Monday, December 14, 2020

DPBioY1 - 2020 - 3.2 Chromosomes

 DPBioY1 - 2020 - 3.2 Chromosomes


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3 marks for your reply
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63 comments:

  1. 1. Does having only one allele present a disadvantage in survival for prokaryotes?
    2. Are all extra/missing chromosome anomalies bad for the organism?
    3. Is it always a requirement for interbreeding species to have the same number of chromosomes?

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    1. To answer your second question, typically it is bad as it leads to a lower production of a specific protein. The only time this is not an issue is if only a single x chromosome is present as it would not affect the gender of the child.

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    2. To answer your third question, in mammals species can only breed with closely related animals that have the same number of chromosomes. In other groups it is possible however to breed different species together such as with frogs.
      Citation
      https://news.berkeley.edu/story_jump/with-interspecies-hybrids-it-makes-a-difference-whos-the-dad-and-whos-the-mom/

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    3. For your first question, If you mean an individual has only one allele of a certain gene, it can be a disadvantage depending on the gene. If someone only has one allele, and it's of a trait such as sickle cell anemia, then this will cause then lots of pain, but having one sickle cell allele and one healthy allele is better because they will still produce sickle cells, but they won't be as overwhelming as they would with only the sickle cell allele. If you mean as a whole species there is only one allele, that probably means that particular allele is the most advantageous to the that species.

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  2. 1. What are some ethical considerations with karyograms?
    2. Have there been any observed cases of chromosomes splitting or fusing in a population or individual?
    3. What are theorized origins of plasmids?

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    1. To answer your second question, it is believed that human chromosome 2 is actually the fusion of two chromosomes that our primate ancestor had.
      This article supports that claim: https://www.discovermagazine.com/the-sciences/the-mystery-of-the-missing-chromosome-with-a-special-guest-appearance-from-facebook-creationists
      This article denies that claim: https://www.icr.org/article/human-chromosome-2-fusion-never-happened/

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    2. In regards to your first question, I found that there are many ethical factors that would need to be considered. Many people believe that seeing genes and basing an abortion on thoses gene abnormalities is ethically wrong. There is also an ethical dilemma regarding gender, as thousands of female embryos are aborted simply because they are female. There are many different perspectives and ethical issues that need to be addressed concerning Karyograms.
      Here is the link:
      http://nandinibio.blogspot.com/2014/10/ethics-of-karyotyping.html

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    3. To answer your 3rd question, yes there are some theories as to how plasmids originated. One theory is that they evolved from primitive replicons.
      More information can be found here: https://pubmed.ncbi.nlm.nih.gov/9602285/

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  3. 1. What is the percentage of a CVS or amniocentesis going wrong and resulting in the death of the fetus?
    2. How the paternal and maternal alleles determined? How do they know which one is what?
    3. What organism has the smallest genome?

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    1. To answer your first question, it is extremely low and is between 1/1000 to 1/43000 depending on the source.

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    2. To answer your last question, the organism with the smallest genome observed is the Carsonella Ruddi which has just 182 genes, for reference humans have a round 20,000 to 25,000 genes. It is a symbiotic bacterium, here is a website that should explain in more detail. https://www.nature.com/news/2006/061009/full/news061009-10.html

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    3. To answer your second question, we know which allele is paternal and which is maternal based on genetic testing of every party involved. If specific traits are only found in one parent then we know which allele comes from which parent

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    4. 1-chances of a miscarriage are relatively low; there is a 1% risk in amniocentesis and a 1%-2% risk in CVS.

      https://www.essentialparent.com/lesson/diagnostic-tests-in-pregnancy-amniocentesis-and-cvs-explained-6182/

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  4. 1. How many plasmids do Prokaryotic cells typically have?
    2. Are there any organisms that have more chromosomes than humans?
    3. How does prokaryotic DNA stay protected?

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    1. To answer your first question, the number of plasmids in Prokaryotic cells vary greatly depending on the organism but you can find the “plasmid copy number” by observing the cell. Here is a website that should go into more detail. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839616/#idm139892270227104title

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    2. To answer your third question, the nucleoid region is protected along with the rest of the cell by the cell wall, which adds another layer for structure and protection. Here is a website that might help. https://courses.lumenlearning.com/boundless-biology/chapter/prokaryotic-cells/

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    3. To answer your second question, yes there are many organisms with more chromosomes. Humans have 23 pairs of chromsomes, whereas chimpanzees and hedgehogs have 24 pairs, pineapples have 25 pairs. There are many more, but those are a few examples

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    4. For the first question, I could not find a direct answer on how many plasmids are in prokaryotic cells, but I did find that there are more than 4,600 complete sequences of plasmids in bacteria, eukaryotes, and archaea.
      Hope this helped!
      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379921/#:~:text=With%20the%20revolution%20of%20sequencing,and%20eukaryotes%20have%20been%20determined.

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  5. 1- Since plasmids in bacteria hold DNA and are shareable , have scientists ever used them to cure, or help maintain any illnesses or genetic abnormalities?
    2- How close are scientists to being able to use genetic testing to pick which traits they want their children to have?
    3- How often are genetic abnormalities beneficial, or detrimental to an organisms health?

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    1. For your third question I found that due to the rate of mutation in humans, the percentage would be about 1/1000 beneficial mutations per individual per generation. Hope this helped :)
      http://www.cs.unc.edu/~plaisted/ce/genetics.html#:~:text=We%20note%20that%20the%20maximum,selective%20advantage%20of%20at%20most%20.

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    2. In response to your second question, I am not sure. I was only able to find timeline of what has occurred and the technology that has been invented. The main reason that there isn't much research on genetic engineering of embryos is because of the ethicality of it. There have been clinical trials of genetic engineering of adults who have sickle cell animeia or beta-thalassemia that have been successful thus far.

      https://www.synthego.com/learn/genome-engineering-history

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    3. For your third question, Yes plasmids are used primarily in gene therapy and proteins replication https://www.intechopen.com/books/plasmid/plasmids-as-genetic-tools-and-their-applications-in-ecology-and-evolution

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    4. In response to your first question, scientists have been recently researching the use of plasmids in developing cures or treatments for a few different illnesses, such as e. coli. Below is an article that explains the work currently being done really well, I hope this helps!

      https://www.contagionlive.com/view/researchers-discover-new-ways-plasmids-work-to-make-bacteria-more-resistant

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  6. 1. Is karyotyping the way that chromosomes are numbered?
    2. Can prokaryotes of the same species have different alleles?
    3. Is there a way to use plasmids to attack prokaryotes or can prokaryotes tell if a plasmid may be harmful.

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    1. For your first question, Karyotyping helps line up the chromosomes so that a sample of chromosomes can be given their assigned numbers. These numbers are assigned based on the size and centromere location of the chromosome. https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/13%3A_Modern_Understandings_of_Inheritance/13.1%3A_Chromosomal_Theory_and_Genetic_Linkage/13.1C%3A_Identification_of_Chromosomes_and_Karyotypes

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    2. 2- There is genetic variation within Prokaryotes due to transformation, conjugation, and transduction. As far as alleles, since prokaryotes only have one chromosomes that means it only has on allele for a certain gene.

      https://www.austincc.edu/rohde/CHP9&10.htm

      https://www.nature.com/scitable/topicpage/some-organisms-transmit-genetic-material-to-offspring-6524963/

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    3. 3- Certain plasmids, specifically Col plasmids, are plasmids that contain genes that can kill bacteria. They code for bacteriocins. It is not common for the plasmid to attack the host but it can to other prokaryotes.

      https://courses.lumenlearning.com/boundless-microbiology/chapter/plasmids/

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  7. 1.How can plasmid characteristics help scientific advancements?
    2.What is the rarest chromosomal abnormality? which chromosome does it affect?
    3.Which eukaryotes are not diploid organisms? how many chromosomes do they have?

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    1. To answer your 1st question, plasmid characteristics, such as their small size and ability to carry only 1 or 2 genes, help to make scientific advancements, like treating or curing diseases. They help because scientists can insert small amounts of DNA into other cells which then allow the cell to do what the scientists would like.
      More information can be found here: https://www.intechopen.com/books/plasmid/plasmids-as-genetic-tools-and-their-applications-in-ecology-and-evolution

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    2. To answer your 2nd question, though no abnormality has officially been named the rarest, an extremely rare chromosomal abnorality is distal trisomy 10q, in which the end of the q portion of the 10th chromosome appears three times instead of two.
      Source: https://rarediseases.org/rare-diseases/chromosome-10-distal-trisomy-10q/#:~:text=Chromosome%2010%2C%20distal%20trisomy%2010q%20is%20an%20extremely%20rare%20chromosomal,in%20cells%20of%20the%20body.

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    3. In response to your third question, a few examples on haploid organisms are most green algae and some fungi. An example is Chlamydomonas, a green algae, which have 17 chromosomes.

      https://biology.stackexchange.com/questions/56061/haploid-eukaryotes
      https://www.uniprot.org/proteomes/UP000006906#:~:text=Chlamydomonas%20reinhardtii%20is%20haploid%2C%20and,with%2014%2C000%20protein%2Dcoding%20genes.

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  8. 1. Is it possible for any chromosome to be copied three times, or does this only happen with certain chromosomes like 13?
    2. Is it possible for a prokaryotic cell to not have a plasmid after cell division? If so, what would that cell do without the plasmid?
    3. What type of genes do plasmids usually carry?

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    1. Question 3- Plasmids can have genes that aid in antibiotic resistance, reporter genes, and transgenes. I found an article that explains each of these kinds of genes :)

      https://sciencing.com/kinds-genes-plasmids-have-17096.html

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    2. In response to your second question, if a prokaryotic cell loses a plasmid during replication, it would most likely not have any notable changes outside of the genes the plasmid controlled. However, if the plasmid was essential to surviving the environment the bacteria was currently in, it would most likely die as a result.

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  9. 1) Have there been any changes to the X chromosome over time?
    2) Can the DNA contained in the placenta be different from the fetus?
    3) What do they stain the chromosomes with during Karyotyping?

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    1. Question 3- During Karyotyping scientists stain the chromosomes with a dye called Giemsa Dye. This is the kind that allows us to see the individual banding of the chromosomes.

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    2. To your first question, unlike the Y chromosome, the X chromosome has not changed much from when it evolved over a million years ago from autosomes. This article will be best for more information: https://www.nature.com/articles/s41598-020-58997-2#:~:text=Abstract,approximately%20180%20million%20years%20ago.&text=The%20results%20of%20our%20study,occurred%20throughout%20our%20evolutionary%20history.

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    3. In response to your second question, the DNA in the placenta and in the embryo both have the same base primary sequences, but the ultimate structure of the DNA itself is what can make them different. Below is a source that helped me answer this question, I hope this helps!

      https://news.yale.edu/2020/07/15/simple-twist-dna-determines-fate-placenta#:~:text=Although%20the%20primary%20sequences%20of,of%20DNA%2C%20N6%2Dmethyladenine.

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  10. 1) So how come the Y chromosome is said to disappear in 4.6 million years but the X chromosome does not?
    2) Are there any chromosomal abnormalities that don't have negative effects?
    3) How come not all Prokaryotic cells have Plasmids?

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    1. In response to your third question, the reason not all prokaryotes have plasmids is because plasmids divide separate of the cell. This means that plasmids divide on their own and there is not process to ensure that plasmids are divided between the daughter cells. So, plasmids aren't in all prokaryotes because there is no cell regulation for it.

      Textbook page 150

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    2. For your first question, the reason the Y chromosome is disappearing, is speculated to be because of a mutation- like how cancer is caused by a mutation in the DNA. This article has more information: https://www.theatlantic.com/science/archive/2019/12/men-lose-y-chromosomes-cells-they-age/603013/

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  11. Question 2- From what I have read, I understand that the DNA of the placenta and the fetus are the same.

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    1. Dang this was meant to be a response to Ari's Second question lol

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  12. 1. Can they extract DNA from cell older than the fetus?
    2. Is there anything with more chromosomes than a kiwi?
    3. How many times/ how long did it take for the modern karyograph to be done?

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    1. In response to your second question, yes. The highest chromosome count of an organism is 1,440 from the Ophioglossum reticulatum, or Adder's-tounge fern.

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    2. In response to your second question, there is, in fact, something with more chromosomes than the lovely little kiwi. There's a type of plant called the adder's tongue fern with a whole 720 pairs of chromosomes! Here's the link for your proof, hope this helped! :)

      https://www.guinnessworldrecords.com/world-records/most-chromosomes#:~:text=The%20organism%20with%20the%20highest,adder's%20tongue%20fern%20Ophioglossum%20reticulatum.

      https://biomysteries.wordpress.com/2013/08/25/largest-chromosome-number-of-ophioglossum/

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  13. For your first question, there has been a case of a man having two y chromosomes. It's called XYY syndrome, and is not very easy to find which causes misdiagnosis' or for it to be missed completely. It is not a big change in their behavior or physicality, but there's more information here: https://rarediseases.org/rare-diseases/xyy-syndrome/#:~:text=Males%20with%20XYY%20syndrome%20have,the%20sperm%20prior%20to%20conception.

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  14. In response to question 2, eukaryotic cells do not contain plasmids most likely due to the larger genotype they have when compared to prokaryotic cells, therefore, they wouldn't need DNA gained from their environment.

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  15. 1. What happens when someone has multiple different genetic disorders?
    2. What species of animal has the most similar DNA to humans?
    3. What other information can be gained from karyotypes outside of chromosome related disorders?

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    1. Chimpanzees and bonobos are the animals that the most genetically similar to humans

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    2. 3. From karyotypes we can know the amount of chromosomes, gender, presence of disorders, and we can analyze varying g-bands and compare organisms like with the DBQ.

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    3. 1. When researching this question, I found a new term that came up more frequently. Not all disorders are simply caused by a single gene mutation that results in a single symptom. Some disorders can be a result of mutations on multiple different genes and result in many complex symptoms. These are called multifactorial disorders and they can also be heavily influenced by environmental factors. Some illnesses that occur as result of multiple genetic mutations include breast cancer, diabetes, and Alzheimer's.
      https://www.medicinenet.com/genetic_disease/article.htm

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  16. 1. What genetic disorder is the most dangerous or fatal?
    2. Can genetic disorders develop, or are you just born with them?
    3. Are there any advantages organisms with more pairs of chromosomes have over those with less?

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    1. To answer your 1st question, cystic fibrosis is the most common fatal genetic disorder

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    2. To answer your 2nd question, genetic mutations can be caused by external environmental factors as well as heretically transferred genes. One example would be Type-2 Diabetes

      https://medlineplus.gov/genetics/understanding/mutationsanddisorders/complexdisorders/

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  17. 1. What is the most common genetic mutation
    2. Are there any beneficial genetic mutations?
    3. What are the most common causes of mutations?

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    1. 1. I believe the most common is Downs Syndrome followed by Cystic Fibrosis and Thalassemia.
      This site provides basic details as well as symptoms of the 7 most common genetic disorders: https://www.sonashomehealth.com/most-common-genetic-disorders/

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    2. 2. This question was actually pretty fun to research! Although much less frequent, there are beneficial genetic mutations that some lucky people experience. One genetic mutation can make getting type 2 diabetes 65% less likely despite being exposed to intense risk factors. An LRP5 mutation can significantly increase bone density and make it very difficult to break bones, even in very dangerous circumstances. There is a "protective" mutation that disables a gene and creates a sort of immunity from HIV. Beneficial mutations like this are being studied in hopes that one day medications can be invented that mimic these natural properties.
      https://www.pnas.org/content/113/10/2554
      https://www.goliath.com/random/8-super-cool-genetic-mutations-found-in-humans/
      There are also some beneficial mutations that we learned about in class. One largely beneficial mutation that most of us have today is the ability to digest lactose. This occurred because of one mutation that was passed down to future generations years ago and allowed a higher quality of living. The sickle-cell anemia mutation that has a connection to a higher resistance to malaria is also an example of a beneficial mutation.

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    3. 3. The most common type of gene mutation is base substitution (also known as a point mutation). This occurs when RNA Polymerase mistakenly adds the wrong base pair during the transcription process, or when DNA polymerase does this in the DNA replication process. This can result in an entirely different amino acid than what was intended for the coding gene or a sequence that no longer functions at all. Other means of genetic mutations include deletion (failure to add/copy the base), the production of two copies for one base (duplication), and insertion (the addition of one or more new bases to the sequence). All of these changes to the original gene can create mutations that are often more harmful or neutral than beneficial.
      https://www.nature.com/scitable/knowledge/library/mutations-are-the-raw-materials-of-evolution-17395346/

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  18. 1. Since plasmids have separate replication what determines the varying rate of that?
    2. When I was doing the gene comparison activity there were chunks of the sequences that would be a repeating N. Does this mean they don't know what it is yet? Is it noncoding?
    3. Are centromeres only purpose their use in division?

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  19. 1) Why do some foods have DNA, and what does this look like?
    2) If there are so many alleles, how do scientists know what is the base human genome and what is an allele?
    3) What are the benefits of having two copies of the same chromosome in eukaryotes vs having one copy in prokaryotes?

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  20. Well prokaryotic organisms have way less DNA compared to eukaryotes, especially humans. Another thing to consider is that on karyotypes when you look at those similarities you are looking at the supercoiled chromosomes. Prokaryotes do not supercoil or create chromosomes so you wouldn't be able to compare them in the same way.

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DPBioY1 - 2020 - 2.9 & 8.3 Photosynthesis

DPBioY1 - 2020 - 2.9 & 8.3 Photosynthesis  2 marks for your questions 3 marks for your reply 2 marks for submitting on time