Monday, December 14, 2020

DPBioY1 - 2020 - 3.1 Genes

DPBioY1 - 2020 - 3.1 Genes


2 marks for your questions
3 marks for your reply
2 marks for submitting on time

68 comments:

  1. 1. Can someone please explain genome sequencing techniques in an easier to understand way?
    2. Are there 23 or 46 chromosomes? I'm not sure of the terminology.
    3. Are alleles what are put on punnett squares?

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    1. For question 2, I am referring to in humans

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    2. For your 2nd question, in humans there are 23 pairs of chromosomes and 46 chromosomes in total.
      https://www.genome.gov/about-genomics/fact-sheets/Chromosomes-Fact-Sheet#:~:text=Humans%20have%2023%20pairs%20of,a%20set%20number%20of%20chromosomes.

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    3. For your third question, yes, alleles are used for the different boxes of a punnet square, which then reveal the possible allele combinations for offspring.

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    4. For your first question, basically they used gel electrophoresis to identify the nucleotides one at a time. These nucleotides were also unique, I am assuming by putting different markers on them such as found in the hershey and chase experiment.

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    5. In humans there are 46 chromosomes or 23 pairs of chromosomes.

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    6. There are 46 chromosomes within DNA

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    7. For your 3rd question, here is a website with details on how to use a punnett square:
      https://ib.bioninja.com.au/standard-level/topic-3-genetics/34-inheritance/punnett-grids.html

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  2. 1) Why is it called the locus of the chromosome?
    2) What are some examples of a harmful mutation?
    3) How many molecules are in plant genomes?

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    1. To answer your first question, it is called locus due to the fact that it is an exact location and is the latin word for location.

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    2. To answer your second question, some of the more common genetic mutations are sickle cell anemia, cystic fibrosis, and color blindness.

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    3. To answer your third question, plant genomes are really broad, ranging anywhere from 0.063 to 148.8 Gbp. There are very very few genomes that have been created larger than Gbp, and one of the larger ones that has been created us wheat. I apologize I am not able to give a more direct answer, there is an extremely large range of molecule number in plant genomes. Attached is a source going over a few different plant genomes, I hope this helps!

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895188/#:~:text=Plant%20genome%20sizes%20vary%20dramatically,%2C%202017b)%2C%20Ginkgo%20L.

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    4. For your third question, I found that there is no exact number for how many molecules are in a plant genome, but studies have reported that there are more than 40,000. It is proven that plants and humans share a large percentage of genes. Hope this helped :)

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  3. 1. What is an example of a trait which has a large number of possible alleles?
    2. Is there an easy way to distinguish between 'junk DNA' and coding DNA?
    3. What tools are used to see/record specific base sequences?

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    1. To answer your third question, They determine it now through disturbances in electrical current when running the DNA through small pores. It
      From genome.gov

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    2. To answer your first question, it appears that MHC molecules have the most alleles, having over 800 different alleles. MHC molecules that code for immune system cells.

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    3. To answer your second question, the main difference between coding and non coding is that coding code for proteins and non coding do not. Here is a resource. https://medlineplus.gov/genetics/understanding/basics/noncodingdna/

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  4. 1) What is the locus for the sickle cell anemia mutation?
    2) What can promote allele mutation?
    3) When reproducing can gametes have mutated alleles that cause issues?

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    1. Externally, ultraviolet light and carcinogens can cause mutations, but the occur naturally with error in replication, due to the instability of purines and pyrimidines
      https://www.ncbi.nlm.nih.gov/books/NBK21578/#:~:text=Mutations%20arise%20spontaneously%20at%20low,)%2C%20also%20can%20cause%20mutations.

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    2. Sickle Cell Anemia is found on Chromosome 11. It's exact location is 11p15.4.
      https://omim.org/entry/603903

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    3. To answer question 3, it is entirely possible for a gamete to be mutated during a time where it is able to reproduce with another, in which case that baby was extremely unlucky.

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  5. 1. How were scientists able to determine what part of the genome coded for what? And how did they determine which parts were non coding?
    2. How do alleles determine what is expressed? DO they code for proteins or is it something else?
    3. Are mutations normally dominant or recessive traits?

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    1. To answer your third question, it depends on the mutation. Recessive mutations result in loss of function. Reversely, dominant mutations result in gain of function.
      Source: https://www.ncbi.nlm.nih.gov/books/NBK21578/

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    2. To answer your second question, gene expression is determine by the combination of dominant and recessive alleles to display a certain trait. Alleles are apart of genes which are apart of your genome that codes for everything you are, including proteins. There is a website that goes into more detail, I hope this helps! https://sciencing.com/do-alleles-affect-inherited-traits-5178806.html

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    3. In response to question one, this website has a detailed description of how gene functions are discovered, involving a reporter gene and studying it's protein output.
      https://www.ncbi.nlm.nih.gov/books/NBK26818/#:~:text=Clues%20to%20gene%20function%20can,study%20with%20a%20reporter%20gene.

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  6. 1 - Are there any genes that can be messed up that won’t have a strong detrimental effect?
    2 - How were gene loci in chromosomes first discovered?
    3 - How are chromosomes organized?

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    1. In response to your third question, the way chromosomes are organized is that they are supercoiled to make them take up less space in the cell. It is organized into subunits of nucleosomes and the supercoiling will help with gene expression.

      https://www.nature.com/scitable/topicpage/chromosomes-14121320/#:~:text=Chromosomes%20are%20made%20up%20of,also%20helps%20regulate%20gene%20expression.

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    2. To answer your first question, there are mutations which are not harmful, these are called neutral mutations. Albinism is an example of a neutral mutation, which causes people's skin to drain pigmentation and eyes become red and have some light sensitivity.
      https://triplecrit.fandom.com/wiki/Neutral_Mutations

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    3. Loci weren't quite discovered because they aren't a specific piece of the molecule, but are a way or referring to location. As far as I can find, there was not an individual who created this system, but it is a product of different research which led to the locus system being created.

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  7. 1. What is the difference between satellite DNA and variable number tandem repeats?
    2. What exactly are SNPs?
    3. What are common mutations that are neutral?

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    1. In response to your third question, there are many common neutral mutations where the amino acids remain unchanged in the proteins encoded with the mutations. A few common examples of these neutral mutations would be rats being hairless, black bears becoming white haired, and humans being double jointed (although it can be argued that double jointed-ness is a negative mutation). Below are sources talking more about neutral mutations in general, I hope this helps!

      https://www.sciencedirect.com/science/article/pii/S0960982220304267
      https://flexbooks.ck12.org/cbook/ck-12-biology-flexbook-2.0/section/4.10/primary/lesson/mutation-effects-bio

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    2. SNP stands for a single nucleotide polymorphism. This is a variation at a single position in DNA sequence among individuals. If a SNP occurs in gene, then a gene is described as having more than one allele.

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    3. In response to your first question, variable number tandem repeats and satellite DNA are the are the same things, just with different names.

      http://www.bio.miami.edu/dana/dox/vntr.html

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  8. 1.What is an example of a polygenic gene?
    2. What scientists were behind the human genome project?
    3. How long does it take on average for an allele to develop?

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    1. To answer your second question, in the United States James Watson was the main scientist to lead the human genome project (the same Watson from Crick and Watson), later followed by Francis Collins. While often textbooks focus on the American scientists, the human genome project was a global effort that `brought together many different scientists from all over. John Sulston was a main leader on the UK side of the project. There were 6 main countries the contributing scientists came from, which were France, Germany, Japan, China, the UK and the US. Among those 6 countries were about 20 institutions that contributed to genome sequencing. In short, there were many, many different scientists who were behind the human genome project, some were just more recognizable than others. Below is a source going over who all was involved, I hope this helps!


      https://www.yourgenome.org/stories/who-was-involved-in-the-human-genome-project#:~:text=%E2%80%9CThe%20US%20side%20of%20the,and%20later%20by%20Francis%20Collins.

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    2. 3-I think it all just depends! I actually had a hard time finding an answer to this. I think it depends on the type of trait and factors like the environment. Like we were talking about, sometimes pigment takes longer to develop. Or there are many environmental factors that could speed or slow the development of the allele.

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  9. 1. How did the scientists all agree on how to divide the chromosomes during the original sequencing process?
    2. Which country contributed the most to the human genome project?
    3. Is it possible for allele's to develop later on in human life rather than towards the beginning somewhat soon after birth or towards the beginning of one's life?

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    1. To answer question 3, it would depend on the allele being represented. As discussed in class, Huntington's disease doesn't get expressed until fairly later in life, so it is definitely possible for alleles to be expressed later on.

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  10. For your third question, as we talked about in class today, Mrs Mullen had mentioned that typically babies are born with a grayish color eyes and later their eyes develop into a different color based on the allele. She had also mentioned that African American babies typically are born with a much lighter skin color and develop their pigmentation allele as they grow older.

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  11. To answer your second question, in the beginning in the US it was James Watson who began the human genome project, followed soon after by Francis Collins. As for the other countries China, France, Germany, Great Britain, Japan, and the United States were all involved in the genome project. Here is a source, hope it helps! https://www.yourgenome.org/stories/who-was-involved-in-the-human-genome-project

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  12. 1. Is there any one reason why certain alleles are dominant over others or why some can be co-dominant?
    2. How do mutations occur?
    3. What gene has the largest amount of possible alleles?

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    1. In response to your first question, there is no one reason that certain alleles are dominant over others. However, there are multiple reasons for the dominant trait. The first reason is that the recessive gene makes broken proteins that don't function as well and so are less useful. The second reason is that the body needs two good copies of a gene to work properly, otherwise it cannot produce enough of the protein needed for that part of the phenotype. Finally, the reason that some alleles can be co-dominant is that neither allele is recessive and both are dominant.

      https://genetics.thetech.org/ask/ask227#:~:text=The%20simplest%20situation%20of%20dominant,recessive%20allele%20is%20red%20hair.
      https://www.genome.gov/genetics-glossary/Codominance#:~:text=Codominance%20is%20a%20relationship%20between,an%20allele%2C%20from%20each%20parent.&text=In%20codominance%2C%20however%2C%20neither%20allele,of%20both%20alleles%20are%20expressed.

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    2. 3- MHC class 1 and 2 are the gene with the largest amount of possible alleles, having around 200 alleles.
      https://www.ncbi.nlm.nih.gov/books/NBK27156/#:~:text=There%20are%20more%20than%20200,high%20frequency%20in%20the%20population.

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  13. To answer your 2nd question, base substitution is what causes the mutation that produced sickle cell anemia. This is caused by a simple mistake that was made when mRNA was transcribed.
    Source: Bio Lecture 2/17 (also on managebac)

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  14. To answer your third question, the Human Genome Project took 13 years, from 1990-2003.
    Source: https://www.nature.com/scitable/topicpage/dna-sequencing-technologies-key-to-the-human-828/#:~:text=The%20Human%20Genome%20Project%20was,human%20genome%20within%2015%20years.

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  15. 1. Can mutated sickle cells scratch or poke small holes as they travel (or attempt to)?
    2. Does cystic fibrosis make you more susceptible or vulnerable to illness?
    3. A bunch of questions with this one. How does deep bleeding happen in the knees/ ankles/ elbows?? Why is this such a huge concern? What happens? (in relation to hemophilia)

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    1. 1- From my understanding of it, yes this can potentially happen. This morning Mrs. Mullen answered a question that I believe Anders may have asked. She said that unusual clotting can happen in people with sickle cell anemia, and it can potentially be painful because of the possibility of damage.

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    2. 2- Yes it can. This was also something we talked about this morning in class, Mrs. Mullen said that people with cystic fibrosis can be more susceptible to other illnesses.

      https://pubmed.ncbi.nlm.nih.gov/10431168/

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    3. To answer your third question, I found that in people with hemophilia type A, there are some severe circumstances where "spontaneous bleeding" occurs. This means that there are times of significant internal bleeding without a specific cause. And because there is an insufficient amount of clotting factors in people with hemophilia, their bodies are pretty helpless to stop it, and muscles, joints, and organs can be damaged. In areas like the knees/ankles/elbows, this is a concern because it can restrict movement and cause arthritis. Any bleeding to organs such as the brain and kidneys can also have concerning effects. I hope that this helped!
      https://rarediseases.org/rare-diseases/hemophilia-a/

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  16. 1) is there any type of treatment for hemophilia?
    2) What is a human genome made up of?
    3) How many genes are in humans?

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    1. 3: there are an estimate of 30,000 genes in human genome.
      https://www.genome.gov/human-genome-project/Completion-FAQ#:~:text=Each%20chromosome%20contains%20hundreds%20to,an%20average%20of%20three%20proteins.

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    2. to answer your third question, the researchers who explored the Human genome project found that there are between 20,000-25,000 genes in the human body.

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    3. 1- One of the only known treatments for hemophilia is a medical process of several injections called clotting factor concentrates. This form of treatment allows for replacement blood clot factor so the blood is effectively able to clot properly. For more information check this link:
      https://www.cdc.gov/ncbddd/hemophilia/treatment.html#:~:text=The%20best%20way%20to%20treat,concentrates%2C%20into%20a%20person's%20vein.

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    4. To answer your 1st question, here is a website with details on how, where, and what to do treat hemophilia:
      https://www.cdc.gov/ncbddd/hemophilia/treatment.html

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  17. 1- From what I understand, there is the Polymerase chain reaction (PCR) which is used to discover gene mutations.

    https://www.sciencedirect.com/science/article/pii/B9780128092521000031

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  18. 1. How many genes are in plant organism?
    2. How does sickle cell disease affect hemoglobin production?
    3. how do genes develop different in prokaryotic and eukaryotic?

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    2. to answer your second question, I found a website that talks about how people with sickle cell disease have atypical hemoglobin molecules called hemoglobin S, which causes the red blood cell to sickle.
      https://medlineplus.gov/genetics/condition/sickle-cell-disease/#:~:text=Sickle%20cell%20disease%20is%20a,sickle%20%2C%20or%20crescent%2C%20shape.

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    3. to answer your first question I found a website that talks about how there are more than 45,000 genes in plants from the research scientists have done
      https://pubmed.ncbi.nlm.nih.gov/17289424/

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  19. 1. Is there a treatment for sickle cell Anemia, or a cure?
    2. Which scientists worked on the human genome project?
    3. what technology did they use to discover how genes and gene mutations work?

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    1. question 1- a treatment with a potential cure is actually utilizing stem cell transplants in the bone marrow! There are sort of treatments for specific aspects of it. therapy preventing the mass clumping of hemoglobin, medications to improve symptoms, painkillers, and such.
      https://sicklecellanemianews.com/sickle-cell-disease-treatments/

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    2. To answer your first question, there isn't a set cure for adults with the disease, but treatments are mainly aimed at managing the pain and symptoms associated with sickle cell anemia. Stem cell transplants are a potential cure for younger patients with sickle cell anemia, but it is an invasive procedure with many risks. Medications for pain and blood transfusions are the most common routes. Blood transfusions increase the amount of normal red blood cells in the body, which can reduce the effects of the bad red blood cells. Penicillin is also often given to patients with the disease, in an effort to prevent infections that could be life-threatening to someone with mutated hemoglobin.
      https://www.mayoclinic.org/diseases-conditions/sickle-cell-anemia/diagnosis-treatment/drc-20355882

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    3. To answer your second question, there were so many scientists working on the Human Genome Project! It was a world-wide effort, in an effort to prevent bias, split up the daunting task, and compare results from a wide range of scientific perspectives. There were mainly scientists collaborating from 6 countries: the UK, the USA, France, Germany, Japan, and China, each country containing multiple centers and institutes facilitating these studies.
      https://www.yourgenome.org/stories/who-was-involved-in-the-human-genome-project

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  21. 1- I remember in class Mrs. Mullen mentioned the recognition process/ the check system. When it comes specifically to things like replication it is DNA Pol and RNA Pol.

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  22. 1) Does every cell contain all of the chromosomes? If so, how would genetic advancements work if changing the characteristic of one cell wouldn't change that sequence in all of the others? And can a mutation occur in the chromosomes of only one cell but not the others?
    2) What causes the hemoglobin in sickle cell anemia to stick together and form fibrous strands vs staying individual?
    3) Are there circumstances where alleles/mutations differ by more than a few bases? What happens if this occurs?

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  23. 1. How often does mutations occur in chromosomes and/or DNA
    2. What would happen if someone had less than 46 chromosomes in their DNA?
    3. What genetic conditions have a direct effect (negative or positive) on chromosomes and DNA?

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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