notto said:
supersport said:
http://www.psrast.org/junkdna.htm
95% of DNA does NOT code for protein!! How do you like them apples Tom and everyone else?
'One Gene One Trait' hasn't been accepted for quite some time. Something else that is taught in just about every college level biology or genetics class.
You are caught in some kind of late 60's, early 70's time warp or something.
Notto is right, a lot has been discovered about how genes are expressed in the past 30 years. Perhaps you should acquaint yourself with just the basics at the sites below (expression is different for the two basic types of cells, prokaryotic cells vs eukaryotic cells).
Control of Gene Expression
The Paradigm of Differential Gene Expression
This is an extraordinarily complex subject so it isn't possible to even begin to explain gene regulation here. There is more to consider about gene regulation that simply looking at genes that are actively transcribed (used to make proteins, RNAs). The whole genome is actually "tagged" with certain chemical "cues" that directly affect that expression. Here's an interesting article on that:
The Unseen Genome: Gems among the Junk
EXCERPT
The extent of this unseen genome is not yet clear, but at least two layers of information exist outside the traditionally recognized genes. [....]Above and beyond the DNA sequence there is another, much more malleable, layer of information in the chromosomes. "Epigenetic" marks, embedded in a melange of proteins and chemicals that surround, support and stick to DNA, operate through cryptic codes and mysterious machinery. Unlike genes, epigenetic marks are routinely laid down, erased and rewritten on the fly. So whereas mutations last a lifetime, epigenetic mistakes-implicated in a growing list of birth defects, cancers and other diseases-may be reversible with drugs. In fact, doctors are already testing such experimental treatments on leukemia patients.
What most people don't realize is that inheritance/gene expression is not just a case of "me Gene", "you Protein". The DNA is packaged and "tagged" with a number of proteins and chemicals that directely effect how these genes are expressed. Some of these "tags" are often sex-specific, i.e., males and females will have often methylate (add a CH[SIZE=-2]3[/SIZE] "tag") the same alleles for a trait differently which will directly affect their expression. This kind of epigentic marking is called
genomic imprinting.
The fact is there are TWO types of DNA inside of a nucleus. First, DNA in a chromosome is actually a complex of DNA and proteins called histones, generically called CHROMATIN. To find out more about the structure of chromatin use
this link from Kimball Biology Pages On-line. Now why is this important? The way DNA is packaged dictates when or even if the genes within are transcribed (used to make proteins and RNA molecules). The two types of DNA are euchromatin and heterochromatin. Quoting/adapted from the Kimball link above:
Heterochromatin
- is found in parts of the chromosome where there are few or no genes,
- such as centromeres and telomeres is densely-packed;
- is greatly enriched with transposons and
- other "junk" DNA (more on this below);
- is replicated late in S phase of the cell cycle;
- has reduced crossing over in meiosis.
- Those genes present in heterochromatin are generally inactive; that is, not transcribed and show
- increased methylation of the cytosines in CpG islands of the DNA [Link];
- decreased acetylation of histones and
- increased methylation of lysine-9 in histone H3, which now provides a binding site for heterochromatin protein 1 (HP1), which blocks access by the transcription factors needed for gene transcription.
Euchromatin
- is found in parts of the chromosome that contain many genes.
- These are separated from adjacent heterochromatin by insulators. More on insulators
- The loops are often found near the nuclear pore complexes. (This would seem to make sense making it easier for the gene transcripts to get to the cytosol, but there is evidence that as gene transcription proceeds, the active DNA actually moves into the interior of the nucleus.)
- The genes in euchromatin are active and thus show
- decreased methylation of the cytosines in CpG islands of the DNA [Link];
- increased acetylation of histones and
- decreased methylation of lysine-9 in histone H3.
What was previously called "junk DNA (JD)" may not be junk after all and also appears to play a role in gene expression.
The question is not that "junk DNA" isn't "useful", but HOW useful is it .....The phrase "junk DNA"(JD) was coined to describe all DNA that did not code for proteins or RNAs used by the host. This phrase is proving to be something of a MISNOMER.
It DOES NOT necessarily mean useless DNA. While this DNA may not code for host proteins and RNAs,
it does appear that it may indeed have a number of "functions" within the cell.
- 1. JD acts as a regulator of gene expression during development (Ex. embryogenesis)
- 2. JD may serve as enhancers for the transcription of nearby genes.
- 3. Acting as a "double-edged" genetic regulator, JD can also function as "silencers" (in contrast to enhancers that up-regulate transcription) for suppression the transciption of proximal genes. Some of this DNA actually appears to be highly conserved between groups of related species:
From
Junk Throws up Precious Secret Researchers inspecting the genetic code of rats, mice and humans were surprised to find they shared many identical chunks of apparently "junk" DNA.
[*]
This implies the code is so vital that even 75 million years of evolution in these mammals could not tinker with it.
[*]
But what the DNA does, and how, is a puzzle, the journal Science reports.
. . . .
The regions largely matched up with chicken, dog and fish sequences, too; but are absent from sea squirt and fruit flies. (NOTE: We wouldn't expect to find such conserved sequences in organisms so far removed from the vertebrates mentioned)
. . . .
The really interesting thing is that many of these "ultra-conserved" regions do not appear to code for protein. If it was not for the fact that they popped up in so many different species, they might have been dismissed as useless "padding".
We know this because ever since rodents, humans, chickens and fish shared an ancestor - about 400 million years ago - these sequences have resisted change. This strongly suggests that any alteration would have damaged the animals' ability to survive.
[*]
"These initial findings tell us quite a lot of the genome was doing something important other than coding for proteins," Professor Haussler said. He thinks the most likely scenario is that they control the activity of indispensable genes and embryo development.
[*]
Nearly a quarter of the sequences overlap with genes and may help slice RNA - the chemical cousin of DNA involved in protein production - into different forms, Professor Haussler believes.
The conserved elements that do not actually overlap with genes tend to cluster next to genes that play a role in embryonic development.
"The fact that the conserved elements are hanging around the most important development genes, suggests they have some role in regulating the process of development and differentiation," said Professor Haussler.
JD may play a role in regulating translation of proteins
- 4. JD can also be used to create new sequences that generate new proteins. Guess what that is, superport, it’s called EVOLUTION!
From
“Junk DNA” Creates Novel Proteins
DNA sequences long considered genomic garbage are finally getting a little respect. Researchers have figured out how short stretches of DNA that do not normally code for proteins worm their way into genes.
[*]
This can result in the production of abnormal proteins and lead to genetic diseases, such as Alport Syndrome, a rare kidney disease.
But the sequences, sometimes called “junk DNA,” have also allowed humans and other species to create new proteins in a process that has dramatically influenced evolution.
[*]
Gil Ast and his colleagues at Tel Aviv University in Israel have figured out how the sequences, known as Alu elements, are incorporated into genes to create novel proteins. More than 300,000 sequences are poised for insertion into genes—all that’s needed is a single mutation.
Through a process called alternative splicing, humans create multiple versions of a gene and, consequently, multiple proteins. It’s a way of constructing a new protein, while keeping a backup copy of the original version.
Just "WHAT" is "junk DNA"? It is composed of:
- 1. Introns (For an interesting twist on how introns can be "used" read about Inteins or "protein introns"
- 2. Pseudogenes
- 3. Nearly half of this "junk" DNA is parasitic or "selfish" DNA. These mobile elements are DNA sequences that possess coding sequences that facilitate their ability to copy and/or transfer themselves to different regions of the hosts genome. These mobile element specific sequences doesn't code for host proteins that will ever become part of the host tissue or perform a cellular function.
These pseudogenes and mobile elements (which also acquire mutations) accumulate over time and have characteristic patterns that can be used to trace lineages.
I haven't even scratched the surface about what is currently known about gene expression.
That is what Tom, notto, Gracchus and others (kudos to you all for your patience with supersport’s antics), have been trying to tell you. It’s all about EXPRESSION of a particular gene or set of genes.
Let me give you an example. Suppose a woman is pregnant, BUT she’s an alcoholic. The alcohol is going to interfere with when and how certain genes affecting intelligence, etc. are expressed and
result in the following defects “brain damage, facial deformities, and growth deficits. Heart, liver, and kidney defects also are common, as well as vision and hearing problems. Individuals with FAS (fetal alcohol syndrome) have difficulties with learning, attention, memory, and problem solving.” The degree to which the developing embryo/fetus is affected depends on when the mother starts drinking and how much she drinks.
Second example of how elements in the environment can affect expression is to
take the simple case of flower color in some species of hydrangeas. If they can take up aluminum from the soil, then their flowers will be blue or pink depending on how much they take up. Raising the pH of the soil will slow the uptake of the aluminum and result in pink flowers, whereas, lowering the pH of the soil will enable the plant to take up more, producing blue flowers. The genes coding for pigmentation in a plant with pink or blue flowers is the SAME, but the presence of the aluminum is going to modify the pigment, resulting in different colors.
Third example…Let’s take height.
One of Jack the Ripper’s victims, a prostitute Elizabeth Stride was known as “Long Liz” because of her height.
How tall do you think she was? I ask my students this and most will opine that she was probably 6 feet tall or taller. The fact is that she was only 5’ 2’’ tall. However, this made her nearly half a foot taller than most women in Victorian London who averaged 4’ 9” tall.
In the UK now, the average height for a woman is a little over 5’3-4”. Have their genes “mutated” so that women in the UK are taller? NO! It’s has more to do with nutrition. IOW,
it doesn’t matter how many “tall genes” you inherit from your parents, IF you don’t get adequate nutrition at the appropriate time, you will not develop to the height dictated by those genes. Height is also going to be affected by a number of other environmental factors, not just nutrition, but adequate nutrition is crucial.
What you apparently have no conception of here is what genes are or anything about how they are expressed and hence don’t know the difference between the effect of a mutation versus the range of gene expression (the “plasticity” factor) which is often dictated by elements in the environment (both pre-natal and post-natal).