Showing posts with label DNA. Show all posts
Showing posts with label DNA. Show all posts

Thursday, January 4, 2018

Every Day Should Be Mother’s Day

Biology concepts – inheritance patterns, mitochondria, fertilization, lineage, mitochondrial Eve

What do the “The Battle Hymn of the Republic”, Mother’s Day, and all your mitochondria all have in common?

Julia Ward Howe wrote the words for The
Battle Hymn of the Republic after meeting
Abraham Lincoln. She wrote it as a poem,
but also as new lyrics for the existing song
called, John Brown’s Body. I wonder if she
had copyright issues to deal with.
The first two are easy; Julia Ward Howe wrote the Battle Hymn of the Republic as a Union anthem during the Civil War, but just 12 years later proposed a national day of mourning and protest for mother’s of sons who killed sons of other mother’s. She had come to regret her support of the Civil War and wanted July 4th to be converted into a protest day by mother’s to ban future wars.

This didn’t go over that well, but the daughter of one of her followers, Julia M. Jarvis, re-purposed the proclamation to celebrate her own mother’s dedication to church and community. This caught on, and in 1912 Jarvis’ home state of West Virginia officially recognized Mother’s Day. Two years later, President Woodrow Wilson declared that the second Sunday in May should be a national observance of a Mother’s Day.

But what has it got to do with your mitochondria? Well, you owe your mom a debt of gratitude for every one of your mitochondria. All of yours came from hers – Dad played no role in your cellular ATP factories.

Here's how it works. Your somatic cells (all your cells except the eggs or sperm) have two copies of each chromosome, but we know that your chromosomes aren’t the only DNA in your cells. Your mitochondria have their own chromosome; it’s circular like the prokaryotic ancestor it came from during endosymbiosis. How do you inherit that DNA?

In this electron micrograph of the sperm you
can see the dark nucleus which houses the
chromosomal DNA. Above the acrosome, or
head, you can see the mitochondria packed
into around the tail proteins. Their ATP is
used to whip the tail for locomotion.
The egg has loads of mitochondria, about a million in each oocyte (egg cell). On the other hand, each sperm has only about 100. This makes sense, the body must produce billions of sperm, but only a few eggs, so it has to ration the mitochondria to all those sperm cells.

The important issue is where the mitochondria are located. The oocyte mitochondria are inside the egg, waiting for a single sperm to enter and begin the process of making a new human (for example). All the mitochondria of the sperm are located in the first part of the tail, called the midpiece or mitochondrial sheath. This also makes sense, as it is the tail’s movement that propels the sperm toward the egg, All of this tail wagging requires a great amount of ATP.

The sperm meets the egg and fuses with the oocyte membrane, but not all of it enters the egg cell. Only the head, or acrosome makes entrance; it has the haploid chromosomal DNA that is your father’s contribution to your genetic makeup. The sperm midpiece, will all its mitochondria remain on the outside of the egg and does not contribute to you being you.

That is how it came to be that you got all your mitochondria from your mother! We all did. The process is called maternal inheritance of mtDNA, and it is has implications for tracking the history of human life.

A journal cover for the issue dedicated to DNA
repair enzymes. Who says scientists don’t have
a sense of humor? Actually, this may just have been
how one guy showed up to the lab that day; his
mind was on science, not fashion.

Mitochondrial DNA doesn’t change much over time, but it does change. Every time your DNA replicates, mistakes are made. “To err is mammalian,” and your DNA polymerase (polymer = long chain, and ase = enzyme that makes) is mammalian. Consider that the DNA polymerase is adding nucleotides to a growing chain at a rate of about 1000/second – some mistakes are bound to occur.

Most of these mistakes are caught and fixed by a series of proofreading and mismatch repair functions, but some mistakes get through. These random mutations often have no effect on the function of the gene product, but if they aren’t fixed, they become permanent and are passed on the next time the DNA is replicated.

Over time, the changes add up. The 50th generation mtDNA necessarily looks different from the 1st generation DNA. Mutations that hurt the function could very well prevent reproductive success (the ability to mate and produce viable offspring), so the changes that we see over time usually are the ones that have little effect on function.

This random mutation wouldn’t matter much if you got half your mitochondria from Pop and half from Mom, there would be random passing on of mitochondrial DNA and probably some recombination, so  the 50th generation wouldn’t look much at all like the first. But you get all of your mitochondria from Ma, and she got hers from her ma, and she got hers from her ma, ….. so that there is a straight line back in your family history.
 
The rate of mutation and the pattern of mutation
in the mtDNA can not only help us date mtEve, but
can help track the migration of humans out of Africa
and around the world. The numbers with a k =
thousands of years ago.
The maternal inheritance of mtDNA allows scientists to trace family lineage through molecular biology (to balance the sexes, you can trace paternal lineage through the Y sex chromosome as well). In fact, with a large enough sample size, you could literally see that all humans are related! Trace the changes in mtDNA backwards far enough and they will all converge on a single female; the mother of all mothers - “Mitochondrial Eve.” This isn’t the same as a Biblical Eve – just the last female to whom we are all related. We don’t know who mtEve was, where mtEve was, or when mtEve was because we don’t have enough samples from enough generations.

The most current estimate is that mtEve lived about 200,000 years ago, although the timing is just that, an estimate. The sampling and math are dependent on knowing the rate of mutation of the hypervariable regions (part of the mtDNA that mutates faster than the other parts) and knowing that this rate has been constant and predictable. Does that sound like the biology you know? The assumption doesn’t invalidate the idea of mtEve, it just makes sending her birthday card difficult.

Even if we don’t know who Eve was, we can talk about her “daughters.” These are the unnamed females to whom we can trace back large numbers of living and deceased humans. Geneticist Bryan Sykes wrote a book called The Seven Daughters of Eve in 2001, but we now consider that we have really defined about 10-12 daughters. With twelve daughters, there must have terrible fights over bathroom time!

Bryan Sykes named his seven daughters of Eve
based on the first letter of the haplotype designation
each already had. Example, haplotype U became
Ursala – he must have seen Bond girl Ursula Andress
in Dr. No recently.

Why would maternal inheritance of mtDNA be a good idea? Current theories hypothesize that this a mechanism by which only genetically strong sperm will reach the egg, and only genetically strong mitochondria will be inherited. With only a few mitochondria in the sperm, they must perform well in order for the sperm to reach the egg. If genetic mistakes have been made during meiotic production of sperm, then chromosomal errors might be accompanied by mitochondrial errors. A fast swimmer indicates a genome without harmful mutations. So the strongest genes get to the egg.

On the other hand, the effort to reach the egg means lots of ATP production, which also means lots of oxygen produced by oxidative phosphorylation. Oxygen can be damaging; the mitochondria probably aren’t in good shape at the end of the race. The sperm may be like salmon. The strongest make it up stream, but they end up so broken down that one trip is all they get; the damage would prevent the next round of their sperm from being prime material.

Why would evolution choose to pass on damaged paternal mitochondria when you have perfectly fine maternal mitochondria laying around in the hundreds of thousands. The chances are greater that the mother’s mitochondria are normal at this point, so the paternal versions are denied entry. Makes sense.

But some organisms just have to rock the boat. Blue mussels (family Mytilidae) and some freshwater mussels have two different types of mtDNA, called F and M – how original. The female passes on the F type to her sons and daughters, while the males pass on the M type to just their sons. Called doubly uniparental inheritance (DUI), females are homoplasmic (one type and males are heteroplasmic (two types).

Males are usually F type dominant in their somatic cells, but M type dominant in their spermatozoa. The females must be F type dominant in all cells, since they only have one type. The interesting part is that both male and female embryos get M type mtDNA, but in those destined to be females, the M type are degraded within 24 hours.

A 2009 study shows that the sex determination and inheritance of the male mtDNA are not coupled, and the female has complete control over whether the male type will be inherited and maintained. But there are occurrences of females with some M type, and males with only F type. Therefore, maternal inheritance is more stringent than DUI ------  Or is it?

This is a Schistosoma mansoni egg. It looks
like a cartoon bubble; I keep expecting it to
say something. S. mansoni is an exception
for trematodes, it has two sexes (is dioecious),
whereas most others are hermaphroditic.
The function of the spine on the egg is not known,
but it may help the egg stick to the wall of the blood
vessel in the host.
In some cases, like honeybees, mice, and a parasitic worm called Schistosoma mansoni, there can be “leakage” of paternal mtDNA into the fertilized egg. Even in some mammalian species other than humans, including sheep and mice, the tail of the sperm can penetrate the oocyte. This gives a zygote with many copies of female mtDNA and a few copies of paternal mtDNA. For some reason – I assume there is a reason, although I don’t know it -- this occurs more in crossbreeding (interspecific breeding – between species), than when two animals of the same species are bred.

In the breeding of animals of the same species, if there is paternal mtDNA present, it is degraded in the fertilized egg. Near the time of birth, they might have only a trace of paternal mtDNA left, but the mechanism by which this occurs is not known. During this time, there is the small chance that male mtDNA could recombine with female mtDNA and gum up the workings of strict maternal inheritance. In any case, there has been only one documented case of a paternal mitochondrion in a child, and this case was clouded by issues of infertility. Does this child feel disconnected from his great, great, great, great grandmother?

So much for animals - how about plant inheritance of chloroplasts and mitochondria? Do they follow the same rules – let’s find out next time.

Ellen L. Kenchington, Lorraine Hamilton, Andrew Cogswell1, Eleftherios Zouros (2009). Paternal mtDNA and Maleness Are Co-Inherited but Not Causally Linked in Mytilid Mussels PLoS One DOI: 10.1371/journal.pone.0006976

For more information or classroom activities on maternal inheritance, mitochondrial Eve, or fertilization, see –

Maternal inheritance –

Mitochondrial Eve –

Fertilization -

Thursday, November 16, 2017

On Geometry And Genomes

Biology concepts – linear chromosomes, circular chromosomes, taxonomy, replication, telomere


Organization is helpful in learning and work,
and apparently in crafts. But there is a fine
line between organization and obsessive
compulsive disorder.
Everyone (teenagers excepted) knows that getting organized helps you to learn and work. When you group tasks, items, or facts, it helps in remembering or working with them. In biology, grouping organisms has a history as old as language.

In the older grouping systems, the name of an organism was a phrase that described some characteristic of the organism. When a new relative was identified, the name phrase had to be lengthened to separate this new organism from those similar to it. As you can imagine, the names got very long very fast.

In the 1750’s, Carolus Linnaeus developed a much easier system of naming. In his “trivial system,” each organism had two descriptors in its name; a binary naming system. Linnaeus’ system (and others) of taxonomy (taxis is Greek for “arrangement”) is based on shared characteristics.


Carolus Linnaeus (he let me call him Carl) had many
names. His knighthood name was Carl von Linne, his
born name was Carl Nilsson Linnaeus. In his naming
system Linne came up with the name mammal, so I guess
he named himself again.
At first, it was the characteristics people could see that were used to group organisms. Then it was the characteristics on the macroscopic and the microscopic levels. Now it is based on molecular characteristics, forming both a taxonomic classification and an evolutionary tree; this is now called the science of phylogenetics.

Molecular characteristics usually mean DNA. Differences in DNA sequence and in the number of mutations that have occurred provide a relationship between organisms. Using these factors, a time line for their divergence can be estimated. We changed the ways we determine similarity, and that changed the rules. With new rules come new exceptions.

Many of the DNA rules start with chromosomes (chromo = color and soma = body, this comes from the dark and light banding pattern of stained DNA). Cellular DNA is very long and very thin, perhaps only 12-22 nanometers wide (about 1/5000 the width of a human hair). In this form, it can only be seen with an electron microscope.

In eukaryotes, this DNA becomes complexed with many proteins during cell division so that all the DNA can be packed up and moved more easily to the daughter cells.  Called chromosomal packaging, the DNA is wound around proteins called histones, then folded many times over, so that the finished chromosome is packed 10,000 times more compact than the original DNA helix. This is the packed DNA that we see as dark and light bands and gives it its name.


DNA packaging with proteins is a eukaryotic characteristic, unless 
I find an exception! The DNA wraps around the histones, then the 
histones line up into a coil, then the coils fold up into the
chromatid. Total packing – about 10,000 fold; it takes a piece of 
DNA 1.5 cm long and makes it 0.0000002 cm long!
By definition, a chromosome is a piece of DNA that contains genes that are essential for the survival and function of the organism. This implies that there may be other pieces of DNA that contain genes that are not necessary for survival.

The molecular rules of biology state that prokaryotes have one chromosome, a single piece of double stranded DNA that contains all the genes that the prokaryote (archaea or bacteria) needs. This is efficient for the organism; it is one stop shopping for replication of all its instructions and only two chromosomes (after replication) need to be segregated to the two daughter cells that are being made.

And here begins our exceptions. There are several prokaryotic organisms that have more than one chromosome. That is to say, their essential genes are located on more than one piece of DNA.

The first identified example of multiple chromosomes in a prokaryote was Rhodobacter sphaeroides, a photosynthetic species of true bacteria that can also break down carbohydrates it takes up. This bacterium was found to have two chromosomes, although one was more than three times the size of the other.

Genes encoding essential products for making proteins and carrying out day-to-day functions are located on each of the two R. sphaeroides circular chromosomes. There are other genes that exist on both of the chromosomes, but appear to be turned on and off via different signals. This implies that the same gene may serve its function at different times in the organism's life, or under different environmental conditions.

R. sphaeroides is by no means the only prokaryote that possesses multiple chromosomes. More than a dozen different groups of bacteria have at least some members with more than one chromosome. This includes Vibrio cholerae, the causative organism of the disease cholera. V. cholerae is responsible for a diarrheal infection that affects more than 3-5 million people per year and causes 130,000 deaths each year.


This is a crown gall in a birch tree caused by R. radiobacter.
Like in cancer tumor in animal tissues, a gallis unregulated 
growth. In grape vines, it has been responsible for the ruin 
of entire Kentucky vineyards. Kentucky makes wine?
In addition to these organisms there is Agrobacterium tumefaciens, whose name was recently changed to Rhizobium radiobacter. This is a very interesting two chromosome bacterium. It usually is a pathogen of plants, forming galls (tumors) on several cash crops, such as nut trees and grape vines. This is an important tool in the molecular biologist’s toolbox, since it has been found that R. radiobacter easily transfers DNA between itself and the plants it infects, via lateral gene transfer (a subject we have discussed in depth, When Amazing Isn’t Enough and Evolution of Cooperation). But R. radiobacter goes further, it can also cause disease in humans who have poorly functioning immune systems. For folks battling cancers, HIV, or other diseases that wreak havoc with their ability to fight off infections, R. radiobacter can cause bacteremia (bacteria colonizing the blood) or endopthalmitis (infection of the two hollow cavities of the eye).


The second molecular rule of biology is that prokaryotic chromosomes take the shape of a circle; the DNA forms a single loop. This shape is helpful in terms of replicating the prokaryotic chromosome prior to cell division. Start anywhere, and you can keep going to replicate the entire thing.  In point of fact, they don’t start just anywhere, but one start point (called an origin of replication) leads to complete replication.

There are advantages to having a circular chromosome. Prokaryotic chromosomes do not complex with proteins to become more densely packed, so it remains as a thin, long molecule. This means that fewer proteins are needed to maintain a circular, prokaryotic chromosome. In addition, since replication requires the doubling of just one piece of DNA from one origin of replication, this takes less time and fewer proteins to accomplish. Together, these features of a circular chromosome result in a more efficient and simpler process, with fewer chances for mistakes to be made.


Borrelia burgdorferi, a spirochete (spiral) bacterium was
Named for the researcher who discovered, it in 1982, Willy
Burgdorfer. It is one of the few pathogens that can function
without iron; it uses manganese instead. The ways this bug
gets around the rules is astounding.
However, there are exceptions in which prokaryotes have linear chromosomes. The Borrelia burgdorferi bacterium has a single chromosome, but it has the geometry of eukaryotic chromosomes, a line segment with two ends. This was the first prokaryote found to have a linear genome, way back in 1989. This lyme disease pathogen has one major linear chromosome and other pieces of smaller DNA that are circular or linear (which we will discuss in the next post); you just can’t trust a pathogen to follow the rules. Other prokaryotes that have linear chromosomes include our friend R. radiobacter. Even more interesting, while this pathogen has two chromosomes; one is circular and one is linear. How does that happen?

The previous discussions do not mean that all prokaryotes with multiple chromosomes or linear chromosomes are disease-causing agents, just the interesting ones. Since they cause pathology in animals or crops, they hit us in the wallet. It makes sense that we have studied them in more detail and have discovered their hidden exceptions. There are probably thousands of innocuous prokaryotes that have more than one chromosome or have linear chromosomes, we just don’t have a reason to look at them in that much detail.

There may be more than one way that prokaryotes end up with linear chromosomes. In some cases, the linear chromosomes still have bacterial origins of replication, indicating that they may have evolved from circular chromosomes. There is also evidence that some linear chromosomes might have developed from other linear DNAs in the cell, something we will talk about next time.

The rules of defining prokaryotes and eukaryotes also state that eukaryotes have linear chromosomes. The essential genes are stored on more than one piece of DNA, and these pieces have two ends apiece, like a line segment in geometry.

Linear chromosomes are a disadvantage because it is hard to replicate the ends. Because of the way that DNA replicates, the ends of the chromosomes, called telomeres, end up being shortened every time the DNA is replicated. Over time, this leads to shorter chromosomes that might lose DNA sequences that the cell needs in order to function.

Some lines of evidence suggest that telomere shortening is a direct cause of ageing. The loss of important sequences at the ends of chromosomes cases cells to perform at less than optimal levels, and mistakes and toxic products then build up and lead to larger dysfunctions of cells, organs, and systems, ie. getting old.


This is a very simple cartoon depicting recombination. When
sequences are exchanged, it isn’t necessarily a 1:1 exchange.
Sometimes parts of genes are sent one way but not the other,
So new genetic sequences can result. Some help, some hurt, and
some have no effect until the environmental conditions show
them for what they are. Most exchanges do not increase diversity
to any great degree, but the fact that some do has helped move
evolution along.
On the other hand, linear chromosomes may promote genetic diversity. In eukaryotes, the division of the cell requires each chromosome to be replicated, then the matching chromosomes of a pair (one from mom and one from dad) line up together. This is a prime opportunity for the chromosome to exchange some sequences in a process called homologous recombination; a mixing of genes beyond just getting one from each parent.

However, a study published in 2010 indicates that the geometry of the chromosome doesn’t matter when it comes to recombination rates. Scientists took a circular chromosome organism and linearized its genome (they cut it so it had ends). They also did the reverse experiment, taking a linear chromosome organism and circularizing its DNA.

In both cases, there was no change in the rate that its DNA recombined and produced slightly different offspring (the two circular chromosomes after replication can swap some pieces). So geometry does not appear to affect genetic diversity – so why did each type evolve? Good question – that can be your Nobel Prize project.

Next week we will continue the discussion of exceptions in DNA structures, including DNA that isn’t part of a chromosome, and mitochondrial and chloroplast genomes that don’t look like they should.



Casjens SR, Mongodin EF, Qiu WG, Luft BJ, Schutzer SE, Gilcrease EB, Huang WM, Vujadinovic M, Aron JK, Vargas LC, Freeman S, Radune D, Weidman JF, Dimitrov GI, Khouri HM, Sosa JE, Halpin RA, Dunn JJ, & Fraser CM (2012). Genome stability of Lyme disease spirochetes: comparative genomics of Borrelia burgdorferi plasmids. PloS one, 7 (3) PMID: 22432010

Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, & Muller D (2014). Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Molecular phylogenetics and evolution, 73, 202-7 PMID: 24440816

Suwanto A, & Kaplan S (1989). Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. Journal of bacteriology, 171 (11), 5850-9 PMID: 2808300


For more information or classroom activities on prokaryotic chromosomes or eukaryotic chromosomes, see:

Prokaryotic chromosomes –

Eukaryotic chromosomes –
http://www.windows2universe.org/earth/Life/genetics_intro.html

Wednesday, January 27, 2016

An Infectious, Genetic Disease? Better Sleep On It.

Biology concepts – thermoregulation, sleep, genetic disease, infectious disease, central dogma of molecular biology, form follows function


Even rats have to get some sleep. It was nice to have the sleeping cap,
but unnecessary for a sleep deprivation study. Not a good use of
research dollars.
“I’m dying for a good night’s sleep.” Is this just hyperbole, or an impending warning of death? For laboratory rats, sleep deprivation does kill. During their insomniac downward spiral, the rats tend to get hot and can’t cool down – you know, they can't thermoregulate (see Can’t We Just Go With The Flow). This doesn’t mean that a loss of the ability to thermoregulate is what kills the rats, but it does suggest a connection between sleep deprivation and the hypothalamus.

We looked at the hypothalamus in our story of endothermy. This evolutionarily old brain structure implements a set point temperature for the body and receives information about the temperature of different parts of the body. When the body temperature deviates from the set point, the hypothalamus initiates bodily mechanisms to normalize the temperature.


Apparently one of the effects of sleep deprivation is that you
become semi-transparent.
People with severe insomnia tend to sweat more and have higher core temperatures even though they say they are cold. They also have extreme high blood pressure, pulse, and appetite. These symptoms suggest that sleep deprivation messes with the hypothalamus, since functions of the hypothalamus include themoregulation, sleep, hunger, thirst, reproductive readiness in females, and stress responses. What scientists don’t know yet is just how sleep deprivation actually kills the rats or harms people.

Dying from a lack of sleep is not just a rat problem, a few very unlucky humans die from it as well. Fatal familial insomnia (FFI) is a very rare genetic disorder; it has been reported in only 40 families worldwide. Before describing the truly horrible way these patients die, let’s look at what causes the disease.

FFI is caused by a point mutation in the gene for the prion protein PrPc. A point mutation means that one nucleotide on the DNA is changed, which leads to a change in the protein coded for by the DNA. Three unit (nucleotides) segments of the RNA (made from the DNA template) work together (called a codon) to code for one protein building block (amino acid). In the case of FFI, the amino acid called aspartic acid is changed to one called asparagine, and this changes the protein’s shape. 


The left image shows mRNA bases recognized in sets of three
(codons) by tRNAs with amino acids attached (Ser = serine, tyr =
tyrosine). The amino acids are linked to because proteins. The
lower section is the genetic code, showing which amino acids are
coded for by which codons. The right image shows how proteins
fold. The primary structure is the amino acid sequence. The
secondary structure comes from interactions of adjacent amino acids,
including spirals called helices or sheets. The tertiary structure comes
from the folding up of the entire protein, while the quaternary
structure comes from the interaction of different proteins into a
larger complex.
PrPc is made up of 250 amino acids linked together in a chain. Each different amino acid carries a different shape and charge and will interact with every other amino acid differently. The sequence of amino acids in a protein cause it to fold into a specific shape. It is the protein’s conformation (shape) that determines its function. This is the opposite of what we determined for evolved organism characteristics, where form follows function (see Do You Have To Be Ugly To Hear Well?). With proteins – function follows form!

Mutation of that single amino acid at position 178 (aspartic acid is negatively charged, while asparagine is positive) causes the folding, and therefore the function, of the protein to change. Aspartic acid is sometimes abbreviated "D", while asparagine is called "N"; therefore, the mutation is often indicated as D178N (D at position 178 is changed to N).

Many genetic mutations result in no change in amino acid, or a change that bring a large enough change the shape to cause a change in function. But when it does, good or bad things can happen. On one hand, the altered protein might confer an advantage to the organism, one that promotes survival in the environment or after an environmental change.This positive selection through reproductive advantage become the new normal – and this is evolution

On the other hand, the change in amino acid sequence, form, and function could be destructive. Disease might be the result, or perhaps a change in the organism that reduces reproductive success. One of these two results is what occurs with the FFI mutation of the prion protein.

When the mutated prion folds differently, it forgets its day job and moonlights as a sinister evil force. Every other prion protein it contacts, WHETHER MUTATED OR NOT, is coaxed into changing its shape. The new prions turn to the dark side, then change other prion proteins they contact, multiplying the effect. The poorly folded prion proteins will stick together, come out of solution, and form solids (plaques) where they settle out. In different prion protein diseases, this settling out occurs in different parts of the brain. In FFI, it is the hypothalamus.


In the top image, the PrPc on the left is properly folded. The green
represents alpha helices and the blue arrows represent beta-pleated
sheets. The right image shows the malfolded version of PrPsc. It is a
tighter structure, which partially explains why protein-degrading
enzymes don’t work on it. . The lower cartoon shows that the PrPsc
can force the PrPc to assume the improper form, and these then
aggregate into plaques.
The prion plaques are longer lived then the regular prion protein; normal cellular enzymes whose job it is to degrade proteins won’t work on prion plaques. And worse, if some of the malfolded protein is transferred to another animal, the recipient will develop plaques and disease as well. That makes this an infectious disease that isn’t caused by a bacteria, fungus, parasite, or virus. The prion is an infectious protein! What a terrible exception to the rules of infectious diseases.

We see here a protein that can replicate itself (not by building more of themselves, but by changing the form of normal proteins), and that makes it a repository of biologic information. This is an exception to the central dogma of molecular biology, which says that DNA is the sole information storing material.

FFI moves from person to person through heredity, but if a non-affected person comes into contact with some brain material from an FFI patient and that material entered their bloodstream, it can be transmitted this way as well. A prion protein disease called Kuru is famous for being transmitted from person to person.

The Fore tribe in Papua New Guinea once observed a ritual wherein they honored a dead tribe member by eating part of their brain (called ritualistic mortuary cannibalism - gasp!). Because of this, there was an epidemic of Kuru in this tribe in the early 1900’s. Over a period of 3-6 months victims would become unsteady, irrational with bouts of laughter, and then degrade mentally and physically to the point of death. There are more than twenty known prion diseases (mad cow disease, Creutzfeldt-Jakob, scrapie, etc.), and Kuru suggests that some might have no genetic component, only person to person transmission.


A member of the Fore tribe is shown on the left. This tribe used
to celebrate the lives of departed members by eating their brains.
This spread a prion protein disease called Kuru, a protein disease
that is infectious! The Fore tribe still lives in Papua New Guinea,
although there are fewer of them than before Kuru.
The differences between the various prion diseases are based on the specific prion protein mutation, what part of the brain is attacked, and how potent the prion is at refolding normal prion proteins. For instance, the D178N mutation in FFI also occurs in Creutzfeldt-Jakob Disease (CJD), but a normal polymorphism (an amino acid change that doesn’t change form or function) at position 129 determines the fate. If amino acid 129 is methionine, the the person gets FFI, if it is valine, then they get CJD. 

The families that suffer from FFI have the D178N mutation, and also pass on the polymorphism for methionine (M) at position 129. Even more gruesome, some cases of prion protein diseases can be sporadic, not associated with either an inherited mutation or transmission. The malfolded prion can very rarely arise out of nowhere in isolated individuals.

The mutated PrPc is passed on via inheritance. You get one copy of each chromosome from each of your parents, so for an individual gene, you might get two normal copies, 1 mutant copy and 1 normal copy, or 2 mutant copies. Some diseases require that you must inherit two mutant copies for symptoms to show (recessive), but other require only one mutant copy (dominant, it dominates the trait from the other parent).

FFI is autosomal dominant (not associated with the X or Y sex chromosomes), so the chance of getting a mutant copy and the disease if one parent has it is 1 in 2; these are bad odds. But, if everyone with FFI dies, then why is the disease still showing up in families. Remember that we said above that some genetic diseases can, but don't have to, affect reproductive success. Unfortunately for those with FFI, the symptoms appear in the victims’ fifties, after they have had children. Natural selection doesn’t eliminate FFI from the population because FFI doesn’t appear affect reproduction.

The first symptoms of FFI include sweating while feeling cold. Later, the ability to get a good night’s sleep is lost, followed closely by the inability to nap. As the disease progresses, there are panic attacks, phobias, and no sleep whatsoever. After 4-6 months, mental abilities start to degrade. In its final stages unresponsiveness precedes death. 

This is especially sad way to die, because during the majority of the disease course the patient is aware of everything going on. At least with middle to late Alzheimer’s disease the patient is blissfully unaware of their dementia.


For both the gross and microscopic images, the left example is from prion protein disease victim, while the right example is from a normal brain. The brains on the left show how great the loss of tissue can be in Creutzfeldt-Jakob disease. The microscopic image from the diseased brain shows the plaques and the resulting holes in the brain structure. The small gaps in the normal brain on the right are a result of shrinking of tissue after it was on the slide.
On autopsy, the hypothalmus of an FFI sufferer looks like it has been hit with a shotgun blast. Holes are present in the tissue, representing areas where neurons have been lost due to inflammation and triggered cell death. The affected area of the brain takes on a spongy appearance, so prion protein diseases are lumped together and called transmissable spongiform encephalopathies (encephalon = brain and pathy = disease). Unfortunately, there are no cure, treatments, or vaccines for any of these prion diseases.

It is the hypothalamus' control of sleep cycles and circadian rhythms that promotes survival in animals. But what about plants? They don’t have a hypothalamus. Can they suffer from loss of circadian activity? In a word – yes!  And this will be our starting point next time.


For more information or classroom activities on prion proteins, central dogma, infectious or genetic disease, the genetic code or protein structure, see:

Prion protein and diseases –

central dogma of molecular biology –

infectious disease –

genetic disease –

genetic code –

protein structure –
nwabr.org/sites/default/files/learn/bioinformatics/AdvL5.pdf