Cathy Key North Carolina Central Univ

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Genomics at North Carolina Central University

Course Overview

BIOL3100 Geneticsat NCCU is divided into 4 main topics: classical genetics (25%), molecular genetics (40%), population genetics (10%) and genomics (25% course).

The course begins with a review of mitosis in the context of cancer and meiosis in the context of nondisjunction (Turner's and Klinefelter's Syndromes) and moves into Mendelian Genetics and modifications to Mendel's findings.  Pedigree charts and twin studies follow and then the course takes a molecular track.  During the molecular genetics portion of the class, students review the basics of DNA structure, transcription, and translation and special focus is place on the importance of properly splicing pre-mRNA transcripts using a case study I created that uses beta-thalassemia and RNA-based gene therapy (  We then move into Genomics focusing on the Human Genome Project and the Drosophila melanogaster annotation project. 

BIOL4400 Introduction to Researchis a non-didactic semester long course.  Students can elect to take 1-3 credit hours.  Three credit hours in my lab means 15 hours of work per week.  This work can be making reagents for the lab, participating in wet-lab research (Drosophila crosses or molecular techniques), or conducting genomic annotation research.


Genomics was introduced into Genetics at NCCU in the 2009-2010 academic year.  Individual students were assigned genes in Fall 2009 in two course, one of which was Genetics.  This did not work well, because we had only Drosophila mojavensis contigs and I was too new to it all.  Spring 2010 worked much better.  I reused some of the contigs I claimed in Fall 2009 and student groups of 3-4 were used. Two of the six groups found one gene and used Gene Model Checker.  However, they used the two T.A.'s out-of-class hours in order to accomplish this much. 

In the BIOL4400 Introduction to Research course, a group of four students successfully annotated two Drosophila mojavensis contigs, presented a poster at the College of Science and Technology's Undergraduate Research Day Spring 2010.  The contigs were submitted to GEP.

Over the years, annotation during BIOL4400 (Introduction to Research) for undergraduates worked well, with successful contig submissions. In BIOL3100 (Genetics) Walk-through tutorials from GEP website were helpful to those students in favor of reading and thinking.  Oral presentations at the end of the semester went well also: good peer pressure for success in annoation.  Caution: wait until students have completed Genome Browser research before introducing them to the Gene Model Checker. 

In 2015 I joined a committee to write a series of modules on 'Understanding Eukaryotic Genes". I introduced it to Genetics lab students in Spring 2016 as beta-tester.  After pre-/post-quiz revisions were completed, I implemented the quizzes and collected data during the 2016-2017 academic year.  Notably, in Summer 2017, students were assigned the SIX "Understanding the Eukayrotic Gene" Modules and had a much easier time annotating!  First time I've ever been able to submit complete contigs from undergraduate Genetic students!See Lab Schedule below.

Lessons Learned and Future Plans

1.) Students need more time. 

2.) I need to sell Genomics.  

The Genomics section of the text I use (Genetics: A Conceptual Approach by Benjamin Pierce) is execellent.  I now have a powerpoint based on the text figures and a few personel touches to enlist students in the genomics cause.  Also, I find that it is helpful to use a weather forecast analogy when explaining the gene prediction models.  Channel 4 may call for snow in some locations, Channel 11 may call for snow in slightly different locations on the map,  which one is right?  Only way to know is to see for yourself.  


For the 2010-2011 year, I am aiming to give students 20-24 hrs of class time to work on annotation projects.  I plan to incorporate more GEP materials (simple intro to BLAST was very good).

Syllabus: 4 weeks Genetics Summer 2017

North Carolina Central University

Department of Biological & Biomedical Science


4 credit hours

                          Genetics: A Conceptual Approach 5th Edition by Benjamin A. Pierce. MacMillan Press. The genetic textbook is required – it will be used immediately and frequently.

you must obtain a copy – it is a course requirement.

Contact Info:

Dr. Cathy Silver Key


2246 Mary Townes Science




Office Hours:

MTWR 3:50-4:30 a.m.

Or by appointment


Class Meetings

Lecture              2235 MTSB on MTWR 1:20-3:50 p.m.

Lab                    2181 MTSB

Section 01 CRN#10535: 9:00 A.m.-12:30 p.m



Course Website: found at NCCU Blackboard site - then look for Genetics section you are enrolled in.


Required Text: 

REQUIRED Textbook title: Genetics: A Conceptual Approach FIFTH Edition by Benjamin A. Pierce, 2014 Publisher = MacMillan Higher Ed.

Course Description:  The course is divided into three general topics: ‘classical’ genetics (50%), ‘molecular’ genetics’ (50%). Prerequisites: Grade of “C” or better in BIOL 2200 . A study of the broad areas of Mendelian inheritance, linkage, sex-connected inheritance, multiple alleles, multiple genes, molecular genetics, mutation, population genetics, chromosomal aberrations, and application of genetics problems. In lab, concepts of genetics are applied to answer questions in the model organism, yeast, and human or other eukaryotic cells.

 Student Learning Outcomes


Given a genetic problem, students should be able to distinguish amongst different types of inheritance patterns (autosomal vs. sex, domininant/incomplete/co-dominance vs recessive, epistasis vs. hypostatic, maternal vs paternal) by analyzing pedigree charts to predict genotypes and phenotypes, designing monohybrid/dihybrid crosses and solving the crosses using Punnett and Branch methods.


Given a gene, student should be able to describe its expression in the context of the Central Dogma of Molecular Biology (CDMB) including the processes of replication, transcription (eukaryotic and prokaryotic), DNA repair, mRNA-processing, epigenetics, genomics/RNAi, and translation: Additionally, students should be able to predict phenotypic outcomes of mutations affecting the CDMB.


Students will have two oral projects: Genetics of Me (GOM) that ties together transmission and molecular genetics concepts focused on a trait that runs in the student family and a Genomics Research Project in which student groups will annotate an assigned gene on a DNA contig from different fruit fly (Drosophila) species.  Students will demonstrate their ability to research literature and problem solve using bioinformatic research techniques by orally presenting their results from each research project before a group of peers.


After completing a series of six Modules using Bioinformatics tools in lab, students should be able to draw and label a model of a gene including the transcription start site (TSS), 5’UnTranslated Region (UTR), exons, introns, 5’ & 3’ splice sites (GT/GU and AG, respectively), start codon, stop codon, the polyadenylation signal sequence (AATAAA/AAUAAA) and polyA tail.   Students should be able to explain the significance of each portion of the gene structure as applied to gene expression. Additionally, students should be able to use the Bioinformatic tools to annotate an unknown gene given in a practical.

 '''Student_Learning_Objectives:''' appear at the beginning of each Powerpoint slide. Use them to focus your studies.


  • ACADEMIC HONOR CODE Undergraduate Student Code of Academic Integrity North Carolina Central University is dedicated to instilling in its students the highest principles of integrity and responsibility. In this regard, students are expected to demonstrate respect for these principles in the performance of their academic activities. Academic dishonesty, which is a violation of academic integrity, will be dealt with according to the provisions of the Student Code of Academic Integrity. Academic Dishonesty is defined as any conduct that is intended by the student to obtain for him/herself or for others an unfair or false evaluation in connection with any examination or other work for academic credit. Cheating, fabrication, plagiarism, and complicity are examples of conduct that is academically dishonest. For definitions of cheating, fabrication, plagiarism, and complicity; please visit the pdf document at .
  • Penalties for Academic Dishonesty The penalty for academic dishonesty will be imposed by the instructor responsible for assigning the final grade in the course. The penalty will be assessed in relation to the gravity of the offense, the type of academic exercise on which the offense occurred, and the weight of that exercise in the computation of the final grade.

 a. For an academic dishonesty act committed in an exercise counting for up to 10 percent of the final grade, the penalty will be the grade of F/Zero for the entire exercise or parts of it.

  b. For an academic dishonesty act committed in an exercise counting for between 11 and 24 percent of the final grade, the penalty will be the grade of F/Zero or a reduced grade for the exercise.   

  c. For an academic dishonesty act committed in an exercise counting for 25 percent or more of the final grade, or for final examinations and papers, the penalty may be as severe as the grade of F for the course.

  The penalties for refusing to respond or failing to respond within 48 hours to the formal charge of academic dishonesty will be an automatic F/Zero for the exercise in cases of category (a) or (b) above, and an automatic F/Zero for the course in cases of category (c). In addition, the charge of academic dishonesty will stand and will be recorded.

 The dean of the school shall check the records of all students reported for academic dishonesty, and refer all cases of second offenses to the Academic Integrity Board.

 The penalty for a second act of academic dishonesty committed anytime before the offender’s graduation may be as severe as suspension or expulsion.


Student Disability Services

Students with disabilities (physical, learning, psychological, chronic medical, etc.) who would like to request accommodations and services are required to register with the Office of Student Disability Services (SDS) in Suite 120 in the Student Services Building.  Please contact the SDS Staff at (919) 530-6325 or email  If you are NEW to SDS, please contact the office for an appointment. If you had accommodations previously, you can resubmit a request by visiting our website at and clicking on the Accommodate Link.  Students are expected to update their accommodations each semester, preferably during the first 2 weeks of each semester.

In addition to or in lieu of contacting Ms. Lee, veterans with wounds of war including PTSB and TBI are encouraged to alert the instructor of needed accommodations. (veterans can also contact Tomeka Davis at 919-530-5312)

 Student Support/Ombudsperson

The Student Ombudsperson is available to assist students in navigating unexpected life events, (e.g. short-term illness/injury, loss of a loved one, personal crises) and guide them to the appropriate University or community resources. Students may also receive assistance with resolving some emergency financial concerns, understanding NCCU policies or general problem-solving strategies. Schedule an appointment by contacting the Student Ombudsperson in the Office of the Dean of Students, G-06 Student Services Building, at (919) 530-7492 or

  Classroom Policies'

''''''<b><b>CLASS ATTENDANCE<b>:         “Students are expected be present and on time at all regular class meetings and examinations. Each instructor is required to drop a student from the class roll when that student has been absent from class for the number of class meetings that equals a two-week period. Students representing the University on official business which will require absences beyond the two-week period must make         pre-arrangements to be absent from classes at the specific request of their University sponsor.” A student who misses two weeks of classes will be assigned a grade of NW or NF according to the University’s Attendance Policy. (Student Handbook 2011-2012, pg 38)'

' For Genetics…In adherence to the NCCU attendance policy, you may be dropped from this course if you accumulate more than 4 total unexcused absences from lecture or more than 2 lab periods'

' Role will be called for the first week of class.  After that, students will be required to sign in as you enter the classroom.'

 ASSIGNMENTS:   All assignments must be turned in during the class period in which they are due or within the time frame of the online assignment.   Late assignments will NOT be acceptedunless you notify me (preferably beforedue date) and/or of a documentable, reason. Students are responsible for missed material. This includes lab quizzes, lab assignments, VICE, ICES, SM online quizzes, exams, and lab work. Students are responsible for viewing all animations/videos indicated in schedule and/or on PowerPoint slides and studying the appropriate pages of the assigned chapters.

If you will be on an athletic or academic trip – plan to turn your assignment in early. You also need to present me with documentation before your trip, so that I may consider excusing you. Be mindful that you are still responsible for all class work. Documented disabled individuals and veterans will need to discuss any accommodations with instructor.

Types of assignments: ICE= In Class Exercise.  They are posted on Bb under assignments.  Print them out and bring on day indicated in schedule.  Failure to print will result in 10%  point deduction. SM= Study Module; these are NOT turned in, but are used to study for the Bb Online Quiz.  There are 3 SM Online Quizzes during the semester. VICE= Video In Class Exercise.  LaQuiz = lab quiz; LICE= lab in class exercises. Only one VICE during the semester…  Only limited time will be allowed during class; therefore, you are welcome to work on ICE and VICE assignments prior to class.

'Genetics of Me (GOM) Project-  This assignment will be completed in lab and includes 3 small assignments and one major oral presentation. The objective' it to study a trait in your family and orally present it at the end of the semester.

You are to investigate your family’s genetic history.  If you are unable to do so, you may pick a disease you are interested in.  All topics must be approved by Dr. Silver Key. Details are posted on Blackboard. All students must turn in the 3 small assignments as an individual. Due to time constraints groups of 2 or 3 students may combine for a presentation, but if the class is small, then folks may present individually.


'Genomics Research Project'Completed in lab. The objectiveis to figure out whether or not a gene that is known to exist in one species of Drosophila, Drosophila melanogaster, is conserved in other species of Drosophila (either Drosophila eugracilis or Drosophila ficusphila). Your hypothesis is that the order of the genes (synteny) and the sequence of the genes (size of exons, kinds of amino acids in the exons, etc) is conserved from one species to another until you find evidence to the contrary.

'Class Participation:   'Students are expected to come to class ON TIME prepared to participate (read Chapters, view videos ahead of class). Cell phones, pagers,… ALL means of electronic communication should be turned off while in class– no text messaging, talking on phones, replying to emails, doing late assignments, etc.  You should only be thinking about Genetics and what is being discussed in class that day.  Repeated use of electronic equipment for uses other than coursework, will negatively affect your grade.

Instructor has a cell phone for emergency use only – ie., to communicate with Security if needed.

Food, drink, and gum are notallowed in the classrooms! (Exception: you may have 1 closed container of water)

If you are asked to leave the classroom for disruptive behavior, disrespectful behavior, not dressing appropriately… in other words, not following Classroom Policies, and you refuse to leave, this is considered a Criminal Offense, and security will be called to remove you from class and give you a citation.

 Exams    Exams in this class are quite challenging.  Studying daily is essential to absorb the vast amount of detailed information and concepts for this course. Exams will consist of 70 objective (multiple choice, matching, select-all-that-apply, and true/false) questions and 1 short answer question. ONCE YOU BEGIN THE EXAM, YOU WILL NOT BE ALLOWED TO LEAVE THE ROOM FOR ANY REASON. For each day of your exam use the following exam checklist:

  • Bring 2 number 2 pencils with you.  
  • You are allowed 1 closed container of water
  • Use the restroom facilities prior to coming to the exam
  • Bring facial tissues, cough drops, etc with you
  • Verify that all electronic communication devices are off or silenced and they are not to be out or in your pocket during the exam
  • 'EXAM FORMAT:  The lecture exam format will include 50-70 questions worth 2 points each and one short answer question (5-10 points) for a total of 150 points. Each exam is worth 15% of your grade. The following types of questions will compose the exam: select-all-that-apply ('SATA), multiple choice (MC), matching, and sometimes true/false (T/F) . Exams will be on SCANTRON. Lab exam will follow similar format.

'Communication:'   Officially, NCCU requires you to use an NCCU email account: it reduces viruses and it looks professional when you correspon for internships, jobs, and other enhancement programs. Check your Blackboard every evening to see if any announcements concerning class have been posted: change in schedule, change in due dates, changes in exam dates, adverse weather announcements.

' Bonus: ' Only bonus opportunities are bonus questions on exams.  If seminars occur, the instructor may allow bonus opportunities for attendance.

 Library Services: Need references for papers?  Want to avoid plagiarism?  Need a place to do group work?  Need a quiet place to study with loaner laptops and ipads?  Visit the library!  One-on-one sessions offered as needed.  Here is the contact information:


              Chat 9 a.m.-

              Call:(919) 530-6473

              Text at:(919) 799-2182

              Follow tweet:@ShepardLibrary

              Like library:James E. Shepard Memorial Library

              Online including JournalFinder, NCLive,

             Journals at Ovid (Biomedical), Triangle Research Libraries Network (TRLN) Interlibrary

             loan (ILL) services, LibGuides, ect.


<b>Academic Services:  For help with course studies and career services, visit ‘support services’ at


  • 70% of your overall semester grade will be from exams: 4 lecture exams + 1 lab exam.

Graded Element

Point Value

Total points

Percentage of Course Grade

4 lecture exams

4 x 162



Study Modules, ICEs, Case Studies, Video Worksheets and In-class participation, which includes following class and university policy.

Each worth 5-20 points




Lab work: lab sheets, LICEs, participation (see above) and multiple quizzes.

Worksheets/homework/ progress reports, quizzes


(may be more points, but only 10% of total grade)


Genomics Research Project on the Drosophila annotation research project done in lab which culminates with an oral presentation.

1 per semester



Genetics of Me assignment and oral presentation

3 assignments 5-10 pts each and oral presentation (50 pts)







'Final Grading Scale'

90-100%           A

80-89%              B

70-79%              C

60-69%              D

< 59%              F


''''Lecture 1:20-3:50 p.m. MTWR 2235 MTSB

'Dr. Key Office Hours: 3:50-4:30 p.m. MTWR 2246 MTSB'



'Reading Assignment and Lecture Topic'

In absence of page #s, assume study whole chapter for Summer Session 1.

'ICE/SM# Due (& Animation assignment)*'

'*'Nothing to turn in for animations, but are assigned

  1. SM papers are not turned in; rather they are study tools to help prepare you for the Bb online quizzes



'Memorial Day – no class'




'Chapter 1' Introduction

'Chapter 2 Cell Cycle & Mitosis section 2.1'

'Chapter 23': pp 661-672 and pp 674-678

  • Chapter 1, 2 and 23 study as per page numbers indicated.
  • (Mitosis animation)



'Chapter 2': Meiosis Section 2.2pp 20-37

'Chapter 4': Non-disjunction pp 83-84

'Chapter 8': Aneuploidy pp 222-223.

'Chapter 3': Mendelian Genetics: Mono & di-hybrid crosses: Punnett Square Probability & Branch Method

  • 'ICE#1 Non-disjunction'
  • (Meiosis animation)
  • Powerpoint slide problems
  • 'ICE#2 Branch Method'





'Chapter 5 section 5.1' pp 104-110 Degrees of Dominance


  • 'Online Quiz on SM#1 due by 11 p.m.'
  • (Genetic variation animation & X-linked inheritance)
  • Powerpoint slide problems on Incomplete and Co-dominance
  • 2 Website tutorials for dominance:



'Exam #1 on all above chapter readings, animation, Powerpoints, ICE and SM quiz assignments.'



'Chapter 5.2' (pp 110-113) & 5.5(pp126-128) Environment, Epigenetics and Epistasis

'Chapter' 10: Structure of DNA review


  • 'ICE#3 Epistasis'
  • Chapters 5 & 10
  • Four DNA experiment website tutorials:
  1. Griffith’s Transforming Principle:
  2. Avery, McCarty & Macleod:
  3. Hershey & Chase:
  4. Watson, Crick, Wilkens, Franklin:

W 6-7

'Chapter 12:' Replication

  • Basics
  • PCR
  • Telomeres
  • Chapter 12
  • (All 4 Replication animations + 1 PCR animation)
  • 'Online Quiz on SM#2 due by 11 p.m'




'Chapter 18 Gene Mutation &' DNA Repair BER, NER, Mismatch Repair, Direct DNA Repair of single-strand damageAnd HR/NHEJ repair of double-strand (ds) DNA breaks to study human disease




'EXAM #2 All reading assignments, animation & video assignments, Powerpoints, ICEs, SM and SM online quizzes.'



'Chapter' 13 Transcription

  • Prokaryotic – transcription unit, core promoter
  • Eukaryotic – enhancers, regulatory promoters for cell specific gene expression


  •  (Transcription animation)
  • 'ICE#5 Prokaryotic Transcription vs Eukaryotic Transcription'




'Chapter 14' RNA processing Chapter 14RNAi


  • (2 RNA processing animations)
  • 'ICE#6 RNA processing (above animations will help)'
  • 'VICE#1 on Nova RNAi video'

    Nova video:


'Chapter 15' The Genetic Code & Translation

'Chapter 6:' Human Genetics

  • Pedigree


  • 'ICE #7 Gene Expression and Mutation'
  • (translation animation)
  • 'ICE#8 Pedigree Analysis'


M 6-19

'EXAM #3 All reading assignments, animation & video assignments, Powerpoints, ICEs, SM and SM online quizzes'

T 6-20

'Chapter 6:' Human Genetics

  • Twin studies
  • Adoption study

'Chapter 16:' Control of Prokaryotic Transcription

  • Lac operon



W 6-21

'Chapter' 21: Epigenetics

'Chapter 8': Chromosome Variation

  • 'SM#3 Online Quiz due by 11 p.m.'
  • 'ICE#10 Epigenetics'
  • View Ted Talk on Epigenetics: – take notes
  • 'Chapter 8 pp. focus on Downs Syndrome'
  • 'ICE#11 Two Genetic Ways to Downs Syndrome Phenotype'

R 6-22


' Chapter 4:' Sex Determination

'Chapter 20': Genomics

  • 'Chapter 4 pp.' focus on Y chromosome & different ways of determining gender
  • 'Chapter 20 pp'
  • 'ICE#12 Gene Structure'





 6-25 or Mon


' EXAM #4:  All reading assignments, animation & video assignments, Powerpoints, ICEs, SM and SM online quizzes for dates: 6-20-17 to 6-22-17'

Grades due in Banner







Laboratory 9:00 a.m.-12:30 p.m. MW 2181 MTSB


All 6 'Understanding Eukaryotic Genes' Modules followed by class of 9 completely annotating and submitting 6 genes on 2 contigs.





'W 5-31'

  • Safety & Policies
  • Pre-course Assessment
  • Learning the Gene Quiz A
  • 'GEP online survey and quiz (recommend to do this BEFORE class)'
  • 'Print & Bring' Understanding the Eukaryotic Gene Module #1 &#2
  • 'Print & Bring ppt' on the Drosophila gene known as Tra
  • Student information sheet
  • Tra Powerpoint presentation
  • Turn in screen shot of finished online survey and quiz
  • Show videos for Module 1:
    • Genome Browser Video
    • Evidence Tracks Video
  • Turn in Module#1 & #2

'M 6-5'

Print & Bring ppt Understanding the Eukaryotic Gene Modules #3, #4 and #5

  • Turn in GOMA#1project proposal & name of at least 1 gene
  • Watch videos in class for Module #5 (splicing & phase video – should help a little with #3) #2 and #4 videos
  • Turn in Modules #3, #4, and #5 by end of class

'W 6-7'

  • Print & Bring ppt Understanding the Eukaryotic Gene Modules #6
  • Introduction to other online websites needed:
  • 'NCBI BLAST       '
  • 'Gene Record Finder'
  • ''
  • Begin assigned Gene Annotation Project (GAP)*
  • 'Quiz on BLAST video'
  • 'Turn in Homework on Module #4'
  • Watch videos in class for Module #6
  • Turn in at end of lab class:
  • Modules #6
  • BLAST Exercise
  • Gene Record Finder Exercise
  • Flybase Exercise
  • Start on Annotation Project
  • Turn in tblastn snapshots and a list of in coordinates for exon in isoform.

'M 6-12'

Continue working on Gene Annotation Project (GAP)*



'W 6-14'

  • Continue working on GAP*
  • Introduction to Gene Model Checker website.
  • Turn in GOMA #2on gene mutation and product
  • Turn in homeworkon your assigned gene.
  • Turn in reports on isoform/gene.

'M 6-19'

Continue working on GAP*

  • Turn in Project Report draft.
  • Turn in Pedigree for GOMA #3project

'W 6-21'

Group Oral Presentations on:


             Gene Annotation Project (GAP)

             Genetics of Me ('GOM)'


  • Turn in FINAL Project Report
  • Audience Evaluation forms for other groups for each presentation
  • Copy of instructor rubric for each presentation
  • Self and group member evaluation for each presentation


  • 'Gene Annotation Projects (GAPs):'

' - contig3 Drosophila ficusphila'

'- contig 20 Drosophila eugracilus'

=== Syllabus ===