Biology 3592A Chapter Notes - Chapter 3: Centromere, Pyrimidine, Kinetochore

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tealsea-lion742

18 Sep 2016

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Chapter 3 - human gene structure and function. Phenotype: observable traits that are the result of the expression of genetic information. Estimated 20,000 protein coding genes in the genome, but many genes can generate multiple products, which explains why we have more than 20,000 kinds of proteins in us (via alternative splicing, protein modification, proteins working together ) Proteome: the hundreds of thousands of proteins that can be encoded by the human genome. Genes tend to cluster on certain parts of chromosomes, sometimes in families. Many genes code for functional rnas (noncoding rnas or ncrnas) On autosomes, there are two copies of each gene - on the maternal and paternal chromosome. Usually both genes are expressed, but there are exceptions. Allelic imbalance: different levels of expression from the homologues, at most extreme only one homologue expresses its gene. The central dogma: dna -> rna -> protein.

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Discussion

Hi All - this week you will learn about DNA - the molecule of life! You may think that protein-coding genes are the most important, but results from the Human Genome Project revealed that only about 2% of our DNA codes for protein - so what about the rest of the "junk DNA" (or non-protein coding portion of the genome) - is it functionally important? Yes! Scientists are learning how "the non-protein-coding portion of the genome is of crucial functional importance: for normal development and physiology and for disease". I would like you to please choose a topic with regards to the non-protein coding portion of the genome (this will introduce you to gene regulation which we will cover in chapter 11) or you may also choose to write about a topic that describes a mutation in any protein that is involved in DNA replication, transcription, or translation (we did not talk about all of the enzymes involved in those processes). Please list your reputable source - this is worth 0.5 pt (even if you use one of my sources below) and tell me WHY you chose your topic (this is worth 1 pt.) please try to briefly explain your topic to the best of your knowledge - I don't expect you to write a lot of detail about your topic - it might be hard to understand (which you are welcome to comment on in your paragraph)!

Examples to choose from (but not limited to) include: noncoding RNAs (snRNAs, miRNAs, siRNAs, snoRNAs, piRNAs, lincRNAs) and RNA therapeutics:

LIST:

1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119351/ (Development of microRNA therapeutics is coming of age)

2. http://www.umassmed.edu/rti/ (RNA Therapeutics Institute)

3. http://www.genengnews.com/insight-and-intelligence/rna-based-therapeutics-and-vaccines/77900520/

4. http://genesdev.cshlp.org/content/26/21/2361.full (Biology of PIWI-Interacting RNAs: new insights into biogenesis and function inside and outside of germlines)

5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265212/ (PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression)

6. http://www.news-medical.net/news/20121203/microRNAs-play-an-important-role-during-embryonic-development.aspx

7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578617/ (the role of microRNAs in cell fate determination)

8. http://news.berkeley.edu/2017/01/13/scientists-reprogram-embryonic-stem-cells-to-expand-their-potential/

9. http://www.the-scientist.com/?articles.view/articleNo/40871/title/The-Second-Coming-of-RNAi/

10. http://web.mit.edu/newsoffice/2013/cardiac-development-needs-more-than-protein-coding-genes-0124.html (long non-coding RNA molecules)

11. http://www.alzforum.org/news/research-news/new-role-micrornas-torpedoes-sink-neurons(microRNAs)

12. http://ghr.nlm.nih.gov/condition/rothmund-thomson-syndrome (mutation in human helicase gene)

13. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633371/ (mutation in mitochondrial helicase gene called TWINKLE)

14. http://sfari.org/news-and-opinion/news/2013/in-autism-related-disorders-rna-turns-out-to-be-key (RNA topoisomerase)

15. http://ghr.nlm.nih.gov/gene/TERC (dyskeratosis congenita - mutations in the TERC gene - the RNA component of telomerase)

16. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853347/ (Top3beta is an RNA topoisomerase that works with Fragile X syndrome protein to promote synapse formation)

The following 3 articles discuss long non-coding RNAs - there are many examples in each article so you only need to talk about one example - not the whole article:

1. http://www.sciencedirect.com/science/article/pii/S2468054016300063 (mechanism of action and functional utility)

2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5084630/ (dysregulated expression in ovarian cancer)

3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736767/ (stem cells)

skyminnow948

Question 1

1 pts

Cystic fibrosis is caused by nonsense and missense mutations in the CFTR gene, which encodes for a chloride channel. You are studying cystic fibrosis patients to determine what mutation they possess in the CFTR gene. The difference between the mutant and wild type CFTR genes can be uncovered by examining the CFTR:

	DNA
	mRNA
	protein
	tRNA

Question 2

1 pts

You decide to identify the CFTR mutation by analyzing the genomic DNA of your patients compared to healthy individuals. You specifically are looking to see whether a specific 3' gene truncation has occurred in the patients. You will determine this using hybridization techniques with samples from healthy and CF patients. Which of the following will allow you to accomplish this?

	Using an RNA probe complementary to the region not removed by the truncation.
	Using an RNA probe complementary to the region removed by the truncation.
	Using an DNA probe complementary to the region not removed by the truncation.
	Using an DNA probe complementary to the region removed by the truncation.

Question 3

1 pts

You would like to ensure that this experiment (to determine whether patients have a specific CFTR gene truncation using hybridization) is properly controlled. Which of the following samples must you test?

	The genomic DNA of a healthy individual who does not have cystic fibrosis.
	The genome of a CFTR patient known to have the specific truncation you are trying to identify.
	The genome of a CFTR patient with a missense mutation but full length gene.
	The genome of a healthy individual married to a CFTR patient with the specific truncation you are trying to identify.
	The genome of a patient with muscular dystrophy, which can be due to a trucation in the dystrophin gene.

Question 4

1 pts

To conduct the hybridization experiment, you are trying to decide between using a DNA or RNA probe. Which would be ideal to use and why?

	As both are composed of nucleic acids, using either would result in identical results.
	An RNA probe because RNA has uracil bases.
	An RNA probe because it could also be used in a translation experiment.
	A DNA probe because it is more stable than RNA.
	A DNA probe because RNA cannot bind to DNA.

Question 5

1 pts

Which of the following will lower the Tm of a given DNA strand?

	Increasing the percentage of GC base pairs.
	Raising the pH of the solution from neutral to basic.
	Decreasing the buffer concentration from 50mM NaCl to 5mM NaCl.
	None of the above.

Question 6

1 pts

One step of the Hershey/Chase experiment involved blending the virus/cell mixture before centrifugation and probing the pellet for radioactivity. Why was the blending step necessary?

	To collect the bacteria at the bottom of the tube.
	To break open the bacteria to release the genome.
	To separate the bacteria from the bacteriophages.
	To be able to detect the radioactivity.

Question 7

1 pts

Imagine Hershey/Chase had used an RNA virus (genome composed of RNA) instead of a DNA virus in their experiment. Would radioactivity still have been found in the pellet?

	No, because only DNA can be labeled with radioactivity.
	No, because the RNA genome would not enter the bacteria upon infection.
	No, because while DNA and RNA nucleotides are similar, they are not identical.
	Yes, because DNA and RNA nucleotides are similar.
	Yes, because genome in any form (DNA, RNA, protein) would be labeled similarly.

Question 8

1 pts

Griffith and Avery's transformation experiments allowed us to identify that DNA is our genetic information. Which of the following scenarios would result in bacterial cells that are capable of killing mice upon injection?

	Heat killed non-virulent bacteria is added to a live virulent bacteria strain.
	Heat killed virulent bacteria is added to a heat killed non-virulent bacteria strain.
	A heat killed virulent bacteria that is treated with a nuclease, is then added to a non-virulent bacteria strain.
	Heat killed mouse cells are added to a non-virulent bacteria.

Question 9

1 pts

The human genome consists mostly of non-coding DNA. Which of the following are benefits of this?

	Random DNA mutations generally won't affect RNA and protein function.
	It is faster to duplicate the genome when these are present.
	The existence of introns can lead to multiple variations of proteins encoded by a single gene.
	It is unlikely transposons would exist in the genome if there was too much protein coding DNA.

Question 10

1 pts

Andrew Murray's sister, Andrea, is adding to her brother's work on chromosomes. She is using cells that are unable to synthesize adenine (âade) and histidine (âhis). The plasmid she is currently working with consists of an origin of replication and the Ade gene.

Following her transformation of the plasmid into her yeast, what media will the cells be plated on to select for cells that have picked up the plasmid?

	Media containing histidine
	Media containing adenine
	Media lacking adenine
	Media lacking histidine

tealcockroach755

1. What recent research has indicated that studying Down Syndrome may hold a key to cancer growth and slowing tumor growth? In your answer be sure to mention the DSCR1 gene, angiogenesis suppression, and why individuals with Downâs Syndrome rarely have solid tumor growth. 2. Select your favorite chromosome and list the following: Three disorders that are found on this chromosome, Indicate the type of disorder (dominant, recessive) and the type of numerical or structural aberration. 3. Assume that crossing over does not occur in the region of each chromosome that is associated with the centromere. You have 46 centromeric regions in each cell, 23 that are copies of the DNA in your motherâs egg and 23 that are copies of the DNA fatherâs sperm. a. For any given gamete, what is the probability that all the centromeric regions will be copies of the same ones that you received from your mother? b. It has been estimated that the average person is heterozygous for at least 2,000 protein forming genes. How many different kinds of gametes is it theoretically possible for each person to produce? c. Considering the maternal and paternal origin of the centromeric regions alone, how many different kinds of gametes can you produce? 4. Find a current article on Telomerase (within the last year). Summarize the article and answer the following: What is telomerase? Why is it viewed as the fountain of youth? Attach the abstract or the first page. 5. Promiscuous Sun Flower has five lovers, but she has decided that the only true father of her child can have her hand in marriage. Sunâs Blood type is A- her five suitors blood types are as follows: a. Maury AB+ b. Elmer O+ c. Willie A- d. Jiggs B- e. Cousin it B+ 6. What is the epigenome. Explain why the study of the epigenome may not follow normal Mendelian genetics 7. Explain what is meant by the statement âWomen are just as hemizygous as menâ. 8. After having 10 children you remarryâ¦â¦ What is the probability of you now having a boy and then a girl, and then a girl, and then a boy, and then a boy or a girl, and then a girl? You now have 16 childrenâ¦â¦ 9. The genetic code has four codons for the amino acid Valine (GUG, GUC, GUU, GUA). Organisms have evolved to use some codes more than other codes. Which of the valine codes would you expect to be preferentially used in the genome of an algae growing in a hot spring at Yellowstone Park? EXPLAIN your answer 10. You discovered a new virus that needs to be studied. You begin by digesting the virus with protease (an enzyme that completely digests all proteins) until only amino acids remain. You then determine that the base composition of the viral nucleic acid is 38% Cytosine, 35% Glycine, 15% Thymine, and 12 % Adenine. To which class could this virus belong? EXPLAIN YOUR ANSWER a. Single-stranded RNA Virus b. Double-stranded RNA Virus c. Single-stranded DNA Virus d. Double=stranded DNA Virus e. None of the above because there is not enough information given to make a guess. 11. Adenine is found in numerous biological molecules (for example, DNA, RNA, NADH, ATP). You are now asked to explain the evolution of adenine and at least 5 of these biological (Adenine containing) molecules and how they may have evolved (the order).

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Biology 3592A Chapter Notes - Chapter 3: Centromere, Pyrimidine, Kinetochore

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