" This class is a project-based introduction to the engineering of synthetic biological systems. Throughout the term, students develop projects that are responsive to real-world problems of their choosing, and whose solutions depend on biological technologies. Lectures, discussions, and studio exercises will introduce (1) components and control of prokaryotic and eukaryotic behavior, (2) DNA synthesis, standards, and abstraction in biological engineering, and (3) issues of human practice, including biological safety; security; ownership, sharing, and innovation; and ethics. Enrollment preference is given to freshmen. This subject was originally developed and first taught in Spring 2008 by Drew Endy and Natalie Kuldell. Many of Drew's materials are used in this Spring 2009 version, and are included with his permission. This OCW Web site is based on the OpenWetWare class Wiki, found at OpenWetWare: 20.020 (S09)"

This lab course supplements ĺÎĺĺĺŤIntroduction to Evolutionary Biology and EcologyĄ_ĺĺö. Although it does not replicate a true lab experience, it does encourage greater familiarity with scientific thinking and techniques, and will enable exploration of some key principles of evolutionary biology and ecology. This lab supplement focuses on visual understanding, application, and practical use of knowledge. In each unit, the student will work through tutorials related to important scientific concepts and then will be asked to think creatively about how that knowledge can be put to practical or experimental use. Upon successful completion of this lab supplement, the student will be able to: Display an understanding of Mendelian inheritance as applied to organisms in virtual experiments; Describe the process of natural selection and understand how it will alter populations over generations and under a variety of selection pressures; Understand how the process of speciation is affected by isolation and selection pressures; Understand predator-prey dynamics under a variety of ecological conditions; Distinguish between biomes in terms of their structure/climates as well as the types and diversity of organisms that inhabit them. (Biology 102 Laboratory)

Students are introduced to the concepts of evolution by natural selection and digital evolution software. They learn about the field of evolutionary computation, which applies the principles of natural selection to solve engineering design problems. They learn the similarities and differences between natural selection and the engineering design process.

Students learn how engineers apply their understanding of DNA to manipulate specific genes to produce desired traits, and how engineers have used this practice to address current problems facing humanity. They learn what genetic engineering means and examples of its applications, as well as moral and ethical problems related to its implementation. Students fill out a flow chart to list the methods to modify genes to create GMOs and example applications of bacteria, plant and animal GMOs.

Though biology as we know it today is a relatively new field, we have been studying living things since the beginning of recorded history. This introductory course in biology starts at the microscopic level, with molecules and cells, then moves into the specifics of cell structure and behavior. Upon successful completion of this course, students will be able to: Describe in general terms how life began on Earth; Identify early scientists that played important roles in furthering our understanding of cellular life; Describe the characteristics that define life; List the inorganic and organic molecules that are necessary for life; List the structure and function of organelles in animal and plant cells; List the similarities and differences between animal and plant cells; Describe the reactions in photosynthesis; Explain how the different photosynthetic reactions are found in different parts of the chloroplast; Describe the sequence of photosynthetic reactions; Explain the use of products and the synthesis of reactants in photosynthesis; Explain how protein is synthesized in eukaryotic cells; Describe the similarities and differences between photosynthesis and aerobic respiration; List the reactions in aerobic respiration; Explain the use of products and the synthesis of reactants in aerobic respiration; Describe the similarities and differences between anaerobic and aerobic respiration. (Biology 101; See also: Psychology 203)

This lab course supplements Introduction to Molecular and Cellular Biology. Although it does not replicate a true lab experience, it does enable further exploration of some key principles of molecular and cellular biology. In each unit, the student will work through tutorials related to important scientific concepts, and then will be asked to think creatively about how those concepts can be put to practical or experimental use. This lab course also contains activities devoted to learning important techniques in scientific study such as microscope use, DNA extraction, Polymerase Chain Reaction, and examination of DNA microarrays. Upon successful completion of this lab supplement, students will be able to: Identify the important components of scientific experiments and create their own experiments; Identify the molecular differences between proteins, fats, and carbohydrates, and explain the molecular behavior of water; Describe the process of photosynthesis; Describe the process of cellular respiration; Identify the differences between DNA and RNA; Describe the entire transcription/translation process, from gene to protein; Explain how recombinant genomes are formed; Use critical thinking to find ways that any of the above natural processes might be altered or manipulated; Explain how to use a compound light microscope for data collection; Explain how to conduct and use various experimental techniques, including DNA extraction, PCR, and DNA microarrays. (Biology 101 Laboratory)

This lesson uses the fundamentals of protein synthesis as a context for investigating the closest living relative to Tyrannosaurus rex and evaluating whether or not paleontologist and dinosaur expert, Jack Horner, will be able to "create" live dinosaurs in the lab. The first objective is for students to be able to access and properly utilize the NIH's protein sequence database to perform a BLAST, using biochemical evidence to determine T rex's closest living relative. The second objective is for students to be able to explain and evaluate Jack Horner's plans for creating live dinosaurs in the lab. The main prerequisite for the lesson is a basic understanding of protein synthesis, or the flow of information in the cell from DNA to RNA during transcription and then from RNA to protein during translation

Students make two different formulations of imitation Silly Putty with varying degrees of cross-linking. They witness how changes in the degree of cross-linking influence the putty properties.

Students explore the relationships between genetics, biodiversity, and evolution through a simple activity involving hypothetical wild mouse populations. First, students toss coins to determine what traits a set of mouse parents possesses, such as fur color, body size, heat tolerance, and running speed. Next they use coin tossing to determine the traits a mouse pup born to these parents possesses. These physical features are then compared to features that would be most adaptive in several different environmental conditions. Finally, students consider what would happen to the mouse offspring if those environmental conditions were to change: which mice would be most likely to survive and produce the next generation?

" This course provides a foundation for understanding the relationship between molecular biology, developmental biology, genetics, genomics, bioinformatics, and medicine. It develops explicit connections between basic research, medical understanding, and the perspective of patients. Principles of human genetics are reviewed. We translate clinical understanding into analysis at the level of the gene, chromosome and molecule; we cover the concepts and techniques of molecular biology and genomics, and the strategies and methods of genetic analysis, including an introduction to bioinformatics. Material in the course extends beyond basic principles to current research activity in human genetics."

Basic molecular structural principles of biological materials. Molecular structures of various materials of biological origin, including collagen, silk, bone, protein adhesives, GFP, self-assembling peptides. Molecular design of new biological materials for nanotechnology, biocomputing and regenerative medicine. Graduate students are expected to complete additional coursework. This course, intended for both graduate and upper level undergraduate students, will focus on understanding of the basic molecular structural principles of biological materials. It will address the molecular structures of various materials of biological origin, such as several types of collagen, silk, spider silk, wool, hair, bones, shells, protein adhesives, GFP, and self-assembling peptides. It will also address molecular design of new biological materials applying the molecular structural principles. The long-term goal of this course is to teach molecular design of new biological materials for a broad range of applications. A brief history of biological materials and its future perspective as well as its impact to the society will also be discussed. Several experts will be invited to give guest lectures.

The genetics of eye color are more complex than commonly believed. This interrupted case study uses the story of a blue-eyed couple with a brown-eyed child to explore the possible scenarios that could result in this outcome. The case emphasizes the link between Mendelian genetics and the underlying molecular basis of the phenotype. It is appropriate for upper-level undergraduate biology majors with a good understanding of eukaryotic gene regulation and Mendelian genetics.

This course focuses on the latest scientific developments and discoveries in the field of nanomechanics, the study of forces and motion on extremely tiny (10-9 m) areas of synthetic and biological materials and structures. At this level, mechanical properties are intimately related to chemistry, physics, and quantum mechanics. Most lectures will consist of a theoretical component that will then be compared to recent experimental data (case studies) in the literature. The course begins with a series of introductory lectures that describes the normal and lateral forces acting at the atomic scale. The following discussions include experimental techniques in high resolution force spectroscopy, atomistic aspects of adhesion, nanoindentation, molecular details of fracture, chemical force microscopy, elasticity of single macromolecular chains, intermolecular interactions in polymers, dynamic force spectroscopy, biomolecular bond strength measurements, and molecular motors.

This web simulation allows students to explore adaptive radiation of a fictitious group of birds called Pollenpeepers over a period of 5 million years. A hurricane blows some birds to 3 very different island groups and students identify the changes that take place over time and their causes including different climates, food, competition and predators. Each of the three island groups are compared to the original habitat with respect to topography, temperature, growing season and type of vegetation. Students read about the competition that the birds face when they arrive five million years ago, look at the amount of seeds, insects and flowers present and whether the number of predators is high, medium or low. They can then go forward in time a million years at a time and see the changes that have taken place in the population of pollenpeepers in each of these time periods. Instructions to operate the simulation are included as well as a species gallery where students can explore adaptive radiation in lemurs, Galapagos finches, Hawaiian silverswords, tenrecs and Hawaiian fruit flies.

In this activity students analyze a family’s pedigrees to make a claim based on evidence about mode of inheritance of a lactose intolerance trait, determine the most likely inheritance pattern of a trait, and analyze variations in DNA to make a claim about which variants are associated with specific traits. This activity serves as a supplement to the film Got Lactose? The Co-evolution of Genes and Culture (http://www.hhmi.org/biointeractive/making-fittest-got-lactase-co-evolution-genes-and-culture). The film shows a scientist as he tracks down the genetic changes associated with the ability to digest lactose as adults. A detailed teacher’s guide that includes curriculum connections, teaching tips, time requirements, answer key and a student guide can be downloaded at http://www.hhmi.org/biointeractive/pedigrees-and-inheritance-lactose-intolerance. Six supporting resource and two “click and learn” activities are also found on the link.

This case study investigates the applications of genetics to medicine by exploring one of the first examples of a pharmacogenetic test to enter mainstream clinical practice. Pharmacogenetics examines how genetic variations in an individual correlate with responses to a specific medication in order to develop tailored medical treatments. Through a scenario based on clinical observations, students learn about acute lymphocytic leukemia as well as the wide range of individual responses to the drug used to treat it. Then, students interpret data similar to those initially published in scientific journals in order to construct an understanding of how genetic variation can be used to "tailor" medical care. Lastly, students are asked to apply their understanding of what they have learned in the case by making the appropriate medical recommendation based on a particular individual's genotype.

In this unit you will learn how advances in genetics could change the way in which diseases are diagnosed and managed. The advent of predictive medicine, based on more detailed DNA profiling of individual genotypes using technologies like gene chips, rather than screening for one gene at a time, may shift the relationship between doctor and patient. People will be seeking advice on how to manage their susceptibilities or genetic risks, rather than looking for treatment for an already existing disorder.

Subject assesses the relationships between sequence, structure, and function in complex biological networks as well as progress in realistic modeling of quantitative, comprehensive functional-genomics analyses. Topics include: algorithmic, statistical, database, and simulation approaches; and practical applications to biotechnology, drug discovery, and genetic engineering. Future opportunities and current limitations critically assessed. Problem sets and project emphasize creative, hands-on analyses using these concepts.

Students create and decode DNA for man’s best friend to observe how variations in DNA lead to the inheritance of different traits. Strips of paper that represent DNA are randomly selected and used to assemble the dog's DNA. Students read the DNA and create a drawing of their pet, and compare it with others in the class to check for similarities and differences.

The discovery of restriction enzymes and their applications in DNA analysis has proven to be essential for biologists and chemists. This lesson focuses on restriction enzymes and their applications to DNA analysis and DNA fingerprinting. Use this lesson and its associated activity in conjunction with biology lessons on DNA analysis and DNA replication.