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CSB349H1 Lecture Notes - Lecture 2: Chromatin, Nucleolus, Ctcf

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yellowcattle940
29 Mar 2017
School
UTSG
Department
Cell and Systems Biology
Course
CSB349H1
Professor
Alan Moses

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Document Summary

Where do genes come from: they are already there, they are copied and diverge to become new genes. Gene duplication and divergence is a major source of new genes. The different hemoglobins have slightly different functions and different affinities for oxygen. Ancestrally, there was a single globin gene and that gene duplicated and diverged to give us variations. In the proteins: acquired subtle mutations that changed themselves biochemically, the different forms of globin then would have the different affinities for oxygen. Fetal and embryonic hemoglobin have more affinity for oxygen. Most genes probably diverge in their proteins and their gene expression. Hox gene: they originated through tandem duplications, all animals have an array of hox genes on the chromosome, throughout evolution, the entire cluster of hox genes duplicated over and over again. 2, 4, 6 hox gene clusters in animals: entire groups of genes can be duplicated so you end up with a tandem array of similar genes.

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Related Questions


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 ~80°C (175°F). It has adapted so that its enzymes are most functional at the elevated temperatures, compared with many organisms’ enzymes that function best ~37°C (98°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 “Central Dogma” 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 prokaryotes’ ability to “fix” 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 athlete’s foot, use ergosterol to maintain healthy membranes. Animal cells do not make ergosterol, they use a similar lipid – cholesterol.
9. During retrovirus infection, a DNA copy is made of the virus’s RNA genome. A cut is made in the host cell’s 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 (“70S” ribosomes) than eukaryotic cells (“80S” 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 cell’s 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 they’re 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:
• What types of infections can be treated with the following drugs?
o Penicillin
o Clotrimazole
o Azithromycin
o Tamiflu
o Raltegravir
• Why are these drugs (above) safe for you to take? That is, why don’t they kill your cells?
• 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?

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 Down’s 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 mother’s egg and 23 that are copies of the DNA father’s 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. Sun’s 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 “Women are just as hemizygous as men”. 8. After having 10 children you remarry…… 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 children…… 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).