“The Cell, Lokiarcharum, And RRNA”

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“The Cell, Lokiarcharum, and rRNA”

For your primary post, please respond to one of the following three topics with a post of at least 125 words that addresses each point given in the instructions. Also, please reply to at least one fellow student on any topic.

Topic 1

: Introduction to the Cell. Watch the Khan Academy video “Introduction to the cell” (1)* and then address the following issues.

  • (a) In the video, the narrator says that we might think that since cells are so small, that they must be simple, but “nothing could be further from the truth.” What did he mean by that?
  • (b) Describe features that are only found in eukaryotic (but not prokaryotic) cells.
  • (c) Did anything in this video surprise you, or was it mainly a recap of material you already knew?

Topic 2 [article]: Lokiarchaeum. Read about Lokiarcheum in the article by Yong (2)* and/or the article by Zimmer (3)*. Both articles describe recently discovered evidence about a previously unknown organism. Then, address the following issues:

  • (a) Lokiarchaeum may be a “transitional form” between archaea and eukarya. What evidence suggests this?
  • (b) Describe one way that this relates to this week’s lesson.
  • (c) Cite whichever article you use. If you use both, cite them both. There’s no particular reason why you should need any other source, but if you do use any other source, you must cite it, too.

Topic 3 [research]: Carl Woese. Carl Woese (b. 1928, d. 2012) worked out a new method for classifying organisms based on RNA from their ribosomes. This is called ribosomal RNA (rRNA). Research Carl Woese’s research on the Internet, and then address the following issues:

  • (a) Describe the basic logic of this Woese’s approach. In other words, how can you tell if two organisms are closely-related or distantly-related from their rRNA?
  • (b) Name one of Woese’s most important findings.
  • (c) Describe one way that this relates to this week’s lesson.
  • (d) Don’t forget to cite your source or sources!

References (in Strayer Writing Standards format).

  1. Khan Academy, November 29, 2017. Introduction to the cell,  https://www.youtube.com/watch?v=5KfHxF6Vhps
  2. Ed Yong, May 6, 2015. New Loki microbe is closest relative to all complex life,  http://phenomena.nationalgeographic.com/2015/05/06/new-loki-microbe-is-closest-relative-to-all-complex-life/
  3. Carl Zimmer, May 6, 2015, Under the sea, a missing link in the evolution of complex cells, http://www.nytimes.com/2015/05/07/science/under-the-sea-a-missing-link-in-the-evolution-of-complex-cells.html?_r=0
 
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Anatomy & Physiology Homework

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Dangerously Thin: A Case Study on the Genetic Code

At 65 years old, Henry Blake was in excellent health and enjoying his first year of retirement. Upon returning from his dream trip to the Great Barrier Reef in Australia, he noticed that his left leg was swollen just inferior to the knee. He already had scheduled an appointment for a complete physical, so he knew that in a few days he would be able to have his physician look at his leg.

Dr. Strickland had been the Blake family doctor for more than 40 years. Knowing that Henry had planned to do some traveling, Dr. Strickland opened with a question that Henry initially found to be a bit out of the ordinary.

“Any chance this swelling showed up after a long flight?”

“As a matter of fact it did,” Henry replied.

“My gut tells me that you may have a clot in that leg, but we’ll have to have a look at it before we’ll know for sure.”

Dr. Strickland knew that Henry’s family had a history of clotting disorders, and he had recently treated Henry’s brother for a deep vein thrombosis (DVT), a disorder that gets its name from the blood clots that form in a vein deep within the leg. A DVT was confirmed by the Doppler ultrasonography results (a test that uses sound to create images of blood flow). Dr. Strickland placed Henry on a “blood thinning” drug called warfarin, which works by preventing clots from forming.

Henry returned to his retirement plans but quickly found himself back in Dr. Strickland’s office after suffering from frequent nose bleeds. A laboratory test called an INR (International Normalized Ratio) was performed. This test measures the time it takes for blood to clot and compares it to an average. The test revealed that the time it took for Henry’s blood to clot was well above what would be expected for the dose of warfarin that he had been placed on. Dr. Strickland immediately took Henry off of his warfarin treatments and asked that he come in every three days for blood tests. Dr. Strickland became concerned when Henry’s abnormal INR results continued long after he had stopped taking warfarin.

Through genetic testing, Henry was found to carry a mutation in a gene for an enzyme called CYP2C9. While the strange name of the gene does not really fully appear to capture the importance of its function, it has a role in breaking down more than 15% of the drugs currently in use, and as many as 35% of people carry a slower acting form of this enzyme. The portion of Henry’s DNA that codes for the CYP2C9 enzyme contains more than 1,400 nucleotides. Henry carries two copies of the CYP2C9 gene, and the tests showed that both of them contain a mutation. On one of these genes, the 1075th nucleotide has been changed from an adenine (A) to a cytosine (C). This mutation converts an ATT triplet code in the coding strand of the DNA molecule to CTT. In Henry’s other CYP2C9 gene, the 430th nucleotide has been changed from a cytosine (C) to a thymine (T). The DNA triplet code CGT in the coding strand becomes TGT as a result of this mutation. Henry was considered a poor metabolizer (PM) because both of his CYP2C9 genes contained a mutation, and therefore he was not making any fully functional enzyme. People who carry two normal copies of the gene are referred to as extensive metabolizers (EM) for their ability to quickly break down drug molecules.

Short Answer Questions

1. Why would someone with this type of mutation be at a much higher risk for overdosing on a prescribed drug?

2. The underlying problem in this case resides in Henry’s “genes.” From what you know about the function of a gene, explain how this problem led to a malfunction in one of Henry’s proteins (the CYP2C9 enzyme).

3. The DNA changes that are described in Henry’s story are changes to the coding strands of the CYP2C9 genes. What is the function of the coding strand and how does it differ from the function of the template strand of Henry’s CYP2C9 gene?

4. Consider the following DNA sequence found on a different portion the coding strand of Henry’s CYP2C9 gene: TTACCGAGA

a. What would be the sequence of the template strand on this portion of the gene?

b. How many triplet codes does this DNA sequence contain?

c. What would be the sequence of the mRNA after this sequence is transcribed?

d. How many amino acids does this portion of Henry’s coding stand actually code for?

5. In the first mutation of the CYP2C9 gene described in Henry’s story, the 1075th nucleotide had changed from an adenine (A) to a cytosine (C). This mutation converts an ATT triplet code in the coding strand of the DNA molecule to CTT. Beginning with this triplet code on the DNA, describe the effect that this change would have on the following:

a. The nucleotide sequence on the template strand of the gene.

b. The mRNA codon that results after this triplet code is transcribed.

c. The anticodon on the tRNA molecule that is complementary to the mRNA codon described above.

d. The amino acid that would be carried by the tRNA molecule described above.

6. In Henry’s other CYP2C9 gene, the 430th nucleotide had changed from a cytosine (C) to a thymine (T). This mutation converts a CGT triplet code in the coding strand of the DNA molecule to TGT. Beginning with this triplet code on the DNA, describe the effect that this change would have on the following:

a. The nucleotide sequence on the template strand of the gene.

b. The mRNA codon that results after this triplet code is transcribed.

c. The anticodon on the tRNA molecule that is complementary to the mRNA codon described above.

d. The amino acid that would be carried by the tRNA molecule described above.

7. From what you understand about enzymes, explain why a change in an amino acid would cause Harry’s enzyme to lose its function.

8. In both of Henry’s mutations, it is the first nucleotide in the DNA triplet code that has been changed.

a. Using the genetic code chart below, create a list of single nucleotide changes in the two affected triplet codes described for Henry’s genes that could occur WITHOUT resulting in a change in the amino acid in the enzyme.

NOTE: The code chart below contains mRNA codons and the amino acids associated with those codons. Your list should contain DNA triplet codes.

image1.png

b. How many triplet code changes did you find that could occur WITHOUT resulting in an amino acid change in the enzyme?

c. Which position (first, second, or third) did the changes occur within the DNA triplet codes you listed above?

d. What would you conclude from the pattern that emerged?

 
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Biology Problem Set Homework

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BICD 110 Fall 2020, Dr. Kiger

Problem Set 8 Lectures 7A-7B

 

Microtubules

 

1. What statement best describes the basis for how/why microtubules are “tubes”?

 

___A. tubulin and tubulin assemble into small filament rings that stack into a tube

___B. tubulin dimers assemble into filaments that spiral into a tube

_X_C. tubulin dimers assemble into parallel protafilaments that fold into a tube

___D. MAPs bind and curve the tubulin dimers so that filament assembly forms a tube

___E. ATPase activity of kinesin motor proteins bends a sheet of protafilaments into a tube

 

2. What is a shared property of both actin and tubulin subunits with respect to microfilament and microtubule dynamics, respectively?

 

___A. predominantly added to filament/protofilament (+) ends.

___B. predominantly added to filament/protofilament (−) ends.

___C. equally efficient at being added to both ends of filament/protofilament.

___D. added along the length within an assembled filament/protofilament.

 

3. During dynamic instability of microtubules, within the tubule…

 

(i)…the -tubulin subunits: (ii)….the -tubulin subunits:

 

___A. undergo ATP hydrolysis ___A. undergo ATP hydrolysis

___B. undergo GTP hydrolysis ___B. undergo GTP hydrolysis

___C. remain locked in GDP bound state ___C. remain locked in GDP bound state

___D. remain locked in ADP bound state ___D. remain locked in ADP bound state

___E. remain locked in GTP bound state ___E. remain locked in GTP bound state

 

(iii) Compare and contrast the above properties of tubulin subunits in microtubule ‘dynamic instability’ to those of actin subunits with microfilament ‘treadmilling’, providing key details. What is similar? What is distinct?

 

 

 

 

 

 

 

4. Define ‘critical concentration’ (Cc) as it relates to microfilament and microtubule formation, as well as to the different ends of the polymers. Define steady state.

 

 

 

 

 

 

 

5. Fill in the blanks.

 

Microtubules are typically not static structures. _____Dynamic instability_____ is the phrase used to describe how a microtubule undergoes alternating periods of rapid growth and shrinkage, called _____rescue_______ and ______catastrophy_________, respectively. These dynamics occur with growth happening at the microtubule ____positive (+)_____ ends, since the ____negative (-)_____ ends are typically inaccessible while stabilized at the ______MTOC_______. At the microtubule minus-ends, you will invariably find the specific microtubule subunit, __________________, which directly interacts with another tubulin subunit, __________________ in -TuRC. Growing microtubule ends are normally stabilized by __________________ ‘caps,’ while ___GTP____ hydrolysis can lead to rapid disassembly.

6. Compare and contrast the proteins, -tubulin and formin (what do they do? how do they do it? where do they do what they do?).

 

 

 

 

 

 

 

 

 

 

 

 

7. Name and describe the organization and roles for the three different major classes of microtubules that contribute to mitosis.

 

Microtubules and Motor proteins

 

8. Motor proteins are what kinds of enzymes?

 

 

 

9. Draw and label a simple cartoon of the general protein domains found in common between the structures for different types of motor proteins. Indicate the ‘motor’ region and what specific types of proteins interact with the different protein domains.

 

 

 

 

 

 

 

 

 

10. Which of the following properties is not shared by all myosins? May be one or more than one answer.

 

___A. the ability to bind ATP

___B. the formation of homodimers

___C. the ability to bind F-actin

___D. the presence of a head domain

___E. the ability to do work

___F. the ability to bind G-actin

 

11. In the model for myosin movement on microfilaments, the power stroke occurs during:

 

___A. binding of ATP.

___B. hydrolysis of ATP.

___C. release of phosphate (Pi).

___D. release of ADP.

___E. the assembly of a myosin thick filament

 

12. Match the cell functions on the right with the specific motor (A-F) most likely involved. You may use an answer more than once or not at all.

 

A. Myosin I ________ Cilia movement

B. Myosin II ________ Cell contraction

C. Myosin V ________ Organelle and vesicle transport (>1 correct!)

D. Kinesin I ________ Microtuble plus-end directed sliding

E. Kinesin 5 ________ Microfilament to membrane tethering

F. Dynein ________ Microfilament plus-end directed vesicle transport

13. All of the following statements describe Kinesin I except:

 

___A. Kinesin I is a (−) end-directed motor.

___B. Kinesin I transports vesicles along microtubules.

___C. Kinesin I binds and hydrolyzes ATP to produce movement.

___D. Kinesin I is composed of two heavy chains and two light chains.

___E. Kinesin is a (+) end-directed motor.

 

14. With respect to motor protein function, specifically what effect would the addition of AMP-PNP (a non-hydrolyzable analog of ATP) have on axonal transport? Why?

 

 

 

 

 

 

 

 

15. You purify what appears (by protein sequence homology) to be an ATPase protein complex that is required in a cell free assay for endosome intracellular transport. You call it Endomytin. You want to determine if Endomytin acts as a motor protein, and if so, to characterize its motor properties. Name three basic criteria (properties or predictions about protein function) that you expect if Endomytin is a motor protein, AND how you would test Endomytin for each of these properties.

 

 

 

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Epigenetics Reaction Paper

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You will be writing a 1,000 word Reaction Paper in this course using the instructions and links found below. You will be completing the following tasks and gathering the following information for your paper:

  1. Watch the epigenetics video from PBS. Begin your paper by defining epigenetics in your own words and discussing your reaction to the video. (Here’s an additional link if the first link is not working – https://www.dailymotion.com/video/x1luqdj)
  2. Interview your family members and complete the Family History-Dr. Oz.pdf.  Find out which disease(s) you are most at risk for.
  3. Research and locate one article on epigenetics and whatever disease you are most at risk for (select a study on research conducted on humans) from a reputable academic source:

Reputable Sources:

  • journal articles
  • government publications based on research

Do not use:

  • magazines of any sort, whether they are on paper or online
  • Websites of any type, including epigenetics websites
  • Wikipedia

How to Perform Your Research

  • Use the College Library in person or online (log in with your new MDC ID number (the one that is all numbers). Your password is the last four digits of that same MDC ID unless you have changed it.

Read the epigenetics article you find. Continue your paper with a discussion of the epigenetics article. Be sure to paraphrase (put things in your own words) and be sure to cite the author(s) of the article you find using APA style (see the section below on using APA style). Aim for about a page for this part of your paper.

  1. Discuss the concept of epigenesis in light of your family history and the article you read. Aim for one page for this section of your paper.
  2. Complete the Living to 100 Questionnaires. Integrate your findings on the questionnaire into your discussion. Aim for another page.
  3. Discuss how you can improve your health and longevity in light of your findings in this questionnaire, your understanding of epigenetics, and your knowledge of your family history. This should be your final page.

You can go over or under a page for any of the sections of the paper as long as your total paper is 1,000 words not counting the references.

General Rules for an “A” Paper (check your paper against this list)

◻    1,000 words

◻    Original work; plagiarism free!!

◻    Double-spaced, 12-point font, 1-inch margins

◻    Covers all 6 tasks

◻    Spellchecked

◻    College-level grammar

◻    Cite your article APA style (author & year within body of paper; full reference at end)

◻    No abstract, no cover

◻    Place your name and reference number on the first page. Use page numbers.

 
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