Tag Archives: membrane

Signal sequence and translation of secreted or membrane-bound proteins

I’ve been looking for a good animation illustrating how signal sequences of proteins are bound by signal recognition proteins (SRPs) that bring ribosomes into contact with the Endoplasmic Reticulum (ER) during translation, and I’ve finally found one. This particular animation has no narration, but it does show the process of translation fairly well. Note that once a signal sequence emerges from the ribosome, it is captured by SRPs and the whole system is taken to the membrane. This video illustrates the process in prokaryotes, which is very similar, except that prokaryotes don’t have ERs, but do secrete material through the plasma membrane. It turns out that just about everything else is the same though; just imagine this as being a larger Eukaryotic cell and the membrane being that of the ER, not the plasma membrane.

A second video that I’ve come across at the same site  but much more recently, shows the process as it occurs in Eukaryotic cells. The animation is much less realistic, but the message is the same.


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Posted by on September 4, 2013 in Uncategorized


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This week in General Bio

This week we are examining the plasma membrane, what its composition is and some of its properties. Biological membranes are primarily organized based on the chemistry of phospholipid molecules. Even in the rare cases (like mitochondria) where proteins actually outnumber phospholipids, the membrane retains its basic organization. That is, it has a hydrophobic interior sandwiched between two hydrophilic surfaces. This structure is created by the orientation of the phospholipid bilayer – that is, two layers of phospholipid molecules. Each layer is arranged with its hydrophilic ‘head group’ on the outside and the hydrophobic ‘tail’ on the inside.

In addition to the phospholipids, plasma membranes are also comprised of cholesterol molecules that contribute to the rigidity of the membrane and a variety of membrane proteins. Amongst the membrane proteins are:

1. Transport Proteins (channel and carrier proteins)

2. Enzymatic Proteins

3. Cell-Cell Recognition Proteins

4. Receptor Proteins

We discussed the function and some examples of each of these major types of proteins, with special attention paid to transport proteins. Why transport proteins? Because one of the most basic functions of the plasma membrane is to keep things on one side or the other of the membrane. Because the membrane is quite good at this, transport proteins are required to move things from one side to the other in a controlled manner.

In discussing the movement of molecules, we defined diffusion and provided some examples of how it works. In general, diffusion is due to the random motion of particles leading to a net movement of particles from regions of high concentration to regions of low concentration. After this process has acted for some time, equilibrium is reached. This does not mean that particles cease moving, but that there is no further net change in concentration likely. See a video animation of this process provided by McGraw Hill at:

The same principle may operate across a membrane if it is permeable to the solute in question. Again, the rule is that molecules (the solute) moves from regions of high concentration to regions of low concentration.

Osmosis, or the diffusion of water, operates by the same principle. The only difference is that osmosis describes the movement of water molecules(solvent) through a membrane rather than that of particles (solute). A good demonstration of this can be seen in the microscopic video presented below. In this film, blood cells (RBCs and WBCs) are observed under conditions of changing solution ‘tonicity’. Watch the lower left corner of the image to see what solution the cells are being exposed to. In isotonic solutions (ones of equal solute concentration), there is no net movement of water. In a hypertonic solution, water moves out of the cell and the cells shrink. In a hypotonic solution, water moves into the cells and ruptures them.

Once we understand these concepts, we can appreciate the difference between passive and active transport. Passive transport is when solutes are allowed to move ‘with’ or ‘down’ the concentration gradient – this requires no input of energy. Active transport is the movement of solute molecules ‘against’ or ‘up’ the concentration gradient and therefore requires energy input to achieve.


Posted by on September 12, 2012 in Education


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Inner Life of the Cell Link

Here’s a link to the ‘Inner Life of the Cell’ animation. Unlike the original version that I knew several years ago – and unlike the one I played in class today, this one had a monologue to guide the student on what is going on. A lot of the description is too technical for intro students, but the generalities are what I think is important.

I would love to get a version of this video to embed into my general bio handbook, but I’ve got to research the copyright permissions on that first.

biology, school, education, cell, animation, molecule, diapedesis, motor, actin, microtubule, vesicle, transport, membrane, protein

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Posted by on September 6, 2012 in Uncategorized


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This week in General Bio

This week we are studying the cell.

We have already discussed the importance of the cell in defining life (The Cell Theory) and talked about why this is a meaningful definition of life. I also spent a little time discussing viruses and how they defy this definition, but are often included or excluded depending upon the view or purpose of the investigator / student. (i.e. Viruses fail to be alive if the Cell Theory is used as the definition, but they are often considered alive by microbiologists for the purpose of classification, discussion of evolution, etc).

We began by recalling when in history people first realized that there was a microscopic world existing at all. This led into a talk about classification and how life falls into two major groups of cells, Prokaryotic and Eukaryotic. There are a number of key differences between these types of  cells, but I focus on just a few: 

1. Prokaryotic cells tend to be smaller

2. Prokaryotic cells have closed circles of DNA, Eukaryotic cells have linear chromosomes

3. Prokaryotic and Eukaryotic ribosomes are different from one another

4. Prokaryotic cells lack membrane-bound organelles (most notably, the nucleus)

We discussed other features, but I think these are the hallmark differences. Prokaryotic cells span two domains of life, the bacteria (which I tend to focus on) and the archae (which are more ancient and often extremophiles). Eukaryotic cells fall into four kingdoms: animalia, plantae, fungi and protista. With a quick discussion about some differences between these groups, I shelved all but animals and said that this was the group we would focus on for the remainder of the semester (with some exceptions such as photosynthesis).

What makes these four kingdoms similar is their Eukaryotic cell type. As I stated above, one feature of Eukaryotic cells is their membrane-bound organelles. These organelles are how the cell divies up its many tasks into separate functions and gets each of them done by some specific structure. In addition to discussing true organelles, we also discussed other structures and their functions (Ribosomes, plasma membranes, cytoplasm, cytoskeleton)

We finished up Tuesday’s class after just introducing all of the players. Today we will be putting some of them together to show how they function as parts of a larger organization. The three things I have in mind to walk through are: 

1. Energy Pathway – how solar energy gets converted into chemical energy, how that energy is stored (not getting into this part much) and then how that energy is brought back out and converted into a more usable form (ATP) that is put to work to make cells do things.

2. The Central Dogma – fleshed out this time with names of some of the processes. Initially focusing on how information is transformed into something that can actually do work (proteins). Then discussing how these proteins are made in a little more detail (cytoplasmic vs secretory proteins). This lets us talk about the ER, Golgi, Ribosomes and even ends with exocytosis.

3. Phagocytosis – I’m an immunologist, so I think about how macrophages attack cells and other foreign particles all the time. This is a good way to reverse the process of exocytosis and talk about endocytosis. Following endocytosis, we can then bring lysosomes and peroxisomes into play and discuss how they function to break down these ‘non-self’ items so that they become harmless (I’ll end by quickly tying this into the immune system’s antigen display mechanism – but without any detail).

That may be enough for them today. Depending upon questions, things can either go much quicker or drag out for the balance of the class. I expect that we will finish this material with enough time to at least get started with the next chapter – membranes. I like this chapter anyway and I think it’s the chapter that puts the students into the ‘mind’ of the cell the best. If you focus on a membrane and how it handles transport and diffusion, you are zoomed in so close, that suddenly, the cell feels large and familiar.

Lastly, I am really hoping to find an great animation of cellular processes that made the email loop of Penn a couple years ago. Cross your fingers – I have no idea where I might get a copy.

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Posted by on September 6, 2012 in Uncategorized


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