Biology 2 Chromosome Structure & Karyotyping PDF

Subject Code: Biology 2 Learning Guide Code: 7.0 Chromosome Structure & Karyotyping Lesson Code: 7.1 Chromosome Structure & Karyotyping Time Frame: 60 minutes (2 sessions)...

Subject Code: Biology 2 Learning Guide Code: 7.0 Chromosome Structure & Karyotyping Lesson Code: 7.1 Chromosome Structure & Karyotyping Time Frame: 60 minutes (2 sessions) Actual Time Component Task Time allocation Allocation Target Know the objectives. Hook Engage in the topic. 30 mins (Session 1) Ignite Comprehend the lesson. Perform the Navigate 30 mins (Session 2) karyotyping activity Knot Take the assessment. MATERIALS NEEDED To complete this learning guide, you need the following: 1. pen; 2. paper; 3. phone/tablet/laptop; 4. stable internet connection; 5. scissors; and 6. glue/tape. TARGET After completing this module, you are expected to: 1. describe the levels of DNA packing in a chromosome; 2. determine the significance of karyotyping in genetics; and 3. demonstrate how karyotypes are analyzed and used in the detection of chromosomal abnormalities and its associated disorders through paper cut-and-paste simulation. HOOK Do you like to travel? When travelling, are you a heavy or a light packer? How do you pack your things? One of the best and common ways that people used to efficiently pack clothes in a suitcase is the rolling technique as seen in Figure 1, because it certainly maximizes the space in your suitcase. Figure 1. Rolling clothes to pack it in a suitcase. From “Here Are the Three Best Ways to Pack a Suitcase,” by D. Revel, n.d. (https://www.travelchannel.com/roam-blog/news-deals/here-are-the- 3-best-ways-to-pack-a-suitcase). In the public domain. PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 1 of 17  Have you ever wondered how the DNA that is about 2 meters long fits in the 5-8 μm nucleus? Suggest a strategy by which the DNA was successfully enclosed inside the nucleus. From “ Sticky Note Clip Art,” by Ocal, 2011 (http://www.clker.com/clipart-sticky-note-2.html). In the public domain. In this learning guide, you will discover how the DNA is packed into chromosomal structures and the significance of this packaging. You will also learn what is karyotyping and assume to be a cytogeneticist to predict the developmental condition of newborn babies through analyzing their karyotypes. IGNITE Instructions needed to make and maintain a living organism is stored within every living cell in the information containing elements called genes. As shown in Figure 2, genes are sequences of DNA or RNA found in the nuclei of eukaryotic cells. Each chromosome contains many genes used to create proteins that play a central role in a variety of biological processes. Deoxyribonucleic acid (DNA) is the genetic material of all living things from unicellular to multicellular organisms. Since DNA directs all the cellular activities, it is considered as the blueprint of life, therefore, this blueprint must be inherited by all of the progenies of a parent cell (Cooper & Hausman, 2007). Figure 2. Genes are segments of DNA that constitute a chromosome. From “Slide show: How genetic disorders are inherited,” by Mayo Foundation for Medical Education and Research, 2020 (https://www.mayoclinic.org/tests-procedures/genetic-testing/multimedia/genetic-disorders/sls- 20076216) From the previous lesson, you have learned that the cell cycle has one main goal and that is to accurately copy the vast amount of DNA in the chromosomes and then segregate it into new daughter PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 2 of 17 cells for reproduction and continuity of life. The daughter cells must be genetically identical thus it requires that each cell receives a complete copy of the entire genome (complete set of DNA). The size of the genome varies in organisms. A human cell contains DNA which measures about two (2) meters in total length. This must be contained within a nucleus with a diameter of less than 10 μm (Griffiths et al., 2005; Lodish et al., 2016). It can be compared to fitting a 2 km thread in a pea that is 1 cm in diameter. Hence, if all of the DNA in a human body from all of its cells are unraveled, its length would be 50 times the distance from the earth to the sun (Griffiths et al., 2005). THINK IT OVER How are these instructions physically organized so that the enormous amount of information required for the development and maintenance of even the simplest organism can be contained within the tiny space of a cell? Structure of Eukaryotic Chromosomes The double stranded DNA molecules of eukaryotes are packaged into particular number chromosomes inside a cell. The DNA is packed into 46 chromosomes for a human cell. The key to the efficient packaging of DNA into chromosomes is the establishment of an increasing level of organizations between the DNA and the specialized proteins that bind to it as illustrated in Figure 3. Specific molecular mechanisms ensure that though the DNA is heavily compacted, it remains accessible to all of the enzymes and other proteins that act on it while preventing it from becoming tangled and unmanageable (Alberts et al., 2014). Chromosomal Levels of Organization Figure 3. DNA organization into chromosomes. Adapted from Concepts of Genetics (10th edition, p. 302) by W. S. Klug, M. R. Cummings, C. A. Spencer, M. A. Palladino, 2012, San Francisco, California, USA: Pearson Education Inc. © 2012 by the Pearson Education Inc. PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 3 of 17  DNA - Each chromosome consists of a single long molecule of DNA. Nucleosome – is the basic unit of chromatin structure. DNA extracted from a nucleus and treated with varying salt concentrations appears like “beads on a string” under the electron microscope. The “string” is composed of free DNA called “linker” DNA connecting the bead-like structure which are the nucleosomes (Griffiths et al., 2005). Nucleosome is consisting of the DNA and a core of chromosomal proteins called histones. Histones is a family of small, positively charged proteins thus it is capable of interacting with a negatively charged DNA (Lodish et al., 2016). There are five major types of histone proteins termed H1, H2A, H2B, H3, and H4. Nucleosomes are formed when the DNA makes a 1.7 (147 bp) turn around an octamer core composed of two units of each histones H2A, H2B, H3, and H4 (Alberts et al., 2014). This winding of DNA onto histone acts somewhat like spools achieving the first level of packaging. 30-nm chromatin fiber – When nucleosomes are further packed on tip of one another, it generates a 30-nm diameter chromatin fiber initially called solenoid (Klug, Cummings, Spencer, & Palladino, 2012). This second level of coiling is achieved by the assistance of H1 histones. H1 is bound to the DNA as it enters and exits the nucleosome. It runs down the center of the structure pulling adjacent nucleosomes together into a regular repeating array. The solenoids that are arranged in loops are attached to a nonhistone protein called scaffolds. Along the DNA are special regions called scaffold attachment regions (SARs) where the scaffold binds. This mechanism is responsible for the additional supercoiling of the DNA into succeeding levels of organization 300-nm chromatin fiber - During prophase of mitosis, chromosomes need to condense into structures of much greater width and decrease in length several fold generating the condensed chromosomes observed during metaphase. Therefore, the 30-nm structures should be further folded into a series of looped domains producing a more compact structure of chromatin fiber that is 300-nm in diameter. Chromatid – The 300-nm chromatin fiber coils further to form one of the longitudinal subunits of the metaphase chromosome which is the chromatid that is 700-nm in diameter. The DNA assumes this particular organization during cell division. This highly condensed structure during mitosis reverts back to its decondensed and uncoiled state (chromatin) as it enters the interphase of the cell cycle after chromosome separation and cell division. As it progresses into the cell cycle, these chromatins that are dispersed throughout the nucleus become visible chromosomes once again. THINK IT OVER Why are chromosomes not condensed all throughout the cell cycle? PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 4 of 17  Go to the following links to better understand the role of chromosomes and visualize the process of DNA packaging. https://www.youtube.com/watch?v=IePMXxQ-KWY https://www.youtube.com/watch?time_continue=7&v=gbSIBhFwQ4s&feature=emb_logo Karyotyping Karyotyping is the process of sorting and identifying chromosomes to detect changes in its shape, size, and gene positions (Shemilt et al., 2015). There are two types of chromosomes in eukaryotes. These are autosomes and sex chromosomes. Autosomes are any chromosomes that are not sex chromosomes. As its name implies, sex chromosomes are chromosomes responsible in determining the sex of an organism which could either be of two kinds, an X or Y chromosome. In particular, humans have 46 chromosomes on its somatic cells where 22 of the pairs are autosomes while the 23rd pair is the sex chromosomes. Karyotype is an ordered display or diagram of the full set of an organism’s chromosomes arranged in homologous pairs (two chromosomes except sex chromosomes with identical features i.e. length and centromere placement) with respect to size, shape, number, and banding pattern. Analysis of karyotypes allow the determination of the sex of an organism and the detection of chromosomal abnormalities that are associated with some inherited defects such as diseases and with certain types of cancer (Alberts et al., 2014). Through comparison of karyotypes, one would obtain information about the genetic condition of a person. Take for example the karyotypes displayed below. Figure 4 shows the karyotypes of a normal male and female. On the other hand, it can be seen that there is an extra sex chromosome in one karyotype and a missing sex chromosome in another karyotype displayed in Figure 5. Figure 4. Traditional human karyotypes of (a) normal female and (b) normal male. Adapted from Concepts of Genetics (10th edition, p. 180) by W. S. Klug, M. R. Cummings, C. A. Spencer, M. A. Palladino, 2012, San Francisco, California, USA: Pearson Education Inc. © 2012 by the Pearson Education Inc. PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 5 of 17 Figure 5. Karyotypes of individuals with (a) 47 chromosomes and (b) 45 chromosomes. Adapted from Concepts of Genetics (10th edition, p. 181) by W. S. Klug, M. R. Cummings, C. A. Spencer, M. A. Palladino, 2012, San Francisco, California, USA: Pearson Education Inc. © 2012 by the Pearson Education Inc. An extra, missing, or defective chromosome would significantly influence the growth and development of organisms particularly humans. Two of the human abnormalities characterized by aberrant chromosomes are Klinefelter syndrome (47, XXY) and Turner syndrome (45, X). The karyotypes of individuals with the said abnormalities are reflected in the images above. Individuals with Klinefelter syndrome have ambiguous sexual development, referred to as intersexuality. They are generally tall and have long arms and legs and large hands and feet. They usually have genitalia and internal ducts that are male, but their testes are rudimentary and fail to produce sperm. At the same time, feminine sexual development is not entirely suppressed. In Turner syndrome, the affected individual has female external genitalia and internal ducts, but the ovaries are rudimentary. Other characteristic abnormalities include short stature, cognitive impairment, skin folds on the back of the neck, and underdeveloped breasts. More information about disorders associated with chromosome abnormalities will be given in the next lessons. Meanwhile, karyotypes of humans and other organisms vary from one another because each has its own unique genetic composition as displayed in Figure 6 and 7. The procedure to generate a karyotype involves isolating the somatic cells of the organism of interest. The cells will be cultured and treated with a drug to stimulate mitosis. The cells will be arrested at metaphase. It will be stained and the specimen will be viewed under a microscope equipped with a digital camera. An image of the chromosomes will be taken and will be displayed on a computer monitor. Using a digital software, the chromosome will be paired and will be arranged according to their appearance (Reece et al., 2014). THINK IT OVER Why should the chromosomes be arrested and observed during the metaphase stage? PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 6 of 17 Figure 6. Karyotype of Platycodon grandifloras (Balloon Flower) with tetraploid (4 sets) of chromosomes. From “Karyotype analysis of obtained tetraploid in medicinal plant (Platycodon grandiflorus),” by F. Yang, L. Li, E. Rong, Y. Yongbo He, X. Zhao, & Y. Wu, 2015, Journal of Medicinal Plants Research, 9(9), p. 298, Creative Commons Attribution License 4.0. Figure 7. Karyotype of cattle (Bos Taurus L.) From “G- and R-banded prometaphase karyotypes in cattle (Bos taurus L.),” by L. Iannuzzi, 1996, Chromosome Research, 4, p. 450, Copyright 1996 by the Rapid Science Publishers PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 7 of 17  NAVIGATE Assume that you are a cytogeneticist and perform karyotyping on two newly born babies. Perform the activity and fill out the worksheet. Activity adapted with modifications from Karyotyping Lab. (n.d.). Retrieved from https://mi01000971.schoolwires.net/cms/lib/MI01000971/Centricity/Domain/2027/Karyotyping%20L ab.pdf KARYOTYPING ACTIVITY Materials: Pen Scissors Glue/ tape Phone/PC Internet connection Procedure: 1. Print the karyotype layout worksheets and the scatter sheets. From the chromosome scatter sheet, carefully cut out each of the chromosomes so they will fit into the layout worksheet. On the other hand, you may opt to select and crop the images of the chromosomes in the scatter sheets, “cut” or “copy” and “paste” it into the karyotype layout sheet to perform the activity. 2. Arrange the chromosomes into homologous (same structural features and pattern) pairs, using your karyotype reference sheet as a guide. Hint: Laying the cut chromosomes directly on top of the matching chromosomes or comparing it side by side on the karyotype reference sheet will help you in this process. 3. Begin gluing or “pasting” each pair of chromosomes onto the karyotype layout worksheet. Hint: You may have abnormalities in your karyotype (more or less than 46 chromosomes), so maintain the number of chromosomes you were given. 4. Once you are done gluing or “pasting” all chromosomes to the layout sheet, complete the activity by answering the questions in the worksheet. You may browse the internet or any reliable source (e.g. genetics books) to deduce the disorder of the babies if applicable. 5. Attach your layout sheet to the activity worksheet and submit it to the teacher either as a soft copy (e.g. scanned copy) or a printed copy. PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 8 of 17  Name: _______________________________________ Section: ______________ Karyotype Layout Worksheet Scatter Sheet A 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 9 of 17  Name: _______________________________________ Section: ______________ Karyotype Layout Worksheet Scatter Sheet B 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 10 of 17  Reference Sheet Normal Human Karyotype PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 11 of 17  Scatter Sheet A PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 12 of 17  Scatter Sheet B PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 13 of 17  Karyotyping Activity Worksheet Karyotype of baby A: 1. What is the sex of the baby? (1 pt) ___________________________________________________________________________ 2. Is the karyotype normal or abnormal? (1 pt) ___________________________________________________________________________ 3. If you conclude that the karyotype is abnormal, what is your basis? Where can the defect be found on its karyotype? (2 pts) ___________________________________________________________________________ 4. If the baby has a chromosomal defect, what disorder does he/she have? Research your answer from reliable sources. (1 pt) ___________________________________________________________________________ 5. Describe the disorder of the baby and how it will affect its development. (2 pts) ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ Karyotype of baby B: 1. What is the sex of the baby? (1 pt) ___________________________________________________________________________ 2. Is the karyotype normal or abnormal? (1 pt) ___________________________________________________________________________ 3. If you conclude that the karyotype is abnormal, what is your basis? Where can the defect be found on its karyotype? (2 pts) ___________________________________________________________________________ 4. If the baby has a chromosomal defect, what disorder does he/she have? Research your answer from reliable sources. (1 pt) ___________________________________________________________________________ 5. Describe the disorder of the baby and how it will affect its development. (2 pts) ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 14 of 17  KNOT In summary, the genetic material of a eukaryotic cell is contained in a set of chromosomes, each formed from a single, enormously long DNA molecule that contains many genes. The DNA is tightly folded by binding to a set of histones and nonhistone proteins. This complex of DNA and protein is called chromatin. Mitotic chromosomes are produced as a result of the coiling and condensation of chromatin fibers of interphase into the characteristic form of chromatids. When chromosomes are at the highest level of organization, it can then be used to generate a karyotype so that chromosomes may be examined to identify possible genetic problems that cause a particular disorder. For your quiz, answer the following: I. Check Your Understanding. Summarize what you have learned from the lesson by filling out the table below. (5 pts) Levels of Organization Key Descriptions DNA Nucleosome Solenoid 300-nm chromatin fiber Chromatid II. Reflection. Do you think it would be practical and beneficial to require karyotyping for newborn babies? Why or why not? (5 pts) __________________________________________________________________________________ __________________________________________________________________________________ __________________________________________________________________________________ __________________________________________________________________________________ __________________________________________________________________________________ __________________________________________________________________________________ Scoring Guide: Indicators 2 pts 1 pt Content Content indicates synthesis of Content indicates thinking and ideas, in-depth analysis, and reasoning with analysis, complete details that accurately however, supporting details are responds to the prompt. lacking. PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 15 of 17  Organization Logical progression of ideas Organization is somewhat with a clear structure that present, however connection enhances the body of thought. between ideas is incomplete. Conventions Uses complete sentences where errors do not impact readability and are not disruptive of the main thought. REFERENCES Alberts, B., Bray, D., Hopkin, K., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P. (2014). The Structure of Eukaryotic Chromosomes. In M. Morales (Ed.), Essential Cell Biology Fourth Edition (pp. 184-186). New York, NY, USA: Garland Science, Taylor & Francis Group. Griffiths, A. J. F., Wessler, S. R., Lewonth, R. C., Gelbart, W. M., Suzuki, D. T., Miller, J. H. (2005). The Chromosomal Basis of Inheritance. In An Introduction to Genetic Analysis 8th edition (pp. 88-89). W.H.Freeman & Co Ltd. Ianuzzi, L. (1996). G- and R-banded prometaphase karyotypes in cattle (Bos taurus L.). Chromosome Research, 4, 448-456. Klug, W. S., Cummings, M. R., Spencer, C. A., Palladino, M. A. (2012). Concepts of Genetics 10th edition. San Francisco, California, USA: Pearson Education Inc. Klug, W. S., Cummings, M. R., Spencer, C. A., Palladino, M. A. (2012). DNA Organization into Chromosomes. In B. Wilbur (Ed.), Concepts of Genetics 10th edition (pp. 300-303). San Francisco, California, USA: Pearson Education Inc. Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Bretscher, A., Ploegh, H., Amon, A., Martin, K. C. (2016). Structural Organization of Eukaryotic Chromosomes. In Molecular Cell Biology Eight Edition (pp. 327-229). New York, USA: W. H. Freeman and Company. Mayo Foundation for Medical Education and Research (MFMER). (2020). Slide show: How genetic disorders are inherited. Retrieved from https://www.mayoclinic.org/tests-procedures/genetic- testing/multimedia/genetic-disorders/sls-20076216 National Human Genome Research Institute (NHGRI). n.d. Karyotype. Retrieved from https://www.genome.gov/genetics-glossary/Karyotype Shemilt, L., Verbanis, E., Schwenke, J., Estandarte, A. K., Xiong, G., Harder, R., Parmar, N., Yusuf, M., Zhang, F., Robinson, I. K. (2015). Karyotyping human chromosomes by optical and X- ray ptychography methods. Biophysical journal, 108(3), 706–713. https://doi.org/10.1016/j.bpj.2014.11.3456 Ocal. (2011). Sticky Note Clip Art. Retrieved from http://www.clker.com/clipart-sticky-note-2.html) Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P.V., Jackson, R. B. (2014). Meiosis and Sexual Life Cycle. In B. Wilbur (Ed.), Campbell Biology Tenth Edition (pp. 254-256). USA: Pearson Education Inc. PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 16 of 17 Revel, D. (n.d.). Here Are the Three Best Ways to Pack a Suitcase. Retrieved from https://www.travelchannel.com/roam-blog/news-deals/here-are-the-3-best-ways-to-pack-a- suitcase Yang, F., Li, L., Rong, E., Yongbo He, Y., Zhao, X., & Wu,* Y. (2015). Karyotype analysis of obtained tetraploid in medicinal plants (Platycodon grandiflorus). Journal of Medicinal Plants Research, 9(9), 294-300. https://doi.org/10.5897/JMPR2015.5763 Prepared by: Leody Mayme A. Monteveros Special Science Teacher I PSHS-SOUTHERN MINDANAO CAMPUS Reviewed and Approved by: MICHELLE B. DUCUSIN Special Science Teacher V/Team Lead (Biology) PSHS-ILOCOS REGION CAMPUS PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology 2: SY 2020-21 Biology 2-G10 Page 17 of 17