two very complex biology questions

Factual Questions
1

Hey
I have two incredibly interesting and thought-provoking biology questions for anyone who can answer them.

  1. Say non-disjunction occurs in a spermatogonium, leading to a spermatozoon with 24 chromosomes: 22 autosomes and 2 sex chromosomes, X and Y (XY). Now, say that non-disjunction also occurs in an oogonium, leading to an egg cell with 22 autosomes and no sex chromosome. Now, the problem is this: Should fertilization occur between these two cells (yes, I do realize how rare this occurrence is, but humor me), what would the outcome be? Theoretically, we should have a normal child (46 chromosomes: 44 autosomes, 2 sex chromosomes, X and Y, both being paternal.) But would it work in reality? Does the body “know” that something is wrong, even though we do have homologous chromosomes (XY)? Is this a rare case of Klinefelter’s Syndrome? Explain, please!

  2. This question regards the genes themselves. Now, you may or may not know of the existence of introns, exons, and non-coding genes. The former and the latter serve no apparent purpose; they are merely garbled information, sequences of nitrogenous bases and nucleotides that make no sense. They don’t code for anything. NOTHING. There are no phenotypes corresponding to them. But they must be there for a reason. What is it? Why does our DNA contain segments that are not translated? Why is it that the mRNA that is utilized in the cytoplasm only contains codons corresponding to the information found on the exons? What do the introns and the non-coding genes (which, I hear are found between every single “coding” gene) do? Were they crucial for the survival of our unicellular ancestors? Are they there to stop the body from being “confused”? Please share your thoughts (I say thoughts because I hear there is no explanation to this as of yet)

Thank you in advance for your assistance,
ghady

2

  1. No idea whatsoever.

  2. The best explanation that my Biology 200 teacher has come up with is that not everything is there for a purpose. If it wasn’t evlutionarily unadvantageous for them to be there, there’s no reason for them to have been eliminated. It seems unlikely that they would have been useful to unicellular ancestors as the amount of non-coding genetic material is MUCH larger in eukaryotes than prokaryotes. Two more notes: my teacher suggested that especially transposons could have played a role in evolution, increasing variation and mutation, and second that either retroviruses arose from certain transposons (retrotransposons) or that retroviruses lost their vrial envelope and stayed in our DNA as retrotransposons.

Also, not all non-coding regions are useless. Areas that aren’t translated into mRNA often serve as gene promoters (ie, they indicate when and where transcription should begin). There is, in fact, information in the non-coding regions, it just isn’t the kind that needs to be transcribed.

3

I recently read a book (I think it was Blood Music by Greg Bear, but I could be wrong) where it was mentioned in passing by super-intelligent beings that DNA segments which do not code for proteins are actually a highly compressed form of genetic memory, dating from our earliest ancestors to our parents.

I thought it was an interesting bit in an even more interesting story, but it wasn’t explored in any depth.

4

Basically, the zygote would be an inviable tertraploid with a 2n number of around 100. When the gametes of diploid organisms undergo meiosis ia a gamete with n chromosomes. the two fuse, and a haploid zygote is formed. The DNA replicates to form paired chromosomes, and then begins dividing. If nondisjunction occured, the zygote would have doubled chromosomal mass and would spontaneously abort.

"They don’t code for anything. NOTHING. "

Wrong. They don’t code for anything we can figure out. I believe the current hypothesis is that they have both regulatory and structural functions that have simply yet to be discovered. For one, without introns, recombinant formation of unique antibodies would be near impossible, as there wouldn’t be any recombination in the V regions of the antibody operon.

It is also possible that they are responsible for differential morphology observed in the C-value paradox, i.e. why Amphiuma means and the pufferfish have such wildly different genome sizes and yet relatively similar physiological makeups.

5

Interesting related ranking

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6

As for question 1, while I don’t know the answer, I do know that some chromosomes act differently according to whether they come from the mother or father. They are distinguished by whether or not they are methylated. An example is a gene whose effect is to cause the mother to have elevated blood glucose level to the benefit to the fetus and the detriment of the mother. This gene is expressed only when it comes from the father. I have no idea if it is on the X chromosome, but it seems likely that there would be some problem with both the X and Y coming from the same parent.

As for question 2, current research is showing that these so-called non-coding regions, while not leading to the manufacture of proteins are still crucial. I believe the RNA itself has enzymatic action. That is apparently why they are conserved during evolution.

I speak not as a biologist, but as one who reads various science magazines.

7

See the November 2003 issue of Scientific American, the article titled “The Unseen Genome: Gems among the Junk”. The “noncoding” sections of DNA don’t transcribe into proteins, but they are read and transcribed into RNA that may have active biochemical functions. In addition, there may be a third level of information dispersed through the entire cellular mechanism.

8
  1. My WAG is that the offspring would be normal. It’s entirely possible that there are many people who have this genetic make-up and may never know it. However, there may be some problem with oocyte development if sex chromosomes are missing, for it appears that in most cases of sex-chromosme-related defects (according to some hasty Google searching), it is the sperm that is lacking a sex chromosome (i.e. in Turner’s syndrome) and not the egg.
  2. As others have stated above, the non-coding regions of the genome play a role in regulating gene expression (i.e. promoters), DNA replication (i.e. telomeres) and chromosomal structure. Additionally, the introns within the coding region of a gene can allow alternative splicing of mRNAs. One gene I studied could be spliced into at least four different mRNA isoforms, each encoding a protein with a different combination of functional domains. This is why the completion of the human genome sequence is only a very small step in understanding how our genes work- each of those full-length gene sequences may each be sub-divided into a myriad of other gene products with distinct activities.

chorpler: I love Greg Bear’s work, he works the hardest at making his science fiction seem plausible than most any other writer out there. And, the fact that his stories all have a biology bent and often take place in my former hometown of Seattle is a plus.

9

I had the same thought. The process is called imprinting, where activity of different genes are controlled by the methylation process Hari Seldon mentioned depending on which parent the chromosome came from. I don’t have a cite handy, but off the top of my head, I think that’s why it was so difficult to clone mammals; imprinted genes are evidently very important during development, and DNA from an adult cell lacks the proper imprints.

I don’t know if there are any important imprinted genes on the X chromosome, but my hunch would be no, since it can come from either parent. Someone with this genetype would probably develope more or less normally, but that’s just a guess.

10

I would like to reiterate that the zygote from 1) would NOT be viable and would spontanteously abort. There are no tetraploid humans.

11

Ilsa Lund: If I’m reading the OP correctly, he’s describing a union between a sperm with 22 autosomes + one X + one Y and an egg with 22 autosomes and no Xs. How would such a union result in a tetraploid? By my math, this gives you a zygote that is 2n for the autosomes plus an X and a Y= a genetically “normal” boy.

12

Ahhh, Okay. I misintepreted the OP as having two diploid gametes. I guess the offspring would be male, although the viability of the sperm would be highly suspect.

13

Question #1: You’d have a male offspring of questionable quality. I don’t know of specific genes on the sex chromosomes that are imprinted, but if imprinting occurs, the result of the unholy union you propose would be less than ideal.

Imprinting is simple in principle: for some genes, uniparental inheritance will not do. There is an excellent discussion of the topic here and another worth reading here.

If the X and Y chromosomes encoded entirely different genes without overlap, all the concern over imprinting might be much ado about nothing. However, as is explained here, pseudoautosomal regions exist on the X and Y chromosomes. Perhaps, some of the loci within the pseudoautosomal regions undergo imprinting. If so, then inheriting both an X and a Y from Dad would not be a good thing.

14

Allow me to correct my previous error. Haploid gametes of chromosome number n combine to form a diploid zygote, which replicate prior to first division.

15
  1. Why wouldn’t he just be a normal male? I don’t understand the significance of imprinting in this case.
16

Assume there are two genes A & B, both essential to normal development & life. Assume that these genes both undergo imprinting and are both encoded on the pseudoautosomal regions of the X and Y chromosomes. For simplicity’s sake, also assume that the X and Y chromosomes carry the same alleles of genes A & B.

Normally, baby gets one copy of A and one B from Mom, and one of each from Dad. That’s a darn good thing, too. Because of imprinting of Mom’s gene A, it doesn’t work in baby, though gene B works great. In Dad’s case, the situation is inversed; imprinting renders gene B inactive in baby, with gene A functioning. Since genes encode for proteins, in this scenario, all the gene A protein product is derived from paternal gene A, while all the gene B protein product is of maternal origin.

What happens when both gene A & B originate from Dad? Gene A is fine (though Baby gets a double dose-lets assume that that produces no bad effects) but gene B is completely inactive. The lack of gene B expression in this example is why the progeny is abnormal.

A noteable caveat, though, is that to my knowledge, no imprinted genes have been identified on the pseudoautosomal regions of the X and Y chromosomes. That doesn’t mean they don’t exist, but, if there were no imprinted genes, the baby should be OK.

17

There are cases of uniparental disomy resulting in births. Accoring to http://www.medgen.ubc.ca/wrobinson/mosaic/upd.htm , it was confirmed in 1980. So the answer to number 1 is yes, possibly.

18

Another point on question #2:
By having long strings of “useless” information (as far as we’ve determined), you also reduce the number of harmful mutations that can occur. When there is a greater amount of unused information, there is a greater probability of a mutation in that area, thus reducing the risk of mutations to the good stuff.

19

This doesn’t seem valid to me. You decrease the chance that any given mutation will affect something “important”, but it seems like you should also increase the chance of getting a mutation in the first place, and by the same factor. If you need a certain amount of encoding DNA, then the chance of a cosmic ray striking one of those important bits isn’t going to be any less, just because there’s another unimportant bit nearby.

20

Question #1:

Uniparental disomy (UPD) usually refers to isolated loci (only parts of the genome). Whole genome paternal uniparental disomy results in a complete hydatidiform mole. Whole genome maternal uniparental disomy results in ovarian teratomas. Neither of these are compatible with live births. UPD over a locus results in a number of conditions – Beckwith Wiedemann, Angelman, Prater Willi to name a few syndromes.

Complete nondisjunction in both the sperm and the oocyte would lead to complete tetraploidy. This has never been reported in the literature, although occasional tetraploidy is seen in cancer cells and the like. It is assumed that these would be spontaneously aborted early, and therefore never seen.

Whole genome complete triploidy is seen though, with a couple of reports of near-term stillbirths and even a few live births. It results in a highly misformed fetus with hydatid like growths on the placenta. This is presumably due to complete nondisjunction in either the sperm or the oocyte with normal fertilization.

Question #2:

I have just been through the run-around about the “junk DNA” question in the GD evolution vs. creation thread. I am getting a PhD right now by searching non-coding regions, and let me assure you that the vast majority of non-coding regions in vertebrates do absolutely nothing. We have a very good way of telling whether something is under functional constraint (whether it is needed in evolution), and most noncoding DNA is obviously not needed. There are estimated to be 1.4 million Alu repeats in the human genome, at around 300 basepairs per repeat. This is only one of many elements. Noncoding repetitive DNA accounts for over 40% of the human genome – these are simple repeats found throughout the genome. Yes, they may have some general structural role or may serve as “padding” to absorb mutagenic radiation and make the probability of hitting good DNA less. But the vast majority of it is remnants of retroviruses and just simple repeats that do absolutely nothing.

There are pieces that do have function – for instance regulatory regions, which we find more of these every year – but these are not the simple di- or tri-nucleotide repeats or dead retroviruses. There are functional genes hidden in the midst of megabases of repeats that are very difficult to work on because our current method of genome sequencing cannot assemble these pieces into the larger chromosome “contigs” due to the repeats. There are repetitive elements that have function, like centromeres and telomeres. I’m not talking about any of these, which make up a small percentage of non-coding DNA.

The vast majority freely evolves without functional constraint. Large insertions and deletions apparently cause no phenotypes. It is basically irrelevant.