Genetics
Online Genetics Textbooks:
http://highered.mheducation.com/sites/007246268x/student_view0/index.html
http://www.nature.com/scitable/ebooks/essentials-of-genetics-8/contents
Teacher's email address: kathynotghi@gmail.com
All assignments must be submitted to this email address only!
Key: 
Test or Quiz
assignment due will be emailed to Mrs. Notghi
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Weekly Assignments:
Week 1
8/21-8/22
Objectives/Tasks: Lab Safety/Scientific Method
Introduction to Lab Safety: http://www.gwd50.org/cms/lib01/SC01000859/Centricity/Domain/158/lab%20safety.ppt
Introduction to Scientific Method: http://www.gwd50.org/cms/lib01/SC01000859/Centricity/Domain/158/scientific%20method.ppt
Read Unit 1.1 in the online textbook: http://www.nature.com/scitable/ebooks/essentials-of-genetics-8/contents
*Take power notes for quiz next class
8/23-8/24
Objectives/Tasks: Characteristics of Life
Quiz over the class discussion and 1.1 in online textbook
Characteristics of Life: http://www.gwd50.org/cms/lib01/SC01000859/Centricity/Domain/158/Chapter%201a.ppt
Review powerpoint slides and take notes
You will begin reading "The Hot Zone" by Richard Preston. 
Online book: http://projectavalon.net/THE_HOT_ZONE_Richard_Preston.pdf
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Week 2
8/25-8/28
Quiz over chapter 1 The Hot Zone/Characteristics of Life
Introduction to Biochemistry: http://www.gwd50.org/cms/lib01/SC01000859/Centricity/Domain/158/Biochemistry.ppt
Review slides in Biochemistry 22-93.
Continue reading chapter 2 of "The Hot Zone." Online book: http://projectavalon.net/THE_HOT_ZONE_Richard_Preston.pdf
8/29-8/30
Quiz over Chapter 2 The Hot Zone/Biochemistry Slides
Film "Extraordinary Measures" Genetics Disease Part 1
Genetics Case Study: Form/Work in groups of 3-4
8/31-9/1
Objectives/Tasks: Clinical case reports have been the earliest form of medical communication.
A clinical case report or case study is a means of disseminating new knowledge gained from clinical practice...
Thus, a clinical case report is expected to discuss the signs, symptoms, diagnosis, and treatment of a disease.
Your case study report is on Pompe disease, where you will discuss the signs, symptoms, diagnosis, and treatment of the disease using a case study format.
Work on Pompe Disease Case Study in Groups of 3-4
Read "The Hot Zone" Chapter 3
OWL Link for formatting your Case Study: https://owl.english.purdue.edu/media/pdf/20120820092738_670.pdf
you must also include an abstract in your case study. Use APA formatting for science
Example of a case study: https://awc.ashford.edu/PDFHandouts/Case_Study_Sample_Annotated_08.31.2015.pdf
How to write a good case study: https://awc.ashford.edu/tocw-guidelines-for-writing-a-case-study.html
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Week 3
9/4 No School
9/5-9/6 Film "Extraordinary Measures" Part 2
9/7-9/8 Complete your reading of "The Hot Zone" until end of the novel.
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Week 4
9/15-9/18 Work on Pompe Disease Case Study
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Week 5
9/19-9/20 Work on Pompe Disease Case Study
9/21-9/22 Work on Pompe Disease Case Study
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Week 6
9/28-9/29 Pompe Disease Case studies due
Case Study Grading Rubric
Each item is rated on the following rubric.
1= Very poor
2 = Poor
3 = Adequate
4 = Good
5 = Excellent
Group Members: _______________________________________________________
_______________________________________________________________________
Assigned Case Studies: ____________________________ Date:__________________
Item Score
1. Evidence of preparation (APA formatted correctly, the evidence you did your research) 1 2 3 4 5
2. Content (group presented accurate & relevant information, appeared knowledgeable about the case studies assigned and
the topic discussed, offered strategies for dealing with the problems identified in the case studies)
1 2 3 4 5
3. Science connection (group identified scientific peer-reviewed resources to help with the problem/issues)
1 2 3 4 5
4. Methodology (clear and logical organization, effective introduction and conclusion, creativity
1 2 3 4 5
5. Discussion/work (group works together on assigned case studies, good use of time, involves classmates)
1 2 3 4 5
Total Score: ________ (sum of Items 1-5)
Total Score : ________
Comments:
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Homework: Review the following information/recommendations about studying Genetics and taking power notes:
1. Genetics is extremely conceptual. We cannot see genes. We cannot see genotype create phenotype. We cannot see meiosis segregating different alleles, or fertilization combining different alleles. We work with models, diagrams, and simulations. Even if we work with actual organisms (e.g. ears of corn with yellow and purple kernels), we still end up deriving our understanding from the ratio of phenotypes, and not the phenotypes themselves. And, ratios are not helpful in understanding our own genetics, since few of us have the several hundred siblings required for statistical validity.
Recommendation: develop a strategy to introduce the concepts using phenotypes directly, rather than ratios of phenotypes. Do so using phenotypes that can be recognized as relevant to human phenotypes (e.g. hair color).
2. Genotype and phenotype are just words. Without a direct connection between the two, an understanding of how one leads to the other, many students remain mystified. It is hard to relate meiosis to genetic inheritance if we don't see the relationship between chromosomes (more specifically, genes) and organismal characteristics.
Recommendation: Link the genetics unit to the transcription/translation unit, and extend this to include the effects of mutations on gene function. Use at least an example with straightforward biochemistry (e.g. pigment production, perhaps hair color). Morphological characteristics (polydactyly, earlobe attachment) require a brief excursion into embryology as well.
3. Dominance is mysterious. This is a specific aspect of the genotype/phenotype problem; without an understanding of how an allele displays dominance over another allele, one is reduced to memorizing the examples rather than the underlying principles.
Recommendation: Work with an example that is both relevant to you and has a clear explanation for why some alleles are dominant over other alleles. Pigmentation (e.g. hair color) is particularly helpful here.
4. Different inheritance patterns as currently described in textbooks are hard to fathom. What is the difference between dominance, co-dominance, and partial dominance? What makes some things special enough that we refer to multiple alleles? Why do some texts mention that two alleles may be co-dominant at the molecular level, but at the phenotypic level show dominance or partial dominance? In actual organisms, it turns out that nearly every gene has multiple alleles, and strict dominance is not only relatively rare but is simply one end of a continuum of various degrees of partial- and co-dominance. This continuum is referred to by geneticists as an "allelic series," for which dominance relationships depend on which alleles are being compared.
Recommendation: If we can begin with clear examples, where we can develop an understanding of why one allele might be dominant over another, we can then understand these patterns of inheritance in their own right. We can then develop a naming system if we so choose. At least the terminology won't drive the instruction, but rather aid in the discussion of the principles you have already learned.
5. Punnett Squares are intelligible only to those who understand what they are trying to show. Because of their abstract nature, they are not a helpful learning tool for you. It often becomes a matter of filling in the table by rote, rather than using the table to facilitate probability calculations.
Recommendation: Begin with a simpler, more representational form of diagram--maybe little drawings of eggs and sperm. This provides a clue that we're concerned with the genes in the gametes. Then, we can ask what possibilities there might be for the gametes...do they get the allele that originally came from Mom or the one from Dad? It's an either/or situation, which seems to be 50:50. OK, now in the current mating, what are the possibilities for egg/sperm combinations? This type of representation might have a better chance of relating the meiotic outcome in the gametes to the genotypic outcome in the progeny. Only after we understand this concept do we see that the Punnett Square is a kind of shorthand for this more laborious reasoning process.
6. Students often do not relate genetics to DNA. These are typically discussed in different units, at different times in the semester. It takes a special effort to connect the dots and build the larger picture. There is, it seems, some danger in beginning the genetics unit with Mendel's work (even though it is historically appropriate). Without the connection to DNA, students often infer that "genes" are some form of mysterious "trait-bearing particles" that are produced in the organs which they affect. Interestingly, this view is close to the "pangenesis" model of inheritance that was developed in the wake of Mendel's discoveries, and before the recognition of the role of DNA in inheritance.
Recommendation: Your teacher will build the genetics unit around the molecular biology. This will automatically occur if we emphasize the mechanisms by which genotype determines phenotype.
7. It's easy to understand that we get half our DNA from Mom and half from Dad, so it should be easy to understand that we are diploid. It should be easy to understand that gametes must be haploid. But the process of meiosis confuses everyone terribly, perhaps because students tend to get lost in the details and terminology.
Recommendation: For the unit on genetics, focus your thinking on the function of meiosis, rather than the mechanism. The important concept is that we've got to get one copy of each gene, and not both, into the gametes. There's the allele we got from Mom, and the allele we got from Dad; each gamete gets one or the other.
8. It is difficult to see beyond the examples to the fundamental principles. Students often memorize Mendel's peas as a wholly separate phenomenon from coat color in guinea pigs and recognize neither as relevant to human genetics.
Recommendation: Begin with examples that appear more directly relevant. (e.g. hair color). After the initial concepts are in hand, then look at additional organisms, to illustrate that they, too, follow the same principles.
9. The simplified nomenclature of an uppercase letter for one allele (e.g. A) and a lowercase letter for another allele (e.g. a) often creates the misconception that every gene has only two alleles. This seriously interferes with linking genetics to evolution (and, in fact, is the reason that Mendel's work was initially thought to contradict evolution).
Recommendation: Begin with examples for which many alleles are known to exist, and for which you already recognize that there is great diversity (e.g. hair color). Emphasize that for every gene there may be many alleles in the population overall, but that a single individual can carry only two--one from Mom and one from Dad.
10. Alleles are mysterious. First of all, it is another odd "science word" that is unlike anything used in normal English. This, alone, poses a hurdle for some students. Second, it is unclear what alleles are if we don't know where they come from. If we begin to grasp that alleles might be the results of DNA mutation, then we may reject this notion if we have internalized the idea that a gene can have only two alleles (dominant, A, and recessive, a).
Recommendation: Emphasize the origin of alleles as mutations--errors in DNA replication. [More precisely, they mostly result from inaccurate repair of DNA damage caused by ionizing radiation, chemical mutagens, or oxidative damage by oxygen radicals.] Emphasize that alleles are "different versions" of the same gene, much as color and color are different spellings of the same word. Since DNA damage can (and does) occur at any location within a gene (and within the whole genome), and cannot be controlled or prevented, mutations occur continuously at a low rate--generation after generation after generation. If a mutation occurs in a gamete and makes it into a zygote that develops into an adult, then the new version of the gene (the new allele) becomes part of the population's genetic diversity. This should be relatively straightforward in the context of recommendation 9 above, examples in which a great deal of genetic variation is readily recognized by students.
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11. Mutations are mysterious. Genetics is commonly presented as the inheritance of alleles that already exist within populations. This simplifies the genetics unit in some ways but leaves two difficulties. First, students do not necessarily see where alleles come from (#10 above), and second, the "mutations" discussed in the evolution unit seem somehow different from the stable alleles discussed in the genetics unit.
Recommendation: Follow the appearance of a new allele, from DNA damage and inaccurate repair to alteration of the protein encoded by the mutated gene to the phenotype that results from alteration of the protein. There are a number of clear opportunities for this. Hemophilia in some of the descendants of Queen Victoria is among the best since the data point to Queen Victoria herself carrying the new mutation. Hemoglobin-S (sickle cell) is also good in that the phenotype is clearly related to the protein, though we have no record of the time of origin of the allele. It would also be appropriate to follow a hypothetical instance of a new allele arising in a gene that students have already been studying (e.g. hair color).
Concepts to study for Test #1
9/28-9/29 A. Origin of Life
Open Powerpoint: http://www.biologyjunction.com/Origin%20of%20Life.ppt
Take Power Notes on Powerpoint
B. Possible Origin of Macromolecules
Open Powerpoint: http://www.saburchill.com/IBbiology/chapters03/images/THE_ORIGINS_OF_LIFE.ppt
Take Power Notes on powerpoint
C. Read Chapter 9 in Genetics textbook (Chemistry of the Gene) (pp. 206 - 220)
Link to the textbook: https://archive.org/stream/FundamentalsOfGenetics/2.principlesOfGenetics7thEd.-R.Tamarinmcgraw-hill_2001#page/n5/mode/2up
10/2-10/3 Cumulative Test #1
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Week 7
10/4-10/5 Objective/Task: The Cell
**Do these Practice Quizzes:
https://www.cliffsnotes.com/study-guides/biology/biology/the-biology-of-cells/quiz-movement-through-the-plasma-membrane
https://www.cliffsnotes.com/study-guides/biology/biology/the-biology-of-cells/quiz-structure-of-prokaryote-and-eukaryote-cells
Watch Powerpoints:
Introduction to the Cell (Chapter 3) take power notes on http://www.biologyjunction.com/cell%20structure%20revised.ppt
Study PowerPoint on Cell Theory: wsscience.weebly.com/uploads/7/7/3/8/7738444/celltheorylessonandtimeline.ppt
Watch Bozeman Videos: https://www.youtube.com/watch?v=aczbMlSMr8U
10/9-10/10 Quiz over Cell
Objective/Task: Begin work on cell membrane review
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Week 8
10/11-10/12 Cellular Membrane Review
Cell Membrane Review: https://www.nature.com/scitable/topicpage/cell-membranes-14052567
Watch the following link: Take power notes:
The Cell: http://www.gwd50.org/cms/lib01/SC01000859/Centricity/Domain/158/Cells--ch%203%20new%20book.ppt
Homework/Flipped Class:
Protocell membranes: Watch lecture on "Protocell Membranes" ( Jack Szostak from Harvard/HHMI)
https://www.youtube.com/watch?v=CJ5jh33OiOA
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Week 9
10/13-10/16 Cell Membrane Quiz
10/17-10/18 Take power Notes on the following:
Introduction to Mendelian Genetics: http://www.gwd50.org/cms/lib01/SC01000859/Centricity/Domain/158/Mendels%20genetics%20PP.ppt
Pedigree Powerpoint: www.saburchill.com/IBbiology/chapters03/images/05PEDIGREE%20CHARTS.ppt
**(Watch powerpoint before you begin pedigree assignment)
Genetics Assignment: In-class practice
The Starting Point: My Family -- Inheritance of Brown Hair Color
Section 1:
Building Pedigrees
Let's Build a Family Chart: a Pedigree of My Family
Aunt Molly has brown hair. She married Uncle Sven, who's blonde, and all five of their kids have brown hair like Aunt Molly. But her sister, Aunt Jess, also has brown hair, and Uncle Tage has blonde hair, but their son is blonde! Why doesn't Aunt Jess's son have brown hair, like Aunt Molly's children, do?
Let's see if we can figure this out. Hmm....what do we know? Let's start by drawing a couple of simple diagrams to keep track of Molly and Sven's family, and to keep track of Jess and Tage's family. We'll use circles for females, and squares for males, and we'll color these symbols brown or light tan to match the hair color. What would this give us?
A. Do Now: Draw a pedigree chart for Molly/Sven and Jess/Tage
Of course, Molly and Jess are sisters, and they have a number of brothers and sisters (including Dad!). Add them, and Grandma and Grandpa both with brown hair to the diagram.
B. Do Now:
It still isn't clear why Jess and Tage have a blonde child, but Molly and Sven do not. Maybe we can find out about Grandma's and Grandpa's parents, and their parents, and so on. ... After some searching, we've learned a bit about Grandpa, but we haven't learned very much about Grandma. Grandpa's mother was blonde! But his father had brown hair, and his father's parents had brown hair. Diagram them:
C. Do Now:
This helps somewhat! Grandpa's mother was blonde, so maybe Jess inherited something from her that made it possible for her to have a blonde son (my cousin John). But what could this be? Maybe we'll have to wait until I get married, and we can see what my children are like.
..... many years pass .....
Now I have 3 children, and one of them is blonde! John has two sons, one of whom is blonde. Here's what our family pedigree is like now: Diagram
D. Do Now:
I can understand how John would have a blonde child, since he's blonde himself, and his dad is blonde. But how did I get a blonde daughter? I have brown hair, my husband has brown hair, my parents have brown hair, and so did my grandparents. My great grandmother had blonde hair, but how could her hair color reappear so many generations later?
E. Do Now and answer the question:
Section 2: Summarizing what you have learned
The Difficulty in Discovering the Mechanisms of Inheritance by Studying Human Populations
As we see in the pedigree chart you completed previously, Jess and Molly both have brown hair and married men with blonde hair. Yet, their children show different hair colors--Jess's son is blonde, while Molly's children are all brown-haired. Shouldn't Jess have had some brown-haired children, too? It's hard to know...she had just the one son. Could Molly have had a blonde child if she'd had more children? Maybe, but neither family has a large enough number of children to be able to discover what all of the possibilities are. We know, for example, that in humans, children tend to be either boys or girls, with equal probability. Jess's one child could have been male or female, but happens to be male. Hed she had another child, that one might have been male or female...but she didn't have another child, so we can't tell for sure. Molly had more children, 2 girls and 3 boys, which is closer to the 50:50 ratio that we think is reasonable. Still, it's not perfect. Rather than being a ratio of 1:1, it's a ratio of 2:3. Their parents' generation might be better to study since they had more children. For them, the ratio of females to males is 5:4. It looks like the trait of maleness or femaleness might be inherited in a simple manner: each child has a 50% chance of being male and a 50% chance of being female. But it's hard to test this idea with single human families because we just don't have enough children for the numbers to get closer to the 1:1 ratio that this idea suggests we should find.
Hair color--and probably most other traits as well--is trickier. At each generation, members of other families come in, bringing their own versions of the traits into the family. For example, here is a complete pedigree chart of the family above, with arrows pointing to the individuals who married into the extended family, but for whom we have no information.
The fact that many people join the family, bringing with them their own genetic history, makes it difficult to work out the Rules of Inheritance from human pedigrees unless we have a huge amount of information concerning a very large number of families. Perhaps, however, we can begin to identify some of the rules if we study hair color in some other mammals. Some mammals, such as dogs, have larger litter sizes than the typical human (we usually have one child at a time). Also, with domesticated animals, there are many varieties, or "breeds," in which particular hair colors "breed true" -- that is, in which every individual of that breed has the same coat color. Perhaps, if we study some model systems, we can identify the rules that govern inheritance in those species. Then, we can come back to our study of humans, and see if the same rules apply to us.
10/19-10/23 Finish Building Genetics project
*************************************************************************************************************************************************************************** 10/24-10/25 Lab #1 Corn Genetics
PRIOR KNOWLEDGE REQUIRED: Students will research and answer the following questions to prepare for the quiz:
• be able to describe the process of artificial selection and explain how it differs from natural selection
• be familiar with the Mendelian principles of segregation and independent assortment (Law of Segregation, Law of Independent Assortment)
• as well as related terms such as allele, cross, hybrid, F1, F2, and phenotype;
• be able to use Punnett squares to predict genotype and phenotype frequencies in F1 and F2 mono- and dihybrid crosses; and
• understand that gene expression is regulated, often by the products of other genes.
Watch film: Popped Secret: The Mysterious Origin of Corn Link:https://www.youtube.com/watch?v=mBuYUb_mFXA&t=791s
Corn Genetics classwork
10/26-10/27 Corn Genetics Quiz
Begin Corn Lab
**You will need to be able to construct dihybrid crosses common in genetics.
Dihybrid Cross practice problems: https://www.biologycorner.com/bio2/genetics/notes_dihybrid.html
10/30-10/31 Corn Genetics Lab completed (Dihybrid Crossing Mastered) Turn in Lab Report for Group
follow Lab formatting @ Lab Notebook format: http://orion.bme.columbia.edu/lulab/pdf/lab_notebook.pdf
11/1-11/2 Prior knowledge required:
Polygenic inheritance (Traits) Non-Mendelian Inheritance
Polygenic traits are controlled by two or more than two genes (usually by many different genes) at different loci on different chromosomes. These genes are described as polygenes. A polygene refers to a group of genes that when expressed together produce a particular phenotype or trait. Multiple genes are involved in a particular trait to manifest. In humans, height, skin color, and weight are determined by multiple genes that are expressed together. Polygenes allow a wide range of physical traits. For instance, height is regulated by several genes so that there will be a wide range of heights in a population. Accordingly, there are more than 400 genes at play in determining the height of an adult human apart from the non-genetic factors (e.g. nutrition) that influence the trait. The predisposition to type 2 diabetes is believed to be associated with polygenes.
Since there are several genes at play in determining a trait, Mendelian inheritance alone may not explicate the phenotype of an organism. A phenotypic ratio where the effect of a single gene can be predicted would therefore not apply to polygene expression.
Polygenic inheritance often results in a bell-shaped curve when you analyze the population That means that most people fall in the middle of the phenotypic range, such as average height, while very few people are at the extremes, such as very tall or very short. At one end of the curve will be individuals who are recessive for all the alleles (for example, aabbcc); at the other end will be individuals who are dominant for all the alleles (for example, AABBCC). Through the middle of the curve will be individuals who have a combination of dominant and recessive alleles (for example, AaBbCc or AaBBcc).
Polygenic traits tend to result in a distribution that resembles a bell-shaped curve, with few at the extremes and most in the middle. There may be 4 or 6 or more alleles involved in the phenotype. At the left extreme, individuals are completely dominant for all alleles, and at the right extreme, individuals are completely recessive for all alleles. Individuals in the middle have various combinations of recessive and dominant alleles.
Summary
In polygenic inheritance, a trait is controlled by more than one gene.
Examples of polygenic inheritance include height or skin color.
Questions to be answered:
Use the resource below to answer the questions that follow.
Genetics and Eye Color http://www.youtube.com/watch?v=MjBZaed9yzM (1:49)
1. Is eye color a trait controlled by a single gene as it is often taught in schools?
2. Do you think skin color is a polygenic trait? Explain your reasoning, and be as specific as possible.
3. What is an albino? What kind of eyes would they definitely NOT have?
4. What is known about the melanin levels in people with blue eyes?
5. How does polygenic inheritance violate Mendel's rules?
6. Give 3 examples of traits governed by polygenic inheritance.
11/3-11/6 Lab #2 Polygenic Inheritance Lab: Eye Color
11/7-11/8 Polygenic Inheritance Lab: Eye Color (Finish lab and turn in group lab report) due today.
Lab Notebook format: http://orion.bme.columbia.edu/lulab/pdf/lab_notebook.pdf
Introduction to Case Study: http://sciencecases.lib.buffalo.edu/cs/results.asp?search=ebola&Submit.x=17&Submit.y=11
You will draw a number to determine which case study you and your partner will do. Only one partner will draw a number!
* You may not change which case study you will work on.
Case Study Link: http://sciencecases.lib.buffalo.edu/cs/results.asp?search=ebola&Submit.x=17&Submit.y=11
1. The Ebola Wars: Advanced Edition
This case study was written for students to review foundational aspects of virology and to examine Ebola virology.
2. CAMEL Question: Can Applied Math Extend Life?
This directed case study examines differences between the exponential and logistic growth models in biology and how they are applied to solve real ...
3. Hunting the Ebola Reservoir Host
This one-hour introduction to the study of infectious diseases uses recent research on the Ebola reservoir host to motivate students to consider th...
4. BSL-4: Authorized Personnel Only
This case study is based on the 2014 Ebola epidemic that spread to multiple highly populated countries in West Africa, making it the largest and mo...
Case Study Grading Rubric: see rubric in class on wall.
**In addition, be sure to have 5 references (One is "The Hot Zone" you read). Be sure to have at least 10 citations, 5 of which must come from "The Hot Zone" which you read.
Each item is rated on the following rubric.
1= Very poor
2 = Poor
3 = Adequate
4 = Good
5 = Excellent
Group Members: _______________________________________________________
_______________________________________________________________________
Assigned Case Studies: ____________________________ Date:__________________
Item Score
1. Evidence of preparation (APA formatted correctly, the evidence you did your research) 1 2 3 4 5
2. Content (group presented accurate & relevant information, appeared knowledgeable about the case studies assigned and
the topic discussed, offered strategies for dealing with the problems identified in the case studies)
1 2 3 4 5
3. Science connection (group identified scientific peer-reviewed resources to help with the problem/issues)
1 2 3 4 5
4. Methodology (clear and logical organization, effective introduction and conclusion, creativity
1 2 3 4 5
5. Discussion/work (group works together on assigned case studies, good use of time, involves classmates)
1 2 3 4 5
Total Score: ________ (sum of Items 1-5)
Total Score : ________
Comments:
11/9 Polygenic Lab due/ Introduction to Case Study
11/13-11/14 Case Study: Bring your own technology
11/15-11/16 Case Study: Bring your own technology
11/17-11/21 Case Study: Bring your own technology
11/27-11/28 Case Study: Extended time to finish/using in class technology*
11/29-11/30 Case Study: Extended time to finish/using in class technology*
12/1-12/4 Structure and Function of DNA and RNA
Case Study due 12/4. Any papers received after this date will receive a lowered grade
12/5-12/6 DNA to RNA to Protein: Transcription and Translation
Structure and Function of DNA and RNA
Review:
- https://www.nature.com/scitable/class-room-content/dna-transcription-4151693
- https://www.nature.com/scitable/topicpage/translation-dna-to-mrna-to-protein-393
- https://www.nature.com/scitable/definition/transcription-dna-transcription-87
- https://www.youtube.com/watch?v=WsofH466lqk
- https://www.youtube.com/watch?v=5bLEDd-PSTQ
- Read/Watch the entire Module: http://authoring.concord.org/activities/22?show_index=true
12/7-12/8 Quiz on Structure and Function of DNA and RNA in Protein Synthesis
12/11-12/12 Lab #3 Building a Protein
12/13-12/14 Lab #3 Building a Protein-Lab Notebook due
12/15-12/18 Review for Midterm
12/21-12/22 Midterm:
*Students who formally exempted with the district form signed by me are finished and do no further work as semester is completed for you.
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Family Tree (Pedigree) of Genetic Disease Project
Name_____________________
Project Overview:
In this project, you will create a pedigree chart for at least 3 generations of your own family, friends, or acquaintances.
You will chart the heritability/passing of a genetic disease for three generations of your family, friends, or acquaintances.
Clearly, indicate and label the traits you are tracing using the correct format you have learned in class.
You will need a key on each pedigree chart. Use the letters below to indicate a particular allele (upper-case letters for the dominant allele and lower-case letters for the recessive allele).
You will need to include a Punnett Square for each generation to determine the probability of the disease occurring and the actual outcome.
You will need to ask questions of your parents, grandparents, or any other family member with an in-depth knowledge of your family tree. You can use your creativity in the design of the pedigree chart, but proper pedigree symbols must be used. Make sure that you number each generation and individual with correct symbols.
O = female with trait represented by circle colored O = female without trait represented by empty circle ½ of circle colored representing a carrier
[] = male with trait represented by square colored [] = male without trait represented by an empty square
Pedigree requirements:
I. Choose 1 Genetic Disease to investigate based on information obtained from your family, friends, or acquaintances that the disease exists in their family tree.
You will need to use your investigative skills and conduct a thorough genetic interview. You should include notes you obtained from the interview on a page
labeled “Genetic Investigation”
II. Each pedigree should contain a minimum of 3 generations. If your family does not have enough generations you will have to use a different family.
III. Each pedigree should be typed using an online template. No handwritten pedigrees will be accepted.
IV. Each pedigree should have a key; use appropriate pedigree symbols.
Also, note for each individual:
A. Genotype (when able)
B. Phenotype
C. Name of a relative. Use first name and last name as an initial. For example, Joe Smith should be
identified on the pedigree as Joe S.
V. Use an online pedigree template such as https://www.familytreetemplates.net/preview/Pedigree_Chart
Research Disease requirements:
Genetic counselors help prospective parents determine the probability of their children being born with a genetic disorder. During this project,
you will act as a genetic counselor for families with a history of genetic diseases. Some genetic diseases are sex-linked, which is determined by
a gene on the sex chromosome and shows a different pattern of inheritance in males than in females. Other genetic diseases are not sex-linked.
Be sure to cite in-text and provide a Reference page using APA style. Please see Rubric before submitting. No resubmissions will be accepted.
Upon your investigation, interviews, and research, you must determine if the genetic disease is sex-linked or not.
Express the sex-linked genotypes as follows:
Unaffected men = XR Y Unaffected women= XR XR or XR Xr
Affected men= Xr Y Affected men= Xr Xr
Genetics Investigation:
1. A genetic counseling begins with what is known about his or her clients. Determine what genetic disease is present in the family. Determine the genotype of each family member.
2. Construct the Punnett Squares to determine the possible genotype outcomes of the F1 generation, F2 generation, F3 and any subsequent generations, if included.
3. Use the results of each of your crosses to complete the table.
_____________________________________________________________
Mother’s Genotype Percentage of Percentage of
Affected Females Affected males
______________________________________________________________
Homozygous Dominant
______________________________________________________________
Heterozygous
______________________________________________________________
4. Determine the odds and risk of the youngest generation producing a child with the genetic disease. Use a Punnett Square to make this determination.
Explain how you would counsel an individual or couple based on these predictions.
5. Research the following items associated with the disease:
a. History and discovery of the disease.
b. Population statistics for the disease.
c. Genetic Disease: Cause and Symptoms.
Be sure to identify which gene(s) are affected by a complete discussion
and photos of patients exhibiting the disease attached (use generic photos of the disease.
Do not include family or friend’s photos).
d. Control or Treatment of Genetic Disease: Be specific and detailed about these!
Include current gene therapy being used. Be sure to include gene therapy vectors centered on viruses if available.
e. Funds allocated currently/forecasted to be allocated to treating/or identifying the disease
f. Future forecasting of disease in the population. Include available data and statistics.
Grading Guidelines and Rubric for Family Pedigrees and Analysis
Please copy/turn this sheet in with your project!
RUBRIC
Name: _______________________________________
Genetic Disease: ________________________________
Grading of this project will be based on five main topic areas:
Pedigrees Points Possible Points Earned
A. Genetic Disease investigated. Identify individuals interviewed. Attach interview Notes title “Genetic Investigation” Genetic Punnett Squares are included per instructions.
(10 pts)
B. The pedigree should contain at least 3 generations of males and females. You must include the following for each individual: (15 pts)
Genotype (when able)
Phenotype
Name of relative (first name and last initial)
Key attached
Each pedigree must be typed or attached using an online template. No handwritten copies to be submitted.
C. Sex-Linked determination of Genetic Disease (5 pts)
D. Odds and risks of the genetic disease. Explanation of how you would correctly provide genetic counseling to potential parents. (10 pts)
E. Research is complete on the genetic disease (20 pts)
History and discovery
Population statistics
Cause and symptoms
Control and Treatment
Funds allocated/or forecasted
Future forecasting of disease in populations
F. All work submitted APA style with correct in-text citations and Reference list. Photos are attached. (10 pts)
TOTAL: 70 points
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B. All students who have not met this requirement (averaged less than a 'B' for both quarters) will report to class during their
assigned midterm times and take the midterm at their scheduled times. No early in class midterms will be given. Failure to take the
in class, midterm will result in a grade of zero.
C. Students who formerly exempted on paper with a minimum of a "B" in each quarter do not need to attend
class and will be assigned no work as they have completed all requirements for Semester 1.
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Happy Holidays to you!!!
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3rd Quarter Lessons
1/16-1/17 Linking Mitosis and Meiosis
Objectives: Review gene transmission in Mitosis and Meiosis
Read:https://www.nature.com/scitable/topicpage/mitosis-meiosis-and-inheritance-476
1/18-1/19 Objective: Review Ploidy/Lifecycles
Read: https://www2.estrellamountain.edu/faculty/farabee/biobk/BioBookmeiosis.html#Ploidy
Diploid vs. haploid
Read: https://www2.estrellamountain.edu/faculty/farabee/biobk/BioBookmeiosis.html#Comparison of Mitosis and Meios
Somatic cells (mitosis) vs. gametes (meiosis)
Linking Mitosis and Meiosis Practice worksheet
Objectives: Review Asexual (Mitosis) and Sexual (Meiosis) reproduction
1/22-1/23 Watch In-class film: http://www.pbs.org/wgbh/nova/miracle/divide.html
1/24-1/25 Linking Mitosis and Meiosis /finish watching the film
Read/Watch/Complete tutorial: Link
http://www.floridastudents.org/PreviewResource/StudentResource/122586
Objectives: Mitosis and Meiosis both involve cell division, yet they transmit genetic material in very different ways.
What happens when either of these processes goes awry? Cancer
How does Cancer grow?
Read/Watch: http://www.pbs.org/wgbh/nova/body/how-cancer-grows.html
Assignment/ Watch: http://www.hhmi.org/biointeractive/eukaryotic-cell-cycle-and-cancer (due at end of class)
Complete and turn in: The Eukaryotic Cell Cycle and Cancer (Student online handout)
file:///C:/Users/p00097901/Downloads/Cellcycle-Worksheet%20(1).pdf
1/26-1/29 Pop Quiz
Complete The Eukaryotic and Cell Cycle online Worksheet from the previous class (30 minutes)
Objective: Cell Growth
Read the following: https://www.biology.iupui.edu/biocourses/N100/2k4ch39repronotes.html
Assignment: After reading the previous information, answer the following questions and turn in at end of class period: No extensions!!
You make work with one partner.
1. Explain the 6 stages of development common to all animals.
2. What is a gamete? fertilization? A zygote?
3. Explain the major features in the formation of the human embryo at the days mentioned above.
4. What is the difference between a morula, a blastula, and a gastrula?
5. What is the primitive streak?
6.What tissues are produced from the 3 germ layers ectoderm, endoderm, and mesoderm?
7. What is the inner cell mass and what is its significance?
8. What structures form from the neural groove, the somites, and the pharyngeal arches?
9. Name at least 4 teratogens.
1/30 Objective: Cancer Film: Introduction to Cancer Biology
https://www.youtube.com/watch?v=46Xh7OFkkCE&list=PLBt3OR94jWPwnyWo-sm5PFRDPvWDrO9Si&index=10
Bozeman Science Video: https://www.youtube.com/watch?v=UopUxkeC4Ls
Why Haven't We Cured Cancer? https://www.youtube.com/watch?v=7tzaWOdvGMw
1/31 Gilda's Club Presentation-Cancer
Students are responsible for the in-class work on 1/30 as homework/review
2/1-2/2 Objective: Mistakes in Meiosis: Read the 2 links below to help you solve the worksheets below
Link: https://www.somsd.k12.nj.us/site/handlers/filedownload.ashx?moduleinstanceid=1607&dataid=5397&FileName=Nondisjunction-Tutorial-HELP.pdf
Link: http://ib.bioninja.com.au/standard-level/topic-3-genetics/33-meiosis/non-disjunction.html
Online Worksheets to complete in class: due at end of class and no extensions are given. You may work with one partner.
https://www.somsd.k12.nj.us/site/handlers/filedownload.ashx?moduleinstanceid=1607&dataid=5398&FileName=Meiosis_and_Nondisjunction_worksheet.pdf
https://www.somsd.k12.nj.us/site/handlers/filedownload.ashx?moduleinstanceid=1607&dataid=5399&FileName=Nondisjunction_worksheet.pdf
2/5-2/6 Objective: Research Personalized Medicine to treat Cancer
Today you will spend time learning to use COSMIC and the Cancer Cell Line Encyclopedia. Browse through each site and learn how it is set up.
Cancer Genome Project: http://www.sanger.ac.uk/science/groups/cancer-genome-project
for practice Go to COSMIC►CANCER BROWSER
(If cancer browser does not load go to direct link): http://cancer.sanger.ac.uk/cosmic/browse/tissue?hn=carcinoma&in=t&sn=breast&ss=NS
Cancer Cell Line Encyclopedia: https://docs.cancergenomicscloud.org/docs/ccle
2/7-2/8 Objective: Cancer Genome Project: You/one partner will use Cosmic to research the specific cancer assigned to you using PERSONALIZED MEDICINE.
Link: http://www.sanger.ac.uk/science/groups/cancer-genome-project
scroll down to Key Projects, Collaborations, Tools & Data
Then click on COSMIC ►CANCER BROWSER
(If cancer browser does not load go to direct link): http://cancer.sanger.ac.uk/cosmic/browse/tissue?hn=carcinoma&in=t&sn=breast&ss=NS
NO EXTENSIONS WILL BE GIVEN ON THIS PROJECT FOR ANY REASON. CHOOSE YOUR PARTNER WISELY!!!
DIRECTIONS FOR PROJECT:
1. You will be assigned one of the following tissue type cancers
Adrenal gland (2853 / 10844)
Autonomic ganglia (842 / 8074)
Biliary tract (1723 / 7036)
Bone (1705 / 9496)
Breast (10625 / 49875)
Central nervous system (17033 / 55813)
Cervix (616 / 6647)
Endometrium (3722 / 18764)
Eye (1370 / 4207)
Fallopian tube (3 / 10)
Female genital tract (site indeterminate) (1 / 13)
Gastrointestinal tract (site indeterminate) (140 / 1517)
Genital tract (208 / 683)
Haematopoietic and lymphoid tissue (109459 / 425725)
Kidney (4805 / 17458)
Large intestine (47946 / 194248)
Liver (5078 / 18760)
Lung (36884 / 178144)
Meninges (896 / 5136)
NS (3164 / 6892)
Oesophagus (3070 / 13894)
Ovary (4988 / 23799)
Pancreas (7804 / 16446)
Paratesticular tissues (2 / 3)
Parathyroid (320 / 2917)
Penis (20 / 84)
Pericardium (2 / 4)
Peritoneum (222 / 524)
Pituitary (882 / 4389)
Placenta (1 / 51)
Pleura (514 / 1844)
Prostate (2346 / 21052)
Retroperitoneum (1 / 1)
Salivary gland (477 / 2666)
Skin (17322 / 44653)
Small intestine (587 / 1804)
Soft tissue (11980 / 43961)
Stomach (3517 / 25622)
Testis (185 / 2165)
Thymus (144 / 1094)
Thyroid (27144 / 75970)
Upper aerodigestive tract (4480 / 19526)
Urinary tract (7691 / 21913)
Vagina (6 / 34)
Vulva (164 / 576)
2. YOU WILL THEN GO TO CANCER BROWSER TO INVESTIGATE YOUR TYPE OF CANCER TISSUE ASSIGNED
A. On Tissue Selection choose the tissue type
B. Choose Include all on Sub-tissue selection, Histology Selection, and Sub-Histology Selection
C. Scroll down to Genes where you will include the graph with Top 20 Genes, as well as the separate graphs for Genes With Mutations and Genes Without Mutations
D. You will then include the Mutation Matrix (include all data)
E. You will then include the Distribution showing the distribution of the different types of mutations
F. You will then include the Variants which are the mutations in the selected tissue/histology (use mutation tab only)
G. You will then include the Samples (10 of the mutant/10 of the non-mutant samples)
H. In addition, you will then include in your Research Project:
1. A complete description of the tissue type you have been researching.
2. Where is the tissue type located in the human body?
3. What diseases affect this tissue type?
4. What current treatments are available for diseases of this tissue type. Include traditional medicine as well as gene therapy, if currently available?
5. Predict what future treatments may become available to treat diseases of this tissue type.
6. Include a Reference page APA style for all your sources including COSMIC (only use Peer-Reviewed Sources, i.e. HHMI, CDC, Mayo Clinic, .gov, .edu, .org). Do not use sites that are not peer-reviewed.
2/9-2/12 Objective: Continue with Cancer Genome Project using COSMIC
2/13-2/14 Objective: Continue with Cancer Genome Project using COSMIC
2/15-2/16 **Cancer Genome Project using COSMIC due today** email to kathynotghi@gmail.com (No hard copies are accepted).
2/20-2/21 Objective: Understanding Genetic variation – mutations, alleles, phenotypes
Read: Link: http://www.genetics.edu.au/publications-and-resources/facts-sheets/fact-sheet-2-variations-in-the-genetic-code
Link: https://ghr.nlm.nih.gov/primer/mutationsanddisorders/genemutation
Link: http://kidshealth.org/en/parents/about-genetics.html#catgenetic
**Answer the following questions. You may work with one partner. (Due at the end of class with no extensions!)
1. What is a gene mutation?
2. How are gene mutations classified?
3. What are de novo mutations?
4. Describe and give an example of polymorphism?
5. How can gene mutations affect health and development?
6. Are gene mutations ever repaired? If so, how?
7. Do mutations ever have positive effects? If so, how?
8. What are the different types of gene mutations? List and describe each type?
9. How can changes in mitochondrial DNA affect a person's health? List and describes diseases associated with these changes?
10. What are complex or multifactorial genetic disorders? Give at least 2 examples and describe each example?
11. Some individuals are predisposed to developing a genetic disease. If so, then why do some members of a family develop a genetic disease
while other members of the family do not?
12. How can statistics provide information about genetic diseases?
13. How are genetic diseases named? Provide an example of a genetic disease and how it was named?
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2/23-2/26 Objective: Practice and Apply DNA Mutation Worksheet: You may work with one partner.
Link: https://www.youtube.com/watch?v=OlBSiKRnPXs
Link: https://www.youtube.com/watch?v=MOtRqBs0jxE
Genetic Code and Amino Acid Translation chart link: http://www.soc-bdr.org/rds/authors/unit_tables_conversions_and_genetic_dictionaries/genetic_code_tables/
2/27-2/28 Objective: Practice and Apply DNA Mutation Worksheet. You may work with one partner (due today end of class with no extensions for late work).
Gene Mutation Important points you must know:
Mutations Can Alter Proteins-Three Examples
1. A mutation is a change in a gene's DNA (genotype), and a mutant is a corresponding expression (phenotype).
2. Mutations include single base changes, deletions, additions, or moved sequences in genes that encode proteins or in regulatory genes.
3. Learning how a mutation alters a protein can explain how a disease arises.
4. Germline mutations can be inherited, whereas somatic mutations cannot.
Types of Mutations
Point Mutations
1. A point mutation is a change in a single base. In a transition, a purine replaces a purine or a pyrimidine replaces a pyrimidine. In a transversion, a purine replaces a pyrimidine or vice versa.
2. A missense mutation is a point mutation that changes one amino acid to a different one.
3. A nonsense mutation is a point mutation that changes an amino acid encoding codon to a stop codon, which halts translation. A stop codon that changes to an amino- acid coding codon, lengthens the protein.
Deletions and Insertions Can Cause Frameshifts
1. Inserting or deleting bases in DNA alters the gene's reading frame, causing a frameshift mutation.
2. A tandem duplication repeats a section of a gene.
Genetic Code and Amino Acid Translation Chart
Understand how the chart works, the number of Amino Acids, Start and Stop Codons
3/1 - 3/2 Objective: Quiz on Genetic Mutations
Begin Research on Recombinant DNA and Clones
What is Cloning? Link: http://learn.genetics.utah.edu/content/cloning/whatiscloning/
Clone a Mouse! (The Click & Clone Activity) Link: http://learn.genetics.utah.edu/content/cloning/
Test Yourself for understanding cloning! Link: http://learn.genetics.utah.edu/content/cloning/cloningornot/
Animal Clones: Double Trouble? Link: https://www.sciencenewsforstudents.org/article/animal-clones-double-trouble
Like Mother, Like Daughter Link: https://www.sciencenewsforstudents.org/article/mother-daughter
3/5-3/6 Objective: Differentiate Genetic Engineering vs. Selective Breeding
Link: https://gmo.geneticliteracyproject.org/FAQ/how-does-genetic-engineering-differ-from-conventional-breeding/
Link: https://www.yourgenome.org/facts/what-is-selective-breeding
Read: CC - the first cat clone Link: http://news.nationalgeographic.com/news/2002/02/0214_021402copycat.html
Read: List of cloned animals Link: https://en.wikipedia.org/wiki/List_of_animals_that_have_been_cloned
Think Tank: Due before next class period (you may work with one partner)
When is Cloning an Option?
Newspaper headlines screamed it, everyone was talking about it - A SHEEP WAS CLONED! Scientists created an exact duplicate of a sheep from a body cell. For some time no one could duplicate the work done in the Scottish lab. Then a mouse was cloned, and now a number of mice clones have been produced. In the sheep and mouse cloning, a body cell was removed and its nucleus placed into another animal's egg cell. Then, an electrical current was sent through the cell, and it started dividing. A physicist in Chicago has announced that he is setting up a laboratory to do human cloning. If laws are passed against it, he says, he will move his lab to another country.
Anthony Luning was more than curious about cloning. Starting with one apartment building, he now owned enough land to make him the richest man in Charlotte. Being rich, however, doesn't keep tragedy from happening to you. One day his five-year-old daughter, Lucy, was crossing the street and was hit by a drunk driver. By the time the ambulance came, she had suffered serious brain damage. In the emergency room, doctors put her on a respirator, and her heart was beating normally. Mr. Luning was told, however, that she probably would never regain consciousness. He was devastated. In Charlotte, a group of scientists was working on cloning a cow from the body cell of a cow that was a high milk producer. They used Mr. Luning's property for their herd, and he had been following their progress. As a businessman, he saw the potential for the process. Now, as a parent, he had another idea. Dr. Irene Smith was the head scientist on the project. Mr. Luning called her several weeks after the accident. He told her he was willing to spend every cent he had to bring his daughter back. He wanted her to clone his daughter from one of her body cells. If the doctor in Chicago could do it, so could she.
1. What should Dr. Smith do? Give three reasons why Dr. Smith should not clone Lucy and three reasons why she should.
2. If Mr. Luning offers her not only money but future funding for her research, should this make a difference in Dr. Smith's decision?
3. Dr. Smith would be the first to clone a human, and she could have the most modern laboratory with everything that she could possibly need. Should this play a part in her decision?
4. Should scientists do everything that they are technologically capable of doing? Give four arguments to support your answer.
5. Will there be a market for human cloning? Why or why not?
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3/7-3/8 Objective: The Human Genome (Complete and submit Think-tank from last class)
Link: https://www.genome.gov/pages/educationkit/download.html
Link: https://www.yourgenome.org/facts/timeline-history-of-genomics
Link: https://www.ck12.org/biology/human-genome/lesson/The-Human-Genome-Project-Advanced-BIO-ADV/
Read the information on the Human Genome Project and do the Practice Module (orange button practice)
Answer the following questions and submit before the end of class:
1. What are/were the goals of the Human Genome Project?
2. Is the DNA sequence information generated by the Human Genome Project available to anyone, and if so, how?
3. What is maintained in the GenBank?
4. What are single nucleotide polymorphisms?
5. What is ENCODE?
Human Genome Think-Tank: Begin/Due before the end of next class period (you may work with one partner)
Who May See the Results of DNA Testing?
In 1990, Robert was employed by the Institute. It was the job he had always wanted because it involved working in the chemical industry His degree was in chemistry, but when he graduated there were very few jobs in the industry and he had done other work for five years. Robert has worked for the Institute for 10 years and rarely has thought about the physical exam they had made him take at the time of his employment. They had explained that blood was being taken for genetic testing and that this information, along with other medical information, would remain within the company and that only he could have access to it. He asked why this was being done and they said it was for insurance purposes.
Very recently a neighbor of Robert's was murdered. The police had no suspects, but they were looking in the neighborhood. They questioned Robert and told him that they had some blood from the crime scene and were trying to find a match for it. They asked if Robert would give them a blood sample. Meanwhile, the police learned that Robert worked for the Institute. They contacted the company asking for the DNA profile they compiled on Robert when he was employed.
1. Should the company give Robert’s profile to the police? Why or why not?
2. Should Robert volunteer to give his blood to the police? Why or why not?
3. What should the police do in order to get Robert's profile? List three possibilities.
4. Is there some way that Robert can stop the Institute from giving his profile to the police?
5. How could Robert have avoided this dilemma?
6. Suggest at least three legal problems that the police could face if they look at Robert’s profile and use it in their investigation.
7. If Robert is accused of this crime, should the court admit this evidence? Why or why not?
8. Courts sometimes deny the police the right to take a person’s blood for DNA examination. Why is this situation different?
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3/9-3/12 Objective: Complete the Human Genome Think-Tank questions from last class /submit no later than today
3/13-3/14 Gattaca film 
3/15-3/16 Gattaca film
Class Debate on Genetic Engineering
3/19-3/20 Objective: Genetic Engineering: Cloning
Film: Genetic Mutations Hidden Mutations (National Geographic)
Link: https://www.youtube.com/watch?v=Kk2yHeRoc9w&list=PLlWJv9aHC-ncyGemgFaH0eWX06aA-k9e8
Objective: Designer Babies? Is this the future?
Links: https://www.technologyreview.com/s/535661/engineering-the-perfect-baby/
https://qz.com/1041609/a-highly-successful-attempt-at-genetic-editing-of-human-embryos-has-opened-the-door-to-eradicating-inherited-diseases/
https://qz.com/574731/2015-was-the-year-when-we-decided-it-was-ok-to-genetically-engineer-human-babies/
3/21-3/22 Short Film.
Possible quiz
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Spring Break********************************************************
4th Quarter Lessons
4/2-4/3 Genetic Engineering/Technology Classwork
Computing Life
Work on questions
4/4-4/5 Genetic Engineering/Technology Classwork
Computing Life
Work on questions
4/6-4/9 Genetic Engineering CRISPR
Submit classwork from prior two classes
Teacher facilitated: https://www.youtube.com/watch?v=mXNW_dJotP4
Teacher facilitated https://www.youtube.com/watch?v=MnYppmstxIs
https://www.youtube.com/watch?v=4YKFw2KZA5o
After the films answer the following questions using the information you gleaned from watching. (Quiz)*
1. What is CRISPR technology? Describe how it functions?
2. What does this technology have the potential to offer society?
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4/10-4/11 Genetic Engineering CRISPR
Read the articles below and research to answer fully questions 3, 4, and 5. Due at the end of the class block today. Individual submissions only.
3. What are some potential drawbacks of the CRISPR technology? Name and describe at least 3 possible drawbacks.
4. What can scientists do right now with genetic engineering technology? Name and describe at least 3 uses.
5. What advancements do you expect to see within the next 10 years?" Name at least 3 possible advancements with explanations for each.
Read:
https://www.sciencenews.org/article/first-human-embryos-edited-explore-gene-function?utm_source=editorspicks092417&utm_medium=email&utm_campaign=Editors_Picks
Read: https://www.sciencenews.org/article/gene-editing-human-embryos-yields-early-results?mode=magazine&context=548
Read: https://www.mnn.com/green-tech/research-innovations/photos/12-bizarre-examples-of-genetic-engineering/mad-science
Read: https://www.taconic.com/taconic-insights/gems-design/crispr-genome-engineering-advantages-limitations.html
Read: https://www.omicsonline.org/open-access/ethical-issues-in-genome-editing-using-crisprcas9-system-2155-9627-1000266.php?aid=70914
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4/12-4/13
Objective: Explore Genetically Modified Organisms
GMO's Think Tank
Due today before the end of class (you may work with one partner)
Genetically Modified Agricultural Products
It was only the second meeting of the group, but everyone was excited. Kent was going to run the meeting and he was hoping to have a large turn out at the school in Lawrence. As the meeting time approached, Kent and his friend Emily began setting up chairs and placing leaflets around the room. This meeting would address an important issue. Many farmers in the area grew GM (genetically modified) corn and soybeans, but these crops were used mainly in animal feed. Outside of Lawrence, a company was doing research on genetically modified food. This company, Ingerm, Inc., was working with tomatoes that produced a protein to combat disease, as well as a variety of green bean that made its own insect repellent.
Although the products were far from market ready, Kent and his group were very worried about the possible outcomes. In the United Kingdom, there have been extensive protests against GM foods and Kent was in touch with some of the protestors. He had some ideas from them. One of those ideas was to sneak onto the property of the company at night and destroy the fields of growing GM tomatoes, strawberries and green beans. Kent was going to introduce this idea at the meeting.
1. Should the group consider Kent's suggestion? Give three researched legal/or other reasons why they should protest in this way and three reasons why they should not.
2. What might possible legal ramifications occur if the organization proceeded with Kent's plan?
3. Suggest three other protests and/or actions that the group could try.
4. In the United Kingdom, some groups have done more than destroy property; they have actually hurt scientists and their families. Is this an acceptable protest? Why or why not? Would this technique work in the United States? Explain why or why not providing your findings from research.
**Be sure to list all sources retrieved APA style in References and cite any direct quotes and sources used to answer the questions.
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Objective: Genetic Presentations (Out of class work and preparation may be required)
4/16-4/17 Genetics Presentation work
4/18-4/19 Genetics Presentation work
Rubric for Genetics Presentations:
Category Scoring Criteria
1. Organization (15 points) The type of presentation is appropriate for the topic and audience.Information is presented in a logical sequence.
2. Content (15 points) Introduction is attention-getting, lays out problem well, and establishes a framework for the
rest of the presentation.Technical terms are well-defined in scientific language appropriate for the target audience.
The presentation contains researched peer-reviewed, accurate information. Material included is relevant to
the overall message/purpose. An appropriate amount of material is prepared, and points made reflect well their relative
importance. There is an obvious conclusion summarizing the presentation and an assessment given to test the audience's
understanding of the presentation.
3. Presentation (15 points) Speakers maintain good eye contact with the audience and are appropriately animated
(e.g., gestures, moving around, etc.). Speakers use a clear, audible voice. Delivery is poised, controlled,
and smooth. Good language skills and pronunciation are used. Visual aids are well prepared, informative,
effective, and not distracting. Length of presentation is within the assigned time limits or no less than 7 minutes
and no more than 10 minutes. Information was well communicated to and well received by all.
____________________________________________________________________________________________________________________________ Total Points out of 45
GENETICS PRESENTATION TOPICS
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Objective: The Genetics of Behavior
Genes Contribute to Most Behavioral Traits
1. Until recently studies on behavior were limited to empiric risk estimates and adoptee and twin studies. Now SNP (single nucleotide polymorphism) patterns can be correlated with disease symptoms.
2. Candidate genes for behavior control are being sought among genes that control neurotransmission and signal transduction.
Eating Disorders
3. Twin studies suggest that there is a considerable genetic component in eating disorders.
4. Genes that produce proteins involved in appetite control are candidates for the etiology of eating disorders.
Sleep
5. Numerous genes appear to influence sleep, although the necessity for sleep is unknown.
6. Narcolepsy is prevalent in some families but has clearly been shown to be an autosomal recessive gene in dogs.
7. A Utah family has provided the first evidence for a "biological clock" in humans. A gene called "period" was located near the tip of the long arm of the chromosome. As well, the "Period" has counterparts in several species of animals.
Intelligence
8. Intelligence is an ill-defined, but complex trait with substantial genetic and environmental effects.
9. IQ tests were first developed in the early 1900s. IQ scores are a useful predictor of success in school, but caution must be exercised in labeling individuals or groups of individuals.
10. Genetic disorders that affect neurological function can affect intelligence in patients. Give and explain a number of genetic disorders affecting neurological function.
11. Single genes that affect intelligence are the subject of an intensive search. A few candidate genes have been identified.
Drug Addiction
12. Drug addiction is a compulsive behavior that exhibits tolerance and dependence.
13. Imaging techniques have identified regions of the brain involved in drug addiction.
14. Genes implicated in drug addiction are involved in the biosynthesis of neurotransmitters, reuptake transporters, neurotransmitter receptors, and components of signal transduction pathways.
15. DNA microarray tests are revolutionizing the analysis of addictive behavior and demonstrating the pattern of gene expression during drug use.
Mood Disorders
16. Mood disorders represent the extremes of normal behavior and are difficult to separate into genetic and environmental components. Because the symptoms of a number of mood disorders are similar, diagnosis may be difficult.
17. Depression and bipolar disorder may both involve a deficiency of serotonin. Selective serotonin reuptake inhibitors (SSRIs) have become popular treatments replacing older tricyclic drugs. Although depression has been correlated with deficiencies in the serotonin transporter, assigning specific genes to bipolar disorder has been difficult.
Schizophrenia
18. Schizophrenia may be difficult to diagnose, but generally affects thinking rather than mood. High heritability and risk of recurrence suggest a genetic component to schizophrenia.
19. Concordance in identical twins also demonstrates that a significant environmental component exists in schizophrenia. Familial studies have implicated numerous loci in schizophrenia.
20. Dopamine and glutamate levels are altered in schizophrenics.
Human Origins and Evolution
Human Origins
21. Propliopithecus and Aegyptopithecus were monkey-like species that lived about 30 to 40 million years ago. Both are possible ancestors of gibbons, apes, and humans. Hominids (human ancestors) appeared about 4 million years ago. Four million years ago bipedalism opened up new habitats for australopithecines who walked upright and used tools. There were several types of australopithecines, and one, A. garhi, may have been a direct ancestor of Homo. A newly described species, Keynanthropus platyops, may have been yet another australopithecine or a contemporary.
22. Dryopithecus lived 22 to 32 million years ago and may have walked onto grasslands. His behavior and adaptations are described.
23. Hominids were ancestral to humans only. By 2 million years ago, Australopithecus coexisted with the more humanlike Homo habilis. Later H. habilis coexisted with H. erectus, who used tools in more complex societies. H. sapiens either coexisted with or arose from H. erectus 300,000-500,000 years ago. The Neanderthals were contemporaries of Homo erectus and were displaced by the Cro- Magnons. By about 28,000 years ago the Neanderthals no longer existed while the Cro-Magnons gave rise to modern humans.
Modern Humans
24. Evidence from the discovery of cave art demonstrates that by 14,000 years ago our ancestors had the ability to use symbols and had developed fine hand coordination. A preserved man from 5,300 years ago is genetically like us. A few genetic changes have occurred in humans over time in modern man.
Objective The Genetics of Molecular Evolution
25. Evolutionary distances between living and extinct organisms can be estimated by studies that examine similarities and differences among chromosomes and sequences of proteins and nucleic acids. The more alike two organisms are on a molecular level, the more likely it is that they share a common descent.
Objective: Comparing Genomes/Genes
26. Whole genome comparisons indicate that humans differ from chimps by only 0.5 percent of their protein-encoding genes. Small differences at the genome level can translate to large differences in phenotype. This may result from changes in developmental control genes where a mutation in a single gene can exert great effects on phenotype. The similarity of all vertebrate genomes is seen in the comparison of the human and pufferfish genomes.
27. Only 40% of the human odorant receptor genes are functional. During the later stages of human evolution, a sense of smell may not have been the survival factor that it was in our ancestors.
Objective: Comparing Chromosomes
28. Chromosome banding patterns are highly conserved in higher primates. All mammals have identically banded X chromosomes.
29. Synteny is the correspondence of gene order in chromosomes in different species. Identifying regions of synteny can reveal information about species relatedness and the evolutionary history of chromosomes.
Comparing Protein Sequences
30. Many proteins are very similar in amino acid sequence in different species. Homeobox proteins are transcriptional factors that control developmental processes in many organisms.
Homeobox genes are highly conserved throughout evolution. Mutations in homeobox genes can cause disease in humans or bizarre morphological anomalies in flies and mice.
Comparing DNA Sequences
31. The degree of evolutionary relatedness between two species can be estimated using DNA hybridization and observing how quickly the DNA forms hybrid double helices. Comparison of DNA sequences between organisms reveals evolutionary relationships and is an important step in determining the function of newly isolated genes. DNA obtained from preserved extinct organisms can be amplified and compared to DNA sequences in modern species.
End of Presentations list
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4/20-4/23 Work on presentations
4/24-4/25 Work on presentations
4/26-4/27 Work on presentations
4/30 Work on Presentations
5/3-5/4 Genetics Presentations for # see class list posted eligible Senior exemptions signed upon completion of presentation
5/7-5/8 Genetics Presentations for # see class list posted eligible Senior exemption signed upon completion of presentation
5/10-5/11 Genetics Presentations for # see class list posted eligible Senior exemption signed upon completion of presentation ( due no later than
1: 10 p.m. on May 11, 2018).
5/14-5/15 Genetics Presentations for
5/16- 5/17 Genetics Presentations for All presentations must be finished by today**
5/18 Final Class Day-No presentations today (Teacher is proctoring AP Exam).
Please schedule a day for your final exam if you have not exempted Genetics Honors. The sign-up sheet will be posted in class.
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Objective: Molecular Clocks
1. Molecular clocks apply mutation rates to timescales in order to estimate when two individuals or types of organisms most recently shared ancestors.
2. Parsimony analysis selects likely evolutionary trees from DNA data.
Neanderthals Revisited
1. Molecular clocks have been used to examine the relationship of Neanderthals to modern humans.
2. Analysis of available DNA sequence data suggests that humans and Neanderthals did interbreed.
3. Mitochondrial DNA analysis suggests that Neanderthals and modern humans last shared a common ancestor 550,000 to 700,000 years ago.
Choosing Clues
1. Genes change (mutate) at different rates. Sometimes different conclusions arise from comparing different sequences.
2. Mitochondrial DNA clocks trace maternal lineages, and Y chromosome sequences trace paternal lineages.
3. Analyses of mitochondrial DNA and Y chromosome information has been used to examine the origin of modern humans in Africa or in many regions and the migration pattern of native
Americans from Asia.
4. Mitochondrial DNA and Y chromosomal DNA support an "out of Africa" origin of Homo sapiens about 200,000 years ago.
5. An "out of Mongolia" model for the origin of Native Americans is supported by mitochondrial DNA and Y chromosomal DNA. Contributions from other Siberian populations are evident.
Eugenics
1. Eugenics is the control of individual reproduction for societal goals.
2. In the early twentieth century, several different eugenic policies were promoted and implemented.
3. Positive eugenic policies aimed to maximize the genetic contribution of those deemed acceptable or superior (positive eugenics).
4. Negative eugenics policies were designed to minimize the contribution of those considered inferior.
5. Some aspects of genetic technology also affect reproductive choices and have been compared to eugenics.
6. The goal of genetic screening is to alleviate human suffering rather than to change society.
7. Laws have been proposed and passed in many nations around the world to prevent genetic discrimination.
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Objective: Genetics of Immunity
The Importance of Cell Surfaces
1. Foreign antigens (molecules) elicit an immune response from a host.
2. Antibodies and cytokines produced by the immune system attack foreign antigens.
3. As many as 20,000 genes in the human genome may be, directly or indirectly, involved in an immune response.
Blood Groups
1. Results of early transfusions were inconsistent.
2. With the discovery of human blood groups systems, properly matched donor and recipient types resulted in successful transfusions.
3. Blood types, including the ABO groups, Rh factor, and others, result from self-antigen patterns on red blood cells.
4. Rh incompatibility may put a fetus at risk.
5. RhoGAM can be used to prevent Rh incompatibility.
The Human Leukocyte Antigens
1. In addition to blood group antigens, a large number of cell surface molecules are recognized by the immune system.
2. Many of the cell surface proteins that help to establish immunity are encoded by the approximately seventy genes of the major histocompatibility complex (MHC) located on chromosome 6 in humans.
3. Class I and II genes of the MHC encode human leukocyte antigens (HLA).
4. Class III genes produce plasma proteins involved in the immune response.
5. HLA antigens on leukocytes are involved in the processing of foreign antigens.
6. HLA proteins are each encoded by several genes with many alleles and as a result only 2 in every 20,000 unrelated people match for the six major HLA genes by chance.
7. Individuals with certain HLA combinations have an increased risk of developing certain HLA-linked diseases.
Objective: The Immune System
1. At the cellular level, the immune system consists of various types of lymphocytes and macrophages.
2. The immune response consists of an immediate, generalized, innate immunity and a slower, more specific adaptive immunity.
Physical Barriers and the Innate Immune Response
1. Skin, mucous membranes, tears, and saliva are examples of physical and chemical barriers that keep pathogens from entering the body.
2. Pathogens that breach this barrier encounter an innate immune response consisting of inflammation, phagocytosis, complement, collectins, and cytokines.
The Adaptive (Acquired) Immune Response
1. The innate response is rapid (minutes) while the acquired immune response must be stimulated to action and takes days to respond.
2. The acquired immune response is divided into the humoral and cellular immune responses. Both of these responses differ from the innate immune response in that they are more complex, highly specific and each has a cellular component with memory.
3. The humoral response involves B cells that secrete antibodies in order to neutralize, clump, and stimulate the destruction of pathogens by recognizing and binding specific foreign antigens.
4. Antibodies are made of Y-shaped polypeptides consisting of constant and variable regions.
5. The astounding diversity of antibody binding activities is due to a shuffling of gene pieces (exons) encoding antibody polypeptide products in B cells.
6. In the cellular immune response, helper T cells stimulate B cells to manufacture antibodies and cytotoxic T cells to secrete cytokines.
7. Some T cells bind to nonself cells and virus-covered cells and burst them. Other T cells function to coordinate the immune response.
Objective: Abnormal Immunity
Inherited Immune Deficiencies
1. Inherited immune deficiencies represent defects in the genes that encode proteins involved in immunity.
Acquired Immune Deficiency Syndrome
1. Acquired immune deficiency syndrome is caused by HIV.
2. HIV replicates very rapidly, and T cell production matches it until the immune system is overwhelmed and AIDS begins.
3. HIV is a retrovirus that injects its RNA into host cells by binding receptors.
4. Reverse transcriptase then copies viral RNA into DNA.
5. HIV uses the cell’s protein synthesis machinery to mass produce itself; then the cell bursts, releasing the virus.
6. Reverse transcriptase and protease inhibitors have been effective in slowing down HIV.
7. A new fusion inhibitor was introduced in 2002.
8. HIV continually mutates and may become resistant to drugs.
Autoimmunity
1. In autoimmune disorders, autoantibodies attack healthy tissue.
2. These conditions may be caused by a virus that borrows a self-antigen, T-cells that never learn to recognize self, or healthy cells bearing antigens that resemble nonself antigens.
3. Some conditions thought to be autoimmune may actually reflect an immune system response to retained fetal cells.
4. Mutations in some genes may present the symptoms of an autoimmune disease.
Allergies
1. An overly sensitive immune system causes allergies.
2. In an allergic reaction, allergens bind to IgE antibodies on mast cells, which release allergy mediators.
3. A subset of helper T cells secrete cytokines that contribute to allergy symptoms.
Objective: Altering Immune Function
Vaccines
1. Vaccines are disabled pathogens or their parts that elicit an immune response, protecting against infection by the active pathogen.
Immunotherapy
1. Immunotherapy uses immune system components to fight disease.
2. Hybridomas are artificial cells that consist of a B cell fused with a cancer cell and produce monoclonal antibodies (Mabs) that can target specific antigens.
3. Cytokines boost immune function and destroy cancer cells.
Transplantation
1. Autografts transfer tissue from one part of a person's body to another.
2. Isografts are tissue transfers between identical twins.
3. Allografts involve tissue transfers between members of the same species. These transplants can cause tissue rejection reactions.
4. A Xenograft is a cross-species transplant. A danger of these transplants is that they can set off a hyperacute rejection.
5. Graft-versus-host disease involves a rejection of recipient tissues by transplanted bone marrow.
6. The success rate of transplants is improved by the use of immunosuppressive drugs, by stripping antigens from donor tissue, and by matching donor to the recipient.
A Genomic View of Immunity-The Pathogen's Perspective
1. Analyzing the genomes of pathogens may reveal the molecular basis of pathogenesis.
Crowd Diseases
1. Crowd diseases readily spread through populations and can cause epidemics.
2. Native populations with no immunity can be devastated by the introduction of new diseases.
Bioweapons
1. A variety of pathogens have been adapted to military use including anthrax.
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***If you are exempting the final exam:
1. All classwork, presentations, and any quizzes must be completed by ____May 11, 2018______________
Congratulations on completing Genetics Honors! 