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erinhornet258Lv1

28 Sep 2019

Please read the New York Times article from May 21, 2010: Researchers say they created a âsynthetic cell,â by Nicholas Wade. http://www.nytimes.com/2010/05/21/science/21cell.html

Then, think about what you would do if you were going to engineer a new type of bacterial cell, with a genome that you could assemble from bits and pieces of other organismsâ genomes. What problems could you solve?

NOTE: This is a thought experiment only; you donât need to do hours of Internet research to answer these questions.

1.If you were going to create a bacterial cell from scratch, what product/function/process would you want it to carry out? Why do you think this is an important process?

2.You know that DNA codes for RNA, and (most) RNAs code for proteins, and that (for the most part) proteins carry out the important functions of the cell. For your âsynthetic cell,â where would you get the genes that would enable you to target your synthetic bacteria to the process you described in #1?

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Elin HesselLv2

28 Sep 2019

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After working through the macromolecules in your friendâs extremely pale burrito, you look at her and think you might have an idea about what is going on. You ask Maria, âDo you usually eat like this?â âYup,â she says, âI love all the carbs, rice, and bread, as well as cheese. Sometimes I eat a piece of fruit or some carrot sticks. And energy drinks!â You then point out to your friend that she seems to be getting very little protein, a major class of macromolecules. But she is getting plenty of carbohydrates and lipids in the form of animal fats.

1. While your body can convert the monomers of macromolecules from one to the other, it has to have the raw materials in the form of the appropriate atoms. You explain to your friend that when she eats proteins, they are broken down into amino acids through the process of INSERT ANSWER and can then be rebuilt into new proteins through the process of INSERT ANSWER.

a. If your body does not take in protein, but only carbohydrates and lipids, what atoms will it be missing? Hint: There are two, and you can figure this out by comparing the structures of the monomers for proteins and carbohydrates as well as the basic structure of lipids. INSERT ANSWER

b. For the above atoms, how many electrons are in the outer shell? INSERT ANSWER

c. For the above atoms, what type of bond will they make within the amino acid monomer? INSERT ANSWER

d. Even if your friend does obtain the correct atoms, there are still a couple amino acids that your body cannot manufacture from scratch, but must be ingested. What are these amino acids? INSERT ANSWER

e.Why might a lack of protein or the wrong types of proteins lead to your friendâs fatigue? INSERT ANSWER

Class 6: Viruses (and Cells, continued)

Making connections: viruses and microbes Match the cell biology concept (on page 1) with an important application of that concept (on page 2). Then answer the follow-up questions at the bottom of page 2.

Cell Biology concepts
1. Bacteria that cannot construct new cell wall material become fragile and break down.
2. During influenza infection, the viral enzyme neuraminidase is required to release new viruses from the host cell in which they were made. Once released, the new viruses can infect many additional cells.
3. Thermus aquaticus is a bacterium found in hot springs and can live at temperatures up to ~80Â°C (175Â°F). It has adapted so that its enzymes are most functional at the elevated temperatures, compared with many organismsâ enzymes that function best ~37Â°C (98Â°F).
4. Until the isolation and investigation of retroviruses, scientists thought that RNA could be copied from DNA, but DNA could not be copied from RNA. Research on this class of viruses led to an update to this âCentral Dogmaâ of biology.
5. Some bacteria have adapted, so that the enzymes involved in making cell wall materials have a slightly different shape and can no longer be bound by certain drugs.
6. Rhizobia are bacteria that colonize the roots of certain plants (legumes, including beans and peas). The host plant benefits from the prokaryotesâ ability to âfixâ nitrogen, converting N2 from the atmosphere into a form that is usable by the plant.
7. Many species of bacteria contain the enzyme cellulase. More than 10 billion such bacteria and other symbiotic microbes may be found in a single milliliter of material from inside the digestive system of ruminant mammals.
8. Fungi, including those that cause athleteâs foot, use ergosterol to maintain healthy membranes. Animal cells do not make ergosterol, they use a similar lipid â cholesterol.
9. During retrovirus infection, a DNA copy is made of the virusâs RNA genome. A cut is made in the host cellâs DNA and the DNA copy of the viral genome is pasted into the host chromosome by a viral enzyme called integrase.
10. Prokaryotic cells contain smaller ribosomes (â70Sâ ribosomes) than eukaryotic cells (â80Sâ ribosomes). Both types of ribosomes synthesize proteins, but the macromolecules they use to do it are somewhat different.

2
Applications
_______ Oseltamivir, also called Tamiflu, binds and inhibits the viral protein neuraminidase.
_______ Clotrimazole is a drug that is used to treat certain infections. It interferes with synthesis of ergosterol, a lipid involved in phospholipid membranes.
_______ Penicillin is a drug that interferes with synthesis of peptidoglycans (these are biological molecules that are part protein and part carbohydrate) that are present in certain cell walls.
_______ HIV is often treated with several drugs that inhibit different parts of the viral replicative cycle. Raltegravir is an example of a drug that interferes with the integration of viral genes into the host cellâs chromosome.
_______ Cows, like other vertebrates, lack the ability to breakdown cellulose. Yet they are able to live on a diet of grass and other vegetation high in cellulose.
_______ Enzymes isolated from extremophiles have been very useful in laboratory research. For example, Taq polymerase facilitates PCR, a revolutionary technique for production of DNAs of particular sequences, which requires cycling reactions through high temperatures.
_______ Plants and animals require nitrogen to make biological macromolecules, however theyâre unable to convert atmospheric nitrogen (N2) into a biologically useful form.
_______ Azithromycin is a drug that binds to 70S ribosomes and blocks synthesis of any new proteins.
_______ Methicillin-Resistant Staphylococcus aureus (MRSA) can cause life-threatening infections of the skin and bloodstream. One of the reasons MRSA infections are so serious is that they are resistant to treatment by many antibiotics, including methicillin and penicillin.
_______ The enzyme reverse transcriptase, isolated from retroviruses, is an important tool in molecular biology research. Scientists interested in learning what genes are turned on in particular cells use it to make DNA copies of RNAs they are studying (The DNA copies are useful because they are more stable).

When you have completed the matching activity, answer these follow-up questions:
â¢ What types of infections can be treated with the following drugs?
o Penicillin
o Clotrimazole
o Azithromycin
o Tamiflu
o Raltegravir
â¢ Why are these drugs (above) safe for you to take? That is, why donât they kill your cells?
â¢ Cancer cells are your own human cells that have become deregulated so that they divide and pile up in an uncontrolled way. Many chemotherapy drugs treat cancer by interfering with cell division and other cell processes.
o Why are there so many more side effects for individuals undergoing chemotherapy than for individuals taking antibiotics?

*Please don't answer with photos, DO NOT UPLOAD PHOTO, it's hard to read.

I post this question twice, please don't answer this post if you already answer the other one, if you can answer different answer that's fine. REASON WHY I POST IT TWICE, I NEED TWO DIFFERENT VIEW.

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)