between cells and anchor this bridge to cytoplasmic elements inside cells. The two differ only on how the bridge is formed.

Belt desmosomes form a complete ring of bridge around cells while spot desmosomes form the bridge only at certain points or spots between cells.

If the desmosome between cells do not form well, then the cells can come off in layers and fluid will accumulate between them. This is what happens when a blister is formed. Notice that a piece of skin (layer of cells) separates from the underlying cells and fluid fills the space created. Eventually, the blister dries up and the separated piece of skin dies and peels off.

In this case, the adhesive junction or bridge between cells collapses.

Tight junction – holding on tight

2009-02-01T00:02:00.005+08:00

Epithelial cells by the nature of their function as linings or as glands must always “hold on to each other”. Cells lining our intestines for example, must hold on to each other to prevent any material from passing between them. This ensures that anything that goes through our bodies passes through them (the intestinal cells) for proper processing, and not between them. So how is this possible? Well, intestinal cells as well as most other epithelial cells are attached to each other by junctional complexes, a primary component of which is the tight junction.

Tight junctions function as seals between and around epithelial cells. These consist of closely apposed plasma membranes of adjacent cells with no space at all between them. Thus, nothing escapes between cells.

For example, urine remains inside our urinary bladder and does not leak through it because of tight junctions. The contents of our intestines and stomach are kept inside our bodies because of tight junction. Food is absorbed by the cells but once absorbed cannot leave the cells. Contents of our body do not leak through our skin because of tight junction.

These are just some examples of the importance of tight junctions between cells.

By the way, gap junctions mentioned in my Nov 17 (intercellular communication) post, also are components of junctional complexes. Another component is the adhesive junction and this will be the subject of a future post.

We can learn from cells about ... quality control

2009-01-30T11:22:00.007+08:00

Do you know how rigid is “quality control” in cells? Extremely rigid, - especially in the making of our T lymphocytes. An estimated 99% of developing T cells do not mature, so only 1% survives and “sees the light of dawn”. Imagine that, only 1% survives the rigid development process! If that is not extremely rigid for you, then I don’t know what is.

T lymphocytes originate from the bone marrow but undergo development and maturation in the thymus. Here (in the thymus) they are well insulated from untimely and extraneous exposure to foreign substances as they undergo development and maturation. The developing lymphocytes are only exposed to foreign elements once it is certain that they can indeed recognize what is foreign and what is self. The thymus has extensive blood-thymus barrier that makes sure this proper environment is maintained.

A mature T cell (the "graduate" of “Thymus University”) must be able to do two important things:
a)recognize self from non-self (foreign) and
b)express receptors that can bind antigen plus self-MHC molecules*

If the T cell during its development untimely develops or does not develop those two attributes, then it undergoes apoptosis or cell suicide, (please see Nov 6 post, cells commit suicide).

So, many cells die on the road to development and maturation and only the elite 1% “graduate” from the “Thymus University”. Can you believe that?

This extremely rigid “weeding out” process is very important for the integrity of our own immune system. Imagine what will happen if the T cell “graduate” cannot recognize foreign from self? Then the T cells will attack our own cells (self)! This by the way is what happens when we suffer from auto immune disorder. What happened to the development of T cells here? This will be the subject of a future post.

So in essence, that is quality control in the cellular world. If the cell does not develop properly, then it is signalled to commit suicide. Only the best survives, no “pwede na” (that’s ok or half-baked) graduates (or end products) here. Is this rigidity at all possible in the human world? What do you think?

--------
*Major Histocompatibility Complex

Why follow rules?

2009-01-29T22:12:00.006+08:00

Following rules is very important in human society as well as in the cellular world. The difference is, cells follow rules “religiously” while humans tend to circumvent or even break or bend the rules. Maybe one of the reasons why we have problems in society is because we tend to do just that – either circumvent rules or break them.

I think we can learn a thing or two from cells. In the cellular world, everything flows smoothly. There is no chaos or anarchy. Why is this so? Well, because cells follow the rules or laws of nature.

For example, take a look at how cells generate energy...

When cells generate energy, they follow steps so there is no build up of both resources and products. There is always an enzyme that facilitates all processes every step of the way. Every process flows smoothly. No step is ever by-passed, there are no short cuts. The metabolic pathway that is followed is always the one that is the most energy efficient given the resources available. Every molecule in the cell "knows" its role and just awaits its turn to play its role. There is no jockeying for position because each molecule has its own time and place for action. There is no "me first, you later" in the cellular world.

Cells follow the rules of nature. We have the choice whether to follow rules of man or of nature. We have choice or freedom to choose, cells don’t have. So maybe there is really no parallelism. Cells “can’t help it” (but follow) but we can choose to follow or not. However, I strongly believe that if we just listen to our heart, we will also choose to follow the “laws of nature”.

In the cellular world, cells follow the laws of nature because these are programmed into their cellular “being”. I believe that in the human world we also have similar “laws of nature” programmed into our own being. However, we have problems knowing what these laws are because they are sometimes masked by the many distractions we have along the way. Many of us are beginning to sense however that indeed there are laws of nature that are also programmed in us. This is the reason why books like “A Purpose Driven Life” for example are so popular these days. We are now beginning to discover what our own “laws of nature” are.

Cells “know” their laws of nature and follow them “religiously” as I said earlier. We are just beginning to discover or rediscover our very own “laws of nature”. Once we do that and follow them, then I’m sure that our world will also flow as smoothly as that of the cellular world.

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

2009-01-28T13:59:00.005+08:00

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?

2009-01-27T17:39:00.006+08:00

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.

How did the chloroplast get its name?

2009-01-26T19:50:00.004+08:00

source of image: http://gcse.wemew.org/data/Plant_cell.png

Years before the advent of powerful microscopes and other techniques for visualization of cells, simple microscopes only showed large cell organelles. One of the largest organelles is the chloroplast and microscopists simply used descriptive terms to explain what they saw.

Thus, chloroplast simply means “green particle” because that is how it appears under the microscope. In the same manner, leucoplast means “white particle” and vacuole is an "empty space or small cavity".

CoQ, do we really need it?

2009-01-24T18:59:00.003+08:00

Why is there so much hype about the importance of CoQ or CoenzymeQ (a.k.a. CoQ10, ubiquinone)? Do we really need it?

Well, CoQ is a naturally occurring substance that is found in our membranes especially the membranes of the ER (see Nov 21, 23), peroxisomes (see Nov 15), lysosomes (see Nov 19), and vesicles (see Jan 11). It is most abundant in the cristae of our mitochondria (see Jan 1-5) as it functions as one of the electron acceptors during energy production.

Because it can accept and transfer electrons, CoQ can therefore act as antioxidant too. Thus, it is usually recommended as a dietary supplement especially in adults and individuals with diminished energy-producing capacity.

There is thus a biological basis for all the hype about this substance. However, its role in preventing heart failure still has to undergo more tests.

Since CoQ is fat soluble, it is best taken during meals that contain oil and fat.

Why is it better to water plants in the morning?

2009-01-23T18:45:00.004+08:00

Why is it better to water plants in the morning? Why, because water is needed by plants in the light-dependent phase of photosynthesis.

Plants and other photosynthetic organisms start the light-dependent phase of photosynthesis as soon as there is light. During this process, light energy trapped by chlorophyll splits water into an oxygen molecule and 4 protons. The oxygen diffuses out of the plants (and this is what we breath in) while the protons (or hydrogen ions) are used to generate energy molecules.

What happens then if we water our plants late in the afternoon? Well, I think you know the answer to that - this does not give the plants enough time to generate more energy as well as to release more oxygen.

The energy molecules generated here are used for the carbon fixation or the light-independent phase of photosynthesis.

By the way, since plants release oxygen during this process, this is another reason why we have to thank a green plant. Don’t you agree?

Why should we thank a green plant?

2009-01-22T17:53:00.005+08:00

Why, because plants do photosynthesis. Photo what? Photosynthesis, that’s what.

So what is this photosynthesis thing? Well, it is nature’s solution to the energy and carbon drain from our biosphere.

During photosynthesis, energy from the sun is transformed into chemical energy in the form of ATP and NADPH. Then this chemical energy is used to fix carbon atoms from carbon dioxide into large organic molecules like carbohydrates. These carbohydrates are then available to other organisms like us for our own energy needs.

We can see that light energy from the sun is needed in photosynthesis. The first stage (conversion of light energy to chemical energy) in photosynthesis is a light-dependent process. The second stage (fixing of carbon into carbohydrates) is light-independent so it can occur even in the absence of light. However, it still needs the products from the light-dependent process.

In order to make use of light energy, a family of green pigment molecules called chlorophyll serves as the trap for light energy. Thus, the only organisms that can make use of light energy are those that have chlorophyll, like the plants, some bacteria and some protists. Plants store chlorophyll in their chloroplasts.

Even if we stand under the sun all day, we will never be able to do photosynthesis and make our own energy molecules. All that we will be able to do is get sunburned. Why, because we do not have chlorophyll like the plants.

This is the reason why we sometimes see some posters that asks the question, “Have you thank a green plant today?”

saying hello without goodbye

2009-01-21T22:29:00.002+08:00

Hello,
I was out for a week but was not able to say goodbye. Well, nobody seems to have noticed because I did not receive any inquiry. Anyway, I had to attend to some family matters in the province and didn't have a chance to say goodbye before I left.

I just want to tell you that I'm back. I will start my regular post tomorrow and pick up from where I left last time.

See you tomorrow.

Chloroplast

2009-01-14T15:51:00.005+08:00

Source of image: http://www.helpsavetheclimate.com/chloroplast1.gif

Today, we will talk about the other energy generating organelle in cells, the chloroplast. We will also start with its structure and cover its function in future posts.

The chloroplast is much bigger than the mitochondrion. Just like the mitochondrion, it also has both an outer and an inner membrane that are separated by an intermembrane space. However, it still has a 3rd membrane which consists of flattened sacs called thylakoids. These thylakoids may be stacked together and form the grana (sing. granum) or may be unstacked and form the stroma thylakoids.

Chloroplast just like the mitochondrion also has its own DNA, mRNA, and ribosomes. These are located in the stroma.

marked for “death”

2009-01-13T17:29:00.004+08:00

Do you know that cells mark certain proteins for “death”? I placed death in quotations because proteins are not alive, so they don’t die. Rather, they are degraded or broken into smaller units. However, “marked for death” is certainly a more catchy title than “marked for degradation”. Don’t you agree?

Anyway, our cells are constantly synthesizing proteins, exporting them, as well as degrading them. Since proteins form structures as well as act as enzymes and information molecules in cells, their amounts have to be constantly regulated. There should not be too much or too little of them inside the cell. Getting rid of excess proteins is thus a carefully controlled process.

The first step in the process is to mark the potential candidate for degradation. This is done by attaching ubiquitin molecules at several points in the protein where the lysine residues are found. Ubiquitination is the mark of “death”. Once marked, then large complexes of protein enzymes called proteasomes attack and break the protein into small pieces. Ubiquitin is thus the marker and proteasomes are the executioner in the “death” of a protein molecule. After the process, ubiquitin detaches and is recycled for future use.

So, if you are a protein molecule, beware of ubiquitin!

entropy and cells

2009-01-12T19:54:00.004+08:00

Somebody asked me how I decide which topic to talk about in this daily blog. Actually, when I started this blog, I first focused on the main topics of Cell Biology. Thus, my first post (after the Intro) was about the basic requirements of cells and cell design. After that however, I would shift between cell design and the misconceptions that I usually encounter in textbooks or in students. Later, there is really no pattern in my posts. I would just talk about either the first topic that comes to mind or I would try to relate my post to the occasion as what I did last Christmas. Now, I talk about what ever inspires me for the day.

So what inspires me today? Yah, what? Well, I let my mind wonder through my “library” about cells and it paused on the concept of entropy. I know entropy is taken up more in physics, but entropy is also very much related to life. Why?

Well, the natural order of things (including living things) is towards entropy or towards increasing disorder. Living things which are highly organized therefore must keep on doing something to prevent this disorder. So what is this something? This something is – generate energy and use this energy to prevent entropy.

Yes, this is the main reason why we must always generate energy. We have to maintain the order in all our cells. We have to maintain our structures, our high degree of organization, so we will be able to function. Thus energy production is a continuous process. We cannot stop generating energy. We need a constant source of energy therefore, so we can “bank against entropy” as how Lewis Thomas put it.

Vesicles

2009-01-11T15:05:00.005+08:00

Different kinds of vesicles abound in cells. They come in all sizes and content but they all transport something, be it towards the nucleus or towards the cell membrane or between cell organelles. Anyway, one thing is common among these vesicles; they usually have coats and markers. The coats generally indicate their source while the markers indicate their destination.

For example,3 types of coats are used by cells when they transport substances between the ER and Golgi: coatomer I (COP I), coatomer II (COP II) and clathrin.

Vesicles carrying newly formed proteins from the ER are coated with COP I while COP II coats vesicles that transfer substances between the different aspects of the Golgi apparatus. If a vesicle has to transport substances from the Golgi back to the ER however, COP II will coat this vesicle.

Usually if a vesicle contains newly finished product from the Golgi then clathrin is used to coat this. Newly synthesized lysosomal enzymes for example are clathrin-coated. Clathrin also coats newly formed endocytic vesicles. Actually these coats all help in the vesicle formation and later on in the transport process.

There are of course different markers for different destinations of these vesicles. So some vesicles are marked for lysosomes only or for “export”only.

Vesicle formation is actually a complex process involving many steps. What is presented here is a highly shortened version. And not all clathrin coats are the same.

the cell's lab table

2009-01-10T21:05:00.005+08:00

Do you know that cells have "lab tables"? Yes have. These are the ribosomes, the small non-membrane bound organelles composed of proteins and ribosomal RNA (rRNA).

Ribosomes consists of large and small subunits. The small subunit has a site for binding mRNA, a P-site for binding peptidyl tRNA and an A-site for binding aminoacyl tRNA. As you can see these sites are used during protein synthesis. Thus, ribosomes serve as the surface or the lab table for the synthesis of proteins.

By the way, the large and small subunits are manufactured separately in the nucleolus and also released separately to the cytoplasm. They remain as separate entities until the synthesis of proteins starts.

why water

2009-01-09T15:50:00.005+08:00

It has been raining lately and this made me think of water. In my Nov 7, 2008 post (water world), I mentioned that water is the most abundant component of cells. In that post, I corrected a common misconception, that water is a universal solvent. It is not! It's just a very good solvent but it definitely is not a universal solvent!

In today's post, I will try to answer why water is the most abundant component of cells. Well, the reasons are because of its physical and chemical properties.

What are these properties? Among its important physical properties are: high specific heat, high heat of vaporization, high heat of fusion, high surface tension. Its dipole moment as well as its ability to form hydrogen bonds are its important chemical properties.

So what is so important about these physical and chemical properties? Well, because of its physical properties, water remains as liquid in a large range of temperature. It takes a lot of energy before water can be converted to vapor (high heat of vaporization) or solid (high heat of fusion). It can also absorb a lot of heat before its temperature changes even one degree centigrade (high specific heat). Thus, water does not easily get heated nor cold and this stability is very important for cells. The high surface tension causes water molecules to create a film on surfaces and this is very important especially in maintaining breathing surfaces.

The chemical properties of water are of course the reasons why water is a very good solvent and can also participate in many biological processes.

So there you are, those are the reasons why water is the most abundant component of cells.

Counting ATPs

2009-01-08T18:43:00.004+08:00

Students usually ask me how to count the number of ATPs formed during cell respiration. So I have prepared the following table that summarizes how and where ATPs are formed.

Before we go to that however, I just wish to point out that there are two ways by which ATP is formed. One is through substrate level phosphorylation and the other is through oxidative phosphorylation. During substrate level phosphorylation, 1 molecule of ATP is formed during each process. During oxidative phosphorylation however, 2 or 3 molecules of ATP are formed per process depending on the first hydrogen acceptor. If FAD is the first hydrogen acceptor, then 2 ATPs are formed while 3 ATPs are formed if NAD is the first hydrogen acceptor.

Another thing, we have to multiply by 2 all the ATPs formed because there are 2 molecules of pyruvic acid formed after glycolysis.

Reaction Type of Phosphorylation ATPs formed
Glucose to Pyruvic acid Substrate level 2 (net)*
Pyruvic acid to Acetyl CoA Oxidative 3 x 2
Krebs cycle and Ox-Phos Oxidative (NAD) 9 x 2
Krebs cycle and Ox-Phos Oxidative (FAD) 2 x 2
Krebs cycle Substrate level 1 x 2
G3P to 1,3DPGA in glycolysis* Oxidative via GP shuttle 2 x 2

* 4ATPs are actually formed. However, 2ATPs are used to prime glucose for the process.

**one step during glycolysis converts glyceraldehyde3phosphate(G3P) to 1,3diphosphoglycerate(1,3DPGA). This releases hydrogen ions and electrons that are accepted by NAD and brought to the mitochondrion through a glycero-phosphate shuttle (GP). So only 2 ATPs (instead of 3) are formed here (even if NAD is the acceptor) because 1 ATP is used to "pay" the GP shuttle.

of energy, equilibrium and imbalance

2009-01-07T21:56:00.007+08:00

If you remember, I gave a quote (Dec 7 post) from Lewis Thomas about membranes. The last portion of that quote is: "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".

Today, I would like to focus on the line "... you have to be able to hold against equilibrium, maintain imbalance,..."

This line usually confuses students because they think that biological systems always try to maintain equilibrium and balance. So when I tell them the contrary, they get confused. How then do we remove this confusion?

Well, what I usually do is I ask them the questions: "What are the contents of cells?, What is the composition of the fluid surrounding cells?, What is the composition of earth?" Once they give the answers, they then realize that indeed cells have different composition from their immediate surrounding and from the earth. And the only way for cells to have a different composition from their surroundings is to "hold against equilibrium and maintain imbalance." This is of course only possible because of membranes and active transport. The membranes keep the substances inside cells and active transport maintains this difference in composition. And the only way cells can do this is by having a constant supply of energy.

Energy is thus needed to go against equilibrium and maintain imbalance. These make cells alive and different from the surroundings. Hooray for imbalance!

junk food and energy generation

2009-01-06T21:48:00.002+08:00

Have you ever wondered why we call certain food as “junk food”? We usually understand that “junk food” has little or no nutritional value, right? Well, that is correct in a certain sense. However, there is another aspect to why “junk food” is junk, and this is related to what we have just covered in the last few posts about energy generation in cells.

One important process in energy generation is the maintenance of the proton gradient (see Jan 4 post). As mentioned: “This gradient drives the ions to move back to the matrix and as the ions pass through special channels that are associated with ATP synthase, ADP is phosphorylated to ATP.”

As you can see, the proton gradient is the one that drives the (hydrogen) ions to move back to the matrix and as they pass through special channels, energy (ATP) is created. If this gradient therefore is reduced or dissipated, then the driving force will no longer exist and no ATP is formed.

So what does this have to do with junk food? Well, here’s the connection. Some junk foods contain chemicals (usually the preservatives or coloring used) that reduce this proton gradient or driving force. How? These chemicals sequester or “smuggle” across the membrane the hydrogen ions without passing through the special channels with ATP synthase. Thus, no ATP is formed.

So, do you still wonder why “junk food” is junk?

energy generation in the mitochondrion, a summary

2009-01-05T20:15:00.003+08:00

I have made this concept map to summarize all the processes of energy generation in the mitochondrion. I hope that you find it useful.

Energy generation in the mitochondrion, part 3

2009-01-04T21:12:00.000+08:00

This is a continuation of yesterday’s post. We are now in the final phase of energy generation, the oxidative phosphorylation. This process takes place along the cristae of the mitochondrion. This is the reason why I mentioned in one of the previous posts that the more folds or cristae there are, the larger the area for energy generation.

Oxidative phosphorylation is the only phase wherein oxygen is used. However, as mentioned before, preparation for this final phase actually starts during the formation of AcetylCoA from pyruvic acid.

The hydrogen ions and electrons that are generated during the Krebs’ cycle are transferred by the hydrogen acceptors to the different enzymes along the cristae of the mitochondrion. Here the electrons are transferred from one electron acceptor to another along the cristae while the ions are pumped across the cristae to the intermembrane space (see post on the structure of the mitochondrion). The ions thus create a proton gradient across the cristae. This gradient drives the ions to move back to the matrix and as the ions pass through special channels that are associated with ATP synthase, ADP is phosphorylated to ATP.

Oxygen acts as the final hydrogen acceptor as the electrons and ions rejoin each other and form water in the process.

Energy generation in the mitochondrion, part 2

2009-01-03T17:53:00.006+08:00

source of image: www.britannica.com
As mentioned in yesterday’s post, the next 2 phases of energy generation in cells are Krebs’ cycle and oxidative phosphorylation.

Krebs’ cycle is also known as citric acid cycle because the first substrate formed is citric acid. This process occurs in the matrix of the mitochondrion.

This cycle is an 8-step process that changes AcetylCoA to citric acid and the latter into oxaloacetate. Main products of this cycle are Hydrogen ions and electrons which are immediately received by Hydrogen acceptors and transferred to the last phase or oxidative phosphorylation. By-products of this cycle are CO2 and H2O.

Only 2 ATPs are actually produced in the Krebs’cycle itself. However, since it is coupled with the last phase, oxidative phosphorylation, 22 more ATPs are produced through the coupled reactions.

We will talk about the last phase of this energy generation in tomorrow’s post.

Energy generation and the mitochondrion

2009-01-02T19:57:00.002+08:00

Energy generation or cell respiration consists of 4 phases: glycolysis, conversion of pyruvic acid to Acetyl Coenzyme A, Krebs’ cycle and oxidative phosphorylation.
The last 3 phases of energy generation take place inside the mitochondrion while the first phase takes place in the cytoplasm of a cell.

Glycolysis is an anaerobic process (does not need oxygen to proceed) that involves breaking down of a sugar molecule (usually glucose) into 2 molecules of pyruvic acid. If oxygen is still not available after this process, then pyruvic acid is converted into lactic acid in animal cells and into ethyl alcohol in plant cells.
If oxygen is available however, the 2nd phase of energy generation takes place, that is, pyruvic acid is converted to Acetyl Coenzymne A in preparation for the 3rd phase of the process.

Glycolysis yields 4 molecules of ATP (the energy currency of cells) but the net yield is only 2 molecules of ATP because 2 molecules are used up to prepare glucose for the process. On the other hand, phase 2 or the conversion of pyruvic acid to AcetylCoA yields a net of 6 ATP molecules.

The last 2 phases of cell respiration are coupled. That is, one cannot occur without the other. We will thus talk about these 2 in another post.

Mitochondrion

2009-01-01T13:13:00.004+08:00

source of image: www.britannica.com

I thought a good way to start the New Year right is to talk about cell energy and the mitochondrion.

The mitochondrion is an organelle that is involved in energy production. It is a rather complex organelle, it will probably take a few posts to completely its story.

Anyway, just to get started, let’s first talk about its structure today.

A mitochondrion (plural, mitochondria) is usually rod-shaped but this shape can change at anytime under varying conditions. It has a double membrane, the outer one being smooth and the inner one being thrown into folds called cristae (sing. crista). These folds increase the area for enzymes embedded in it and the more active a cell is, the more folds there are. Thus, a heart muscle cell for example has more cristae in its mitochondrion compared with a cartilage cell's mitochondrion.

There is a narrow space between the outer and inner membranes of the mitochondrion. This space is called the intermembrane space. Another space is found in the middle of the mitochondrion and this is called the matrix space or simply the matrix. Contents in both spaces differ.

The contents of the intermembrane space are somewhat similar to that of the cytosol whereas the matrix space contains many enzymes involved in the Kreb’s cycle process. Ribosomes as well as a circular DNA and tRNA are also found in the matrix.

Stem cells

2008-12-31T11:19:00.001+08:00

It’s New Year’s eve in a few hours. When I thought about which cell reminds me of New Year, stem cells immediately came to mind. Stem cells remind me of new beginnings, new possibilities, new hope. New Year is always exciting for me, so are stem cells.

Of course there are two kinds of stem cells: embryonic and adult. Embryonic stem cells have the potential to be anything, even a whole new organism (especially for some animals or plants). Adult stem cells on the other hand can only give rise to a specific cell line. So we have stem cells for skin or for intestine or for blood.

Using embryonic stem cells for research is of course controversial because of the source and the way the cells are prepared. Technical and moral issues are involved here. Use of adult stem cells is not as controversial and this where most of researches are now focused.

Actually use of adult stem cells has been going on for a long period of time. Bone marrow transplant for example uses the stem cells in the bone marrow as source of new cells to replace damaged or abnormal blood cells of the recipient.

Major biomolecules of cells

2008-12-30T22:52:00.002+08:00

Every cell needs 4 major molecules, little bits of odds and ends, and plenty of water. These major biomolecules are: carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates are used mainly as energy source for cells. However, some carbohydrates are also used as structural components. Cell walls for example consist of carbohydrates. Some components of the cell membrane as well as the extracellular matrix are also carbohydrates.

Lipids on the other hand make up the basic component of the cell membrane. They are also the major backbone of steroid hormones as well as the main form of stored energy.

Proteins meanwhile have both structural as well as functional roles in the cell. Structurally, they are major components of the cell membrane. Functionally, they act as enzymes, hormones, carrier molecules, antibodies, and several other roles.

Nucleic acids are of course the carriers of hereditary information of cells.

cell design 101.6, fat cell

2008-12-29T23:33:00.005+08:00

Do you know that fat and thin people have actually the same number of fat cells? Yes, we have. The only difference is in the amount of fat stored inside the cells. So if somebody is fat, their fat cells appear bigger because of the greater amount of fat stored inside.

We also have two kinds of fat cells: those that store fat as a single large fat droplet and those that store fat as several small droplets. The first cells are called unilocular fat cells and the latter are called multilocular fat cells. The unilocular cells form what we call as white adipose tissue while the multilocular ones are what forms the brown adipose tissue. We have more white than brown adipose tissue.

not all bacteria are bad

2008-12-28T18:26:00.002+08:00

I always see or hear in advertisements that we should get rid of the bacteria in our surroundings thus we need to use a certain brand of alcohol or some antiseptic. However, this idea is rather misleading. It gives the impression that all bacteria are bad. But such is not the case, there are also good bacteria.

Just think for example of the bacteria that degrade the substances in the soil. If these bacteria are not there then we would have been buried by now in all the garbage that we produce. Or think of the bacteria that help us in digestion of food or help process the undigested material in our large intestine. We will have all kinds of digestive disorders if these bacteria are not there.

We have several other examples of good bacteria like the nitrogen-fixing ones or the oil removing ones. However, I think the above examples are sufficient enough to make us rethink about getting rid of all bacteria.

spermless development?

2008-12-27T22:34:00.004+08:00

I have been sitting here in front of my computer thinking of something to write about cells. Somehow, after writing about the egg cell and the sperm cell, I cannot think of anything else to talk about. Of course there is still so much more to discover about cells. I have not even talked about the energy-generating centers in cells yet – meaning the mitochondria and chloroplasts. However, I don’t feel like starting their stories today. Not just yet anyway. So what cell story should I tell today?

Okay, here’s one – do you know that egg cells can start the first stages of development even without the sperm cells? Yes they can!

The first stage of development after fertilization is what is called as cleavage. This simply involves the rapid cell division of the fertilized egg. Experiments have shown than even a pin-prick can trigger this initial stage. However, after dividing several times, the egg cell will stop dividing and will not proceed to the next stage of development which is called gastrulation.

So later stages of development need the combined information coming from both the egg cell and sperm cell but the initial stage of development does not need the information from the sperm cell. Isn’t this amazing?

sperm cell

2008-12-26T22:25:00.004+08:00

source of photo: http://aycu31.webshots.com/image/44110/2002564320883082356_rs.jpg
Since I talked about the egg cell yesterday, I thought I might as well talk about the sperm cell today.

If you look at the picture, you will notice the big difference between the size of the sperm and the egg. What is shown in the picture is only a small segment of the egg cell. A sperm cell is only about 25 micrometers or less in diameter while the egg cell is about 200 micrometers or even more in some animals.

A sperm cell contains only the nucleus which occupies the "head" part of the sperm, plus several mitochondria in the "neck" part. The rest of the sperm consists of the flagellum.

According to http://hypertextbook.com/facts/2000/EugeneKogan.shtml, the average speed of a sperm is "1–4 millimeters per minute".

egg cell

2008-12-25T18:01:00.005+08:00

source of picture:http://encarta.msn.com/media_461516399/egg_cell.html
To me, the egg cell is always a special cell. It is as if it carries all the future of a new organism in itself.

The egg cell is the biggest cell in the body. It can even be seen without the aid of a microscope. It contains so much yolk especially in those animals that develop outside of the female’s body. The sperm cell only contributes its nucleus during fertilization, but the egg cell contributes not only its nucleus but also its cytoplasm and everything in it including the organelles.

During the early stages of development after fertilization, the yolk in the egg cell’s cytoplasm is actually the only source of nutrition for the growing embryo.

By the way, since the mitochondria of a developing embryo only comes from the egg cell, one line of research has tried to follow our supposed to be "Eve" by following the mitochondrial DNA or "mitochondrial Eve" through the ages.

taking a break

2008-12-24T19:48:00.001+08:00

It's Christmas eve here tonight. I'm taking a break from this blog today.
Have a Merry Christmas!

Season's greetings

2008-12-23T22:08:00.001+08:00

Instead of writing some cell story, I just want to greet everyone a very Merry Christmas!

why cells are small

2008-12-22T23:04:00.005+08:00

Sorry I could not find the table I was talking about last time. However, I found the following notes (which can be converted to a table, but I don't have time, sorry) in my notebook:
In a cell, equilibrium through diffusion is attained within 0.00000456 seconds if the distance from the boundary is 0.1 of a micrometer. If the distance is 1 micrometer, then equilibrium is attained within 0.000456 seconds and if the distance is 10 micrometer, then equilibrium is attained within 0.0456 seconds. If however the distance from the boundary is 1 mm, then equilibrium is attained only after 7.6 minutes while if it is 1 cm, then it would take 12.75 hours for equilibrium to be attained.

If we examine the figures above therefore, it is obvious why cells have to be small, that is, they are in micrometers. A red blood cell for example is about 7 micrometers. Just imagine what will happen if a cell is in centimeters, it would take several hours (half a day, actually!) for substances to move from the cell membrane to the cytoplasm. That is not compatible with life at all! And if the cell is as big as a basketball, can you imagine how long equilibrium by diffusion would take? - months maybe or would it be years? Oh no!

why are cells small?

2008-12-21T23:38:00.003+08:00

Why are cells small indeed? Well, it's really the physical and chemical laws that limit cell size. Substances need to move to and from cells and also within cells. If cells become big, it will take a long time for substances to move from one part of the cell to another and this will not be compatible with life. I have an actual table showing how far substances can move if the distance between the cell membrane and the cytoplasm is in nanometers or in millimeters. However, I cannot find the table right now. I promise I will post it sometime soon. As soon as I find it that is.

Suffice it to say for the moment that one should never expect to find a single cell that is as big as a basketball.

what can In give you this Christmas

2008-12-20T23:09:00.003+08:00

The song “What can I give you this Christmas” keeps ringing in my brain as I think about what story to write about cells today. So what can I give you this Christmas? Well, maybe I can share with you how I got fascinated with cells. It all started when I took up Cytology in the undergrad.

As you know, Cytology is the study of cells. It was the first time the course was offered as an elective so our teacher was so excited about it. Her excitement was contagious such that we the students also got excited at learning more about cells. Even if we only had our compound microscope then, our teacher had so many electron micrographs of various cells and their components. I would pour over these micrographs and marvel at the orderliness of everything in the cell.

Later, when I was in graduate school, I took up Cell Biology and this got me even more interested in cells. Eventually, when I started teaching, I taught Cell and Molecular Biology and I was hooked for good. I would read anything and everything about cells and excitedly shared everything I learned with my students. Now I’m extending this love of cells in this blog.

Cilia and flagella

2008-12-19T19:20:00.003+08:00

Some cells have cilia or flagella on their cell surface. What are these structures for? Well, whenever these structures are present one can be sure that there is movement going on.

Cells lining our respiratory tract for example use their cilia to move mucus and trapped particles towards the mouth. Movement is usually towards one direction, so in a sense the cilia act somewhat like escalators that move people or things upwards or downwards.

We are familiar of course with the flagellum of sperm cells. This propels the sperm as it moves along the reproductive tract of females.

Structurally, both cilia and flagella consist of microtubules that are arranged in a specific manner together with associated proteins dynein and kinesin. They only differ in length and number as well as in the kind of movement. Cilia are shorter and more numerous than flagella. Ciliary motion is also more like the power stroke in swimming while flagellar movement is a wavelike motion.

By the way, ciliated unicellular organisms like the Paramecium use their cilia not only for moving about but also for moving food towards their oral groove or "mouth".

Intermediate filaments

2008-12-18T23:41:00.003+08:00

I have talked before about the microtubule and microfilament components of the cytoskeleton. Now let’s turn our attention to the third component, the intermediate filaments.

Intermediate filaments unlike the microtubules and microfilaments are not always present in all cells. When present however, they can indicate the cellular origin of tumors. Why? How?

Well, there is a specific intermediate filament associated with specific cells and tissues. For example: cytokeratin is specific for epithelial tissue, desmin is found only in muscle cells, vimentin is found only in cells derived from mesenchyme, neurofilament is specific for neurons and glial fibrillary acidic protein or GFAP is specific for glial cells except microglia.

By the way, Alzheimer’s is associated with extensive tangles of neurofilament.

Complementarity between structure and function, part II – the squamous cell

2008-12-17T12:07:00.004+08:00

Have you ever seen a squamous cell? You have? Good, because it is my topic for today. I thought I will take a break from looking for something Christmassy to looking at complementarity between structure and function once again. As I mentioned before, this complementarity is a recurring theme in biology so I’m sure we will not ran out of examples. So today is the turn of squamous cells.

Squamous cell is a term given to describe a cell that is thin and flat when viewed from the side and is tile-like (the old-style, honeycomb-like tile) when viewed from the top. This cell never occurs alone but is found in the body as a single layer of cells or as multiple layers of cells.

If occurring as only a single layer of cells, their main function is for rapid exchange of materials. Thus they can be found lining the alveolar sacs of our lungs and the inner lining of blood vessels. When arranged as multiple layers of cells however, they assume a protective function. In this case, we can therefore expect to find them on the surface of our skin, the exposed portions of our digestive tubes, the exposed portions of our reproductive system and any other exposed parts of our body.

Since these layers of cells are always exposed to all kinds of wear and tear, they are thus prone to infections and even cancer. I’m sure you have heard of squamous cell carcinoma or cancer of squamous cells.

the megakaryocyte story (a gift of self)

2008-12-16T14:41:00.005+08:00

I got this picture from: http://path.upmc.edu/cases/case37/images/micro8.jpg Thank you. Sorry, no time to ask permission.

What else can cells tell me about Christmas?

Yah, what else? Hmm...this is getting harder everyday. In trying to think of which cell story reminds me about Christmas, I form a mental picture of cells and their parts. There is a kind of slide show in my mind and I let it ran, then pause for a while, turn around the cell and proceed once more. Now my slide show stopped on... the megakaryocyte.

The megakaryocyte, what kind of cell is it? Well, if you examine the name, “mega” means big and “karyocyte” means a mature cell. So it’s a big, mature cell. Just how big? – about 10 – 15 times bigger than our red blood cells. That’s big! It’s only found in the bone marrow. So if you examine a bone marrow smear under the microscope, it’s the biggest cell around and you can’t miss it, as shown in the picture.

So, what is so special about megakaryocytes and what is Christmassy about it?
Well, megakaryocytes give rise to our platelets by fragmentation of its cytoplasm. Yes, you read that right... its cytoplasm fragments to give rise to platelets, around 2000 – 5000 of them. Imagine that, being fragmented to give rise to little buggers! That is true giving of self, isn’t it?

What remains of the megakaryocyte after this is simply the nucleus with a teeny weeny bit of cell membrane. This then leaves the bone marrow and migrates to the lungs where it is “eaten up” by lung macrophages. I don’t know why it goes to the lungs to die (macrophages are everywhere anyway), but that is how the megakaryocyte story ends.

Glial cells

2008-12-15T14:42:00.003+08:00

Very few people have heard about glial cells. They do not have the same “superstar” status as the nerve cells or neurons. However, glial cells are just as important as neurons in the function of the nervous system. In fact they outnumber the neurons by a ratio of about 10 (glial cells) to 1 (neuron), maybe even more in some parts of the brain.

So what are glial cells? Well, they are known as the supporting cells of the nervous system. They provide support to both the cell body and the cell processes of the nerve cells. However, they do much more than just provide support: they also provide nutrition, form myelin sheath, maintain homeostasis, insulate neurons, and modulate nerve impulse transmission. They also guide neurons in making the correct connections during development. Some glial cells even act as scavengers and clean-up crew because they destroy pathogens and remove dead neurons.

There are specialized glial cells for each of those functions. For example, there is a different glial cell that forms the myelin sheath. A different glial cell also provides nutrition and another acts as scavenger. So they come in different names like microglia, oligodendroglia, astroglia, ependyma, and Schwann cell.

Glia is actually Greek for “glue.” So glial cells kind of “glue” together the components of our nervous system.

cells and the spirit of Christmas

2008-12-14T11:10:00.003+08:00

I am in a Christmassy (is there such a word?) mood today. I sat for a while thinking if there is anything in the cell or about cells that is somehow related to Christmas.

Well, what predominates during Christmas is the spirit of giving. So, is such a spirit present at all in cells? I think I can answer “ yes” to that. I think there is so much giving in cells actually. Just take a look at our soldier cells for example – the macrophages and some of the white blood cells, they are called “soldiers of the body” because they do defend us. In the process of defense however, they must "give up their lives".

In my Nov 26 post, “display, tell, and kiss” I mentioned that macrophages act as APCs or antigen presenting cells. Well, these cells once they “kiss” with the T lymphocytes actually die because the T cells (specifically the killer T cells) punch holes in these APCs and literally these cells “spill their blood”. So these cells die in the process but they have done their duty – that of informing the T cells that there is an infectious agent or an abnormal molecule in the body. Imagine that, that is a true spirit of giving, “giving up one’s life” in the line of duty.
If that does not show the spirit of Christmas, I don’t know what does.

Have a happy Christmas!

Upstream ...downstream

2008-12-13T06:00:00.003+08:00

We usually encounter the terms “upstream” and “downstream” when researchers talk about cell processes. What do they mean by that?

Well, we are familiar with the flow of information in cells or what is usually referred to as the “central dogma” of molecular biology, right? That is, – DNA ---> RNA ---> proteins. Well, upstream means the replication of DNA and the formation of RNA or transcription, while downstream is the formation of proteins or translation. So when the write-up says that the problem appears to be upstream, then it means that something is wrong with either the replication or the transcription process. A downstream problem on the other hand means something wrong with the translation process.

When a cell divides, it multiplies

2008-12-12T14:26:00.003+08:00

When a cell divides, it actually multiplies. Huh? This may not be possible mathematically but it possible biologically. Yes, that is how we get to have many cells, by division.

We all started as one fertilized egg cell. The cell then divided and divided until there are hundreds of millions of cells (refer to Nov 10 post, “cells touch”). See, by division a single cell has multiplied into millions of cells. Imagine that! This cell division is called mitosis.

Through mitosis, new cells are formed to replace dying, dead, or old worn out cells. Through mitosis, new cells are also formed to repair wounds or to even grow new parts. Unfortunately, as a cell becomes more specialized, it loses its ability to divide. Thus, nerve cells which are highly specialized cannot be replaced once they die because there no new source of cells. Other cells however are rather “enterprising”. When they divide, only some of the cells become specialized, the others remain unspecialized and they can keep on dividing and dividing so there is a constant source of new cells. These unspecialized cells are called stem cells.

Skin cells have their own stem cells, so do our intestinal cells and blood cells. Thus we have new skin month and new intestinal cells every week. Sperm cells also have their own stem cells but egg cells do not have any (alas!).

A cell with multiple nuclei

2008-12-11T23:01:00.002+08:00

If the mature red blood cell has no nucleus, the opposite is true for the mature skeletal muscle cell - it has several nuclei per cell. How did this happen?

Well, the myoblasts or young muscle cells start out as uninucleated cells. Sometime during their development however, these cells fused with each other and become surrounded by connective tissue. The fused cells then elongate and develop into what is now called muscle fiber or the mature muscle cell. Thus, a single muscle fiber is equivalent to one muscle cell with multiple nuclei.

Muscle fibers are also bundled together by connective tissue and form what we recognize as our muscles. So our triceps or biceps and other muscles actually consist of bundles of muscle fibers.

Why our red blood cell has no nucleus

2008-12-10T21:19:00.004+08:00

Our red blood cell actually has a nucleus when it starts to develop (while still an erythroblast, see Dec 8 post). However, it extrudes or throws out its nucleus as it matures. Why? Well, to have more space for carrying oxygen which is its main function.

While still developing, our red blood cell actually starts as a big cell with a big nucleus. It also divides several times to produce more of its kind. At the same time, it synthesizes hemoglobin, the molecule that actually carries oxygen. Later, it becomes smaller and smaller and the nucleus becomes more clumped until it (the nucleus) no longer can participate in cell division. When that happens, the cell then extrudes the nucleus. By this time it has produced all the hemoglobin it needs to carry the maximum amount of oxygen.

Since the mature red blood cell has no nucleus, it can no longer make new proteins. Thus, it can survive for only about 120 days. However, we should not worry that we will run out of red blood cells. Our bone marrow continuously produces red blood cells at a rate of about 2 million per second. These are then released into the bloodstream in a regulated manner or as needed by our body.

If you look at the picture of our red blood cells, they look like a doughnuts. What appears like the “hole” is where the nucleus used to be.

Barr body

2008-12-09T14:10:00.004+08:00

Do you know that the discovery of the Barr body was actually through serendipity? Yes, it was. Murray Llewellyn Barr was actually working on the effects of fatigue on the nerve cells of cats. However, he did not find any changes in the nerve cells of fatigued animals. Instead, he noticed a mass of chromatin material on the nuclear membrane of some nerve cells but not all cells. When he crossed checked the sources of those cells, he discovered that they actually all came from female cats. When he examined cells coming from other mammals including human, the same chromatin mass was also observed only in females. He later discovered that this mass of chromatin material is actually a sex chromatin.

This sex chromatin is now referred to as the “Barr body”. It represents an inactivated X chromosome. It is now known that in mammalian and human females, one of the X chromosomes becomes inactivated during development and it appears as a dark mass (Barr body) near the nuclear membrane of their cells. So a female with XX sex chromosome will always show one Barr body, while a male who has XY sex chromosome should have no Barr body on his cells.

The number of Barr bodies observed in cells is always a good indicator of the number of X chromosomes in an individual. Individuals with multiple X chromosomes will have all the X chromosome inactivated (will appear as Barr bodies) except one. Thus, as mentioned earlier, females with normal number of sex chromosomes will always show one Barr body. Some females however have XXX sex chromosomes. Their cells will thus show 2 Barr bodies. Males showing a Barr body in their cells therefore have XXY sex chromosome.

The discovery of the Barr body thus launched a new era of research on genetic disorders.

"blast" means young

2008-12-08T19:45:00.003+08:00

Have you ever noticed that all young cells are called ___blast? Osteoblast for example is a young bone cell while chondroblast is a young cartilage cell. Erythroblast is a young red blood cell while a neuroblast is a young nerve cell. A young muscle cell is called a myoblast and a young while blood cell is a leucoblast... and so on and so forth.... So, if somebody calls you “blasted thing”, it means you are young. Take it as a compliment and say “thank you”. Ha ha ha.... Sorry, I got a weird sense of humor today...

By the way, when a cell is old it’s called _____cyte. So we have osteocyte, chondrocyte, erythrocyte…etc.

one more from Lewis Thomas

2008-12-07T19:09:00.003+08:00

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

2008-12-07T00:01:00.001+08:00

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.

"Lives of a Cell"

2008-12-05T21:36:00.005+08:00

Today I thought I will diverge from my usual post about some cell lessons. Today I would like to share a favorite quotation from an author who made me think about cells in a different way. I'm talking about Lewis Thomas who wrote "Lives of A Cell" sometime in 1971.

I'm lucky I was able to listen to Lewis Thomas in person when I was studying in the US in 1979 - 1980. He was as fascinating in person as in his book.

The following lines are found in the 1st page of his book.
"I have been trying to think of the earth as a kind of organism, but it is no go, I cannot think of it this way. It is too big, too complex, with too many working parts lacking visible connections... If not like an organism, what is it like, what is it most like? Then, satisfactorily it came to me: it is most like a single cell".
- Lewis Thomas
"Lives of A Cell"

What do you think? Why did Lewis Thomas think of the earth as like a single cell?

Another correcting misconception day – about cholesterol

2008-12-04T09:39:00.003+08:00

“Cholesterol is a steroid that is harmful to the body because it causes heart ailments”. This is a very common misconception found in many biology textbooks. It is always mentioned in relation to the chemicals making up cells.

The correction is: Cholesterol is only harmful if present in large amounts. Cholesterol per se is not harmful. In fact it is needed for synthesis of steroid hormones and for maintaining the fluidity of cell membranes.

We have to be aware that there are two kinds of cholesterol in our body: LDL (low density lipoprotein) cholesterol or the “bad” cholesterol and HDL (high density lipoprotein) or the “good” cholesterol. When too much LDL or “bad” cholesterol circulates in the blood, it can clog arteries and increase our risk of heart attack and stroke. HDL or “good” cholesterol on the other hand helps remove the “bad” cholesterol from our arteries.

We also have to be aware that most (about 75 %) of the cholesterol we have is actually produced naturally by our own liver. Only a small amount (25%) comes from the food that we eat. Unfortunately, many people inherit genes from their parents or even grandparents that cause them to make too much LDL. Inheritance plus the kind of food that we eat can therefore cause high LDLs in our blood and this is the one that triggers ailments of our circulatory system.

If high blood cholesterol runs in our family, therefore, a change in lifestyle (like watching our diet and refraining from smoking) plus some medications will probably be needed.

One more thing, if high blood LDL runs in our family, then it is important to watch the diet even of children because deposit of fatty plaques in the arteries starts even in childhood and slowly builds up as we grow older.

Cell design 101.5, skin cell or keratinocyte

2008-12-03T11:42:00.004+08:00

Several kinds of cells make up our skin. However, today, I’m just going to talk about the main cell type or the keratinocyte.

Keratinocytes start from the basal layer of our skin’s epidermis. Here, they divide several times to produce more keratinocytes. Several of them are later pushed up slowly to the surface of our skin. As they move up, they lose their ability to divide but become more specialized by accumulating keratin filaments in their cytoplasm. As more keratin accumulate in their cytoplasm, some are also secreted out into the surroundings of the cell and create a barrier. Thus, nutrients can no longer move into the cells, and they die. The topmost cells of our skin are therefore dead keratinocytes. They are later removed from our skin surface and will be replaced by new cells coming from the basal layer of our skin. Keratin plus other molecules joined with them make our skin waterproof.

The whole process of skin renewal takes about 20 – 30 days. That means every 20 -30 days we have new cells on the surface of our skin. If one has the skin disease, psoriasis however, new skin is produced in less than 20 days. Thus, people with psoriasis have portions of “bumpy” skin.

By the way, formation of new keratinocytes by mitosis usually takes place at night while we sleep. This might explain why our skin suffers if have too many late nights.

microtubules

2008-12-02T19:33:00.002+08:00

So far I have only mentioned the functions of the microfilaments as part of the cell’s bones and muscles or cytoskeleton. To even up matters, I’ll talk about the microtubules today.

The microtubules consist mainly of the protein tubulin which has 2 phases, the alpha and beta tubulin. These tubulin molecules form a tube like structure that can elongate at one end and shorten at the other. This is a continuously occurring process so the microtubules and also the microfilaments are always in a state of dynamic instability. That means that nothing is permanent with the cell’s cytoskeleton.

Microtubules serve as scaffolding inside cells and act as “tracks” on which cells can move organelles, chromosomes, vesicles and other things inside. In other words, they act like bullet trains inside cells. Microtubules are also responsible for the movement of cilia and flagella. Imagine that, molecules that can act as scaffolding, train, and propeller at the same time! Yessiree, those are your microtubules.

In order to do their function however, microtubule need to associate with proteins like dynein and kinesin. These two serve as motors to power the movement of microtubules. If something goes wrong with these motors, then any of the movements mentioned above will not be possible. Sperm cells for example will be immotile if dynein is absent in their flagellum.

cytokinesis

2008-12-01T22:34:00.004+08:00

Cytokinesis is another activity that is generated by the cytoskeleton, particularly the microfilament.

After the chromosomes of a cell separate during anaphase, the microfilaments together with their associated protein, myosin, create a contractile ring somewhere near the middle of a cell. This ring tightens like a purse string until finally the cell is divided into two. This division completes the final stage of mitosis wherein two new cells with the same chromosome number are formed.

Separation of chromosomes and cytokinesis have to be properly coordinated so that the chromosome number of each generation of cells remain the same. If the timing of these two processes is off, we can end up with cells that have abnormal chromosome number or cells that can develop into cancerous ones.

amoeboid movement

2008-11-30T19:14:00.003+08:00

Amoeboid movement is one example of how the microfilaments (the cell’s muscles) function. It is the same kind of movement that is involved in phagocytosis or “cell eating” which is the subject of my post last Nov. 19.

Biology – Online dictionary defines it as “A crawling-like type of movement in which the cell forms temporary cytoplasmic projections called pseudopodia (false feet) towards the front of the cell”.

Aside from the Amoeba, other cells that exhibit amoeboid movement are: neutrophils and macrophages (our professional phagocytes, remember?), monocytes (another kind of white blood cell), Kupffer cell of the liver, as well as cancer cells. Yes, cancer cells. This is the way by which cancer cells metastasize or spread to other parts of the body.

table for cytoskeleton

2008-11-29T06:07:00.004+08:00

Above is the corrected table for the cytoskeleton, yesterday's post.

cell bones and muscles

2008-11-28T23:48:00.005+08:00

The cell has its own bones and muscles called the cytoskeleton. This cytoskeleton has 3 major components: microfilaments, intermediate filaments and microtubules.

These major components are usually associated with other proteins. The association enables them to do several functions like formation of scaffolding inside the cell, ciliary or flagellar movement on the cell surface and internal cell movements like chromosomal movement during mitosis.

A summary of the functions of the cytoskeleton is shown in the table below.

Microfilaments Intermediate Filaments Microtubules
Muscle contraction Support and tensile strength Cell motility
(cilia and flagella)
Amoeboid movement Maintenance of cell shape Chromosome movement
Cell locomotion Formation of nuclear lamina Movement of
and scaffolding organelles
Cytoplasmic streaming Strengthening of nerve cell axons Determination of cell shape
Cell division (cytokinesis) Keeping muscle fibers in Maintenance of cell
register shape
Maintenance of cell shape

I will talk about each of these functions in a future post.

The cell’s post office

2008-11-27T20:05:00.004+08:00

Yes, the cell has a post office. It’s called the Golgi complex or Golgi apparatus after Camilo Golgi, the scientist who identified it.

So what does the Golgi complex do? Well, just like any post office, it receives packages, sorts them, checks their labels and delivers them to the proper destination. It also sends back packages that are defective. However, it is more than the ordinary post office. Why? Because aside from doing all those functions mentioned above, it can also modify the packages, insert more identifying markers, compact and repackage them, and even add some fancy gift tags and ribbons.

The packages I am talking about here are of course the products coming from the ER. If you remember from a previous post (Nov 23, rough ER), I mentioned that the Golgi together with the ER are involved in “membrane trafficking” wherein vesicles move between them and the other parts of the cell.

Yes, the Golgi also sends back to the ER packages that contain defective proteins. Aside from that, it can also insert identifying markers like mannose-6-phosphate, the marker for proteins destined to be part of the lysosome.

The Golgi is also involved in the synthesis of proteoglycans. As the name implies, these are molecules that contain protein and sugars. These molecules are very important components of the cell’s immediate surrounding or the extracellular matrix. Furthermore, the Golgi also adds sulfates and phosphates to various cell products. Sulfation and phosphorylation are important for signaling and sorting. All these add-ons are the fancy gift tags and ribbons that I mentioned.

So as you can see, the Golgi complex is the cell’s super post office.

Oh, and by the way, just like a post office, the Golgi also has a receiving window (its cis face) and a releasing window (its trans face).

display, tell and kiss

2008-11-26T20:04:00.003+08:00

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.

plasmolysis

2008-11-25T20:22:00.003+08:00

I am again in my “correcting misconception” mood today. I encounter so many of them in several biology textbooks and I always feel shivers ran up and down my spine every time I see them. I know that textbooks are the major source of information for most of our teachers so I don’t understand how such books (full of misconceptions) can even be approved as text. I also don’t understand how some authors can write some out of this world information.

Today my topic is about plasmolysis. I was shocked to read this in one textbook - “Plasmolysis explains why your skin wrinkles” What?

Please, plasmolysis does not cause wrinkling of the skin!!!

Plasmolysis occurs in plant and bacterial cells, not in human cells. When plant cells are placed in extremely hypertonic environment, water moves out of the cells by osmosis. This causes the plant vacuoles to shrink and the cell membrane detaches from the cell wall. This is plasmolysis.

Animal cells do not have cell walls so there is no such thing as detachment of cell membrane if cells are exposed to hypertonic environment. So plasmolysis does not occur in animal cells.

Red blood cells shrink or undergo crenation if placed in hypertonic solution in laboratory condition. Under laboratory condition also, blood cells bloat and even burst if placed in hypotonic solution. However, in natural condition these do not happen because our body has a system for regulating water loss and gain such that our individual cells are protected from shrinking or bursting.

cells need chaperones

2008-11-24T18:11:00.003+08:00

Yes, you read that right – cells need chaperones! Cellular chaperones are of course different from the social chaperones that we are familiar with. However, to a certain extent, both kinds of chaperones actually perform similar functions. While a social chaperone ensures that the concerned parties (usually unmarried ladies or gents) behave properly during social occasions, the cellular chaperones also make sure that certain molecules in the cell (especially proteins and nucleic acids) behave properly.

So far, four instances have been discovered wherein chaperones are needed by the cell, but the list may still increase.

The first instance is in the association of the genetic material with histone proteins. When DNA, the genetic material associates with histone proteins as they fold together to form the chromosomes, chaperones make sure that folding is correct.

Second, most chaperones are actually heat shock proteins. Huh? What are those? Well, in the presence of heat and stress, proteins usually tend to misfold and aggregate. The heat shock proteins or chaperones try to prevent this misfolding because protein function is dependent on their proper folding. Once they are misfolded they lose their ability to function properly. One example of a disorder that can happen when proteins are misfolded is mad cow’s disease.

The third instance when chaperones are needed is during the formation of new proteins. As the polypeptide chains exit from the ribosomes during their synthesis, chaperones guide them to fold properly into fully functional proteins.

Lastly, chaperones guide polypeptides as they are transported across the membranes of the mitochondria and ER. The chaperones make sure that the polypeptide chains pass through the membrane properly before they fold over.

As you can see cellular chaperones just like their social counterparts also ensure proper behavior of their molecular protégés.

rough ER

2008-11-23T19:38:00.004+08:00

The presence of ribosomes attached to the cytoplasmic side of this membranous network gives it a rough appearance, thus the name. Its main function is protein synthesis.

Initially, the rough ER does not have any ribosomes yet. Synthesis actually starts in ribosomes that are freely floating in the cytoplasm. However, once the initial sequence of amino acids called the signal peptide, are formed, the ribosomes then attach to the ER and continue with the synthesis. Since different kinds of proteins are being synthesized regularly, a continuous stream of ribosomes attach to the ER thus making them practically integral parts of the ER.

Protein synthesis is a very systematic and closely monitored process. Proteins which are destined for use within the cell are processed separately from proteins that are “exported” out of the cell. Markers are added along the way as the synthesis of proteins progresses. The markers ensure that proteins reach their proper destinations.

The rough ER works closely with the Golgi apparatus. Between the two of them, there is a regular flow of proteins in vesicles. There is even a whole process of vesicular movement between the ER, the Golgi, and the cell membrane that is called “membrane trafficking”. Yes, there is traffic flow in cells, but unlike the chaotic traffic in our society, this cellular traffic is very well coordinated and there are no traffic snarls along the way. Maybe our traffic coordinators could learn a thing or two by observing how cells do their trafficking.

cell design 101.4, nerve cell

2008-11-22T23:20:00.005+08:00

Every nerve cell is as unique as one’s fingerprints. But all nerve cells have something in common. Each one is excitable. Each one can change from a serene, hu hum cell to a fiery, pulsating one. How is this possible?

Well, we are of course familiar with the usual picture of a nerve cell, right? The picture is usually that of a star-like cell, with some cell processes sticking out. These cell processes even differ into two kinds; one is short and highly branching (dendrites), while the other is long and usually non-branching (axon). However, the latter usually terminates in small knob-like endings called axon terminals. So above is a diagram of a nerve cell.

As mentioned earlier, every nerve cell is unique, so this is not really how every nerve cell looks. However, it fairly represents one group of nerve cells called motor neurons.

So back to the question, how can a nerve cell change from a serene to a fiery cell?

Well, nerve cells have a unique way of distributing their channel proteins. Along their cell body membranes, the channel proteins (both leaky and gated) are distributed about almost evenly. So small batches of ions constantly move in or out through leaky channels, while gated channels open or close depending on the presence of some disturbance or stimulus. Then of course, ion pumps like the Na-K-ATPase pumps constantly pull back potassium ions (K+) that sneak out and bale out sodium ions (Na+) that sneak in. But, it’s a different story where the axon of the neuron starts. In this area, the neuron’s membrane is fully studded with Na and K gated channels. So, when the disturbance or stimulus is strong enough, it can set a whole bunch of gated channels open or close. The action is much like a floodgate opening or closing, it is sudden and it creates instant action. Na ions rush inwards while K ions rush outwards. Thus, the nerve cell is usually described as “firing” when it is in this state.

All this action takes place in milliseconds and the nerve cell once more goes back to its resting state, wherein only a few Na and K ions move in and out of the cell until the next disturbance or stimulus comes.

So the way things are arranged in space and time can spell the difference between a humdrum life and an exciting one. However, just like the neuron, we need both kinds of arrangement – one kind makes us grounded, the other kind makes us reach greater heights. Exciting, isn't it?

smooth ER

2008-11-21T14:14:00.003+08:00

In the cellular world “ER” does not mean “emergency room”. Rather, it means “endoplasmic reticulum,” and there are two kinds of them: smooth ER and rough ER.

Our story for the day is about the “smooth ER.” The other kind will be the subject of another post.

Liver cells, steroid hormone-secreting cells, and muscle cells especially abound with smooth ER. In these cells the smooth ER performs different functions.

In liver cells, the smooth ER performs two major functions: detoxification and glucose metabolism especially conversion of glycogen to glucose. People who regularly use drugs have liver cells with very extensive smooth ER. The enzymes of the smooth ER convert the drugs into water soluble compounds that can then be easily eliminated from the body. The detoxifying effect is the reason why drug users need higher and higher doses of drugs.

In steroid hormone-secreting cells, the smooth ER is involved in the synthesis of steroid hormones like estrogen, testosterone and progesterone. While in muscle cells, they serve as depot for Calcium ions.

Changes in Calcium ion levels inside cells is an important signal for activities like muscle contraction and exocytosis. It is thus important to keep low the levels of Calcium ions in the cytoplasm.

In muscle cells, the smooth ER has a special name - “sarcoplasmic reticulum”.

cell design 101.4

2008-11-20T21:09:00.003+08:00

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

2008-11-19T12:41:00.003+08:00

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

2008-11-18T22:41:00.004+08:00

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.

intercellular communication

2008-11-17T12:13:00.002+08:00

How do heart muscle cells synchronize their beat? How do the cells lining our windpipe synchronize the movement of their cilia? The answer my friend is – through rapid intercellular communication.

Neighboring cells maintain rapid communication lines with each other so they can act as a single unit and not as uncoordinated separate units. In animal cells the rapid communication lines (actually pipes) are called gap junctions while in plant cells they are called plasmodesmata.

Gap junctions are pipe-like structures that connect adjacent animal cells. Unlike a pipe however which is made up of one rounded piece, gap junctions consist of 6 pieces that can change orientation and therefore open or close the opening of the pipe.

In the heart for example, only one part, the pacemaker, needs to be receive the activation information but the whole heart responds as an integrated beating unit. This is possible through the opening of gap junctions between adjacent cells which then rapidly spread the information received. The same process allows for the synchronized beating of the cilia in respiratory cells as they move substances from one end of the windpipe to the other end. The peristaltic movement of the digestive tube is also synchronized through the same rapid communication across gap junctions of smooth muscle cells.

Because of their cell walls, plant cells cannot move in any synchronized manner. However, through their plasmodesmata which are small channels not covered by cell walls, the cytoplasm of adjacent cells can communicate with each other and move substances between them. This way, parts of the plant can function as one metabolic unit.

plant vacuoles

2008-11-16T20:14:00.004+08:00

While vacuoles in animal cells are small and temporary, plant vacuoles are big and practically permanent. The vacuoles in plant cells usually occupy about 30% of the cell’s volume but can sometimes become as much as 90%. Why is this so? Well, plant vacuoles have many functions.

First, it can act a storage area of many different things ranging from water, minerals, enzymes, ions, and even toxic substances. The toxin helps protect the plant from being eaten by predators. If we cut a plant, the contents of the vacuoles, generally called cell sap, spill out.

Vacuoles also store pigments. These pigments are responsible for giving us the beautiful colors of flowers and fruits.

The second and even more important function of vacuoles in plant cells is to maintain turgor pressure against the cell wall. Turgor pressure makes the plant firm and rigid.

Vacuoles are surrounded by a special membrane called tonoplast. The tonoplast is selectively permeable and has pumps that actively pump ions in order to maintain the water content of the vacuoles. If you remember, I mentioned before that water moves by osmosis. It always moves to were the solutes are. So if the tonoplast for example pumps in potassium ions, then water follows the ions and moves inside the vacuole. If there is enough water available, then turgor pressure is easily maintained by the plant through this pumping action. The plant then remains firm and rigid.

If there is not enough water however, the vacuole shrinks and moves away from the cell wall. Turgor pressure then decreases. When this happens, the cells plasmolyse and the plant wilts. So vacuoles really help maintain the structural integrity of plant cells.

Oh by the way, some of the other materials stored in plant vacuoles are: opium, rubber, and garlic flavoring.

cells have a detoxification center

2008-11-15T18:49:00.003+08:00

Aside from having a recycling center, cells also have a detoxification center. The center is the peroxisome, another organelle found in eukaryotic cells.

Peroxisomes are so named because they use molecular oxygen for carrying out their function. Just like their cousins, the lysosomes, they can also recycle substances. For example, they breakdown fatty acid molecules into small chunks of carbon atoms resulting in the formation of acetyl CoA. Acetyl CoA is then recycled for use in biosynthetic reactions.

An important and specific function of peroxisomes however is – detoxification. If you are an alcoholic drinker for example, you can expect the peroxisomes of your liver and kidney cells to be working overtime in converting the toxic alcohol to non-toxic substances.

Peroxisomes also remove another toxic substance, hydrogen peroxide, from our system. Hydrogen peroxide is a by product of many reactions so it can readily build up in the cell. To prevent this build up, peroxisomes convert the hydrogen peroxide into water and oxygen.

Abnormality or malfunction of the peroxisome results in severe abnormalities in the brain, liver, and kidneys. Individuals with the abnormality immediately die soon after birth.

cells recycle

2008-11-14T11:46:00.003+08:00

Let’s leave the cell membrane for a while and go inside the cell. Since environmental issues are so popular these days, let’s focus on the original recycling center found inside cells.

Eukaryotic cells have an organelle called the lysosome. This organelle contains hydrolytic enzymes that convert food particles, phagocytosed bacteria or viruses, and old, worn-out cell parts into smaller pieces that are then used, recovered, reused, and recycled by the cell into other functional parts of the cell. Lysosomes can even recover through the process of endocytosis, membranes that are once part of vesicles and receptors.

Lysosomes are so efficient in their function, they will “eat” anything they encounter, break it into pieces, and recycle them. There is practically zero waste inside cells because of lysosomal activity.

Sometimes however, lysosomes can malfunction because of lack of some enzymes. When this happens, substances can accumulate inside the cell and interfere with normal cell function. The cell then gets sick and of course the individual gets sick. Tay Sachs disease and Pompe’s disease are examples of diseases caused by malfunction of lysosomes.

In Tay Sachs disease, fatty proteins accumulate in the brain and affect a baby’s sight, hearing, movement, and mental development. In Pompe’s disease on the other hand, glycogen accumulate inside muscle cells and cause weakness of muscles including muscles of the heart and the respiratory system. The individual may then die of heart failure and/or respiratory failure.

All these for not being able to recycle because the cell's recycling center malfunctioned.

ion channels

2008-11-13T23:55:00.003+08:00

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.

diffusion

2008-11-12T23:52:00.002+08:00

I almost flipped when I encountered this sentence in a biology textbook – “The diffusion of sodium is done against a concentration gradient.” Huh? How can that happen? That is simply illogical.
Diffusion is passive transport. It is always along the concentration gradient, never against it. Diffusion is directly related to the difference in concentrations between two areas. This difference in concentration is called the concentration gradient. Molecules will always move along this gradient, that is, from where the molecules have greater concentration to where they are less concentrated. This movement is called diffusion. So if sodium moves by diffusion, then it’s moving down this concentration gradient, not against it. Molecules can only move against their concentration gradient by active transport.

osmosis

2008-11-11T22:59:00.002+08:00

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

2008-11-10T20:09:00.004+08:00

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

2008-11-09T20:50:00.004+08:00

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 can be cultured

2008-11-08T20:28:00.003+08:00

No, a cultured cell does not go to concerts or view art works or read classical pieces. Rather, a cultured cell is one that is kept in a controlled condition in the laboratory.

Yes, cells are found not only inside the body of an organism but can also be found outside. They can be removed from the organism’s body and cultured in the laboratory. Here they are kept alive for long periods of time where they can even grow and produce more cells.

In fact, the first ever group of cultured cells, the so called HeLa cells, have survived their owner. Henrietta Lacks died a long time ago but her cells (actually taken from her tumor) are still living today in various laboratories. These cells are now being used for various medical researches in cancer, drug tests, cosmetic tests, and many others. For example, Jonas Salk used HeLa cells when he developed and tested the polio vaccine.

water world

2008-11-07T13:37:00.005+08:00

One of the very first lessons in Biology that we usually discuss is the biochemistry of cells. We then note that cells consist mainly of water plus biomolecules and some minerals. If I ask my students the question “why is water the most abundant component of cells?” – One answer that usually comes up is - “because water is a universal solvent.”

Huh? I simply cringe every time I get this answer. Sometimes I even get ballistic! Ugh! Double Ugh! How can one say water is a universal solvent??? Why is this mentioned in Biology books and even in Chemistry books? Water is not a universal solvent! It is just a very good solvent but not a universal solvent. If it is a universal solvent, then we will not even exist. There will be no cells, no plants, no animals, no mountains, rocks or stones. Everything will be dissolved in water. Everything will be in solution. Everything will be…water. In fact the only thing that there will be is…water!

cells commit suicide

2008-11-06T12:31:00.001+08:00

Some cells die because of cell injury but other cells die because they commit suicide. Yes, they do! And why would cells do that? There are various reasons.

One reason is, to remove severely damaged cells and prevent them from being duplicated. Cells generally repair some damages that may develop in them. If the damage is too extensive however, they receive signals to commit suicide rather than pass on their defect to the next generation of cells.

Another reason is to maintain the number of cells in the body. We cannot have too many or too little number of cells. So “old, worn-out cells” that have reached their “expiry date” are told to commit suicide. They are then replaced by new cells through the process of mitosis. In the cell world, there is no such thing as extension of retirement. Any extension is always detrimental to the whole organism. Some cancerous cells for example ignore this “expiry date” so the organism develops cancer.

Still another reason is “body sculpting” during development. In the formation of our fingers and toes for example, the starting form is a whole solid mass. During development, the “in-between” cells in the mass commit suicide and this leads to the formation of separate fingers and toes. Sometimes some cells may not commit suicide so the separation of fingers can be incomplete. Thus, we sometimes see people with partially fused fingers or toes.

The disappearance of the tadpole’s tail as it is transformed to an adult frog is an example of “body sculpting” produced by cell suicide.

There are other reasons for cell suicide but those three are the most important ones.

By the way, the scientific term for cell suicide is – “apoptosis” or programmed cell death.

cell design 101.2

2008-11-05T12:55:00.003+08:00

After eukaryotic cells were formed, one other variation to the cell design was added. This variation is enough to differentiate plants from animals. I am talking about the addition of the cell wall in plant cells.

If one takes a closer look at all plant and animal cells, one will discover that this, the cell wall, is one of only two major differences between these cells. The other difference is the presence of chloroplasts in plant cells. But this will be the subject of a future post. In this post, I would like to focus on the cell wall first.

Imagine that, a major difference between our own cells and those of a rose plant’s for example is simply the presence of cells walls in the rose cells. Amazing! But just this single difference is enough to give us nerve cells that reach out and muscle cells that shorten and elongate. Plant cells cannot have cells that reach out or shorten and elongate, the rigid cell wall prevents that from happening. That’s the reason why plants stay rooted and rigid in one place while we can walk, jump and do cartwheels.

Cells talk

2008-11-04T12:38:00.004+08:00

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.

cell design 101.1

2008-11-03T10:32:00.003+08:00

As our cell story unfolds, observe that after putting together the basic requirements in cell design, a major variation is incorporated. This major variation is the formation of an internal membrane system that encloses the genetic material and several of the biosynthetic machinery molecules. What is/are the result(s) of this variation? Well, we can now recognize two large groups of cells – the prokaryotic cells and the eukaryotic cells. The eukaryotic cells are those with the internal membrane system while no such structure is present in prokaryotic cells. Because of this variation, the enclosed genetic material is now called the nucleus; while the enclosed biosynthetic machinery molecules are now identified as organelles. Isn’t that beautiful? Just one major variation, and a whole new world, the world of eukaryotic cells, with their nucleus and various organelles unfolds.

Is the virus a cell?

2008-11-02T13:56:00.003+08:00

This question becomes easy to answer once the basic requirements of cell design are known. One just needs to check if the 3 basic requirements: cell membrane, genetic material and biosynthetic machinery are all present in the virus. If one does that, then one will discover that the 3rd requirement, the biosynthetic machinery, is missing in viruses. There you have it; the virus cannot be a cell because it lacks the 3rd basic requirement for a cell. This is the reason why viruses have to infect other cells; they need to use the biosynthetic machinery of these cells in order to replicate their own genetic material and form membranes. That’s the only way to form more viruses.