inTRON legacy...is splicing evidence of cell evolution?

We have discussed the fact that unlike prokaryotic RNA, eukaryotic DNA must be spliced or processed before it achieves the status of mature mRNA.

The splicing event is peroformed by the spliceosome.  A recent study highlights the importance of spliceosome components by showing that a rare genetic disease is caused by a mutation in a

snRNPs the "smurfs" of cell biology

snRNP. The spliceosome is a machine made of several snRNPs. These molecular scissors cut precisely the right location on the primary transcript (hnRNA) to remove an intron and promote the ligation of exons. Prokaryotes appear to do just fine without introns.




inTrons freed from the cell?
what do they do now?

So what is the purpose of introns? What overall function do they provide for eukaryotes? Why use such a complex splicing operation for a function which appears to do nothing more than rejoin exon regions? How do evolutionary biologists propose that snRNPs and spliceosomes evolved? Is this good design or is this entire process wasteful because large pieces of genetic material is discarded? Is this wasteful process, therefore, not supportive of the idea that splicing is a designed feature of cell life?

due April 20

Life and Death at the cell level and the Jason Bourne organelle

We have discussed the lipids and proteins which make up the membranes in cells in lecture. Internal cell organelles are also composed of phospholipids and specialized membranes. One of the most bizarre membrane proteins is called the mitochondrial permeability transition pore (mPTP). This is a cluster of proteins which connect the inner mitochondrial membrane with the outer mitochondrial membrane and forms a pore. The pore only forms briefly under extreme cell stress conditions and essentially really messes up the mitochondria so that it reverses its function, and begins consuming ATP which usually kills the cell. In many cases this activity leads to apoptosis also called programmed cell death. This drastic measure often occurs after local cellular stress or stress of internal organs like during a heart attack. Just like Jason Bourne in the Bourne Identity, the identity of the mitochondria is difficult to determine, it is a unique mystery organelle in many ways, and like Bourne, it commits violence when stressed out....or is it that it commits violence to protect itself? Just what could the mitochondria be protecting?

This also raises a question about eukaryotic cell evolution. Mitochondria look like they come from bacteria. And thus it looks like eukaryotes evolved from prokaryotes. It is based on the idea that an ancient prokaryote engulfed another ancient prokaryote and this was the beginning of the evolution on internal organelles.

Perhaps though we are looking at this all wrong, perhaps mitochondria are the intracellular counterparts to extracellular bacteria. We know that many extracellular bacteria perform life supporting functions for higher level organisms. So why not consider mitochondria to be specialized intracellular bacteria which also supply life supporting functions for cells. It would be a design feature consistent with the idea of a master designer of all of life. Could the mitochondria have originally risen from an extracellular source? Or is it too vital to the function of plant and animal cells such that it is more likely that it was inserted upon the first creation of these organisms? Are both theories viable or does the data at hand support one theory over the other?

DUE APRIL 1
 

Questions:

1 What are the different ways that a cell can die?

2 What is apoptosis? What are its benefits?

3 What would be the advantage to having the vital energy producing organelle also double as a death organelle?

4 Considering the idea that the mitochondria is a specialized internal bacterium, are there parallels in function between mitochondria and extracellular free living bacteria with respect to energy production and promotion of cell death?

5 Is the endosymbiosis theory logical with respect to the evolution of mitochondria?

6 Could God have created cells in this manner, by using an endosymbiotic process?

7 What are the supports in favor of endosymbiosis theory and the arguments against it. What do you believe based on the evidence?

8 Could God have created internal bacteria to do things inside our cells, similar to the idea that bacteria do important things for creatures when they are outside of cells?

Evolution of the first cells

evolution of the first cell in the prebiotic soup...why not???
 

Read this wiki about evolution of the first cells.  We have discussed the origin of the first cells.  We have seen that amino acids can be made from small molecules infused into a pre-biotic pond from an early reducing atmosphere.  We have noted that phospholipids can self assemble into certain kinds of membranes when they are place in water.  It may be possible for nucleotides to also self assemble given some kind of template.  A recent report shows that the smallest bacteria only requires 182 proteins. (In comparison how many proteins do animals and plants have?)

Given all of this what would the first cell look like? What are some of the most basic functions it would need?  Describe what you would think the first cell would look like in a purely evolution scenario.  Also what would it have to be protected from? Could a cell evolve given what we know about cells today? 

Due March 18

Membranes and the microbial cockatrice

We are discussing the four organic classes of molecules in class which play important roles in the structure and function of cells. We will soon be talking about membranes of cells and the phospholipids and proteins which are parts of cell membranes.


Phospholipids are amazing molecules. Place them in a watery environment and they self associate into a spherical ball and make membranes. Membranes made of phospholipids are fluid structures which are sticky to themselves, so that they make a barrier which typically defines, in part, the outer boundary of a cell and helps hold things in the cell, yet it remains a fluid. Life would not work without these fluid barriers. Who would of thought of that? What a perfect idea for a membrane, a fluid barrier! We would be very stiff creations indeed if our membranes were not made out of these soapy molecules.


So we see in membranes the same principle we discussed regarding the idea that all macro-organisms are made of smaller pieces or entities we call cells, i.e., membranes are made of lots of smaller parts (phospholipids). Relatedly, we also see modularity, i.e., the parts are somewhat interchangeable and pliable. And this modularity and pliability allows for a lot of things to be stuck in membranes.


But, if phospholipids are sticky (self associate because of hydrophobicity) why don't all cells near one another, stick together and form one big clump....for instance when we bump into each other why don't we form one big glumpy smear of phospholipid humanity on the earth. How do pond organisms swim around with these sticky membranes and not get stuck or fuse together?


In fact this is the secret involved in how some viruses work, they invade cells by fusing their outer lipid membrane envelope with the cell membrane, and they take advantage of this sticky/hydrophobic effect. Works like a charm; the virus fuses to the membrane and releases its contents ( at least some viruses work this way, not all do).


Membranes play important roles in prokaryotic cells also. One prokaryote, the microbial cockatrice has unusual membranes. A cockatrice was a wild dish served at medieval banquets. It was a cooked dish of a rooster fused to a suckling pig. Archaebacteria, as suggested by some microbiologists, are a microbial version of the cockatrice, since they appear to have genomes composed of both prokaryotes and eukaryotes. 
 
However, what is even more interesting is the different kinds of lipids and structures which make up the outer membrane and walls of the archaebacteria. Some archaebacteria have monolayers rather than bilayers in their membranes. They also have different lipids suggesting that the biochemistry involved in making archaebacteria lipids is very different from both eukaryotes and prokaryotes. Their cell wall also contains something called an S-layer which is an intriguing structure. Even more fascinating the flagellum they display is constructed differently from the flagellum of eubacteria.


Questions to answer:


1 Why and how do phospholipids self associate?
2 What prevents membranes from fusing with all other nearby membranes?
3 Could the self assembly of phospholipids be a possible explanation for how the first cell membranes evolved?
4 When phospholipids form membranes in a water based environment, do they make membranes similar to the cell membranes we find in cells today?
5 Explore the structure of the archaebacterial monolayers. How does this contribute to life in the extreme?
6 What is an S-layer and how does it contribute to cell function?
7 We discussed the problems inherent in trying to assemble a flagellum from pieces secreted from the eubacterial cell. How is this problem solved in the archaebacterial flagellum? Or is it solved?

 

DUE MARCH 2

What is cell life?

Welcome to the cell biology blog. This blog is for students in the cell biology course at The Master's College, but anyone is free to join. My name is Dr Francis and I teach the cell biology course. Please feel free to contact me at jfrancis@masters.edu if you have questions about this blog.

What are cells? Cells are often distinguished from viruses, but recent discoveries of some very large viruses suggest that this distinction is becoming more and more fuzzy.

Also, is there such a thing as unicellular life? Can cells and do some organisms exist as single cells? Well I might be going out on a limb but I do not believe that unicellular life exists. That is certainly a statement that is subject to a lot of interpretation. Let me explain.

First, single cells do exist, and some appear to lead independent lives, for instance creatures we call microbes like bacteria or paramecium. So what then does the term unicellular mean? It is a term used to distinguish free living independent cells from those which live in tissues, or the multicellular condition. Cells which live in this multicellular state live in close contact with other cells. But I would argue that all cells live in close contact with other cells.
 

So how likely is it that you are going to find microbes living alone, in a true unicellular state. Take a pinch of soil; you will find thousands of creatures living there, many interacting with each other. Consider an amoeba or paramecium or other pond organism. How many of these creatures do you know who live in their own private pond?!
 

But really, lets get down to the nitty gritty, could you not isolate a single bacterium and give it a nice petri dish with lots of nutrients in the corner of your room? But wait a minute, about every 30 minutes, this guy will generate his own friends, within a few hours a full grown microbial party will be in force. I am wondering just how easy it is to isolate a single living bacterium. How would you do it?

I challenge the microbiology students every year and tell them I will give them an A in the lab course if they can isolate and stain a single bacterium on a single microscope slide. What would you have to do to accomplish this task? ( I might give some credit just for a protocol for how you would do this).

Lets face it. Life is multicellular at every level. But wait. What about those pond organisms? they seem independent. More and more studies are showing that most of these critters carry bacteria around. There is even one strain that lives with a bacterium in its macronucleus. Why in the world would you want to carry a bacterium in your macronucleus? I have asked a lot of people, and no one has given me a satisfactory answer. I have gotten some weird looks ….as if the person is thinking, what the heck is a macronucleus and why do I care?

A lot of single celled pond organisms eat bacteria or algae. But there is one pond organism Paramecium bursarium which eats algae and bacteria but also knows how to ingest some algae and not digest them; instead it keeps them as energy harvesting slaves! Whoa! How does it know to eat some critters and digest them and eat other critters an not digest them? Remember this is a small creature with no brain and no nervous system.

So the questions for the blog today are:

1 Investigate the Mimi virus and explain how it is like cells but also different from cells. Is this a true virus in your opinion?

2 Mimi virus is infected with viruses.  What are these viruses and what  could they being doing inside Mimi virus?

3 What is a macronucleus and why would you want to live there? cheap rent? cozy?

4 How would you isolate a single bacterial cell on a microscope slide?

5 How can Paramecium eat algae but not digest it?

6 What is the advantage to being multicellular?

Blog responses are due Feb 4.

5 What is significant about the concept that all living creatures are multicellular?