Discovering the Genome Module Summary Table for Teachers P. 17 of 17

Discovering the Genome – Module Summary Table – For Teachers p. 1 of 15

Module Where can I cover this Pennsylvania Next Generation Other Resources in my Biology Keystone Eligible Science Standards (Estimated time to curriculum? Content (Websites, related cover module HS-LS1 From Molecules to activities, etc.) sections) Organisms: Structures and Highlights? Processes

HS-LS2 Ecosystems: Interactions, Energy and Dynamics

HS-LS3 Heredity: Inheritance and Variation of Traits

HS-LS4 Biological Evolution: Unity and Diversity

What is This module begins with a video BIO.B.1.2.2 Explain the HS LS1-1 Excellent video introducing introducing the genome and how it functional relationships between Construct an explanation genomics and its uses: Genomics? is studied by researchers. Three DNA, genes, alleles, and based on evidence for how http://www.ontariogenomic short videos highlight applications chromosomes and their roles in the structure of DNA s.ca/about/what-genomics of genomics to food, biodiversity inheritance. determines the structure of and health care. proteins which carry out the Genetic Variation unit: essential functions of life http://learn.genetics.utah.ed Intro video can be used in typical through systems of u/content/variation/ Each video plus unit on DNA & Protein Synthesis; specialized cells. start of mitosis or meiosis when questions - 15 min discussing chromosomes, HS LS1.A: Structure and each for the Intro homologous pairs, etc. Function *Systems of specialized cells video and 3 within organisms help them application videos perform the essential functions of life. (HS-LS1-1) *All cells contain genetic information in the form of DNA molecules. Genes are regions in the DNA that contain the instructions that code for the formation of proteins, which carry out most of the work of Discovering the Genome – Module Summary Table – For Teachers p. 2 of 15 cells. (HS-LS1-1) (Note: This Disciplinary Core Idea is also addressed by HS-LS3-1.) * Multicellular organisms have a hierarchical structural organization, in which any one system is made up of numerous parts and is itself a component of the next level. (HS-LS1-2)

3 application videos Students could “jigsaw” these three BIO.B.2.4.1 Explain how genetic HS LS1.A: Structure and Cracking Your Genetic videos--students will be assigned engineering has impacted the Function Code plus jigsaw activity - Feedback mechanisms to watch one of three videos. They fields of medicine, forensics, and http://www.pbs.org/wgbh/n 40 min will then meet with other students agriculture (i.e. selective maintain a living system’s ova/body/cracking-your- who watched the same video to breeding, gene splicing, cloning, internal conditions within answer the questions. Finally, genetically modified organisms, certain limits and mediate genetic-code.html (also students will be put in mixed gene therapy) behaviors, allowing it to available by searching groups with the responsibility of remain alive and functional YouTube) even as external conditions Video: Food teaching their classmates what they learned. change within some range. Nova: Personal DNA Feedback mechanisms can Testing (12 min.) *Food could be incorporated during encourage (through positive http://www.pbs.org/wgbh/no Genetics unit; Plant Reproduction; feedback) or discourage va/sciencenow/0302/01.ht whenever talking about natural (negative feedback) what is m (also available by selection/artificial selection; or in going on inside the living searching YouTube) whichever unit you cover genetic system. (HS-LS1-3) engineering. GMO’s is a hot topic NOVA: Cracking The Code of discussion and lends itself well HS-LS4-1 (8 min) to incorporating ethical and Communicate scientific societal issues. information that common http://www.pbs.org/wgbh/n Video: Biodiversity ancestry and biological ova/body/cracking-the- *Biodiversity and the concept of evolution are supported by code-of-life.html DNA Barcoding might be used in multiple lines of empirical Select segment 11- Family evidence. studying evolution and Disease (also available by classification; at the very start of searching YouTube) the year when introducing life and its diversity; or when talking about DNA/DNA Technology and identifying organisms by their DNA.

*Health fits well with either DNA & Video: Health Protein Synthesis or Genetics units, especially if you discuss genetic screening, which is a hot Discovering the Genome – Module Summary Table – For Teachers p. 3 of 15 topic of discussion and lends itself well to incorporating ethical and societal issues. This is especially true with the resurgence of 23 & Me and the popularity of DNA testing related to personal genetics and ancestry related information.

Tour of the This module describes genome HS-LS1-6 Tour of Basic Genetics structure and how it relates to Construct and revise an animations: Genome function. It uses videos to explanation based on http://learn.genetics.utah.ed introduce and visually represent evidence for how carbon, u/content/basics/ the human genome. In small hydrogen, and oxygen from groups, students investigate how sugar molecules may combine problems with genome structure with other elements to form can result in genetic diseases. amino acids and/or other large carbon-based molecules. Genome Overview This introductory video fits well BIO.B.1.2.1 Describe how the Excellent animations on with DNA & Protein Synthesis or process of DNA replication DNA and Genes at: the first time you talk about results in the transmission and/or http://learn.genetics.utah.ed Intro video plus chromosomes. It is a clear and conservation of genetic u/content/molecules/ discussion plus entertaining look at these topics information. and sets the stage nicely for further For example: questions - 25 min. detail and discussion. BIO.B.2.2.1 Describe how the What is a chromosome? processes of transcription and http://learn.genetics.utah.ed We would not recommend this as translation are similar in all u/content/chromosomes/intr the main instructional video by organisms. o/ which they learn the material--it’s too fast and with too little detail-- but it can be a great intro and conclusion video. Students could go back after the unit and see how much more they understand. Chromosome Close- This eye opening video fits well to BIO.B.1.2.2 Explain the Available along with other up help introduce DNA & Protein functional relationships between animations and tutorials at Synthesis, Genetics or the first DNA, genes, alleles, and DNA Interactive time you talk about chromosomes. chromosomes and their roles in http://www.dnai.org/c/index. Video, discussion and Students will never think of a inheritance. html (Select - Genome / chromosome in the same way Tour) questions 20 min again! You could also use this when talking about evolution, in Video on how gene terms of gene duplication followed duplication can lead to by mutation to one of the genes. It evolutionary innovation: also discusses DNA repeats. http://www.hhmi.org/biointe ractive/making-fittest-birth- Discovering the Genome – Module Summary Table – For Teachers p. 4 of 15 It is important for teachers to and-death-genes reassure students that they do not need to learn the specific genes and their locations; the idea is to get an appreciation for the many different kinds of genes and non- coding regions that can be located on one short segment of a chromosome. Packaging DNA This video can easily be used BIO.B.1.2.2 Explain the Epigenetics unit: when first talking about DNA or functional relationships between http://learn.genetics.utah.ed chromosomes. It can also be used DNA, genes, alleles, and u/content/epigenetics/ Video, discussion and as a lead in to epigenetics and chromosomes and their roles in questions- 10 min modification of histones. inheritance. Great videos and animations at NOVA Science Now: http://www.pbs.org/wgbh/no va/body/epigenetics.html

Chromosome Video can easily be used when BIO.B.1.2.2 Explain the HS-LS1-4 Arrangement first talking about DNA or functional relationships between Use a model to illustrate the chromosomes or Mitosis. Be sure DNA, genes, alleles, and role of cellular division to walk students through the chromosomes and their roles in (mitosis) and differentiation in Video, discussion and experiments and what would have inheritance. producing and maintaining been seen depending on which complex organisms. questions 20 min model was correct and why.

Genome Structure Karyotyping background and BIO.B.2.1.2 Describe processes HS-LS3-1. Chromosome and and Disease activity could be done during that can alter composition or Ask questions to clarify Karytotypes Unit: Meiosis or Genetics units, although number of chromosomes (i.e. relationships about the role of http://learn.genetics.utah.ed having students also diagram how crossing over, nondisjunction, DNA and chromosomes in u/content/chromosomes/ Do these all together - the mistake would have happened duplication, translocation, coding the instructions for would help them understand the deletion, insertion, and characteristic traits passed Karyotyping Activities: 40-100 min depending process of meiosis even better. inversion). from parents to offspring. http://www.biology.arizona. on how you have your edu/human_bio/activities/ka students present their You might assign each BIO.B.3.2.1 Interpret evidence HS-LS3-2. ryotyping/karyotyping.html group/student a picture of a normal supporting the theory of Make and defend a claim findings and abnormal karyotype; have evolution (i.e. fossil, anatomical, based on evidence that http://learn.genetics.utah.ed them determine the abnormality physiological, embryological, inheritable genetic variations u/content/chromosomes/kar Karyotyping (match with the list) first and then biochemical, and universal may result from: (1) new yotype/ do the research. genetic code). genetic combinations through meiosis, (2) viable errors Discovering the Genome – Module Summary Table – For Teachers p. 5 of 15 Activity occurring during replication, Primate Chromosome Teachers should emphasize that and/or (3) mutations caused Comparison; Compare there is a difference between by environmental factors chromosomes of human, Resources for chromosomal disorders and gorilla, chimp, and Genetic Disorders genetic disorders caused by a HS-LS1.A: Structure and orangutan: gene mutation. The disorders Function All cells contain http://www.utsouthwestern. discussed in the Activity are all genetic information in the form edu/edumedia/edufiles/edu caused by chromosomal of DNA molecules. Genes are cation_training/programs/st abnormalities. The link in the regions in the DNA that ars/chromosome- “Additional Resources” section contain the instructions that analysis.pdf includes both kinds. code for the formation of proteins. (secondary to HS- The primate chromosome LS3-1) (Note: This Genetic Disorders: comparison activity in the right Disciplinary Core Idea is also 1. column could be used as part of addressed by HS -LS1-1.) https://www.genome.gov/10 your Evolution unit when 001204/specific-genetic- discussing evidence for evolution. HS-LS1.B: Growth and disorders/ Development of Organisms In multicellular organisms’ 2. individual cells grow and then https://ghr.nlm.nih.gov/cond divide via a process called ition mitosis, thereby allowing the 3. organism to grow. The http://learn.genetics.utah.ed organism begins as a single u/content/disorders/ cell (fertilized egg) that divides successively to produce many cells, with each parent cell passing identical genetic material (two variants of each chromosome pair) to both daughter cells. Cellular division and differentiation produce and maintain a complex organism, composed of systems of tissues and organs that work together to meet the needs of the whole organism.

(HS-LS1-4) LS3.A: Inheritance of Traits. Each chromosome consists of a single very long DNA molecule, and each gene on the chromosome is a Discovering the Genome – Module Summary Table – For Teachers p. 6 of 15 particular segment of that DNA. The instructions for forming species’ characteristics are carried in DNA. All cells in an organism have the same genetic content, but the genes used (expressed) by the cell may be regulated in different ways. Not all DNA codes for a protein; some segments of DNA are involved in regulatory or structural functions, and some have no as-yet known function. (HS- LS3-1) DNA This module explains why DNA How PCR works sequencing information is http://www.DNAlc.org/resou Sequencing important for the biological rces/animations/pcr.html sciences. It provides a brief description of the technical http://learn.genetics.utah.ed Background readings challenges of DNA sequencing. u/content/labs/pcr/ Students learn the basic principles & discussion - 45-60 of sequencing-by-synthesis, which DNA Sequencing: min. is a widely used next-generation http://www.hhmi.org/biointe sequencing (NGS) technology. ractive/disease/Sequence_ Students will do an online activity Assembly/01.html Activity - 45 min that simulates sequencing strings (Read slides 1-17 and of DNA. watch the videos on slides 2, 6 and 17) This unit can be covered during a DNA Technology unit or added as How Sanger Sequencing a very relevant example to your works DNA replication unit, since http://www.wiley.com/colleg sequencing relies on the principles e/pratt/0471393878/student of DNA replication. /animations/dna_sequencin g/index.html http://www.dnalc.org/resour ces/animations/cycseq.html

http://www.dnalc.org/view/1 5479-Sanger-method-of- DNA-sequencing-3D- animation-with- narration.html Discovering the Genome – Module Summary Table – For Teachers p. 7 of 15

Visit HHMI for DNA Sequencing What Makes a The same genome is in every cell HS-LS3.B: Variation of Traits Stem Cells unit: of your body. Yet different cells in In sexual reproduction, http://learn.genetics.utah.ed Cell a Cell? A different parts of your body look chromosomes can sometimes u/content/stemcells/ and act very differently. The swap sections during the Bioinformatics activity explores several databases process of meiosis (cell that are used by bioinformaticians division), thereby creating new Experiment and other scientists for their genetic combinations and thus research. more genetic variation. The activity, organized by topics, is Although DNA replication is Introductory video and presented such that students tightly regulated and progress from more simple to more remarkably accurate, errors discussion - 15-20 min complex database exploration. The do occur and result in topics expose students to human mutations, which are also a health-related databases as well source of genetic variation. as to databases for multiple Environmental factors can species, which can be used for also cause mutations in comparative genomics. genes, and viable mutations are inherited. (HS-LS3-2) Watch a video that describes one Environmental factors also way a bioinformatician could affect expression of traits, and approach the question: How does hence affect the probability of the same genome produce occurrences of traits in a different types of cells? population. Thus the variation The video introduction fits well in a and distribution of traits unit on DNA and Protein Synthesis observed depends on both or Reproduction & Development genetic and environmental when talking about differentiation factors. (HS-LS3-2), (HS-LS3- of cells during embryonic 3) development. You could use this to start off a cell unit but it does require some knowledge/language of DNA and gene expression. Sickle Cell Disease This could be done in a unit on HS-LS3-3. genetics or when talking about Apply concepts of statistics DNA and protein synthesis and and probability to explain the 20 min. Minimum, mutations. It could also be done as variation and distribution of including discussion - part of population genetics and expressed traits in a evolution. Students utilize the 1000 population 60 minutes if more Genomes database for this activity. questions added using “The 1000 Genomes Project ran HS-LS4-1. graphics on the site between 2008 and 2015. The goal Communicate scientific of the 1000 Genomes Project was information that common Discovering the Genome – Module Summary Table – For Teachers p. 8 of 15 to find most genetic variants with ancestry and biological frequencies of at least 1% in the evolution are supported by populations studied” from around multiple lines of empirical the world. evidence. (http://www.1000genomes.org/abo ut) Genome Size This is a great short activity to do with your class when you first start talking about DNA and protein 25-45 min, including synthesis or when you first mention discussion, questions chromosomes before Mitosis. Students utilize the Animal and whether you have Genome Size database, “a students do the comprehgensive catalogue of calculations and any animal genome size data”(great images of different animals and C additional searching. values flash by on top left!) http://www.genomesize.com/ Huntington’s Disease The OMIM website is a treasure Tutorial for OMIM available chest of information about genetic at: traits and genetic disorders and is http://www.openhelix.com/ 40-50 minutes with great to use during Genetics, after OMIM introduction and the students have some background on DNA and gene discussion expression. This site has a ton more to offer and is connected to the National Center for Biotechnology Information’s (NCBI website http://www.ncbi.nlm.nih.gov/) You could definitely expand this to a full period or more activity.

Cystic Fibrosis This could be done at many places Uniprot tutorials: in the year - during discussions of https://www.youtube.com/c protein structure during DNA & hannel/UCkCR5RJZCZZoV 40-60 minutes with protein synthesis or during TQzTYY92aw introduction and Genetics. The Uniprot site that students will use is amazing - it discussion. contains almost everything that is known about the structure and function of every protein that has been catalogued! It is well worth spending time to learn what is there and spend a day or two there Discovering the Genome – Module Summary Table – For Teachers p. 9 of 15 with your class. Breast Cancer This can be done during Cell Cycle NCBI tutorials available at: and Cancer / Mitosis unit, during http://www.ncbi.nlm.nih.go DNA & Protein Synthesis or during v/guide/training-tutorials/ 20-30 minutes with Genetics. You could also do this introduction and during a Biochemistry unit when covering Protein Structure and Watch video clip, NOVA: discussion include the concept of “domains”. Cracking The Code ( 8 The NCBI Gene site that students min) will use and its various linked sites http://www.pbs.org/wgbh/n is another amazing resource for ova/body/cracking-the- everything connected to DNA, code-of-life.html BRCA1 genes and proteins. Again, it is well worth spending time to learn (Select- Watch the what is there and spend a day or Program. Select segment 30-40 minutes with two there with your class. 11- Family Disease) introduction and The HomoloGene database that discussion After watching the clip, students will also use allows you to discuss the following see what species share genes that questions with the whole are thought to be “homologs” - class or in small groups: similar in structure and evolutionary origin. Try looking at (5-10 min) the Protein information - it is Should Alana get BRCA especially interesting to see which genetic testing for domains are conserved between breast/ovarian cancer species. susceptibility genes? If she tests positive, what options are available to her? If she tests negative, does that mean that she will never develop breast or ovarian cancer? Bioinformatics: Introductory video could be used in a DNA Technologies unit. The What? Why? same is true for all of the activities that follow in this section. Who? Please note that the last problem in the “Real Problems” section Video plus discussion renews itself with a different problem when you reload the - 20min page! Discovering the Genome – Module Summary Table – For Teachers p. 10 of 15 45-50 min for all activities that follow (they can be done in 5-15 minute chunks)

RNA RNA plays an important role in biological systems as the Sequencing: intermediary between DNA and proteins. By measuring the RNA in Up Close with a cell or tissue, we gain insight into the cell/tissue’s function. RNA- the Data sequencing (RNA-seq) is a relatively new technology that allows us to measure RNA in a sample with a high degree of accuracy. In this module we are going to discuss the data generated by an RNA-seq experiment. RNA-seq Data This section could be done in your mRNA Processing Case DNA & Protein Synthesis unit or a Study: DNA Technologies unit. It has http://sciencecases.lib.buffa Readings, short video good basic core content. lo.edu/cs/collection/detail.a and discussion - 20 sp?case_id=849&id=849 Great gene expression graphic min

Gene expression

Nice video on RNA splicing Find new genes (introns/exons)

Detect changes in RNA splicing

RNA-seq Analysis This section could be done in your Discovering the Genome – Module Summary Table – For Teachers p. 11 of 15 10-15 min reading and DNA & Protein Synthesis unit or a discussion DNA Technologies unit. It has good basic core content.

Read Alignment / This section and those that follow Mapping in the rest of the module may be more suited for AP Biology level courses or in an elective course on Basic alignment Genetics/Genomics, etc. They could also be used to help differentiate instruction in an Multimappers Honors Biology classroom. It has (repeated sequences) clear graphics and explanations and ends with creative and challenging activities. Spliced alignment

Reading and discussion 15-20 min

Gene quantification

Simple quantification

Alternative splicing

Reading and discussion 10-15 min

RNA-seq in the World These examples and the accompanying information in the teacher section would be of Reading and interest in any level Biology class discussion 10-15 min when covering DNA and gene expression Activities The questions that accompany the activities would be great to do in small groups and then as a whole class, using the diagrams in the Discovering the Genome – Module Summary Table – For Teachers p. 12 of 15 10-20 min each slideshow to help lead the discussion. RNA-seq Activity 1

RNA-seq Activity 2

RNA-seq Activity 3

RNA-seq Activity 4

RNA-seq Advanced Activity

Browsing This could be done as part of a HS-LS4-2. The Center for Disease DNA Technology unit, when Construct an explanation Control has excellent life Genomes covering Classification and based on evidence that the cycle diagrams of all Diversity of Life or when covering process of evolution primarily parasitic infections! the Immune System. It could also results from four factors: (1) http://www.cdc.gov/parasite be done at the end of the unit on the potential for a species to s/ DNA & Protein Synthesis since it increase in number, (2) the nicely incorporates most of that heritable genetic variation of unit. individuals in a species due to mutation and sexual reproduction, (3) competition for limited resources, and (4) the proliferation of those organisms that are better able to survive and reproduce in the environment Toxoplasmosis This is a short general introduction HS-LS4-4. to Toxoplasma. Construct an explanation based on evidence for how 10 min reading and natural selection leads to discussion adaptation of populations

ToxoDB This section contains a short 5 HS-LS4.C: Adaptation minute video tutorial that uses a Evolution is a consequence of Discovering the Genome – Module Summary Table – For Teachers p. 13 of 15 Video and discussion clear analogy to shopping at the interaction of four factors: 15-20 min Amazon. (1) the potential for a species to increase in number, (2) the genetic variation of individuals in a species due to mutation and sexual reproduction, (3) competition for an environment’s limited supply of the resources that individuals need in order to survive and reproduce, and (4) the ensuing proliferation of those organisms that are better able to survive and reproduce in that environment. (HS-LS4-2) Natural selection leads to adaptation, that is, to a population dominated by organisms that are anatomically , behaviorally , and physiologically well suited to survive and reproduce in a specific environment. That is, the differential surv iv al and reproduction of organisms in a population that have an advantageous heritable trait leads to an increase in the proportion of individuals in future generations that have the trait and to a decrease in the proportion of individuals that do not. (HS-LS4-3),(HS- LS4-4) Adaptation also means that the distribution of traits in a population can change when conditions change. (HS-LS4- 3) Changes in the physical environment, whether naturally occurring or human induced, have thus contributed to the expansion Discovering the Genome – Module Summary Table – For Teachers p. 14 of 15 of some species, the emergence of new distinct species as populations diverge under different conditions, and the decline– and sometimes the extinction– of some species. (HS-LS4-5) Species become extinct because they can no longer survive and reproduce in their altered environment. If members cannot adjust to change that is too fast or drastic, the opportunity for the species’ evolution is lost. (HS- LS4-5) GBrowse This section contains a 12 minute How to get more interesting tutorial demonstrating how to use a data sets at any of the genome browser within the Toxo Databases? Under tracks, Video and discussion - DB database. Speaker uses a nice select - Transcript 25 min. analogy with Google Maps. In Expression Evidence - look addition to be a clearly explained for data sets of interesting tutorial that is very applicable to topics other genome browsers, it is an excellent review of chromosomes, More activities: genes, introns/exons. http://workshop.eupathdb.o rg/athens/2011/index.php? page=schedule

The following sections should be done together and will take 30-45 min of browsing and discussion

Open ToxoDB with This section gets you started on The coding strand (sense GBrowse the activity involving two genes strand or non-template found in the ToxoDB database. It strand) is the DNA strand requires use of the terminology which has the same base surrounding DNA structure, gene sequence as the RNA expression and also from the transcript produced (with previous RNA Sequencing module. thymine replaced by uracil). During transcription, RNA Discovering the Genome – Module Summary Table – For Teachers p. 15 of 15 Pol II binds the non-coding strand (antisense strand, template strand, or transcribed strand) and transcribes their sequence to synthesize an RNA transcript with complementary bases. By convention, the coding strand is the strand used when displaying a DNA sequence. It is presented in the 5' to 3' direction. https://en.wikipedia.org/wiki /Coding_strand Locate RNA This section help you pull up data Sequence Data involving which RNA is being transcribed by which genes, on which days and in which host (cat, human) in the infection cycle of Toxoplasma. Interpreting a It is really exciting to actually work Coverage Plot with this type of sophisticated data in a way that is made readily understandable for high school students! Questions These will be challenging questions - you will need to gauge the format (individual, small group, whole class) that you use with your class. Every wrong answer will provide a window of opportunity for some excellent discussions and further questions.