BIOLOGY 2450: GENETICS SUMMER 2020 SYLLABUSWELCOME! - Please put this syllabus on your desktop

Remember what cognitive scientist, Dr. Art Markman said about thinking more effectively and building “high quality knowledge?” It is not possible to build high quality knowledge if you are distracted by your phone. In our Zoom class or in Ingram 4102 in Summer 2 or when at home studying, put your phone away. Do not check it until end of class at and put it in another room at home when studying. If you have a family or personal emergency that requires a text or phone call from you, please go into hallway or another room to complete it.

Professor: Dr. Julie Westerlund For Summer 1: Zoom classroom Meets 8:30 to 9:50 AM: Monday, Tuesday, Wednesday, Thursday, Friday Attendance is mandatory.

For Summer 2: Classroom Location: Bruce and Gloria Ingram Hall 4104Class Meets 8:30 to 9:50 AM: Monday, Tuesday, Wednesday, Thursday, Friday Attendance is mandatory.. Office: Supple Bldg. 214 Zoom Office Hours: 10:00 to 11:00 M, T, F or by appt or just stop by. Phone: 245-3361 (office), or (512) 560-8276 (cell)Email: jw33@txstate.edu

Important Dates: Last Day to Drop with 100% Refund is June 16Last Day to Drop with Automatic W is July 10Last Day to Withdraw is July 29

TEXTS 1. Required text – Genetics- A Conceptual Approach by Benjamin Pierce. 6th Edition

2. Sapling Plus. Information about it is in Canvas resources.

3. Required lab text: Lab Manual BIO 2450 – Dr. Bergh

4. Sign up for my free Educreations site at Register for the genetics problems videos and create a password (post it somewhere, maybe on yourwall) and all the videos should be there for you. Let me know if you have any trouble seeing thevideos. Students can register by going to the following link:

http://www.educreations.com/sr/F747BB The course code is F747BB if you decide to

go to the Educreations website directly instead and sign up for a free account.

5. Purchase Play-Dough (4 different colors) in small containers. Keep at home in Summer 1.

Course Description and Objectives: This course is an introduction to genetics and provides a strong foundation in the main genetic disciplines, Molecular, Transmission, and Population Genetics If you have worked hard in this course, by the last class day, you will possess a genetics toolkit that will allow you to ponder questions and ideas, and problem solve within these disciplines and interpret stories in the news concerning genetics. A toolkit is a set of tools designed to be used together or for a particular purpose (1). Examples of genetic tools that you will use include the familiar Punnett Square, Chi-Square statistical tests, Hardy-Weinberg equation and many more.

Bring lab clothes in Summer 2 1. Closed Toe Shoes (no sandals or flip-flops)2. Long pants (no shorts or short dresses) 3. Full-shirts (no exposed shoulders, no tank-

tops or spaghetti straps)4. Hair tie (tie long hair back in a pony-tail)

If you are not wearing these clothes, you will not be allowed in the genetics lab

Lab is for 3 hours. Do not ask to leave early.

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This course is built upon Genetics Society of America (GSA) Learning Frameworks: https://genetics-gsa.org/wp-content/uploads/2019/08/GSA-Genetics-Learning-Framework-2015.pdf

Grading Policy: Lecture: 70% Based upon 1) Assignments/Quizzes (worth 10%), 2) Best 3 out of 4 exams (worth 10% each)

and 3) Comprehensive Final Examination (worth 30%). Bring Texas State ID or Driver License to exams

Lab: 30% Based upon attendance, participation, lab quizzes, assignments and written papers

Attendance: Not part of final grade unless you miss more than 6 classes. See note below on attendance. Attendance is taken both in Zoom and during face-to-face in Summer 2.

Make up Exams: No make-up exams. Lowest of the four exams, including missed exam, will be dropped.

Academic Integrity: https://www.txstate.edu/honorcodecouncil/Academic-Integrity.html

It is expected that students will discuss assignments with each other, but any assignment turned in should be your own work. Also, you are not allowed to give aid or seek aid from any source external to the course resources when you take a test. For example, searching for a test answer on Chegg or Yahoo Answers etc. during a test is a violation of the honor code (see below). Those that violate the honor code will be penalized including removal from the class or university.

Learning and teaching take place best in an atmosphere of intellectual fair-mindedopenness. All members of the academic community are responsible for supportingfreedom and openness through rigorous personal standards of honesty and fairness.Plagiarism and other forms of academic dishonesty undermine the very purpose of theuniversity and the value of an education.

Texas State University Honor Code

As members of a community dedicated to learning, inquiry, and creation, the students, faculty, and administration of our university live by the principles in this Honor Code. These principles require all members of this community to be conscientious, respectful, and honest.

WE ARE CONSCIENTIOUS. We complete our work on time and make every effort to do it right. We come to class and meetings prepared and are willing to demonstrate it. We hold ourselves to doing what is required, embrace rigor, and shun mediocrity, special requests, and excuses.

WE ARE RESPECTFUL. We act civilly toward one another and we cooperate with each other. We will striveto create an environment in which people respect and listen to one another, speaking when appropriate, and permitting other people to participate and express their views.

WE ARE HONEST. We do our own work and are honest with one another in all matters. We understand how various acts of dishonesty, like plagiarizing, falsifying data, and giving or receiving assistance to which one is not entitled, conflict as much with academic achievement as with the values of honesty and integrity.

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Your Foundation in the Genetics Course:

1. Attendance: Attendance is mandatory and will be recorded. In case of illness or family emergency, students are allowed up to 6 excused absences. Absences will need to be documented with reason for absence and turned in by a hard-copy written letter on the last day. If you miss more than 6 classes, points will be deducted from your overall grade average as determined by the instructor. Come to class either the Zoom class in Summer 1 and our actual classroom, (Ingram 4104) in Summer 2 in order to develop a solid understanding ofgenetics. Perfect or near perfect attendance is rewarded with borderline grade boost-ups! :)

2. Assignment/Quizzes: Mandatory. Students are expected to complete all 35 assignments and submit them to Canvas by the due date. Plan on completing so that you will understand genetics and be successful on the tests and on the final examination. I don't accept late work but will give you an extra two days beyond the due date for times when you have an emergency. Each day late will result in a 10% reduction. Since I have provided the emergency buffer in allowing two days beyond the due date, there is no reason for you to ask me to accept work that is even later. And, I will also drop your 5 lowest assignments/quizzes. Please organize your time.

3. Course Binder: (My recommendation for you to be successful.)Please note: You may have alternate way to organize in a remote learning environment. My successful geneticsgenetics students in the past when we met face to face always had an organized course binder. If that does not work for you remotely, then find some system of organization. For example, you could organize our class as a folder on your desktop with each of the four tests having a different electronic folder. If you want a good grade in this course, you need to have a system of organization.

Course Binder (2 or 3 inch) that is organized into the following sections. I believe it will be easier for you to print out documents and organize them in a binder but that is not required since we are remote in Summer 1.

Suggested sections: (You can choose how you want to organize but be organized!)Section 1: Syllabus

Section 2: Test Review Questions for Assignment AssignmentsSection 3: Lecture Notes and Handouts (put date on these)

Section 4: Assignment Assignments with time stampSection 5: Practice quizzesSection 7: Practice Tests

Section 8: Information on gene that you chose to research on OMIM

How to Succeed: 1. Read the assigned readings before lecture and review the powerpoints in resources after each lecture. 2. Do the assigned problems, check your answers using the solutions manuals that are on Canvas resources. 3. Very important! Watch the Educreations videos that are designed for you as you work through the problems. 4. Work in study groups, visit SLAC genetics tutors and visit me during office hours for further help. 5. Keep your study materials organized in your course binder or in electronic folders. Be organized!!6. Be prepared for the exams by knowing how to approach the problems and understand the concepts and terms.

Barzun's Laws of Learning: Becoming a Scholar

The simple but difficult arts of paying attention, copying accurately, following an argument, detecting an ambiguity or a false inference, testing guesses by summoning up contrary instances, organizing one's time and one's thought for study -- all these arts -- cannot be taught in the air but only through the difficulties of a defined subject. They cannot be taught in one course or one year, but must be acquired gradually in dozens of connections.

Organizing one's time and one's thought for study or Time on Task is the most important for success in geneticsCompleting your assignments will take time. Set aside 3 to 4 hours a day outside of class if you want a good grade in genetics.

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What to do after you have registered for the course (if you have not already).

1. Register for the genetics problems videos and create a password (post it somewhere, maybe on your wall) and all the Educreations videos should be there for you. Let me know if you have trouble seeing the videos. Students can register by going to the following link: http://www.educreations.com/sr/F747BB. The course code is F747BB if you decide to go to the Educreations website directly instead and sign up for a free account.

Bio 2450 Genetics Lab Summer 2020 Schedule (from lab syllabus)

Example: The step by step problem solving Educreations videos for the probability lab worksheet is shown below for Lab 1.

To see them, go to my Genetics Educreations video website.

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Month Lab Description In Class(pages from lab book)

June Probability Worksheet for Probability Lab(22 - 23)

(Find step by step answers onpage 1 of Educreations Videos

(labeled p. 17)

July Quantitative Genetics Quantitative Genetics Worksheet 1 & 2 (61

– 62) (Find step by step answers onpage 1 of Educreations Videos

(labeled p.51)

Please note: The page numbers may be slightly different but the problems are the same.

CLASSROOM CIVILITY

Disruptive behavior in the classroom is prohibited in Section 2.02 of Texas State's Code of Student Conduct. From: https://studenthandbook.txstate.edu/rules-and-policies/code-of-student-conduct.html

The term "classroom disruption" means behavior a reasonable person would view as substantiallyor repeatedly interfering with the conduct, instruction, and education of a class. Examples include

a. repeatedly leaving and entering the classroom without authorization (including coming to class late or leaving early without a valid excuse)

b. making loud or distracting noisesc. persisting in speaking without being recognizedd. resorting to physical threats or personal insults

e. using cellular phones and/or other electronic devices during the class, f. coming to class under the influence of alcohol or a controlled substance other

than prescription medicineg. eating or drinking in the classroom *(see below for allowed items) h. sleeping in class i. reading the newspaper during class

j. using a computer in class or other technology on activities not related to the classk. abusing others verbally or physicallyl. otherwise making offensive remarks

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*Drinks such as water, coffee, soda are fine. *Discreet foods such as a breakfast bar, or granola bar, candy bar are fine too.

However, foods that make others hungry or generate noise such as full-blown breakfasts including breakfast tacos or doughnuts are not allowed. Just be considerate of others trying to learn in class.

Course ScheduleDate Key Words & Concepts Videos and Websites- On tests,

there is an extra credit section that is often based upon this column. Keep information about this in electronic separate folder on desktop.

This column describes your assignments to be completed after the morning lecture. Follow module due dates for assignments and quizzes

MonJune 1

First Day!

Lecture Topic: Introduction to CourseWhat is the illustration on the cover of your textbook? Hint: Check the back cover of your book.

Concept MAP 1 – Introduction to Genetics I of highlighted (p.12) words in Fundamental Concepts after you watch Youtube video Mind Matters Show- Becky on the Concept Map Eukaryotic, Prokaryotic, Cell, Nucleus Gene, Alleles, Genotype, Phenotype, DNA, Chromosome, Chloroplast, Mitochondria

Concept Map 2 of highlighted words

Introduction to Genetics IINucleic Acids, RNA, DNA, A, T, G, C, Chromosomes, Bacterial (Prokaryotic) Circular Chromosome, Human (Eukaryotic) Linear Chromosomes, Replication, Mitosis, Meiosis,

Google a genetic condition or disease found on the human chromosome. Write information about it below:1. Name of condition?_________________2. Type of mutation?________________3. Symptoms of genetic condition?________________To find a gene go to chromosome map: Genes and Disease and pick a gene resulting in a genetic condition. https://www.ncbi.nlm.nih.gov/books/NBK22266/#A274

Find more information about it. From the Genome Data Viewer at

You should already have purchasedyour textbook and Sapling Plus. We use Sapling only for animations.Watch a three-minute video on howto create a concept map. The Mind Matters Show - Becky on the Concept Map or Go to https://www.youtube.com/watch?v=bmncg-Kzhq8Study Actively! Not Passively!

Do Assignment #1 for TuesdayRead Chapter 1 (p.1-12) and take detailed handwritten notes. Answer questions #18, #19, #23, #24, #25, #26 on page 15Go to Resources Tab and Check your answers in the Solutions Manual. Do this with all of your assignments.Make Concept Map 1 and Concept

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Transcription, Translation, Mutations

Make sure you have connector word(s) between your bubbles on your concept map. Example

https://www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_000001405.39

Research further by going toto http://omim.org Online Mendelian Inheritance in Man® An Online Catalog of Human Genes and Genetic Disorders

Describe information about the gene you chose and keep in coursebinder or electronic folder.Why did you choose this gene? Gene Name: Chromosomal Location:Phenotypic characteristic:Mode of inheritance: (How inherited?) Be prepared to share with your group during the next class.

Map 2 (see first column) of highlighted words in yellow.

Take a scan of notes, problems, concept maps and submit to Canvas.

You will be scanning and submitting all of your homework in this course.

Late assignments/quizzes will be reduced by 10% per day until the last day to accept.

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TuesJune 2

Lecture Topic: Introductory Concepts

Words /Concepts should be in notes

Genetics Story – Black Mesa, Arizona

Hopi Native American – Albinism

Albinism gene - OCA2 – Chromosome 15

Role of Melanin and Melanosomes (?)

Diastrophic dysplasia - Chromosome 5 (p.3)

Norman Borlaug – Green Revolution

Genome

DNA

RNA

Evolution

Divisions of Genetics: Transmission, Molecular

Population

Why is population genetics essentially the studyof evolution? (p.5)

Characteristics of a Model Genetic Organisms? Examples of Model Genetic Organisms?

Difference between two genes that each can cause albinism? OCA2 versus SLC24A5 (p.7)

Did zebrafish serve as model organism in the discovery of the human SLC24A5 gene? (p.7)

Gregor Mendel – “Father of Genetics” of modern genetics (mid- 1800’s)

What genetics discipline did Mendel work in?

Recent Developments in Genetics (p.11)

Epigenetics

RNAs (small interfering RNASs, microRNAs)

CRISPR/Cas9 (cover of book!) and Gene Editing

Remember, from the videos, that bacteriophage (a bacterial virus) has also been used in genetics research in genetic discoveries. This is not mentioned in the first chapter of your book because a virus is not considered living or anorganism.

Google: What is Genomics Chapter 1 on youtube https://www.youtube.com/watch?v=mmgIClg0Y1k

Note: Genomics is considered a part of themolecular genetics discipline.

Assignment #2Read Chapter 2 (p.17-23 only) and take notes. What is the blind man’s riddle? How does that analogy compare to mitosis? Do #20, #21 p. 44

Google: Learn Genetics or http://learn.genetics.utah.edu/Select Amazing Cells Select Inside a CellYou may need to enable Flash on your browser settings.

Look through these animations.

Make Concept Map 3 of highlighted words In your notes, describe how prokaryotic cell reproduction differs from eukaryotic cell reproduction. Include words such as origins of replication, binary fission, mitosis, circular chromosomes, linear chromosomesFeatures of eukaryotic chromosomes: homologous chromosomes, diploid, haploid, polyploid, centromere, two sister chromatids, telomeres. Concept Map 3 of highlighted words

Types of Cells

Prokaryotes (Bacteria, Archaea) Eukaryotes,

Differences between prokaryotes and eukaryotes packaging DNA, histones, chromatin, circular chromosomes, linear chromosomes

WedJune 3

Lecture Topic: Structure of Chromosomes, Packaging of DNA in chromosomes

What are the three fundamental events that must occur for any cell to reproduce?

1)_____ 2) ______ and 3)_______Section 2.2 p. 20

1. Genetic information must be copied

2. Copies must separate from each other

3. Cell must divide. Histones organize DNA, condensing it and preparing it for further condensation by nonhistone proteins. This compaction is necessary to fit large amounts of DNA (2 m/6.5 ft in humans) into the nucleus of a cell.Nonhistone is a general name for other proteins associated with DNA. This is a big group, with

Google: Learn Genetics or http://learn.genetics.utah.edu/Select Amazing Cells Select Inside a CellExamine different parts of the animal and plant cell. Listen to the explanation of the different parts of the cell and watch animations.Optional: WatchDr. Jim Boyne’s-(University of Bradford-United Kingdom) Talk: Noncoding RNAS (2013)https://www.youtube.com/watch?v=02_SVWsXdg0

Assignment #3 Read pg 287 Arctic Treks

"It's an amazing technical achievement to get a whole genome out of a hair sample," from 4000 years ago!!Spencer Wells, National Geographic

Read p. 296 (from 10.3) to page 303On page 297 draw structures in notes, Examine each figure in detail so that you can develop a complete understanding of these abstract concepts. Cut out your paper DNA nucleotides that you obtain from your module. Print and then be sure to cut carefully so the shapes are distinct. Build a

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some structural proteins and some that bind only transiently. Nonhistone proteins vary widely, even in different cells from the same organism. Most have a net (-) charge and bind by attaching to histones.

Concept Map 4 of Highlighted WordsStructure of DNA

5’, 3’ carbons in ribose 3′-OH, 5′-Phosphate (polarity)

adenineantiparallel strandscomplementary base pairscytosinedeoxyribonucleotide3’ end of DNA5’ end of DNAdeoxyriboseDNA (deoxyribonucleic acid)guaninemajor grooveminor groovemonomersnitrogenous basenucleic acidsnucleoside phosphatenucleotidesphosphate groupphosphodiester bondspolymerspolynucleotidespurinespyrimidinesribonucleotideribonuclease (RNase)riboseRNA (ribonucleic acid)thymineuracil

Answer questions as you view video DNA -Secret of Photo 51 in Assignment 3.

Describe the appearance of DNA.

Rosalind Franklin discovered ______distinct forms of _______.

What form of DNA is found in cells?

X shape in middle of Photo 51 indicates what?

What do the lines represent in Photo 51?

DNA model with them. Store nucleotides in plastic baggies.

Examine page 299 in detail. Can you find the 3’ end and the 5’ end of DNA…of RNA? Notice that each of the 5’ or 3’ carbons in either the drawing of DNA or RNA is labeled with a number. Count the carbons. They should be five with the 5’ carbon sticking off the ring structure. It is very important that you can identify the 3’ and the 5’ carbon in either RNA or DNA. Can you find those ends on your cut-out nucleotides?

Practice Worked Problems on page 305. Does it make sense?

Answer questions #10 p. 305#14, #15, #16, #17 p.306#26, #28, #32, #34, #35, #38, p.307/8Do Concept Map 4 of highlighted words You just need to just include the highlighted words in your concept map.

View DNA-Secret of Photo 51 -NOVAGo to https://www.youtube.com/watch?v=uYuo72X46pA

Begin viewing at 26:21….[visual of DNA in a beaker] to 34:00 (not long!)

Answer questions in the middle column about the video. Put answers in your assignment.

Concept Map 5 of highlighted words

Types of DNA and RNA sequencesGenome: A genome is an organism’s complete set of genetic instructions. Each genome contains all of the information needed to build that organism and allow it to grow and develop. Haploid organisms have one copy of the genome and diploid organisms have two copies of the genome.

Concept Map 6

Organization of DNA into Chromosomes

centromere (example of heterochromatin)

telomere (example of heterochromatin)

G-rich 3’ overhang of telomerechromatinchromosomes

Concept Map 7Differences between viral, eukaryotic

and prokaryotic chromosomeschromatindouble-stranded DNAsingle-stranded DNAdouble-stranded RNAsingle-stranded RNAcircular chromosomelinear chromosome

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Proteome-Complete set of proteins that occur within a cell, tissue or in an organismTranscriptome- is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells. (see Cech’s slide at 29 min section of talk that is coming up)

Look at the pie chart. What percent of the genome is transcribed (in red?) about 80%!What percent of genome is eventually translated in proteins (in yellow?) about 2%!Human genomes have approximately 3 billion nucleotides (C-value). 2% of the human genome is protein coding DNA and 98% is non-protein coding DNA (does not code for proteins). Some non-protein coding DNA is transcribed into functional noncoding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAssuch as long coding RNAs), while others arenot transcribed or give rise to RNA transcripts of unknown function. eukaryotic genomes: contain both unique

sequence DNA and repetitive sequence DNA (makes up half of human genome)

prokaryotic genomes: contain primarily unique sequence DNA with only repetitive DNA in sequences codingfor rRNAs and tRNAs.

viral genomes: contain primarily unique sequence DNA or RNA

C valueunique-sequence DNAmoderately repetitive DNA p.321 examples: Tandem repeats, interspersed repeats LINES and SINES long interspersed elements (LINEs) short interspersed repeated elements (SINEs)highly repetitive DNA examples: centromeric DNA, telomeric DNAacetylated DNA epigenetic changes

constitutive heterochromatineuchromatinfacultative heterochromatinheterochromatinhistones (found only in eukaryotes

& archaea)looped domainsnonhistonestopoisomerasesplasmidsnucleoid regionnucleousnucleosomesmethylated DNAphosphorylated DNA acetylated DNA epigenetic changes

nuclear membranenucleoid regionrepetitive DNAunique sequence DNAintrons (hint: found only in

eukaryotes)plasmids

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Thurs

June 4

Lecture Topic: Structure of DNAHumans have at least 65% unique sequence DNA in their genome but only 2% of that unique sequence DNA are genes that code for proteins. What is the function of the rest of the uniquesequence DNA? We will find out!Misconception that students often have about bacterial chromosomes: Students sometimes do not realize that the term single chromosome means there is only one chromosome in the organism. They may assume instead that it means single-stranded DNA which is NOT CORRECT. REMEMBER! bacterial chromosomes are made of double stranded (ds) DNA, just as eukaryotic ones are.

The typical prokaryotic genome is one circular dsDNA chromosome, but some prokaryotes are more exotic, with a main chromosome and one or more smaller ones.When a minor chromosome is dispensable to the life of the cell, it is called a plasmid. For example, Borrelia burgdorferi (Lyme disease in humans) has a 0.91-Mb linear chromosome, plus an additional 0.53 Mb ofDNA in 17 different linear and circular molecules.

Just for Fun!Recent Genetic News stories1. Neanderthal Genes, The human and Neanderthal genetic sequences are at least 99.5 % identical (in comparison to other species, chimpanzees are 98% identical Nature 437, 69-87 (1 September 2005) dogs share 18,000 of the 24,000 human genes)

In Figure Above1- Neanderthal Skeleton and Skull2- Modern Human Skeleton and Skull3. Blue Eye Mutation May Have Occurred Fewer than 10,000 yearsago in Europe, (Human Genetics, 2008)Enrichment: Recent News about Neanderthals and Modern Humanshttp://www.npr.org/2010/12/28/132243863/2010-a-good-year-for-neanderthals-and-dnaandhttp://www.newscientist.com/article/dn18869-neanderthal-genome-reveals-interbreeding-with-humans.html What is Central Texas’s most famous human fossil? Leanne, a female skeleton, Homo sapiens, approximately 11,000 years old found near Leander Texas. Leanne would look like modern humans today. http://www.texasbeyondhistory.net/plateaus/prehistory/images/leannes.html

About the new hominid the Denisovans: http://www.nature.com/news/2010/101222/full/4681012a.html

Assignment #4Read pages 312 to 332. Take notes over these sections.How is organelle DNA different from nuclear DNA and what does it code for?Do Concept Maps 5, 6, and 7 of highlighted wordsWhat is the evidence that mitochondria and chloroplasts are more related to bacteria?Heteroplasmy? Homoplasmy?Do the Worked Problems on page 326How is mitochondrial DNA different from nuclear DNA?Do Worked problems 1, 2 page 333Answer #12, #13, #14, #25, #28, #29, #30, #33 on pages 334-336

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Fri

June 5

Lecture Topic: Genetics of OrganellesNote: You do not need to memorize the functions of the different DNA polymerases nor the histone types in eukaryotes! Too many!

Assignment #5Read parts below of Chapter 12 and take notesRead Genetics Story: Topoisomerase,Replication and Cancer on p. 339How does camptothecin inhibit cancer? Does it only affect cancer cells?Review the Cell Cycle on page 23. Examine Figure 2.9. Where does DNA replication occur in the cell cycle? Hint: DNA duplication is the SAME THING as DNA replication.Why does DNA have to replicate?Read p. 340 - How many base pairs (bp) in a human zygote cell? Or any diploid human cell? What is semiconservative replication?Read page 343 to 360.Do Questions #25, #26, #29, #33, #34on page 368-369.Do Concept Map 8 of highlighted wordsNeed drawings of DNA replication in your notesPlease note: E. Coli has a circular DNA chromosome. What is the difference between a primer and a template strand?Why do eukaryotes have to use telomerasein some cells but not all?Does telomerase have RNA in it?Remember: DNA nucleotides can only be added to the 3’ end of DNA. Please examine carefully Fig 12.7 on page 346. Do you see that DNA polymerase (not shown) can only add nucleotides to the 3’ OH that is attached to the 3’ carbon on theDNA ring structure.

View Sapling Animations:12.1 (p 347), 12.2, 12.3 and 12.4 (p.353) and Action of Telomerase animationHow does DNA replication differ betweeneukaryotes and prokaryotes?

Mon

June 8

Lecture Topic: DNA replicationsemiconservative modelConcept Map 8 of highlighted wordsDNA ReplicationDNA helicasesDNA ligaseDNA polymerase IDNA polymerasesDNA primaseinitiator protein (prokaryotes) orORC protein complex (eukaryotes)lagging strand

Amoeba Sisters! Fun Video on DNA replicationhttps://www.youtube.com/watch?v=Qqe4thU-os8

DNA Replication Video with Quizhttp://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter3/animation__dna_replication__quiz_1_.html

Why do we need telomeres and telomerase?

Assignment #6 Genetics Story: Read Death Cap Poisoning on page 373. How could a mushroom kill a person?What does alpha-amanitin do to RNA Polymerase II, (RNAP II)?Read Chapter 13 p. 374 to 391, take notes. Focus on Figure 13.1, Table 13.2, Figures 13.4, 13.6, 13.8, 13.10, 13.11, 13.12, 13.15, 13.16Do Worked Problem 1 on page 392Do Questions #12, #13, #14, #15, #19, #24, #25 and #28 on pages 394-395.

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leading strand3’end of DNA5’ end of DNA(remember nucleotides can only be added onto

3’end!)Okazaki fragmentsorigin of replicationreplicatorprimosomereplication bubblereplication forkreplication unitreverse transcriptaseRNA primerrolling circle replicationcontinuous and discontinuous replicationproofreadingmismatch repairsingle-strand DNA-binding proteinstelomeraseAdding to the 3’ 0H end of DNA

http://www.youtube.com/watch?v=vtXrehpCPEE

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WE NOW BEGIN WORKING ON THE EXTRA PROBLEMS TEST REVIEW PACKET. You need to go to the CANVAS Resources Tab and open up that file. Do Test Review Problems 5.6, 5.8, 5.12, & 5.13 Watch the videos with those problems on the Educreationssite. I will check names so be sure to watch those videos.Do Concept Maps 9 and 10.

Tues

June 9

Lecture Topic: Transcription (makingRNA!)

Concept Map 9 of highlighted wordsTranscription in Prokaryotes: BacteriaDNARNAPromoter (-35 box )- (Consensus Sequence)Promoter (-10 box) – (Consensus Sequence)Polycistronic mRNASigma factor RNA polymeraseterminator sequences Rho-dependent vs. Rho-independenttemplate strandnon template strandConcept Map 10 of highlighted wordsTranscription in EukaryotesDNARNA polymeraseRNA polymerase I (for rRNA)RNA polymerase II (for mRNA and others)RNA polymerase III (for tRNAs and others)General Transcription FactorsCore promoter 1. Initiator for transcription (+1) 2. TATA box (-25 to -30 bp upstream)TATA binding Protein (TBP)Regulatory Promoter 1. CAAT box (See Figure 17.6 p. 498) 2. GC box (See Figure 17.6 p. 498) 3. Enhancers (thousands of bases upstream

Watch video of The Non-(protein) coding

Genome: Finding Treasures in our Junk DNA by Dr. John Rinn [first 26 minutes]

https://www.youtube.com/watch?v=3okle8DKbA8

Questions for Video:Why does he use a cherry pie? 1:44

The long non-coding RNA (lncRNA)

XIST is used for what? (Frame 14:22)

Do you produce this lnRNA?(Answer will depend on your sex)What are some other known examples of lncRNAs? lncRNA RoR? lncRNA FIRE? lncRNA associated with

P.falcipaurm (malaria host)?What is the significance of this slide at frame 22:57 of video?

Why does the speaker say at video

Assignment #7 Read Genetics Story: RNA Molecules and RNA Processing p.399. What wasthe mutation that caused the Tsar’s son Alexei blood to not clot in hemophilia? How does that relate to RNA processing?Read Chapter 14 p. 400-422. Take notes, Make Concept Map 11 Remember there are a lot of details in these chapters. Focus on the big picture. How is RNA processed? Howdoes it differ between eukaryotic RNA and prokaryotic RNA? What arethe roles of small of the newly discovered small RNAs?Focus on the following figures. 14.7, 14.12, Connecting Concepts on page 413, 14.17, 14.19, 14.21, 14.22, 14.23

Do Worked Problem: Problem1, 2 on page 423Do (p.425) #21, #23, #24, #24, #25, #26, #28, #29, #30, #31, #34Do Test Review Question 5.23Watch Video.

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of initiation site (-200 to -1000 or more) and sometimes downstream (+200 to +1000 or more)

Transcriptional activator proteins (Figure 13.6) No terminator sequences in eukaryotestemplate strandnon template strand

frame 26:20 that if remove a pieceof “junk DNA”, and not be able tolive”?Does he evidence for that?

You may stop viewing at this frame 26:20 or for fun watch the rest! Typical Misunderstanding: Examine Figure 13.4 on page 378.Do you notice that RNA nucleotides can only be added by RNA polymerase to the 3’0H end?If that is the case, then the RNA will grow in a 5’ to 3’ direction. Does that make sense? Watch Tom Cech’s talk again Brief History of Non Coding RNAs (2015)https://www.youtube.com/watch?

v=9oPgXr6jAC8 Begin Viewing it at 8:00 min

until 13:00 min and answer the question below.

What are three functions of noncoding (non protein coding) RNA?

1. Ribozymes: biochemical reactions

2. Provide “handles” to hold proteins into a complex such as in telomerase DNA

3. Regulate transcription by recruiting histone modifying enzyme complexes (lncRNAs)

You may watch the rest of the video for fun! Dr. Cech describes the experimental research that helped scientists begin to understand the function of lncRNAs.

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Wed

June 10

Lecture Topic: RNA ProcessingConcept Map 11of highlighted wordsDifferences between eukaryotic and prokaryotic

transcription Transcription and translation coupledPolycistronicMonocistronicRNA enzymes (ribozymes)mRNAIntrons (only in eukaryotes remember)Exons (only in eukaryotes remember)mRNA splicingpoly(A) mRNAspoly(A) polymerase (PAP)poly(A) tailprecursor mRNA (pre-mRNA)spliceosomesnRNAS, snRNPs5’ capping3’ modification-polyadenylationpoly A tailspliceosometemplate strandself-splicing introns (discovered by Tom Cech in

1982…you saw him in the video Brief History of Non Coding RNA

Alternative processingRNA editingtRNArRNA ribosomal proteinsSO MANY RNA TYPES!!Small RNAS siRNA, miRNA,Ribosome assembly in nucleolus snoRNAs, snoRNPs, rRNA, rRNPsCRISPR, CAS protein – (like an immune system

for prokaryotes!) lncRNAS – “dark matter of the genome” examples, XIST RNA (only in females!) eRNAs

How is a gene defined today?Sapling Animation 14.1Animation 14.3

Assignment #8 Read parts below of Chapter 15 and take notes.Genetics Story: Child without a Spleen on p. 429What does the RPSA gene code for?What happens if there is a mutation inthe RPSA gene? How did scientists determine that the condition ICA (absence of a spleen) was due to a mutation in the RPSA gene?Read p.431-435, p 438-452. Study Figures 15.11, 15.17, 15.18, 15.19, and 15.21 Do Concept Checks #1, #4, #5, #7, #8, and #9

Do Test Review Questions Q4.1 (Analytical Approach–Watch Video

Do Worked Problems, Problem #1, #2, and #3 on pages 454 to 456.

Do #5, #9, #15, #16, #17, #22a, #26a, #32, #26, #32, #33, and #35

Do Concept Maps 12, 13, 14, 15, 16, and 17

Need drawings of translation in your notes representing all 3 stagesInitiationElongationTermination

Thurs

June 11

Lecture Topic: Translation

Concept Map 12 of highlighted words

Proteins and Amino AcidsStructure of amino acidsAmino groupCarboxyl groupR groupHydrogen group20 naturally occurring amino acids

What is hereditary hemochromatosis? Google it!

Type 1 hemochromatosis is due to mutations in the HFE gene and is one of the most common genetic disorders in the United States, affecting about 1 million people. Itmost often affects people of Northern European descent.

Is Type 1 hemochromatosis is due

Assignment #9 Read Genetics Story Gene Mutations and DNA Repair on page 515. Have you ever heard of Lou Gehrig’s Disease or ALS? What happened to Lou Gehrig? Can you describe his mutation and how that caused his illness? Read and take notes on pages 516 through Radiation section on p. 532. There is a lot of information in this chapter. Structure

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Peptide bondProtein4 levels of structure of proteinsCheck out how gamers contribute to science by folding proteins!http://fold.it/portal/

Concept Map 13 of highlighted wordsGenetic CodeCodonReading frameFrameshift mutationTriplet codeNonoverlapping code Universal Code (almost)Degeneracy (redundancy) of codeStop codon (or nonsense codons)Start codonWobble in anticodon

Concept Map 14 of highlighted wordsStructures in Translation ProcessStruture of tRNAAmino acid on tRNAtRNA genes RNA polymerase IIIaminoacyl–tRNA (charged tRNA)aminoacyl–tRNA synthetaseanticodon on tRNAPairing between codon (mRNA) and anticodon

(tRNA)RibosomerRNArRNA genesRibosomal proteinsRNA polymerase I

Concept Map 15 of highlighted wordsInitiation of TranslationInitiation in Bacteria-Ribosome binding site (Shine-Delgarno sequence) 8 to 12 bp

upsteam of AUG start site initiator tRNA is fMetInitiation in Eukaryotes – Initiation factors cap binding protein bind to 5’cap on mRNA

40 S ribosomal subunit AUG codon initiator tRNA carries Met amino acid 60 S ribosomal subunit Poly A tail loops the 3’ end back to 5’end thereby stimulating translation!

to a faulty enzymatic protein or a non-enzymatic protein?

From DNA to Protein Required Videos to WatchVideoSteps of Translation from Initiation to Termination by Alila Medical Media https://www.youtube.com/watch?v=qIwrhUrvX-k

Fun Claymation video on InitiationNote: How 3’ poly A tail loops back to 5’ cap site!http://www.youtube.com/watch?v=BrgUQLz6RrM

Do overview tour concerning transcription and translation. Include in paragraph about the concepts presented and usefulness of the animation https://www.youtube.com/watch?v=D3fOXt4MrOM

Fun Video on Proteins throughout bodyhttp://www.youtube.com/watch?v=suN-sV0cT6c

your study around1. Different types of mutations a. Molecular b. Functional 2. Mutation rate3. How chemical and radiation can induce mutations

Do Worked Problem on page 525

Be familiar with the contents of Table18.2 on page 524 on mutations

Other important figures to focus on include: 18.2, 18.3, 18.5, 18.6, 18.8, 18.12, 18.13, 18.14

Watch Sapling Learning Animation 18.1 concerning expanding repeats.

There are a lot of chemical mutagens that are discussed in this chapter.It is a bit overwhelming!Just be familiar with Base Analog: 5-bromouracil Oxidative RadicalsIntercalating agents

You will not expected to memorize these mutagens or how they mutate!Too much information!

What might happen to you and your DNA if you sunbath in Sewel Park? Or anywhere outside? Be specific about the effects of radiation. Your answer should include thymine dimers.

Do Problems at end of chapter 18#2, #3, #17, #18a, #22, #27a, #28 on pages 552 to 554.

Do Concept Map 18 and 19

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Concept Map 16 of highlighted wordsElongation of Translationcharged tRNAwobblereading framemRNARibosome Peptide bondPeptidyl transferaseRibosome moves (translocates) from 5’ to 3”chain-terminating codonscodon on mRNAE siteP siteA sitePolysome (polyribosome)

Concept Map 17 of highlighted wordsTermination of TranslationmRNAtRNARibosomeStop codons UAG, UAA, UGARelease factors Polypeptide (protein)

Friday

June 12

Lecture Topic: DNA MutationsConcept Map 18 of highlighted wordsTypes of MutationsBase SubstitutionTransitionTransversionInsertionDeletionFrameshift mutationExpanding nucleotidesForward mutationBack mutationMissense mutation Special type of missense- Neutral mutationNonsense mutationLoss of Function MutationsGain of Function MutationsLethal MutationSuppressor MutationMutation rateConcept Map 19 of highlighted wordsCauses of MutationSpontaneous mutations Replication errors, strand slippage, unequal

crossing over, deamination, depurination, Induced mutationsMutagen- Base Analogs 5 BU for thymine

Describe how DNA is repaired. Assignment #10In this section, focus on transposons in humans. Read beginning on page 534 Section 18.4 to p.536. Read pages 541 to 543.

In this section (p. 544 to 547) focus on how DNA is repaired. Remember many details here, you just need to know basically how DNA is repaired (not all the steps!) Just look over the figures in this section to gain an understanding as to how it occurs. Not expected to memorize the details!Do Concepts Maps 20 and 21Answer #14 on page 553Do Test Review Questions7.1, 7.2, 7.3, 7.5 and 7.10. Watch Videos on these

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Oxidative radicals Intercalating agentsRadiation induced – thymine dimers

Mon

June 15

Lecture Topic: Transposans and DNA Repair!Concept Map 20Transposable ElementsTransposaseDNA TranspososnsRetrotransposons SINES, Alu sequences LINESTransposable Elements as Genomic Parasites!

Concept Map 21DNA RepairMismatch repairDirect repairBase-excision repairNucleotide Excision RepairDouble Strand Break Repair

Wow!!! 45% of Human genomemade of sequences that are related to transposable elements! p. 536Barbara McClintock on page

539 (what did she do?)

END of TEST ONE MATERIALReview Assignments #1-#10 for Test One on Tuesday June 16

Tues

June 16

Test One over Assignments #1-#10 Assignment #11 Mendel Paper: Read pages 298-303 Student Reading section of Gregor Mendel’s classic paper and the nature of science in genetics courses Authors: JULIE F. WESTERLUND and DANIEL J. FAIRBANKS

{Found in genetics class Canvas resources tab, bottom of list]

“Nature of Science” [NOS] concerns the practice of science and the development of scientific knowledge. This reading guides you though a study of Gregor Mendel’s discoveries in heredity correlated to six major characteristics of the nature of science[NOS].Describe the six major characteristics of the nature of science in a one page (entire page!) essay. You may provide examples of each.

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Date Lecture Assignment is due at next class periodWed June 17

Lecture Topic: Mendel and Nature of ScienceFun stuff to consider! You have been studying molecular genetics for threeweeks. How similar percentage wise is the genetic sequence between individuals within the human species? ___________

How different are two individuals in terms of their nucleotides? _____________

Hint: 1 in every 1000 nucleotides differs.Hint: We have 3,000,000,000 base pairs in our haploid genome. Hint: We are diploid so we have 6,000,000,000 base pairs total

Bacterial Geneticist Rosemary Redfield: How Different are We?https://www.youtube.com/watch?v=8bh35mRD_FI&list=PLgh8WcYegg44oownMBBHKTjjvxf-Z5fc8&index=2

Discussion of Mendel Paper and the six major characteristics of the nature of science

Assignment #12 Transmission Genetics There are two parts to Assignment assignments #12-#34We are no longer doing concept mapping. However, you can choose to continue to do it on your own. Two parts of your Assignment must include:1. Reading and note-taking either through notes or concept maps General Guideline (1/2 or more pages of notes per assignment)2. Answers to problems showing your work! Do not just write answers from solutions manual. Need to show your work!_________________________________________________________1.Read Genetics Story: The Genetics of Blond Hair on page 47.Answer: How did geneticists Kenny and Myles found the gene for blond hair on the short arm of chromosome 9. Hint: Genome-wide association study (but explain what that is!).

2.Read/take notes on Chapter 3 p.48-61. Figures are important to spend time on in this reading. Fig 3.4, 3.5, 3.6, 3.7, 3.9, and Tables 3.2, 3.3, 3.4 and Connecting Concepts, Worked Problems #1, #2 on pages 71-72

3. Do Problems from Lab Manual on page 17. It is found in the Resources Tab and also at the end of this syllabus. Watch the Educreations Videos for the answers.

4. Watch video on Educreations-Lab Manual (p.17 approx), #11 on using the binomial distribution for unordered events problemsFound on web – Educreations web page 1, Do #27, p.75

4.. Do Test Review Questions 11.1, 11.3, 11.4, 11.5, 11.6, 11.7, 11.10, 11.13 You need to watch the videos on these questions6. Do #18, #21, and #22, on page 75Test Review Question 11.13 is shown below.

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Optional enrichment:Dr. Eric Lander (MIT prof) discusses historical development of Mendel’s Laws (old-school lecture with chalk but terrific!!) http://ocw.mit.edu/courses/biology/7-01sc-fundamentals-of-biology-fall-2011/genetics/mendels-laws

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ThursJune 18

Lecture Topic: Crosses in Genetics & BinomialGenotype, Phenotype, True-breeding (pure-breedingstrains) Mendel’s experimental designs, Principle of Segregation, dominant, recessive, Punnett squares, branch diagram, locus, testcrosses, monohybrid crosses, Gain of Function Mutation, Loss of Function MutationUse of Product Rule and Sum Rule, Binomial Distribution in GeneticsWatch Video: Youtube Penguin Prof: Solving Genetics https://www.youtube.com/watch?v=Qcmdb25RnyoWatch video and answer these questions. Her videos are fun and easy to understand!

a. How is an allele different from a gene?b. The Penguin Prof describes the product rule and the sum rule using a Venn diagram. Was this section of the video helpful in your refreshing your understanding as to when to use each of these?c. When you use the word AND, what rule do you apply?d. When you use the word OR, what rule due you apply ?e. What is the probability of having 3 daughters in arow?f. What is the probability of rolling a 3 or a 4 on a six-sided die? g. A trihybrid cross! What is the probability of an offspring ppQqRR from parents PpQqRr and PpQQRR?

Assignment #13 Transmission Genetics Read/take notes on Chapter 3 p. 61to first half of 67. Do Worked Problem on page 65/67. Do Test Review Questions : 11.9, 11.15, 11.16 (a, b), 11.17, 11.18 (a,b), 11.19, 11.20, 11.24a, 11.26, 11.28, 11.31(a, b)Do Problems: #23, #31, #33, #34 on pages 75 to 76.

FridayJune 19

Lecture Topic: Dihybrid & Trihybrid CrossesPrinciple of Independent Assortment, dihybrid crosses, trihybrid crosses (Remember Penguin Prof Video from last lecture?)

Assignment #14 Transmission Genetics Read/take notes on Chapter 3 p. 67 to 73 including worked prob.Required Video to Watch: Chi-SquareWatch Youtube: Bozeman Science Chi squarehttps://www.youtube.com/watch?v=WXPBoFDqNVkCorrection on Bozeman Video: You cannot accept the null hypothesis. You either reject the null or fail to reject null.Do Test Review Questions: 11.8, 11.27, 11.28 & Watch VideosDo Question #41 on page 78.

Monday

June 22

Lecture Topic: Chi Square TestingChi Square Testing (goodness of fit)

Assignment #15 Transmission GeneticsRead/take notes Chapter 2 p. 23 to 40Be sure to carefully read Connecting Concepts on page 27, Counting Chromosomes and DNA MoleculesView Sapling Plus Animation 2.3- Independent AssortmentDo questions #14, #15, #16, #17 on page 43 and #26, #28, #29, #30, #33 and #34See differences between meiosis and mitosis at Nova:http://www.pbs.org/wgbh/nova/miracle/divi_text_13.html

Practice viewing Lilly Anthers in meiosishttps://bio.rutgers.edu/~gb101/lab10_meiosis/meiosis_web/lily_frame.htmlRead Genetics Story on page 81: The Sex of a DragonDoes the warmth of the nest of a bearded dragon make any difference to the production of dragon males? How would climate change affect the sex ratio in bearded dragons?Read/take notes on Chapter 4 pages 82 to 89. Answer questions

21

#3, #4, #5, #7, #8, #17 on pages 102 to 103

TuesJune 23

Lecture Topic: Cell Cycle, Meiosis & MitosisCell Cycle and MitosisEukaryotic chromosomes, karyotype, mitosis, meiosis, sex chromosomes, sex determinationAlteration of Generations Plant Sex! – Penguin Profhttps://www.youtube.com/watch?v=uJNnZtE00ko

HAVE PLAYDOUGH TODAY

Assignment #16 Transmission GeneticsRead/take notes on Chapter 4 p. 89 to 102 including Worked Problems 1 and 2 and Connecting Concepts Recognizing Sex-Linked Inheritance (p.97) Can you explain coat color colorationon a tortoiseshell cat?Read the passage below from our previous genetics book

Watch my 15 minute Educreations video on Genetic Symbolism. You may have already used Drosophilia type symbols in lab.

Do Test Review Problems 12.23, 12.24, 12.26, 12.27 and 12.28Watch videos on these test review problems.Do Problems #23, #24, #25, #26, #27 on page 104.

WedJune 24

Lecture: Genes on Sex ChromosomesSex LinkageBarr BodyRandom X InactivationNondisjunction of sex chromosomes

Assignment #17 Transmission GeneticsRead Genetics Story on page 109 The Odd Genetics of Left-Handed Snails. See Figure 5.17 on page 131What is exception to Mendel’s inheritance patterns in the coiling of snails?Read/take notes on Chapter 5 on pages 109 to 136.

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X Chromosome Inactivation

https://highered.mheducation.com/sites/

9834092339/student_view0/chapter13/

x_inactivation.html

Do Test Review problems 13.6, 13.28, 13.32, 13.33

Be sure to watch complementation testing on the above video from Test Review Problem 13.28!Do problems #12, #13, #25, #26, #29 on pages 139 to 142

Bring a color photo of your cat or a friend’s cat tomorow.

Print and read Cat Genetics.docx from TRACS resourcesWatch Cat Coat Genes PPT at https://facultystaff.richmond.edu/~lrunyenj/bio554/cat/sld001.htmCat Coat Color Genotype Assignment

1. Find a friendly cat2. Determine its coat color genotype using the Cat Coat

Genes pdf and ppt in the links above3. Take a picture of the cat and write the genotype under

the picture.Be prepared to explain to your lab group the genotype of your cat tomorrow.

Thurs

June 25

Lecture: Modified Mendelian InheritanceCat Genetics Cat Population Genetics Cards (turn in July 31)Modified Mendelian InheritanceComplete/Incomplete DominanceCodominancePenetrance/ExpressivityLethal Alleles 2:1Multiple AllelesGene Interaction Recessive Epistasis 9:3:4 Dominant Epistasis 12:3:1 Duplicate Resessive Epistasis 9:7ComplementationSex Influenced and Sex LimitedCytoplasmic InheritanceGenetic Maternal EffectGenomic ImprintingAnticipation (repeating DNA sequences)Genotype influenced by environmentDiscontinuous Characteristics vs. Continuous CharacteristicsPolygenic vs. Pleiotropy (opposites!)Multifactorial characteristics

Assignment #18 Transmission Genetics Read Genetics Story: The Mystery of the Missing Fingerprints on page 145. What and where is the molecular mutation that creates no fingerprints? Read/take notes Chapter 6 p.146 to 155. Do Worked Problems on pages 165 to 166. Do Test Review Questions 11.32, 11.33 11.34, 11.36Watch Videos on these problems

Do Problems #19, #24, #30 on pages 168 to 171

Tutorial on Solving Pedigree Problemshttps://www.youtube.com/watch?v=HbIHjsn5cHo

Fri

June 26

Lecture Topic: Pedigree Analysis Pedigree AnalysisConcordance

Assignment #19 Transmission Genetics Read Genetics Story: Building a Better Banana on page 217Are the bananas that we eat from the grocery store genetically modified organisms (GMOs)?Read/take notes on Chapter 8 p. 218 to 242, Work Problem 1*Importance of these chromosomal mutations in evolutionCheck out the following helpful video on paracentric inversionsand meiosis https://www.youtube.com/watch?v=Z13o9KGltWA

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Do Test Review Problems: 16.4, 16.5, 16.6, 16.13 Do problems #1, #2, #3, #15, #17, #20, #21, #36

Mon

June 29

Lecture Topic: Chromosomal MutationsChromosomal InheritanceChromosomal MutationsImportance of chromosomal mutations in evolutionParacentric, Pericentric InversionsVariations in Number and StructureNondisjunction of AutosomesAneuploidyPolyploidy

Watch Chromosome 2 Formation https://klru.pbslearningmedia.org/resource/evol07.sci.life.evo.genconnect/human-chromosome-2/

Prepare for Test Two over Assignments #12-#19Test 2 Practice Question #4 on Rat colors p. 2 video pageTest 2 Practice Question #5 on Onion Colors p. 2 video page

Tues

June 30

Test Two over Assignments #12-#19

After you take Test 2 and after doing Assignment #20:watch this video on linkage. It is found on page 2 of Educreations video pages.

Assignment #20 Transmission GeneticsRead Genetics Story: Linked Genes and Bald Heads on p. 173Do the Think-Pair-Share question..Common Folkore suggests…Where did the researchers locate the gene for “pattern male baldness?” How did they find it?Read/take notes Chapter 7 p. 174-189Do Test Review Questions: 14.1, 14.2, 14.3, 14.4, 14.6 and watch the videosOptional:For another description of linkage and 2 point testcrosses.View Cal State Northridge Prof Dr. Cindy Malone

View Malones 2 point.pdf on Genetics TRACS resourcesView MIT prof Dr. Eric Lander’s lecture on the historical development of linkage at http://ocw.mit.edu/courses/biology/7-01sc-fundamentals-of-biology-fall-2011/genetics/linkage-and-recombination-genetic-mapsI enjoyed watching his lecture.

Wed

July 1

Lecture Topic: Gene LinkageGene Linkage and Linkage Mapping in EukaryotesRecombination FrequenciesGenetic Maps with 2 genes

Assignment #21 Transmission Genetics Read Chapter 7 p. 189 to 197 or view Malone’s two lectures and take notes on it. If the book is confusing, I recommend Malone’s Lectures. Do Test Review Questions: Q14.2 (Chinese Primrose Problem!...Watch Video!), 14.9, 14.16, 14.17, 14.18Do Problems #3, #4, #5, #7, #10, and #11 on page 209

From Dr. Cindy Malone – California State NorthridgeLecture notes on

Determining map distances between three genes

View Malones 3 point test cross.pdf on our Genetics TRACS resources More examples from Dr. Todd Nickle : Canadian professorhttp://universitygenetics.blogspot.com/p/classical-gene-mapping.htmlSee Dr. Nickle’s Alien Trihybrid Cross video and Determining Gene Order video

Further resources to understand mapping on your Sapling Learning site are shown below:

24

Additional Reading: Read p. 198 to 200 Mapping Human Genes Answer Question #12 p. 209

Watch these videos!

Chinese Primrose Problem Q14.2 - Required video to watch on mapping 3 genes and found on page 2. These required videos found on page 2 of my Educreations

videos are very helpful in understanding how to do the 3 point test cross which is determining the order of 3 genes and the distances between the genes.

Check it out!

Thurs

July 2

Lecture: Gene Linkage involving 3 genesGene Linkage and Linkage Mapping in Eukaryotes3 Point Test Cross (Mapping 3 genes)LOD scoresMapping Human Genes

Assignment #22 Transmission GeneticsRead Genetics Story: The Genetics of Medieval LeprosyQuestion: What did the examination of bacterial leprosy

DNA from medieval skeletons reveal about this horrible disease?

Read Chapter 9 p. 252 to 264 on bacterial and mapping bacterial genes

Read the Concepts Summary page on p.277

Do Review Test Question, Q15.1, 15.3 (Watch Video)

Do #3, #4, #5, #6, #22 on pages 280-281.

Friday

July 3

Lecture: Bacterial Genetics MappingBacterial GeneticsMapping Bacterial GenesFrom Sapling Plus: Video

Educreations Video Page 2

Happy 4th of July!!

Assignment #23 Molecular GeneticsRead Genetics Story: Operons and the Noisy Cell on page 461How does “noise” relate to operons?Read Chapter 16 p. 462 to 475 on E.Coli Lac Operon.

Watch Educreations Video: Mirodiploids on video page 2 for 17.10Below is a link to an interactive tutorial on the lactose operon. Watch it! It will clarify some of the types of mutants.https://www.life.illinois.edu/mcb/150/private/lectures/lac_operon.htmlDo #1, #4, #5, #6 and #19 on pages 486 to 487.

Do Test Review Question 17.10

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For #19, use the gold reference sheet above. You will be able touse this on the test. Are you stuck on #19 of the assignment? Watch my educreations video on a similar problem at the link below. https://www.educreations.com/lesson/view/merodiploid-problems/22823904/?s=Lkw3pm

Summer 2

Monday

July 6

Lecture: Gene Regulation I - BacteriaClass Meets Face to Face in Ingram 4104 Welcome Back! :) (hopefully)Class introductions in small groups.Gene Regulation in Prokaryotes - BacteriaE.Coli Lac Operon

Assignment #24 Molecular GeneticsRead Chapter 16 pages 476 to 484 and Section 9.4 on p. 267Do #7, #8, #9, #11, #26, #30

Tues

July 7

Lecture: Gene Regulation II - Bacteria, VirusesE.Coli - Trp Operon – Attenuation!Handout on Gene Regulation in Bacteriophage –(Virus) Phage Lambda

Assignment #25 Molecular GeneticsRead Genetics Story: Genetic Differences that Make Us Human on page 491. If we humans differ in DNA sequences from chimpanzees by approximately 1 or 2 percent, then how can we be so different?Read Chapter 17 pages 492 to 495, 497 to 508;Focus on Figures 17.5, 17.6, 17.7,17.9,17.10, and 17.13Do Problems #1, #2, #3, #4, #7, #8, #10, #11, #12, #13, #14, #23 on pages 510 to 511.

Wed

July 8

Lecture: Gene Regulation in EukaryotesPromoters, Enhancers, GTFs, HREs, Chromatin Remodeling, Gene silencing, DNA Methylation Control of Gene ExpressionView: http://learn.genetics.utah.edu/content/variation/newtricks/

Bring Play Dough!

Assignment #26 Molecular GeneticsRead Genetics Story: Epigenetics and the Dutch Hunter WinterWhat happened to the people who were fetuses in the Netherlands during this time? What might have happened to their DNA due to starvation of their mothers who were pregnant? What is the thrifty phenotype hypothesis? Read Chapter 21 p. 642 to 647What is epigenetics? Epigenetics has been called “inheritance but not as we know it. P.643 What does that mean?Do Problem #2, #3, #4, #5, #6, #19, #21, #23 on p.659-660

Thurs

July 9

Lecture: EpigeneticsMolecular mechanisms that can create epigenetic phenotypes1. Changes in Patterns of DNA Methylations a. Methylation of Cytosine Nucleotides next to guanine nucleotides How does “royal jelly” lead to a queen bee? p.6462. Chemical Modifications of Histone Proteins3. RNA molecules that affect chromatin structure and gene expression

Honeybees and Epigeneticshttps://www.youtube.com/watch?v=NlBt8qr9B74

Review for Test 3 over Assignments #20-26

26

Nova : Epigeneticshttps://www.youtube.com/watch?v=xG8nt9OlODo

Friday

July 10

Review for Test 3 over Assignments #20 - #26

Monday

July 13

Test 3 over Assignments #20-#26 Assignment #27: BiotechnologyRead Genetics Story: The Origin of Spineless Sticklebacks on page 663. How did spineless stickleback fish originate? What gene was responsible? What was the mutation and how would that affect function? Read Chapter 22 on pages 664 to 665, p.666 (Sec 22.2) to 673. Answer #5 on page 688Read Genetics Story: Editing the Genome with CRISPR-CAS9What did scientists do to restore the dystrophin protein in mice using the CRISPR-CAS9 system? Has this type of gene therapy been done in humans yet?Read Chapter 19 pages 560 to 570 and pages 582 to 586 Do Worked Problem 2 on page 600, Do #4, #5, #6, #7, #24, #17, #30, #38, #39

Tues

July 14

Lecture: Biotechnology 1Recombinant DNA TechnologyRestriction EnzymesEngineered NucleasesCRISPR-Cas9 Genome EditingSeparating and Viewing DNA FragmentsGel ElectrophoresisPolymerase Chain ReactionDideoxy Sequencing -Watch the video: https://www.youtube.com/watch?v=3M0PyxFPwkQ

Next Generation Sequencing

PCR videos (2)http://learn.genetics.utah.edu/content/labs/pcr/

http://highered.mcgraw-hill.com/sites/dl/free/0072835125/126997/animation38.html

New advances in genetics

Watch Gene Editing and CRISPR-CAS9https://www.youtube.com/watch?v=2pp17E4E-

O8

Question to answer in notes. How is the CRISPR-CAS9 system similar to restriction enzymes and how different?Ancestry.com (23 & Me type sites)New York Times article on Accuracy

Assignment #28: BiotechnologyRead pages 586 to 589: DNA Fingerprinting, and p. 596 on Genetic Testing/Gene Therapy. Look very closely at Figures 19.26 and 19.27 and Table 19.3. Do #18, #23.

Wed

July 15

Lecture Biotechnology 2DNA FingerprintingGoogle: DNA InteractiveSelect ApplicationsSelect Human Identification Module and Hit profiling On: http://www.dnai.org/d/index.htmlApplication to DNA profilingForensics – Identification of Humans through DNA

Assignment #29 Population GeneticsRead Genetics Story: The Wolves of Isle Royale on page 749. Why did the population of wolves decrease on Isle Royale?Read Chapter 25 pgs. 750 to 757Do problems #2, #3, #4, #5, #15, #17 and #18 on page 774. Do Test Review Question 21.2 Review again video: Blue-Footed Penguins? (not real but fun) https://www.youtube.com/watch?v=oG7ob-MtO8c

27

9/11 and DNA Profiling videohttps://www.youtube.com/watch?v=ZsyQWTSEkHo

Blackett Family ActivitiesSee http://www.biology.arizona.edu/human_bio/activities/blackett2/str_frequency.htmlRead about Gene Therapy by going to the Learn Genetics siteWrite a paragraph on each of the 4 sections.https://learn.genetics.utah.edu/content/genetherapy/

Thurs

July 16

Lecture: Calculation of Allele FrequenciesAllele FrequenciesGenotype Frequencies Hardy-Weinberg EquilibriumWatch on Youtube Penguin Prof: https://www.youtube.com/watch?v=oG7ob-MtO8c

Assignment #30 Population GeneticsRead Chapter 25, pgs 757 to 760Do Test Review Questions #3, #5 and #6. Do #20, #22, #23, #27, #28a,b on pages 774 to 776Watch Video on Calculation of X-linked Allele Frequencies, Educreations Video page 2

Friday

July 17

Lecture: Is population in Hardy Weinberg Equil?X-linked Allele FrequenciesTesting for Hardy-Weinberg EquilibriumUsing Hardy-Weinberg to Estimate Allele FrequenciesInbreeding

Assignment #31 Population GeneticsRead Chapter 25, pgs 760 to 766Do Test Review Questions #15 and #23, Watch VideosDo #7, #8, #9, #10, #25, #33 (yes, disgusting problem), #34

Mon

July 20

Lecture: Evolutionary ForcesForces that change allelic frequencies:MutationMigrationRandom Genetic Drift Bottle Necks and Founder Effects

Assignment #32 Population GeneticsRead Chapter 25, pgs 766-772 (Table Method is also known as General Selection Model]

Do Test Review Question #26- Must WATCH Video on effectsof Natural Selection on Allele Frequencies [TABLE METHOD]Do Worked Problem on page 768-769…very important

Do Worked Problem on page 768…very importantDo #11, #12, #13, #14, #37, #49 [TABLE METHOD] on page 777

Sapling Learning Mini-Tutorial on Animation 25.1 p. 770Population Genetics Review Videos [Look at the series of optional videos on population genetics] Watch on Youtube Bozeman Science: Solving Hardy-Weinberg Problems

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https://www.youtube.com/watch?v=xPkOAnK20kw

Watch on Youtube Bozeman Science: Natural SelectionBiology Essentials 001https://www.youtube.com/watch?v=R6La6_kIr9g

Watch on Youtube Bozeman Science Examples of Natural Selection Biology Essentials 002 https://www.youtube.com/watch?v=S7EhExhXOPQ

Watch on Youtube Bozeman Science: Genetic DriftBiology Essential 003https://www.youtube.com/watch?v=mjQ_yN5znyk

Watch on Youtube Joseph Ross (Prof at CSU) Lecture on Selection CoefficientStart at 41:48 to the end of videohttps://www.youtube.com/watch?v=nl1DfLITS5Y

Watch Selection Part I on Fitness Watch on Youtube Brad Swanson (Prof at Central Michigan) Selection Part Ihttps://www.youtube.com/watch?v=LPSp9yeKXDw

Watch on Youtube Brad Swanson Selection Part II (optional)https://www.youtube.com/watch?v=8ufyWB8IoIo

Watch on Youtube Brad Swanson Selection Part III (optional)https://www.youtube.com/watch?v=3V8z7p7qpH4

Watch on Youtube Brad Swanson Selection Part IV (optional)https://www.youtube.com/watch?v=j-cU9LRG2ME

Tues

July 21

Lecture: Selection as Evolutionary Force Natural SelectionFinding new allele frequencies after natural selection– use the Table Method (also known as General Selection Model) Mutation and Natural Selection - Equilibrium

Assignment #33 Population GeneticsRead Genetics Story: Taster Gene in Spitting Apes p. 779Can you taste PTC? How did Fischer and his friends discover that the ability to taste PTC arose independently in our differentspecies between human and chimpanzee?Read Chapter 26 p. 780 to 788, p.797 to 796Do #1, #5, #6, #8, #9, #16 on pages 800-801

Wed

July 22

Lecture: Evolution of New SpeciesEvolutionIf evolution is occurring in a population, is that population in Hardy-Weinberg equilibrium? Molecular Variation Formation of New Species SpeciationNeutral Mutation HypothesisBalancing SelectionMolecular ClockConservation GeneticsGoogle: Making of the Fittest: Natural Selection and Adaptation HHMIOr go to Pocket Mouse Video

Assignment #34 Transmission Genetics [Quantitative]Read Genetics Story:Corn Oil and Quantitative Genetics on p. 715Can people predict the oil content of a plant on the basis of its breeding when it is a complex characteristic?Read Chapter 24 p.716 to 726, Do Worked Problem on page741Do Test Review Questions 22.1, 22.4 and 22.5 Do #1, #2, #3, #4, #5, #6, #7, #8, #16, and #17

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http://www.hhmi.org/biointeractive/making-fittest-natural-selection-and-adaptation?utm_source=BioInteractive+News&utm_campaign=5d443884ac-BioInteractive_News_Vol_99_2017_7_12&utm_medium=email&utm_term=0_98b2f5c6ba-5d443884ac-69918469

Thurs

July 23

Lecture: Quantitative Genetics Part 1Continuous TraitsStatistical Tools used in Quantitative GeneticsPopulation, Sample, Mean, Variance and Standard Deviation, Correlation CoefficientRegression

Assignment #35 Quantitative GeneticsRead/Take notes on Chapter 24, p.727 to 734Do: #9, #10, #11, #12, #26, #27, #31

Friday

July 24

Lecture: Quantitative Genetics Part 2Broad Sense HeritabilityNarrow Sense HeritabilitySelection ResponseSelection Differential

Review for Test 4 over Assignments #29 - #35(You will not be tested over Assignment #27 & #28)

Complete: Cat Population Genetics Cards

Mon

July 27

Review for Test 4Turn in Cat Population Genetics CardsTest for Hardy Weinberg Equilibrium in Central Texas Cats

Review for Test 4

Tues

July 28

Test 4 over Assignments #29-#35 Read Chapter 23 p. 696 to 699

Wed

July 29

Lecture: Genetics and CancerRegulation of the Cell CycleProto-Oncogenes, Tumor Suppressor genesReview for Final Examination

Review for final examination (All except #11, #27, #28)

View Molecular Genealogy http://learn.genetics.utah.edu/content/basics/molgen/

Thurs

July 30

Biodiversity of HumansMigration View Molecular Genealogy http://learn.genetics.utah.edu/content/basics/molgen/

Review for final examination (All assignments except #11, #27, #28)

Friday July

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Review for Final ExaminationClass does not meet

Tuesday

Aug 4

Final Examination8:00 to 10:50 AM(if you have a class conflict see me asap)

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Lab I - Probability Lab. [You need to complete this in Summer 1 by June 18]First Watch Video: Youtube Penguin Prof: Solving Genetics https://www.youtube.com/watch?v=Qcmdb25RnyoBasic Probability

What is the probability of getting a head when flipping a coin? The answer, assuming the coin is “fair”, is 1 outof 2 or 1/2. There exist two possibilities: either a head or a tail is possible and we understand that bothpossibilities are equally likely. This is the simple basis for thinking about probability.

By definition, we say that the probability of some event occurring:

P(event )=number of ways an event can occur (or is expected to occur )number of possible outcomes

In our example of flipping a coin, there is only one way of getting a head and there are two possible outcomes:

heads or tails. Thus,

P( H )=12

What is the probability of rolling a “6” on one die? Dice have six sides, all of which are equally likely to landface up when we roll one. The side with six spots is one of those possibilities.

P( 6 )=16

What is the probability of getting an even number with one roll of a die? What is the probability of getting any number 1 through 6 on one roll of a die? Notice that the probability of a100% certain event = 1, and the probability of an impossible event (like rolling a “7” with one die) = 0.

This kind of probability applies directly to genetics. For example, if two parents are Aa heterozygotes, what isthe probability that they will have a child with the genotype AA? We know from Mendelian genetics and thePunnett square that the Aa x Aa cross produces on average 1/4 AA offspring, 2/4 or 1/2 Aa offspring and 1/4aa offspring. From the cross Aa x Aa,

P(AA child )=14

So far we have been estimating probabilities from our understanding of the mechanisms by which theseevents occur. We know that coins have two sides, dice have six sides and we know how Mendelian geneticsworks. However, we can also estimate probabilities from empirical data. For example, about 130 babies out ofevery million born are albinos. We can say that the probability of a child being albino is 130/1 million or1/7700.

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Here there is a direct relationship between the frequency of an event and its empirically estimated probability.Take another example: if 57 out of every 100 automobiles in San Marcos are pickup trucks, what is theprobability that an automobile chosen at random in San Marcos would be a pickup?

P(pickup )=57100

=0. 57

By the way, what is the probability that an automobile chosen at random is not a pickup? That is,

P(not a pickup )=43100

=0 . 43=1−P(pickup )

In other words, if P(event) = the probability of the occurrence of that event, 1-P(event) is the probability ofthat event not occurring.

How do we calculate the probability of more than one event occurring? The rest of this lab and your labexercise will deal with these kinds of probability questions.

The Multiplicative Rule (also known as the “both-and rule” or the “product rule”). The multiplicative rule

describes the probability that events A and B will occur simultaneously.P(A and B )= P(AB ) = P( A ) * P( B )

Example: What is the probability of rolling two dice and getting a “1” on both?

P( 1 and 1 )= P( 1 ) * P( 1 )= 16∗

16=

136

What is the probability of drawing an ace and a heart with one draw from a deck of cards?

P(ace and heart )= P(ace ) * P( heart )= 4

52∗

1352

=522704

=1

52Going back to our earlier genetics problem, if both parents are Aa heterozygotes, what is the probability thattheir child is an AA homozygote? We could use the Punnett square thinking, or we can think about thisproblem another way using the multiplicative rule. Having an AA child means that both parents donate an Aallele to the child. So, the probability of getting an A allele from mom,

P(A from mom )=12

Likewise,

P(A from dad )=12

So,

P(A from mom and A from dad )=P( AA child ) =12∗

12=

14

The Additive Rule (also known as the “either – or rule” or the “sum rule”). The additive rule describes theprobability that either event A or event B occurs:

P(A or B)= P( A ) + P( B) - P(A and B )

where P(A and B) is the probability that both events occur simultaneously. If it is impossible for both events tooccur simultaneously, then P(A and B) = 0.

Example: Drawing from a standard deck of 52 cards, what is the probability of drawing either an ace or aheart? The probability of drawing an ace,

P(ace )= 4

52 (there are 4 aces in a deck of cards)Likewise,

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P(heart )= 1352 (there are 13 hearts in a deck of cards)

The probability of drawing an ace and a heart (i.e. the ace of hearts):

P(ace of hearts)= 1

52

So, P(ace or heart )=

452

+1352

−1

52=

1652

What is the probability of getting either a head or a tail on one flip of a coin?

P( H )= 12 ,

P(T )= 12 and P(H and T on one flip )= 0 .

It is not possible to get both a head and a tail from one coin flip. So, P(H or T )= P( H )+P(T )-P(H and T )

= 12

+12

−0=1

Now, what is the probability that the child is heterozygous, Aa? From the Punnett square we know the answer

is 1/2. We can also figure this out using both the multiplicative and additive rules. There are two ways to make

a heterozygous (Aa) child:Event 1:

P(A from mom and a from dad )=P (Aa child ) =12∗

12=

14 (multiplicative rule)

or,Event 2:

P(a from mom and A from dad )=P( Aa child ) =12∗

12=

14 (multiplicative rule)

So to get a heterozygous child, we can have event 1 or event 2 occur,

P(event 1 or event 2 )=P(event 1)+P(event 2) -P(1 and 2) (additive rule )

=14

+14

−0 (having both occur in one child is impossible )

=12

What is the probability of getting three heads and one tail from four coin flips? We can use the same thinkingas above, taking into account all of the possible ways to get three heads and one tail. For example, we couldhave the series H,H,H,T in four flips,

P(H,H,H,T )=12∗

12∗

12∗

12=

116 (multiplicative rule)

Or we could have H,H,T,H with probability,

P(H,H,T,H )=12∗

12∗

12∗

12=

116 (multiplicative rule)

We could figure out all of the ways to get three heads and one tail and then use the additive rule. However,there is an easier and faster way to think about this problem using the binomial distribution.

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The binomial distributionThe binomial distribution is very useful in genetics. The binomial is used when we are interested in theprobability of repeated independent events where there are two choices (or possible outcomes) for eachevent. The example of flipping four coins discussed above fits this distribution. Notice that we do not careabout the particular order in which the events occur. Three heads and a tail could happen as H,H,H,T orH,H,T,H etc. If we are interested in the probability of a specific series, say H, H, H, T (that is, heads on the firstthree tosses and tails on the last) we would use the multiplicative rule (answer = 1/16). However, if we wantto calculate the probability of three heads and one tail in any order, we can use the binomial.

The general formula for the binomial distribution is the expression:

(p+q )N

Where:p= the probability of an event occurringq= the probability of an alternate event occurringN= the number of observations

In our coin flipping example, an event is getting a head on one flip (p = 1/2); the alternative is getting a tail (q =1/2); N is the total number of coins flipped. From a genetics viewpoint, an event might be a genotype or aphenotype. N would be the total number of individuals observed.

The general formula of the binomial can be expanded (as shown below) for different values of N. Thecoefficients of the terms in the expansion show a symmetry and are arranged in Pascal’s triangle:

N The formula The expanded binomial_______

0 (p+q)0 11 (p+q)1 1p + 1q2 (p+q)2 1p2 + 2pq + 1q2

3 (p+q)3 1p3 + 3p2q +3pq2 + 1q3

4 (p+q)4 1p4 + 4p3q + 6p2q2 + 4pq3 + 1q4 5 (p+q)5 1p5 + 5p4q + 10p3q2 + 10p2q3 + 5pq4 + 1q5

Notice that the coefficient of each term tells us how many different ways a combination of events can occur.The exponents tell us about the arrangement of the events (i.e how many events and how many alternativeevents). An example will make this clear. Back to four coins, what is the probability of getting three heads andone tail on four flips? In this problem, N = 4, p = (probability of getting a head on any one flip) =1/2 and q =(probability of getting a tail on any one flip) =1/2. If we examine the row in Pascal’s triangle for N = 4 we can

find the term that has p3 q in it. Notice that the whole term is 4p3q. This tells us that there are four differentways to flip four coins and get three heads (p3) and one tail (q). So,

P(3 heads and 1 tail) = 4p3q = 4 (1

2)3(

1

2)=

416

=14

If we wanted to flip five coins and find the probability of getting two heads and three tails we would scan the

row for N=5 looking for the term that includes p2 q3 . That would be 10p2q3. There are 10 different ways to

flip five coins and get two heads and three tails.

What is the probability of a family with 4 children consisting of 2 boys and 2 girls? There are six different waysthis can occur according to the order of births: bbgg, ggbb, bggb, gbbg, bgbg, gbgb. The term whichsummarizes the probability for four siblings (N = 4) consisting of two boys and two girls is 6p2q2 where p= the

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probability of a boy and q= the probability of a girl at any birth (i.e. p=1/2, q=1/2). The coefficient (6) gives usthe number of birth orders. The term p2q2 gives the probability of any one particular birth order (e.g. bbgg).So,

P(2 boys and 2 girls out of 4 kids) = 6p2 q2 = 6

16=

38

The other terms in the expansion of (p+q)N where N = 4 are the probabilities of the distributions of boys andgirls. For instance, the term 1p4 describes the probability of having 4 boys and no girls in a family of four, andthe term 4pq3 is the probability of having one boy and three girls in a family of four. The exponent on p tellsyou how many boys are in the family, and the exponent on q tells you how many girls.

Another way to calculate specific terms in the expanded binomial is to use the general formula for thebinomial (also called the factorial method). The probability of x successes in N trials is given as follows:

P(x of event 1 and y of event 2 )=[N!x!y! ] px q y

where:N = Number of observations (= x+y)N! = N(N-1)(N-2)(N-3)…(1)x = the number of successes of event 1y = the number of successes of the other event, event 2p = probability of the first eventq = probability of the second eventThe term in brackets provides the coefficient that tells us the number of possible ways to have x of event 1and y of event 2. pxqy gives us the probability term. This general formula can be used if you don’t have Pascal’striangle or for large values of N.By definition 0!= 1, and x0 = 1

The best way to start is by writing down what you know. For example:p = ? q = ?N = ? x = ? y=?

Let’s go back to the four siblings problem and utilize the general formula. What is the probability that we gettwo boys and two girls in four siblings?

p = 1/2 q = 1/2N = 4 x = 2 y=2

35

P(2 boys and 2 girls )=[N!x!y! ] px q y = [4!

2!2! ] p2 q2

=[4*3*2*1(2*1)∗(2*1 ) ] p2 q2

=6 p2 q2

=6 (12 )

2

(12 )

2

= 616

= 38

This example illustrates how the general formula can be used to get the terms found in Pascal’s triangle.

Consider another example: A trait is determined by a single gene with simple dominance (AA and Aa have thesame phenotype). If both parents are heterozygous for this trait, what is the probability of having fourchildren, with one expressing the recessive trait?

Again, start by writing down what we know:N = 4 childrenx = 3 dominant childreny = 1 recessive childp = 3/4 (the probability of a child with the dominant phenotype – probability determined from Mendel’s 1 st

Law)q = 1/4 (the probability a child with the recessive phenotype)

P(3 dom. and 1 recessive )=[N!x!y! ] px q y = [4!

3!1! ] p3 q1

=[4*3*2*1(3*2*1)∗(1) ] p3 q1

=4 p3 q

=4 (34 )

3

(14 )

= 108256

= 0 . 42

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THIS is part of ASSIGNMENT #12 This is part of your lab grade and you can work on it earlier. WATCH ALL THE Educreations VIDEOS associated with these lab questions.

NAME:_________________________. DUE JUNE 18WORKSHEET FOR PROBABILITY LABInstructions: Answer the following questions by writing the appropriate answers in the blanksprovided. Turn in the worksheet before leaving class today.

1. If two parents are Aa and Aa, what is the probability that they have a homozygous child?a. 1 b. 3/4 c. 1/2 d. 1/4 e. 1/8 1.________

2. You have a coin and a die and toss them both. What is the probability of getting an even number and ahead?a. 1/4 b. 1/2 c. 1/12 d. 8/12 e. 7/12 2.________

3. You have a deck of cards. You choose one card. What is the probability of getting a jack or a club?a. 1/4 b. 13/52 c. 9/12 d. 16/52 e. 5/52 3.________

4. What is the probability of flipping 5 coins and getting a tail on the first flip and heads on the last 4 flips?

a. 1/4 b. 1/2 c. 1/8 d. 1/16 e. 1/32 4.________

5. What is the probability of flipping 5 coins and getting 2 heads and 3 tails in any order?

a. 10/32 b. 1/2 c. 1/8 d. 10/16 e. 1/32 5.________

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6. Considering four gene loci, what is the probability that an individual with the genotype AaBbCcDd will

produce a gamete that has the genotype A B C D ?

a. 1/4 b. 1/2 c. 1/8 d. 1/16 e. 1/32 6.________

7. Consider a tetrahybrid cross (AaBbCcDd x AaBbCcDd), what is the probability that offspring will be

homozygous dominant for all four traits (AABBCCDD)?

a. 1/4 b. 1/16 c. 1/64 d. 1/128 e. 1/256 7.________

8. If a tetrahybrid is test crossed (i.e. crossed to a homozygous recessive individual, aabbccdd), what is the

probability that a phenotypically recessive individual offspring will be produced?

a. 1/4 b. 1/2 c. 1/8 d. 1/16 e. 1/32 8.________

9. In couch potato fleas, pink eyes are dominant to blue eyes and straight wings are dominant to curly. A crossbetween a homozygous pink eyed, straight wing female is mated with a blue eyed, curly winged male. The F 1

progeny are then crossed to produce the F2 generation. What is the probability of producing a blue eyed, curlywinged flea in the F2 generation?a. 1/4 b. 1/2 c. 1/8 d. 1/16 e. 1/32 9.________

10. Considering question 9 again, what is the probability of producing a pink eyed, straight winged flea in theF2 generation?a. 9/16 b. 9/32 c. 1/8 d. 1/16 e. 1/32 10.________

11. What is the probability of a family of 6 consisting of 4 girls and 2 boys?

a. 10/128 b. 15/64 c. 1/64 d. 1/256 e. 15/32 11.________

12. In humans, albino individuals are homozygous recessive for an autosomal gene. If two normal parents

have an albino daughter and a normal son. What is the probability that their son is homozygous?

a. 1/4 b. 1/2 c. 1/8 d. 2/3 e. 1/32 12.________

13. Referring to question 12, what is the probability that the father is heterozygous?

a. 1/4 b. 1/2 c. 1 d. 1/16 e. 0 13.________

14. Again referring to question 12, what is the probability that out of 4 children, 2 are albino?

38

a. 1/256 b. 67/256 c. 5/24 d. 54/256 e. 54/128 14.________

15. Again referring to question 12, what is the probability that out of 4 children, 2 or more are albino?

a. 1/256 b. 67/256 c. 5/24 d. 54/256 e. 54/128 15.________

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For Extra Practice on Probability Read Lab Manual concerning Probability and answer questions below.

1. What is probability?

2. What is the probability of rolling a four with one roll of a die?

3. Define the multiplicative rule, “product rule”?When would you apply the multiplicative rule, “product rule” in genetics problems?

4. Define the additive rule, “sum rule”? When would you apply the additive rule, “sum” rule in genetics problems?

5. Watch Video: Youtube Penguin Prof: Solving Genetics https://www.youtube.com/watch?v=Qcmdb25Rnyo

Watch video and answer these questions. Her videos are fun and easy to understand!

a. How is an allele different from a gene?

b. The Penguin Prof describes the product rule and the sum rule using a Venn diagram. Was this sectionof the video helpful in your refreshing your understanding as to when to use each of these?

c. When you use the word AND, what rule do you apply?

d. When you use the word OR, what rule due you apply ?

e. What is the probability of having 3 daughters in a row?

f. What is the probability of rolling a 3 or a 4 on a six-sided die?

g. A trihybrid cross! What is the probability of an offspring ppQqRR from parents PpQqRr and

PpQQRR?

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Now we get to a little more complicated problems..

1. What are the chances of having 4 boys AND 3 girls in a family?

Think of all the ways this could happen! This is considered an unordered event.

Now, you probably think…I can use the multiplicative rule for each possibility and then sum all the possibilities. For example: Boy Boy Boy Girl Girl Boy Boy =[1/2]6 =1/64 ANDBoy Girl Boy Boy Girl Girl Boy = =[1/2]6 =1/64 AND……..etc. Too much effort!

Hmmm maybe I should use a shortcut method for these “unordered events”?Yes! The General Formula for the binomial! Watch this video below as it is worked out. Watch Youtube Genetics Binomial Expansion from Smart University https://www.youtube.com/watch?v=mP3pBjHx7oo

a. What are the chances of having 4 boys AND 2 girls in a family?

Pascal’s Triangle can also be used instead of the General Formula for a shortcut.

a. What are the chances of having 4 boys and 2 girls in a family? “unordered events” again! Label p=boy event , q = girl event Note: 6 events ……That would be (p + q) 6 Use 7th row

41

b. What is the probability that 4 boys born first and then the last 2 born are girls? This is an ordered event! You cannot use the general formula for the binomial or Pascal’s Triangle for this ordered event.

Now you are ready to complete the probability worksheet.

c. What is the probability of getting all of one gender?

Watch the video https://www.youtube.com/watch?v=mP3pBjHx7oo for the answers!

Extra enrichment (optional)Resource Video: Khan Academy explains how Pascal’s Triangle is derived and used.https://www.youtube.com/watch?v=v9Evg2tBdRk

Answer:1 p6 + 6p5q + 15p4q2 + 20p3q3 +15p2q4 + 6p2q4 + 1q6 is the row to use

Choose 15p4q2 because that would be 4 boys and 2 girls. 15p4q2 = 15/64 or .23 Was that easier?

42

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