which came first riboswitches or ribozymes?

We have discussed RNA a lot in the lecture class.  There is much more to talk about regarding these versatile molecules.  For instance, some RNA molecules can act like enzymes.  Origin of life enthusiasts believe that this supports the notion that early life was RNA based....the RNA world hypothesis. 

But on the other hand, some RNA is regulated by many outside factors.  Some of these factors interact with a region on the mRNA called riboswitches, these are binding sites within mRNA for molecules which help control the production of the protein which results from that particular RNA.  These molecules are the "dependent" cousins of the more independent ribozymes.  It would be interesting to see if ribozymes are controlled by riboswitches or they are dependent on them.

1 Provide an example for how riboswitches work.  What is the advantage of having a switch within the mRNA which is used for the translation process? (i.e., why could not the switch be outside the sequence?).

2 Riboswiches show that mRNA sequences are used for more than just making a protein...the same sequence can bind to factors which control the sequence.  What is the significance of one molecule of RNA having multiple functions?

3 Can you envision a scenario for how roboswitches could have evolved?

Telomeres and Spock



"my what lovely telomeres you have" said the wolf-virus
to the little red-riding hood-cell

 


  Cells have their own version of Spock's famous missive "Live long and prosper."  Cells make this statement using repetitive DNA sequences found on end of chromosomes called "telomeres." Telomeres act as a cap on the end of chromosomes.  They are thought to be another "guardian of the genome" of sorts.  Some scientists believe that longevity is related to telomere length. In fact, telomeres have been shown to be longer in individuals who are healthy and exercising compared to individuals who are under stress.



What's even more interesting is that telomeres are thrown out or lost during cell division so they have to be "remade" using a specific polymerase.



How do telomeres protect DNA?

What is the significance of telomeres being made from repetitive DNA? (what is repetitive DNA and what is it good for?).

What determines how long telomeres are?

How are telomeres related to cell function?

Some bacteria have telomeres,  so from one perspective it looks like they were handed down via evolution.  Why use what appear to be accidental sequences to make the ends of chromosomes? Is there some advantage or design feature inherent in these chromosomal pieces?

inTRON Legacy... the problem of snRNPs (the smurfs of cell biology)

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

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

 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 and therefore not good evidence for design in nature?

location location location, position of chromosomes, gene expression, and bad design?

garage DNA ..what a mess?

The amazing organization of the eukaryotic nucleus was shown in a fascinating article in Scientific American.  It turns out that chromosomes occupy certain locations in the nucleus.  Some chromosomes reside at the periphery of the nucleus and others near the middle.  Some chromosomes also appear to favor being next to "buddy" chromosomes.  It is not yet totally understood why chromosome position is important, except that it is very crucial to cell function.  One nucleoskeletal protein lamin, helps tether the chromosomes in place.  Mutations in lamin are responsible for all sorts of disease conditions, including progeria, or premature aging.


Also it appears that the chromosomes near the nuclear periphery are more quiescent than chromosomes near the center.  The chromosomes in the center are more involved in gene expression.  No one knows how the chromosomes get directed toward a specific place in the nucleus.  I find it quite amazing that this overall structure can be maintained because there is so much DNA in the nucleus.  Remember in its stretched out form DNA is  hundreds of thousands of times longer than the nucleus diameter.   I have trouble just keeping a few power cords untangled in the garage.  Just imagine my garage packed full of tightly wound-up and partially wound-up power cords  and that I need to find one cord in particular to unwind and use and I must do this while literally swimming through a tangled maize of power cords.  I think you would suffer from "power cord" entrapment before you could even reach the power cord you need. 


1 Investigate progeria and hypothesize how nuclear organization could lead to this syndrome and other disease states.  Many diseases are related to chromosome structure and function including cancer, does this support the notion of bad design?....i.e., does the fact that some aspects of cell structure are more involved in promoting disease states show that a designer of the cell or life is unlikely ?




2 Describe how nuclear organization and chromosome location could evolve during the evolution of the nucleus from a prokaryote ancestor? What are some of hurdles that evolution would have to overcome?

the creation of life, the end of vitalism and Dr Venter’s Frankenstein cell

Last year, biologist Craig Venter created the first artificial cell.  Or did he?  Apparently he was able to manufacture a genome and stick it in a bacterial cell which had its DNA neutralized or removed.  Many news outlets claimed that he created the first synthetic life form. 

The creation of a living cell from scratch would be no small feat considering the billions of atoms and thousands of proteins, and hundreds of lipids and carbohydrates that would have to be put in the correct place.  If we used a cooking analogy, it would be like constructing a single cookie one speck of flour and one speck of sugar at a time….that would be some cookie and it would take a long time to get every single speck of flour, sugar, baking soda, salt all in the right place.

However, that is not what Venter did.  So did he really create the first synthetic life form?

One of the nations leading bioethicists, Arthur Kaplan has inferred that this is the end of the idea that life has a spiritual dimension or a “vitalism"; an idea that has persisted in philosophical biology for hundreds if not thousands of years.

1 How did Venter make his genome and insert it into the bacterium?    How did he remove the original DNA?

2 Did he create a living cell?  Share your view.

3 Is this the end of vitalism?

"stretchy pants" and hemidesmosomes

In the movie Nacho Libre',  Nacho is a wrestler (luchador) and likes to wear the "stretchy" pants the luchadors wear.  Living things made out of cells can be very firm like plant structures, but in animals,  cells are very stretchy and can participate in making structures like human skin and other tissues which are very malleable.  In our next topic in class we will discuss how eukaryotic tissue cells communicate with the outside world. Certain outside stimuli involving the extracellular matrix can promote shape change in cells and it can cause them to stretch and contort in ways that seem extreme.  Some cells must be stretched and shaped in order to form the shape of internal organs and for wound healing.  How do you stretch a cell and not break it?  Answer:  very carefully.


In a recent paper in Nature, a mechanism for stretching cells is proposed.  The mechanism centers around fascinating membrane protein complexes called hemidesmosomes.  Hemidesmosomes have been known for quite some time to be attachment structures which attach cells to other cells or the extracellular matrix.  Hemidesmosomes also attach to cytoskeleton components inside cells.  But new studies suggest that hemidesmosomes are also mechanosensors able to detect outside forces which squeeze and stretch cells. Hemidesmosomes communicate with intracellular cell signaling components such as kinases and other proteins.  Here again we have another case where a protein is involved in multiple functions.  The end result of the squeezing and stretching is elongated cells that contribute to the final shape of an internal organ for example during embryogenesis.


1 Review hemidesmosome structure and suggest a mechanism for how they could be involved in cell stretching? 


2 What would be the overal mechanism that would drive the cells to take on shapes which would contribute to the final morphology of an internal organ?


3 How do cells know how much force they can take before they rip apart?

Life on Mixotricha paradoxa

No, this is not a newly discovered planet but a flagellated Trichomonad found in the gut of the termite (Mastotermes darwiniensis). Paradoxa helps digest wood fiber in the gut of the termite. It appears that paradoxa moves by using its flagellum. But a closer inspection shows that the flagellum is perhaps only a steering device and the entire structure moves by the locomotion of hundreds of bacteria on the surface of paradoxa.
 
Thus we can document yet another function for the flagellum.  There are several kinds of bacteria on the surface of paradoxa and some are held in what appears to be specialized brackets on the surface of paradoxa.  Some of these bacteria contain their own flagellum and some of the bacteria are spirochetes.  The spirochetes are thought to provide the locomotion on the surface of paradoxa.  It would seem that a most efficient way for this organism to move would be to communicate with its surface motors when it wants to stop or start or go faster.

And there is good reason to want to move fast because Mixotricha paradoxa is hunted and eaten by other creatures lurking in the shadows.  Maybe this is a good reason to live in a  nice safe place like a termite gut.

Questions:

1 Spirochetes move by rotating.  How can a rotating twisting bacterium promote locomotion of paradoxa and yet stay attached to its host if its entire cell body rotates?

2 If paradoxa communicates with its motor bacteria, what form of communication would this be?

Cellular UPS and bad design

As I have mentioned in class, I think that bacteria and viruses appear to possess  features consistent with the idea that they are designed to deliver agents to cells.  For instance, their size is conducive to cell interaction and many possess elaborate motors , docking and delivery systems.  In fact, the bacterial flagellum which is often advertised as having one function, actually demonstrates many functions, i.e. it is a docking/binding agent as well as a motor, it also appears to be a receptor in some instances.  Thus the flagellum demonstrates co-option; it has more than one function,  an idea that many intelligent design theorists don’t like.  In addition some bacteria can control the actin polymerization inside cells inducing the cells to make “cellular arms” or pseudopods.  Thus they  induce the cell pseudopods to engulf them and they enter the cell in this manner.  Recently, researchers have used  bacteria to deliver a virus to a cell which induced profound genetic changes in the cell.  Viruses themselves possess several elaborate mechanisms for engaging cells and entering cells.  Viruses not only deliver genetic information to cells, but they can deliver proteins, they can control intracellular biochemistry and they can deliver membranes and membrane proteins.  Take for instance the flu virus.  It is an enveloped virus.  Technically when it leaves a cell it takes along some membrane from that cell.  Could it be that everytime you get a flu, you also get some proteins and membrane components from your friends?   What are the long term and short term implications of this?  But then again, viruses and bacteria can cause lots of problems.  If these creatures were designed as extracellular delivery organelles, is this the best design?.... because it appears that with a few "slight modifications" they can become agents of cellular destruction.

Questions:

1 Discuss the microbial extracellular organelle theory as described above.  What are its strengths and weaknesses as a theory?

2 If bacteria and viruses are designed delivery agents, why does our immune system try to eliminate them?  Or does it?

the dreaded dihydrogen oxide cell toxin: beware!!

Dihydrogen oxide is one of the most lethal cellular toxins.  It kills cells by causing them to swell uncontrollably and then burst, or in some cases to shrivel up like a crumpled piece of paper.  However most all cells on earth have been able to resist this toxin by using a membrane protein to prevent its deadly actions.  But even more interesting dihydrogen oxide or water is required for life and the aquaporin channel helps maintain a non-lethal concentration of this precious but deadly fluid.

Aquaporin is a fascinating integral membrane protein.  It is able to "filter" water into the cell by keeping other polar or charged molecules around the same size as water  out of the pore.  Plant, animal and bacterial cells have aquaporin channels. 

Questions:

1 How does aquaporin operate as a selectivity filter?  What would happen to cellular metabolism if it did not operate as a selectivity filter?

2 The complexity and requirement of aquaporin for cellular life appears to be a problem for the evolution of the first cells.  Or is it?  Some plants cells can take in water without aquaporin.  Could this represent a more ancient water controlling mechanism?  Check it out and comment on what you have learned.

cell suicide and the schizophrenic Jason Bourne organelle

We are discussing the lipids and proteins which make up the membranes in cells in lecture.  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? 

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?

membranes of the microbial cockatrice

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.

1 Explore the structure of the archaebacterial monolayers.  How does this contribute to life in the extreme?

2 What is an S-layer and how does it contribute to cell function?

3 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?

Membranes: The amazing phospholipids

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 boundry 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 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).

So my questions for this blog are;

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 posssible 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?

globules, cemetery chambers, and noxious seaweed, what is a cell?

Biologist Henri Milne-Edwards and his contemporaries in the 1800s referred to cells as globules.  Many rejected the term “cell” that Robert Hooke used to describe the dead dried plant cells he looked at under the microscope.  He was considered a botanist when he made this declaration, and therefore most likely the animal cell biologists were not sold on the term "cell" being used to describe animal tissues. A cell was a room and the term was used to describe the small above ground cemetery crypts at that time…..so it was not necessarily a term of endearment.  It also implied that  cells were empty, and many early biologists believed they were filled with some kind of “protoplasm.”

After  the term cell became widely accepted many biologists claimed, based on their observations, that all creatures were made of these small compartments called cells.  Additional cell theories implied that cells were derived from cells and their arrangement determined in part the morphology of living things.  Is this true? Is every living creature with the exception of viruses and prions made  of cells?  Maybe not.  There is an asexually reproducing seaweed called Caulerpa taxifolia. It grows so well that it crowds out all other aquatic plants on the ocean floor.  However it appears to be a giant multinucleate single cell. ( so much for my idea that unicellular life does not exist).  What is bizarre is that this single celled creature can form stem-like, root-like and leave-like shapes as a single cell.

In class we will try to define what a cell is, but here is my question for the blog.  From a teleological  perspective, what is the advantage of multicellularity, what is the advantage of making most every macro-creature out of really really small cells?

A tale of two nucleobionts: Holospora obtusa and Holospora undulata

I got really intrigued about the paramecium endonuclear symbionts.  So this will be the subject of our first research challenge in class.  I got really intrigued because these bacteria  (Holospora)  don't just happen to end up in the macro or micronucleus, they possess specific mechanisms to discriminate and enter these nuclei and they also bind to chromatin.  They even dramatically change their morphology to perform this feat.  This is fascinating because I thought that perhaps viruses were the only creatures which possess designs to invade nuclei.  So what could these nucleobionts be doing?  According to a speculative theory developed by my colleague Todd Wood these creatures might be doing something very significant.  But you will have to find his paper to find out more about this (AGEing).  I cannot give away anymore hints now, but stayed tuned to this blog for more hints.

Bioplasten and Henrietta Lacks

In 1890 german biologist Richard Altmann observed mitochondria in cells and named them the “Bioplasten.”  Mitochondria are everyone’s favorite cell organelle.  Unfortunately we never have enough time in class to discuss thoroughly these fascinating cells.  Wait a minute, ….these are cells?  Well I am going to go out on a limb and say that these are obligate endocytobiotic  bacteria.  However this phenomena is not that unusual because more and more endocytobiotic bacteria are being described. 

So I thought we would use this blog to collect information about these interesting creatures.  Lets start with their abundance.  If these are intracellular bacteria then they are perhaps the most numerous bacteria on earth with estimates of  10²⁶.  This may represent a  good portion of all bacteria on earth.  In fact we could estimate that the mitochondria from one person, Henrietta Lacks,  may be one of the most abundant bacteria on earth, with estimates of 10¹⁷.  (Pallen, Trends in Microbiology, 2011)

Who was Henrietta Lacks?

From WikiPedia:

Henrietta Lacks (August 18, 1920 – October 4, 1951) was an African American woman who was the unwitting source of cells from her cancerous tumor, which were cultured by George Otto Gey to create an immortal cell line for medical research. This is now known as the HeLa cell line.

The story of Henrietta Lacks is a fascinating one and was published in a book last year.  Many many researchers have grown her cells and used them in research, thus her mitochondria are very abundant on earth;  some suspended in a timeless state in freezers all over the world.

One scientist suggests that we name the mitochondrian bacteria as Mitochondrian lacksi.

So here is the first set of questions about mitochondria.

1 What are the current theories regarding the origin of mitochondria?

2 What is the structure of the mitochondrial membrane?

3 Mitochondria provide several functions in cells, what are they?

4 What bacteria do mitochondria resemble the most?

5 Do all cells have mitochondria?

6 Why do mitochondria have DNA? 

social networking bacteria, cellulosaic structures, and greenbeard genes

I was surprised this past week when after writing the “unicellular” blog to find a paper titled “social interactions in a unicellular world. “ Fascinating.  The authors seem to struggle in a way with the concept, because it appears that many “social” interactions among microbes appear to be beneficial and not necessarily competitive.  They even mentioned that Darwin struggled with the concept that living creatures can benefit another creature, without receiving a benefit in return.

One example they used was the cooperation among “unicellular”  DIctyostelium discoideum an amoeba which assembles multicellular structures via cooperation.  The structure they form is a fruiting body which culminates in a spore forming tip. So in the soil this microbe can be very happy living as a disorganized mob, but when it comes time to start a colony somewhere in the beyond, they get organized and form a fruiting body. The authors note that when they get together to organize a multicellular fruiting body, 20% of the cells lyse (kill themselves) to form a cellulosaic structure ( I like that word cellulosaic for some reason).  The cellulosaic structure is apparently a dead stalk which supports the fruiting body.  So how do we explain this apparent act of selfless behavior in this slime mold?  Can slime molds really exhibit  selfless behavior?  Do we really care?  I find it fascinating that biologists are interested in this.  It appears to me that the ideas which embody evolution drive them to see these ideas of selfless or selfish behavior in living organism.  Why are biologists interested in these concepts?

The authors also discuss the discovery of genes which are thought to be responsible for co-operation; these genes are called "greenbeard genes."  They mention the discovery  of the greenbeard gene Flo-1 in yeast which codes for a protein which makes yeast work together.

Questions:

1 Find out more about DIctyostelium discoideum.  What role does it play in nature? 

2 What advantages are there to living as an organism which can experience both a closely nit multicellular stage and a loosely nit unicellular-like stage? i.e.  what could organisms  accomplish living in this way?

3 Why are biologists interested in the concepts of selfless behavior or selfish behavior as demonstrated at the cellular level?

4 How does the Flo-1 gene promote yeast communities?

Unicellular life does not exist…..or how to live in a macronucleus!

In my first blog I mentioned that I do not believe that unicellular life exists.  Well that is one of those statements 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!  How many signs do you see posted around ponds or puddles that say…”get your own pond you scum-bag”, signed Peter Paramecium.

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 to review, my three main questions for the blog today are:

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

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

3 How can Paramecium eat algae but not digest it?

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

Next blog….more weird cells..

cellular angst

This is my first blog in this series.  This blog is primarily intended for my cell biology and microbiology students at The Master's College.  My background is in cellular immunology/microbiology and I have been teaching at the undergraduate level for 20 years.  However I am by no means an expert in this field....there is just too much to know and a lot of things yet to discover about these smallest pieces of life.

I intend on blogging at least once a week to share insights from our classroom lectures and discussions. 

Please feel free to contact me at jfrancis@masters.edu.

So what are cells and what is the advantage to having every living thing made of cells?  How do we define what a cell is anyway?  The traditional way to define them is to distinguish them from viruses.  Viruses are typically smaller than cells and do not have a lot of things which cells have.   Recently some very large viruses with membranes and cellular biochemistry have been discovered.  One of these is the Mimi virus... a pretty big virus. It is bigger than some bacteria.  It has metablic pathways to make amino acids and nucleotides.  So is this is virus or a cell? http://www.microbiologybytes.com/virology/Mimivirus.html



Then there is the issue of unicellular life.  I have a sneaky suspicion that unicellular life does not really exist.  Curiosity peaked.  Stay tuned.

Students please feel free to answer my questions with a reply.