BIOL 243 Lecture Notes - Lecture 1: Non-Coding Rna, Heredity, Chaperone Dnaj

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whitecamel498

17 May 2016

School

University of Calgary

Department

Biology

Course

BIOL 243

Professor

Gordon Chua

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Document Summary

Molecular genetics studies the function of genes (+ their alleles) and proteins. We observe their mechanisms - how they work, how they are passed on, and how variation ends up occurring. Genes are sequences of dna that act as the functional unit of genetic heredity and it"s resulting variation. Variations of each gene are called alleles, and variation results in diverse phenotypic traits. The genome is the entire set of dna, which contains all of the information required to build an organism (this is what"s found in genetic sequencing). Example: for a gene eye color, one allele codes for blue eyes while another allele codes for green eyes. The gene doesn"t code for the phenotype, but for the rna. Genes get transcribed to mrna, then mrna translates the information into proteins. Coding dna, all other rna is non-coding rna. Recall genotype refers to the specific genes inherited and phenotype refers to the resulting visible traits.

Related Questions

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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

Cystic fibrosis is caused by mutations in the CFTR gene, whichencodes for a chloride channel. You are studying cystic fibrosispatients to determine what mutation they possess in the CFTR gene.The difference between the mutant and wild type CFTR genes can beuncovered by examining the CFTR:

(1 point - partial possible)

DNA

mRNA

protein

You decide to identify the CFTR mutation by analyzing thegenomic DNA of your patients compared to genomic DNA of healthyindividuals. You specifically are looking to see whether a specificgene truncation has occurred in the patients. You will determinethis using hybridization techniques. Which of the following willallow you to accomplish this?

(1 point - partial possible)

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

Using an RNA probe complementary to the region removed by thetruncation.

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

Using an DNA probe complementary to the region removed by thetruncation.

You would like to ensure that this experiment (to determinewhether patients have a specific CFTR gen truncation usinghybridization) is properly controlled. Which of the followingsamples must you include?

(1 point - partial possible)

The genome of a healthy individual who does not have CFTR.

The genome of a CFTR patient known to have the specifictruncation you are trying to identify.

The genome of a CFTR patient with a point mutation in a separateregion of the gene but without the disease truncation.

The genome of a healthy individual married to a CFTR patientwith the specific truncation you are trying to identify.

The genome of a patient with muscular dystrophy, which can bedue to a trucation in the dystrophin gene.

To conduct the hybridization experiment, you are trying todecide between using a DNA or RNA probe. Which would be a betterchoice and why?

(1 point)

An RNA probe because RNA has uracil bases.

An RNA probe because it could also be used in a translationexperiment.

A DNA probe because it is more stable than RNA.

A DNA probe because RNA cannot bind to DNA.

Which of the following will lower the Tm of a given DNAstrand?

(1 point - partial possible)

Increasing the percentage of GC base pairs.

Raising the pH of the solution from extremely acidic toneutral.

Decreasing the salt concentration in the DNA solution from 50mMNaCl to 5mM NaCl.

None of the above.

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

(1 point)

A.No, because only DNA can be labeled with radioactivity.

B.No, because the RNA genome would not enter the bacteria uponinfection.

C. No, because while DNA and RNA nucleotides are similar, theyare not identical.

D. Yes, because DNA and RNA nucleotides are similar.

Griffith and Avery's transformation experiments allowed us toidentify that DNA is our genetic information. Which of thefollowing scenarios would result in bacterial cells that arecapable of killing mice upon injection?

(1 point - partial possible)

A. Heat killed non-virulent bacteria is added to a live virulentbacteria strain.

B. Heat killed virulent bacteria is added to a heat killednon-virulent bacteria strain.

C. A heat killed virulent bacteria that is treated with anuclease, is then added to a non-virulent bacteria strain.

D.Heat killed mouse cells are added to a non-virulentbacteria.

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

(1 point - partial possible)

A. Random DNA mutations generally won't affect RNA and proteinfunction.

B. It is faster to duplicate the genome when these arepresent.

C. The existence of introns can lead to multiple variations ofproteins encoded by a single gene.

D. Abundant non-coding genome is a protective feature againstthe consequences of transposition of mobile elements.

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BIOL 243 Lecture Notes - Lecture 1: Non-Coding Rna, Heredity, Chaperone Dnaj

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