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Cells: The Building Blocks of Life Knowledge Probe Primary Knowledge Research Activity Participant Guide www.scme-nm.org Southwest Center for Microsystems Education (SCME) University of New Mexico BioMEMS Topic Cells: The Building Blocks of Life Learning Module This booklet contains three (3) units: Knowledge Probe (pre-quiz) Primary Knowledge Cells Research Activity Target audiences: High School, Community College, University Support for this work was provided by the National Science Foundation's Advanced Technological Education (ATE) Program through Grants #DUE 0902411. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and creators, and do not necessarily reflect the views of the National Science Foundation. Copyright © by the Southwest Center for Microsystems Education and The Regents of the University of New Mexico Southwest Center for Microsystems Education (SCME) 800 Bradbury Drive SE, Suite 235 Albuquerque, NM 87106-4346 Phone: 505-272-7150 Website: www.scme-nm.org Cells – The Building Blocks of Life Knowledge Probe (Pre-Quiz) Participant Guide Introduction The purpose of this pre-quiz is to determine your current understanding of the cell as the basic unit of life, cell types and organization of cells, and the kinds of organelles found in eukaryotic cells. You should take this quiz prior to starting the learning module. This knowledge leads to an understanding of the importance of cells in bioMEMS applications. You will not be graded on this quiz; therefore, answer to the best of your current knowledge. There are ten (10) questions. 1. If electron micrographs consistently show mitochondria grouped around a particular structure in a particular cell type, what might one infer? a. cell is dead or dying b. structure requires a considerable supply of energy c. cell contains DNA d. structure in involved in secretion e. cell is carrying out protein synthesis 2. Which of the following would be present in prokaryotic cells? a. endoplasmic reticulum b. nuclear envelope c. ribosomes d. mitochondria e. lysosomes 3. The cytoskeleton includes which of the following? a. microtubules only b. actin microfilaments only c. endoplasmic reticulum only d. microtubules and actin microfilaments e. tight junctions and microtubules 4. Why are individual cells considered life's fundamental units? a. Are abundant in our world b. Exhibit all of the basic properties of life c. Exhibit some of the basic properties of life d. Are present in the fossil record Southwest Center for Microsystems Education (SCME) App_BioMEM_KP34_PG_021014 Page 1 of 2 Cells Knowledge Probe 5. If all the lysosomes within a cell suddenly ruptured, what would be the most likely result? a. The macromolecules in the cell cytosol would begin to degrade. b. The number of proteins in the cytosol would begin to increase. c. The DNA within the mitochondria would begin to degrade. d. The mitochondria and chloroplasts would begin to divide. e. There would be no change in the normal function of the cell. 6. What type of cell always lacks a cell wall? a. Bacterial cell b. Plant cell c. Animal cell d. Fungal cell e. Prokaryotic cell 7. Chromosomes are a series of entangled threads. What are chromosomes composed of? a. Microtubules b. DNA and protein c. Fibrous proteins d. Cytoskeleton e. Membranes 8. A cell is composed of compounds that include proteins, nucleic acids, lipids, and carbohydrates. A cell is capable of reproduction, but when the compounds that make up a cell are isolated, none of them can reproduce. Based on this, what is cell reproduction an example of? a. Growth b. A molecule c. Adaptation d. An emergent property e. Metabolism 9. Which of the following applications would NOT benefit from the ability to sort and concentrate bacterial cells on a micro-fluidic biochip? a. food safety b. environmental risk management c. DNA analysis d. health diagnostics 10. Cell survival is NOT dependent on which of the following? A cell’s ability to… a. Prevent of DNA mutations. b. Obtain and process energy. c. Convert genetic information into proteins. d. Keep certain biochemical reactions separate from one another. Southwest Center for Microsystems Education (SCME) App_BioMEM_KP34_PG_021014 Page 2 of 2 Cells Knowledge Probe Cells: The Building Blocks of Life Primary Knowledge Participant Guide Description and Estimated Time to Complete This unit provides information on cells, the building blocks of life and how bioMEMS are being used in identify, analyze and cultivate cells. This information is necessary to better understand how bioMEMS use cells to create new diagnostic and therapeutic devices. Estimated Time to Complete Allow approximately 20 minutes Introduction What is a cell? Why should a person who is interested in bioMEMS learn about a cell? Primarily because the emerging field of bioMEMS is rapidly growing. One area of major interest is the development of miniature and portable instrumentation for cell-based microassays and sensor applications. The image on the right is from the Phenotype MicroArray™ (PM), a new tool which offers a panoramic view of cellular events or properties (phenotypes). Just like a battery of tests on a person’s blood can scan the health of vital organs, the PM can scan the physiology of cells, yielding data on hundreds of traits at once. Typical cell-based assays measure only one trait at a time (for example, cell death or DNA synthesis), but the PM can measure up to 2,000 traits--or phenotypes--under hundreds of growth conditions.1 The PM is a valuable tool that lead to the development of safer and more effective drugs by allowing us to better understand how a gene or drug affects living cells.11 The Phenotype MicroArray™ (PM) Environmental Health Perspectives Volume 114, Number 3, March 2006 Some challenges facing investigators are how to incorporate living cells into sensors and diagnostic devices, how to create environmental conditions conducive to cell organization into tissue-like structures, and how to sort and concentrate bacterial cells on a micro-fluidic biochip. Applications in both diagnostic and therapeutic areas such as health diagnostics, environmental risk management, and food safety, are just a few of the areas impacted. All areas rely on a basic knowledge of a cell. To a biologist, a cell is the smallest unit exhibiting the property of life. Cells acquire and use energy; they acquire and organize materials; they grow and reproduce. This unit will introduce the different types of cells, aspects of their growth, and the types of organelles found within cells. Objectives Define and interpret the Cell Theory. Describe similarities and differences of prokaryotic and eukaryotic cells. Identify and describe the functions of cellular structures (cell membrane, cell wall, nucleus, cytoplasm, chloroplast, mitochondria) within a cell. Hooke's Microscope Cells are small, approximately 10x smaller than the visual limits of the human eye. Thus, the discovery of cells was dependent on the development of the microscope, a tool that aided the human eye. In 1662, Robert Hooke built a primitive microscope and used it to observe and describe individual cells of cork. The illustration above shows the microscope used by Robert Hooke and a drawing of the cork showing individual cells or compartments. Robert Hooke's microscope and drawing of a thin layer of cork Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 2 of 10 Cells: The Building Blocks of Life Leeuwenhoek's Observations In 1675, Anton van Leeuwenhoek used a microscope to examine droplets of water. He described a multitude of "animalcules", thus becoming the first person to observe living, single-celled microorganisms.3 Leeuwenhoek's work generated a great deal of excitement; however, it was another 100 years before scientists would describe cells in greater detail. Anton van Leeuwenhoek and his drawings of microorganisms The Cell Theory Plant Cell [Image courtesy of Mariana Ruiz Villarreal] In the 1830's, Matthias Schleiden and Theodor Schwann proposed a set of hypotheses that came to be called the cell theory. The cell theory states (1) all organisms are composed of one or more cells (2) the cell is the structural unit of life (3) cells can arise only by division from a preexisting cell Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 3 of 10 Cells: The Building Blocks of Life Prokaryotic and Eukaryotic Cells Bacteria, Animal cell, Plant cell [Bacteria and Plant cell graphics courtesy of Mariana Ruiz Villarreal] Cells vary in the types and complexity of structures found both internally and externally. However, they can be categorized into two broad types: Prokaryote and Eukaryote. The structurally simpler prokaryotic cells include bacteria (Fig 1), and the more complex eukaryotic cells include protists, fungi, animals (Fig 2) and plants (Fig 3). Prokaryotic and Eukaryotic Cells Common features of Eukaryotic and Prokaryotic cells This figure compares eukaryotic and prokaryotic cells. It points out common features found in both cell types. Despite these common features, many characteristics distinguish these two types of cells. The table lists some of the differentiating features between prokaryotic and eukaryotic cells. Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 4 of 10 Cells: The Building Blocks of Life Prokaryotic Cell Presence of a nucleus Complex membrane-bound cytoplasmic organelles Complex cytoskeletal system Cellulose-containing cell walls (plants) Complex chromosomes composed of DNA and associated proteins Size Eukaryotic Cell Present Present Absent Absent Absent Absent, contain cell walls made of different materials Absent, usually a single circular DNA molecule Very small (0.1-10 mm) Present Present in plants Present Small (10-100 mm) Table 1: Distinguishing Characteristics of Prokaryotic and Eukaryotic Cells The Eukaryotic Cell Compartmentalization is the key to eukaryotic cell function. Eukaryotic cells are larger and more structurally complex than prokaryotic cells. This complexity is largely due to the membrane-bound organelle that compartmentalizes cellular functions. The cell nucleus is the command center of the cell. Surrounded by a porous, double membrane called the nuclear envelope, the nucleus contains the cell's hereditary material (DNA and associated proteins) organized into chromosome. Eukaryotic cells contain an extensive endomembrane system consisting of the endoplasmic reticulum (both smooth and rough forms), the Golgi apparatus, and lysosome. These organelles form an interconnected set of membrane systems that function in compartmentalizing, transporting, and modifying proteins. The lysosomes contain digestive enzymes that break down proteins, carbohydrates, and lipids. Lysosomes process cellular debris as well as food particles. Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 5 of 10 Cells: The Building Blocks of Life Organelles Plant Cell showing organelles, Cytoplasm, Plasma Membrane and Cell Wall [Image courtesy of Mariana Ruiz Villarreal] Two organelles, mitochondria and chloroplasts, function specifically to supply energy to cells. Nearly all eukaryotic cells contain mitochondria. Chloroplasts are found only in photosynthetic cells such as plants and algae (see graphic). All of the organelles are found within the cytoplasm of the cell. For animal cells, the boundary of the cell is defined by the plasma membrane. For plant cells, the boundary is defined by the plasma membrane plus a cell wall composed of cellulose (see graphic). The structure of the animal cell is in part maintained by an extensive cytoskeletal system composed of actin microfilaments, microtubules, and intermediate filaments. Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 6 of 10 Cells: The Building Blocks of Life Growing Cells and MEMS Arrays Whole cells can be removed from a plant or animal and cultured in a laboratory. In the lab they grow and reproduce for extended periods of time given optimal environmental conditions. Cells grown in vitro have become essential tools for the cell and molecular biologist. Applications for animal cell cultures include the following:10 Investigate the physiology or biochemistry of cells (e.g. cell metabolism). Test the effect of various chemical compounds or drugs on specific cell types (normal or cancerous cells, for example). Assist in the generation of artificial tissues (e.g. artificial skin or organ tissue). Generating artificial tissues is an emerging area of biotechnology known as “tissue engineering”. Synthesize valuable biologicals from large scale cell cultures. Biologicals encompass a broad range of cell products (e.g. specific proteins or viruses, therapeutic proteins) MEMS are being developed and tested that challenge the current tools used for cell cultivation. BioPOETS at the University of California, Berkeley has developed a MEMS cell culture array (below left). The array used microfluidics to create an optimal micro-environment for cell cultivation. The right images are cells that have been cultivated in this array. MEMS Cell Culture Array (left). This array creates a microenvironment for growing cells in vitro and in parallel, allowing for the analysis of multiple cell growth conditions. The inset left shows the microenvironment of each array component. The cells on the right were grown in the cell culture array developed at the BioPOETS Lab, UC-Berkeley. [Developed by and courtesy of BioPOETS Lab, UC-Berkeley] To read more about this array, read “Microfluidic Cell Culture Array”, BioPoets, UC-Berkely. Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 7 of 10 Cells: The Building Blocks of Life Summary A cell is the basic unit of life. Cells are highly complex and organized, possess hereditary information and the means to use it, reproduce, acquire and utilize energy, carry out a variety of chemical reactions, engage in mechanical activities, respond to stimuli, and self-regulate. Cells are divided into two main categories: prokaryotic and eukaryotic. Prokaryotic cells and eukaryotic cells share similarities, but eukaryotic cells are more complex structurally. The organelles found in the larger eukaryotic cell compartmentalize cellular functions. Both types of cells can be grown in the laboratory. MEMS applications will aid in the cultivation of cells for the purpose of creating new diagnostic and therapeutic bioMEMS. Food for Thought / Answers 1. What are the major tenets of the cell theory? 2. How are prokaryotic and eukaryotic cells similar? 3. How are prokaryotic and eukaryotic cells different? 4. What is the primary tool of the cell biologist studying cells in the laboratory? 5. How are MEMS being used in cell cultivation? Glossary of Key Terms Actin microfilament - Part of the cytoskeleton of eukaryotic cells, composed of fibrous actin, functioning in cellular structure and locomotion. Cell membrane - A semipermeable membrane that encloses the cytoplasm of a cell. Cell wall - The rigid outermost cell layer found in plants and certain algae, bacteria, and fungi, but characteristically absent from animal cells. Cell Nucleus - The largest of the membrane-bounded organelles found in eukaryotic cells. The nucleus contains the genetic information of the cell (DNA). Chromosome - A linear strand of DNA and associated proteins found in the nucleus of eukaryotic cells that contains genes and functions in the transmission of hereditary information. Cytoskeleton -The internal framework of a cell composed mainly of actin microfilaments and microtubules. Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 8 of 10 Cells: The Building Blocks of Life Cytoplasm - A complex, semifluid, translucent substance found outside the nucleus of a cell. It is composed of proteins, fats, and other molecules suspended in water. Chloroplast - A subcellular organelle contain chlorophyll found in algal and green plant cells. Eukaryote - A single-celled or multicellular organism whose cells contain a distinct membranebound nucleus. Lysosome - A membrane-bound organelle found in the cytoplasm of most cells containing hydrolytic enzymes that function in intracellular digestion. Microtubule: A structure found in eukaryotic cells that is composed of protein, provides structural support, and assists in cellular locomotion and transport. Mitochondria - A subcellular organelle found in eukaryotic cells that use oxygen. They are responsible for energy generation by the process of oxidative phosphorylation. Organelles – Organelles are subcellular structures that provide internal compartmentalization and other functions. An organelle is to a cell as an organ is to the body. Prokaryote - An organism of the kingdom monera (or Prokaryotae), comprising the bacteria and cyanobacteria, characterized by the absence of a distinct, membrane-bound nucleus or membrane-bound organelles, and by DNA that is not organized into chromosomes. References 1 “Cell Scenario: A New Look at Microarrays”. Environmental Health Perspectives Volume 114, Number 3, March 2006. http://www.ehponline.org/members/2006/1143/innovations.html 2 “Fundamentals of BioMEMs and Medical Microdevices”. Steven S. Saliterman. Wiley Interscience. 2006. 3 Life: The Science of Biology, 8th edition, Sadava • Heller • Orians • Purves • Hillis. W.H. Freeman. 2007. 4 Bioinquiry, 3rd edition, Pruitt and Underwood. Wiley. 2006. 5 Cell and Molecular Biology, 5th edition, Gerald Karp. Wiley. 2008. 6 "BioMEMS applied to the development of cell-based bioassay systems", Brenan, Colin J.; Domansky, Karel; Kurzawski, Petra; Griffith, Linda G. 7 “Micro- and Nanotechnology for Biomedical and Environmental Applications”. Proc. SPIE Vol. 3912, p. 76-87. 2000. 8 Microfluidics, BioMEMS, and Medical Microsystems II. Edited by Woias, Peter; Papautsky, Ian. Proceedings of the SPIE, Volume 5345, pp. 17-25. 2003. 9 "Advances in on-chip photodetection for applications in miniaturized genetic analysis systems", Namasivayam, Vijay; Lin, Rongsheng; Johnson, Brian; Brahmasandra, Sundaresh; Razzacki, Zafar; Burke, David T.; Burns, Mark A. Journal of Micromechanics and Microengineering, Volume 14, Issue 1, pp. 81-90. 2004. 10 “Cell Culture”. Arshad Chaudry. The Science Creative Quarterly. Issue 3. August 2004. 11 Phenotype MicroArray ™ can test thousands of cell properties simultaneously. Tim Mullane. Biology.com. EurekAlert! June 25, 2001. http://www.eurekalert.org/pub_releases/2001-06/BI-PMct-0406101.php Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 9 of 10 Cells: The Building Blocks of Life Related SCME Learning Modules BioMEMS Applications DNA Overview DNA to Protein Overview Biomolecular Applications in BioMEMS Support for this work was provided by the National Science Foundation's Advanced Technological Education (ATE) Program. This Learning Module was developed in conjunction with Bio-Link, a National Science Foundation Advanced Technological Education (ATE) Center for Biotechnology @ www.biolink.org. Southwest Center for Microsystems Education (SCME) App_BioMEM_PK34_PG_021014 Page 10 of 10 Cells: The Building Blocks of Life Cells – The Building Blocks of Life Research Activity Participant Guide Description and Estimated Time to Complete This activity provides a research opportunity that will enable you to tie cell structure, function, and growth to bioMEMS devices. You will attain a greater understanding of cells and cellular organelles as presented in the related unit "Cells-The Building Blocks of Life". Estimated Time to Complete Allow several days to complete your primary research and prepare to present your findings in class. Introduction Cells are highly complex and organized, and there is consistency within levels of complexity in different cell types. Knowledge of the organization and function of subcellular organelles provides an understanding of the organization and complexity of the cell. For example, in eukaryotic cells (right), the nucleus and ribosomes are organelles that process information, while mitochondria and chloroplasts are organelles that process energy. The following activity allows you to investigate a specific question about cell structure or function and how your findings relate to the field of bioMEMS. Activity Objectives and Outcomes Activity Objectives State the meaning of cellular organelles structures and functions. Translate the knowledge into a new context of bioMEMS devices. Describe the experimental methodology needed to answer the question they posed. Southwest Center for Microsystems Education (SCME) App_BioMEM_AC34_PG_021014 Page 1 of 3 Cells Research Activity Activity Outcomes Upon completion of this activity, you will have gained an understanding of the importance of cells in the field of bioMEMS. You will have researched a unique aspect of cell structure and function, and extended that knowledge into current or emerging bioMEMS devices that utilize cells. Documentation The documentation for this activity will be a 1 – 2 page synopsis of your research (Be sure to include all resources and references) PowerPoint presentation summarizing your findings Answers to the Post-Activity Questions Research Activity: Cells 1. Consider a question about cell structure or function that you would be interested in answering. 2. Write your question below: 3. Research your question. 4. Write a 1-2 page synopsis of your findings. a. Include the rationale for your choice of an experimental system. b. Would the data required to answer the question be easier to collect by working on an entire plant or animal, or on a population of cultured cells? c. What might be the advantages or disadvantages of working on a whole organism versus a cell culture? d. How can, or how does your question and your findings relate to bioMEMS? 5. Use your synopsis to create a PowerPoint presentation that informs and instructs others about the question and the experimental design strategy you chose to answer the question. Your presentation should also summarize a possible or existing relationship between your findings and bioMEMS. 6. Answer the Post-Activity Questions. 7. You may be asked to present your findings to other participants. Southwest Center for Microsystems Education (SCME) App_BioMEM_AC34_PG_021014 Page 2 of 3 Cells Research Activity Post-Activity Questions 1. How do cells communicate with their environment, including other cells? What happens if the communication is disrupted? 2. Unlike bacterial cells, the nucleus of a eukaryotic cell is bounded by a double-layered membrane with complex pores. How do you think this might affect traffic between the DNA and cytoplasm of a eukaryotic cell compared with a prokaryotic cell? 3. What might the surface area to volume ratio have to do with cell size and complexity? Summary Looking at the emerging field of bioMEMS, one area of major interest is the development of miniature and portable instrumentation for cell-based microassays and sensor applications. Some challenges facing investigators are how to incorporate living cells into sensors and diagnostic devices, how to create environmental conditions conducive to cell organization into tissue-like structures, and how to sort and concentrate bacterial cells on a micro-fluidic biochip. Applications in both diagnostic and therapeutic areas (health diagnostics, environmental risk management, and food safety) are just a few of the areas impacted, and all rely on a basic knowledge of a cell. Support for this work was provided by the National Science Foundation's Advanced Technological Education (ATE) Program. This Learning Module was developed in conjunction with Bio-Link, a National Science Foundation Advanced Technological Education (ATE) Center for Biotechnology @ www.bio-link.org. Southwest Center for Microsystems Education (SCME) App_BioMEM_AC34_PG_021014 Page 3 of 3 Cells Research Activity Southwest Center for Microsystems Education (SCME) Learning Modules available for download @ scme-nm.org MEMS Introductory Topics MEMS Fabrication MEMS History MEMS: Making Micro Machines DVD and LM (Kit) Units of Weights and Measures A Comparison of Scale: Macro, Micro, and Nano Introduction to Transducers Introduction to Sensors Introduction to Actuators Problem Solving – A Systematic Approach Wheatstone Bridge (Pressure Sensor Model Kit) Crystallography for Microsystems (Crystallography Kit) Deposition Overview Microsystems Photolithography Overview for Microsystems Etch Overview for Microsystems (Rainbow Wafer and Anisotropic Etch Kits) MEMS Micromachining Overview LIGA Micromachining Simulation Activities (LIGA Simulation Kit) Manufacturing Technology Training Center Pressure Sensor Process (Three Activity Kits) MEMS Innovators Activity (Activity Kit) A Systematic Approach to Problem Solving Introduction to Statistical Process Control MEMS Applications MEMS Applications Overview Microcantilevers (Dynamic Cantilever Kit) Micropumps Overview BioMEMS BioMEMS Overview BioMEMS Applications Overview DNA Overview DNA to Protein Overview Cells – The Building Blocks of Life Biomolecular Applications for bioMEMS BioMEMS Therapeutics Overview BioMEMS Diagnostics Overview Clinical Laboratory Techniques and MEMS MEMS for Environmental and Bioterrorism Applications Regulations of bioMEMS DNA Microarrays (GeneChip® Model Kit available) Revision: January 2014 Nanotechnology Nanotechnology: The World Beyond Micro (Supports the film of the same name by Silicon Run Productions) Safety Hazardous Materials Material Safety Data Sheets Interpreting Chemical Labels / NFPA Chemical Lab Safety Personal Protective Equipment (PPE) Check our website regularly for the most recent versions of our Learning Modules. For more information about SCME and its Learning Modules and kits, visit our website scme-nm.org or contact Dr. Matthias Pleil at [email protected] www.scme-nm.org