Biology 3334
Cell Biology
Course Syllabus
Instructor: Brent Bill, Ph.D., Assistant Professor of Biology
Office: HPR 107; 903-565-5883
Office Hours: , M 1:00 - 2:00, W 2:00 - 3:00, or by appointment
Email: [email protected]
Class time: MWF 9:05-10:00AM
Class Location: ADM127
Required Text:
Karp, Cell and Molecular Biology 8th Edition
Paperback(ISBN): 9781118886144
OR
Ebook: (ISBN): 9781118883662
Required Online Workbook:
SimBio Custom Modules: Due: 3-6-2017
Action Potentials Explored
Cellular Respiration Explored
Upon completion of your module, please check the “My Work.” All
questions that you have completed will show up in a darker color with a
check box. If it remains white, it has not recorded your work. Please verify
that your work has been recorded, as you are responsible for verifying that
your work has been properly recorded. Only the graded section will be
recorded for you grade.
Please follow the instructions on Blackboard to subscribe to SimUText for
Cell Biology at University of Texas, Tyler - Cost is $10.
Problems or questions? Visit SimUText Support to search our Knowledge
Base and view Video Tutorials.
If you are not able to find the answer to your question, you can submit a
support request from the support page
(http://simbio.com/support/simutext)
If you do not have a computer, SimBio can provide you a link to download
the software to a USB drive, so you can run the program on any public
computer.
Course Description:
This course provides an overview of cell biology, both at the structural and
functional level, highlighting medical implications. This is an intensive course
with a lot of material, so it will be critical that you keep up with reading,
studying, and understanding the material.
Course Objectives:
Biology 3334 is an upper division course that investigates the molecular
basis for cellular function, and assumes prior exposure to General Biology I
(1306 or equivalent), and Organic Chemistry I. The course will build on the
cellular concepts introduced in General Biology, and complements the
introductory course by providing a more thorough presentation of some of the
major aspects of cellular functioning.
1) Our understanding of Cell Biology has grown rapidly over the past fifty
years fueled by evolving technologies including recombinant DNA
technology, antibody production, cell culture, 2nd and 3rd generation
sequencing, site-directed DNA Modification, and the incorporation of
systems and synthetic biology. These techniques allow for a desired piece
of DNA to be isolated, transferred, and utilized within the cell for a variety
of applications. The first objective of this class is to recognize these
advancements, and understand their effects of cell biology.
2) Inherent within the scientific method is a constantly evolving knowledge
base. Scientist routinely form hypotheses based on the existing
knowledge base, and then proceed to strengthen the support for or negate
the initial fact that was the focus of the study; therefore, the second goal of
the class is to understand the current knowledge base of Cell Biology
3) The course will explore conceptual questions that will provide a framework
for understanding modern Cell Biology, and discuss classical experiments
that illustrate how researchers have approached these problems in the
past.
4) The last objective is that the students will be able to distill this knowledge,
and be able to communicate it to the general public.
Grading Policy:
The final grade will be determined as follows:
Pretest
Three exams
Comprehensive final
6 Video-lecture quizzes
4 Multiple Choice Exam Questions
SimBio: Action Potentials Explored
SimBio: Cellular Respiration Explored
Final Essay
20 points upon completion
100 points each(Total 300 points)
150 points
10 points each (Total 60 points)
5 points each (Total 20 points)
20 points
20 points
50 points
Total
640 points
Letter Grades will be assigned based on the following point levels.
A
B
C
D
F
570 ---- 640
505 ---- 570
435 ---- 505
320 ---- 435
Under 320
Exam Policy:
Exam questions will be drawn from the lectures, student written multiple choice
questions, SimBio Modules, and assigned video lectures. They will be a mix of
multiple choice, short answer, and essay. A 3X5” index card will be allowed for
each of the exams. You may fill the front and back with whatever you would like;
however they must be handwritten (no typing). You must take the exams on the
scheduled dates. Please check your calendars now, so that you do not have
conflicts. If an absence cannot be avoided, the professor must be notified in
advance. If a student is unable to take an exam when scheduled, following
appropriate documentation of the absence, the professor will arrange a make-up
exam.
Please note - cell phones are not allowed to be out during any of the exams
in this class. The usage of a phone during the exam is grounds for an
automatic 0.
Documentation
• University Note: Have your professor or coach email me a letter
explaining the reason for the absence due to a prescheduled
University excused absence.
• Doctors Note: If you are sick, please bring proof of your
appointment, and have the doctor explain that you were indeed
sick, and should not or could not attend class.
• Civil documentation: If there are other extenuating circumstances,
please provide the obituary, police report, court documents, or other
evidence explaining the absence.
The Final Exam
The final exam will cover the material between exam 3 and the end of the class;
as well as comprehensive material, meaning that it will cover all material from the
class. It will be important for you to keep your previous exams as study guides.
Final Exam schedule and room will be scheduled by the registrar and, will be
announced closer to the exam date. You will be able to bring a 4X6” index card
for the final exam, front and back and handwritten.
Please note - cell phones are not allowed to be out during the final exam in
this class. The usage of a phone during the exam is grounds for an
automatic 0.
Re-grading Policy:
If you feel that an error was made on the grading of your exam, please attach a
typed statement that explains the error, and turn it in to your professor within 3
days of when the exam is returned. Oral arguments are not accepted. Please
photocopy your exam before turning it in, this way, if it has not been returned,
you may still use the exam as a study guide for the final exam. Please note, the
entire exam will be assessed for errors; therefore, your score may increase or
decrease.
VideoLecturesand“Quizzes”
Therewillbe6online“quizzes.”Thesequizzeswillbebasedonpreviouslecture
material,readinginyourtext(speci@ically“TheHumanPerspective”),andashort
videolecture.Eachquizwillbe10multiplechoicequestions.Youcantakethequiz
asmanytimesasyoulikeandthescoresaveraged;however,whateverscoreis
presentasoftheclosuredatewillberecordedasthe@inalgrade.Closuredatesare
listedbelow.Closuretimein11:59PM.
Quiz1:StemCells
1-27-17
Quiz2:ProteinFoldingDiseases 2-3-17
Quiz3:Channelopathies 3-3-17
Quiz4:OrganelleDisorders(Mitochondrial,Peroxisomal,andLysosomal) 3-3-17
Quiz5:FutureofGeneticsinMedicine 4-10-17
Quiz6:Canceranditstreatments 4-28-17
Multiple Choice Exam Questions
Prior to each exam, students should post 1 multiple-choice exam question to the
multiple choice question discussion on Blackboard based on the material for the
upcoming test. The top 5 questions will be placed on the exam. Each question
posting is worth 5 points. You should include the following information.
1) The Question
2) Five possible answers, only 1 of which can be “all of the above”, “none of
the above”, “both a and b”, etc.
3) Your choice for the correct answer
4) The Rationale of why this is the correct answer
For Example:
1) Who was the first woman to win the Nobel Prize (Physics) and the first
person to win a second Nobel Prize in a different discipline (Chemistry)? Hint:
Her husband and daughter also have been awarded Nobel Prizes!
A) Linus Pauling
B) Rosalind Franklin
C) Marie Curie
D) Gerty Cori
E) None of the above
The correct answer is C - Marie Curie.
Rationale: She won the Physics prize in 1903 for describing radiation and the
Chemistry prize in 1911 for discovering the elements Radium and Polonium. Her
husband shared her 1903 prize, and her daughter won in 1935 for the synthesis
of new radioactive elements. Linus Pauling is the only other person to win two
nobel prizes in different fields (Chemistry 1954 and Peace 1962). Rosalind
Franklin was involved in the description of the structure of DNA, unfortunately
she died prior to the Nobel Prize for the structure of DNA, and prizes cannot be
awarded posthumously; therefore, she did not win the Nobel. Gerty Cori was the
first woman to win the Nobel Prize in Medicine and Physiology for her work on
the catalytic conversion of glycogen.
Please note that all four components should be there to receive full credit.
The purpose of this assignment is to make you critically think about the material
prior to the exam. It will give me an idea of how well you are following the course
material, and let me know of any misconceptions that I might want to review prior
to the exam. Lastly, since the top 5 questions will be on the exam, it will give you
the opportunity to know answers to some of the exam questions.
Cell Biology Take Home Essay Question
I will give you an essay question. It will be due near the end of the course (See
Schedule). I will present a topic in class, and you will be expected to write a 2page essay on this topic. It will follow a format that I will describe in class. It will
require you to synthesize everything that you have learned in the semester, and
propose a series of experiments based on the cell biological techniques and
principles that you have learned. You can use any resource that you can obtain:
journal articles, websites, discussions with the professor, i.e. Dr. Bill, or any other
friend/relative/scientific genius you can rope into helping you. You may work in
groups of 2; however, if you work in a group you must cite your coworker on the
document, and both will receive the same grade. Every student is required to turn
in their own assignment. i.e. If the paper was written by Bob and Jane, I should
receive a copy of the Essay that Says Bob and Jane from Bob, and a copy that
says Jane and Bob from Jane. You will have to do outside research for this
project.
One resource that you may find helpful is the University Writing Center. It is
available free of charge, and is located in the Library. You should plan ahead, as
you will have to make an appointment, although a limited number of walk in slots
are available. Their website is: https://www.uttyler.edu/writingcenter/
ExtraCredit
Therewillbeanopportunitytoreceiveupto25pointsextracredit.Foreach
presentation,video,orpaper;youshouldwriteashort2-paragraphessayona
presentation,video,orpaper.The@irstparagraphshouldsummarizethetopicofthe
presentation,andthesecondparagraphshouldfocusonsomethingthatyoufound
interesting.Thesecondparagraphshouldconcludewithaquestionthatyouhad
basedonorinspiredbythepresentation,video,orpaper.EachEssayisworth5
points,andyoucanuploadupto5intheExtraCreditdiscussionthreadson
blackboard.TheseEssayswillbeduebyApril30,2016.
1) AttendtheBiologyDepartmentSeminar:Fridays,from1-2P.M.theDepartment
ofBiologyhostsaweeklyseminar.Seminarsthatfeaturecellbiologicaltopics
willbelistedbelow.Pleasenote,thesepointsarenotofferedforallseminars,
onlytheonesthatarelistedinthesyllabus,orthatDr.Billadds,andmentionsin
class.
SeminarsTBA
2) DarwinDayVideosorSeminar:February10,2016istheInternationalDarwin
DayCelebrationatUTTyler(http://darwindaytyler.org).Therewillbe4
opportunitiestoattendevents:
VideosandKeynoteSpeakerTBA
3) Reviewpaperspostedintheextracreditfolder.Donotjustcopytheabstract,I
willgiveyou0pointsduetoplagiarismontheessay.Ifyoudonotunderstand
thepaper,pleasefeelfreetostopbyandIwillanswerquestionsthatyoumay
have.
ClassExpectations
• StudentswillbeexpectedtofollowtheUniversityofTexasatTylerHonor
Code.Cheatingwillnotbetolerated,andwillbedealtwithharshly,i.e.azero
ontheassignment,examorprojectattheminimum.
• BeCourteousandontime.
• Silencecellphonesandotherelectronicdevices,anddonotansweryour
phonewhileinclass.Cellphoneusageduringanexamwillresultinan
automatic0ontheexam.
• Discussioniswelcomedduringthelecture,sopleasefeelfreetoask/answer
questions,seekclari@ication,etc.Ifyouneedextrahelp,orwearepressedfor
timeduringclass,pleaseseemeduringof@icehours.
• Youarestronglyurgedtoattendclass,thisisafast-pacedclass,andwewill
becoveringandlargeamountofmaterial.Itisyouresponsibilitytokeepup
withthematerial.Stayingontopofthematerialwillbecriticaltodowellin
thisclass.
• Questionsoverlecturematerialarewelcomedduringof@icehours(orby
appointment),orifmoreconvenient,theycanbedirectedtomeeitherby
phoneore-mail.Pleasedonothesitatetoaskquestions!Pleaserealize,that
ifsubmittedviaphoneoremail,Imaynotreceivethequestionandanswerit
immediately;however,Iwilltrymybest.Forexample,ifyouemailme
Thursdaynightat11:45P.M.thenightbeforetheexam,youmaynotgetan
answeruntilthenextday,whichmaynotbepriortotheexam.
• IfIammeetingwithsomeonepleasewaityourturn.Donotjustwalkin,and
sitdown.Insomeinstances,wearediscussinggradesorotherprivate
matters,anditisunprofessionaltointerrupt.
• Participate:Stayingactivelyengagedinthelectureswillincreaseyour
retention.Therefore,throughoutthelecturesthereareclassquestions.
Pleasevolunteertoanswerifyouthinkyouknowit.Iwillmovearound
theroom,soifthesamepeopleareansweringtonotbesurprisedifyou
getcalledon.
GENERAL:
Ifyouhavedisability,includingalearningdisability,forwhichyourequestan
accommodation,pleasecontactDisabilitySupportServicesof@ices(https://
www.uttyler.edu/disabilityservices/),sothattheappropriatearrangementsmaybe
made.Inaccordancewithfederallaw,astudentrequestingaccommodationmust
providedocumentationofhis/herdisabilitytotheDisabilitySupportServices
counselor.Formoreinformation,callorvisittheStudentServicesCenterlocatedin
theUniversityCenter3150.
Ifyouarerepeatingthiscourseforagradereplacement,youmust@ileanintentto
receivegradeforgivenesswiththeregistrarbythe12thdayofclass.Failureto@ilean
intenttousegradeforgivenesswillresultinboththeoriginalandrepeatedgrade
beingusedtocalculateyouroverallgrapepointaverage.Astudentwillreceivegrade
forgiveness(gradereplacement)foronlythree(undergraduatestudent)ortwo
(graduatestudent)courserepeatsduringhis/hercareeratUTTyler.(2006-08
Catalog,p.35).
TheUniversityWritingCenteratTheUniversityofTexasisaplacefor
undergraduatestudentstoworkontheirwritingprojectsandwritingskills.
Ifyouhaveawritingprojectunderway(forexampleyour@inalpaper),itis
recommendedthatyoumakeanappointmentwithoneoftheirquali@iedtutors.
Theycanassistwithavarietyofconcernsatalmostanylevel
([email protected]).
Non-NativeSpeakers:Forthosethatarenon-nativespeakers,andwouldliketo
improvetheirEnglishSkills;theOf@iceofInternationalStudiesoffersseverallevels
ofIntensiveEnglishLanguageCourses.Ifyouarehavingdif@icultyfeelfreeto
contactthem([email protected]).Ifhavingtroublewithvocabularyspeci@ictocell
Biologyfeelfreetostopbyduringmyof@icehours,andwecanworkonthis
speci@ically.
HelpfulLinks:
Pubmed:Aresourceforaccessingbiomedicalliterature.
• UT-TylerPortal:http://www.ncbi.nlm.nih.gov/pubmed?holding=txutrmlib
Genomebrowsers:Thesewebsitesarerepositoriesforgeneticinformation.Youcan
lookatanentirechromosomeusingthegenomebrowser,orfocusonmoredetailed
informationforaspeci@icgene.
• NationalCenterBiotechnologyInformation:http://www.ncbi.nlm.nih.gov/
• EuropeanGenomeBrowser:http://www.ensembl.org/index.html
• DNADataBankofJapan:http://www.ddbj.nig.ac.jp/
• UCSantaCruzgenomebrowser:http://genome.ucsc.edu/
Gene-speci@icinformatics:Thesewebsitesprovidemoredetailedinformationon
genesandgeneticdisorders.
• OnlineMendelianInheritanceinMan(OMIM):http://www.omim.org
• Genecards:http://www.genecards.org/
• GeneTests:http://www.genetests.org
• GeneReviews:http://www.ncbi.nlm.nih.gov/books/NBK1116/
SelectedAnimalSpeci@icInformatics:Thesewebsitesfocusonthemostpopular
geneticanimalmodels.
•
•
•
•
•
Mouse(Musmusculus)Informatics:http://www.informatics.jax.org/
Zebra@ish(Daniorerio)Informatics:http://[email protected]/
Fly(Drosophilamelanogaster)Informatics:http://@lybase.org/
Caenorhabditiselegansinformatics:http://www.wormbase.org/
Saccharomycescerevisiaeinformatics:http://www.yeastgenome.org/
ProgramstolookatDNAsequence:Sangersequencingproduceschromatograms,as
areadout.Thisreadoutcanbeviewedusinganumberofprograms.Thesewill
covertthedataintoastringofnucleotidesthatcanbeanalyzedfurther.
• APlasmidEditor(ApE)-http://biologylabs.utah.edu/jorgensen/wayned/ape/
• CLCsequenceviewer-http://www.clcbio.com/products/clc-sequence-viewer/
• FinchTV-http://www.geospiza.com/Products/@inchtv.shtml
• SequenceManipulationSuite:http://www.bioinformatics.org/sms2/
index.html
General Science Resources:
•
•
•
•
•
•
•
•
•
HHMI Biointeractive: http://www.hhmi.org/biointeractive/
CSHL DNA interactive: http://www.dnai.org
Science Friday Life Science Education: http://www.sciencefriday.com/
teacher-resources/index.html?subject=3#page/full-width-list/1
GeneEd: http://geneed.nlm.nih.gov/topic_subtopic.php?tid=1
Cell and Molecular Online: http://www.cellbio.com/education.html
Cells Alive: http://www.cellsalive.com
Khan Academy: https://www.khanacademy.org/science/biology
NIGMS: http://publications.nigms.nih.gov/order/
Evolution and cell biology: http://evolution.berkeley.edu/evolibrary/teach/
undergradsyllabus.php
Tentative Schedule
Date
Topic
Chapter
Pages
1-18-17
Syllabus, Introduction to the Cell, Viruses, Origin Of
Eukaryotes
1-20-17
Introduction to the Cell, Viruses, Origin Of Eukaryotes
1
1-29
1-23-17
The Chemistry of Life
2
32-41
1-25-17
The Chemistry of Life - The Macromolecules:
Carbohydrates, Lipids, and Nucleic Acids
2
42-48,7779
1-27-17
The Macromolecules: Proteins
Stem Cell Video Lecture Due. Pretest due.
2
48-62
1-30-17
Proteins and methods of study.
Census: Deadline for all registrations and schedule
changes
2
71-77
2-1-17
Thermodynamics, Enzymes, and Metabolism
3
81-100
2- 3-17
Finish Glycolysis and Regulation,
Protein Folding Video Lecture Due,
Multiple Choice 1 Due.
3
103-111
2-6-17
Go over Review for Exam 1
2-8-17
Fermentations, and then introduction to membranes
3,
4
108,
114-139
2-10-17
Exam 1 (Chapters 1-3), Darwin Day
2-13-17
Movement Through Membranes
4
139-156
2-15-17
The Action Potential: an example of ion flow through a
membrane.
4
159-165
2-17-17
The Electron Transport Chain
5
168-195
2-20-17
Finish ETC, Exam 1 Review Day
5
168-195
2-22-17
Microscopes and Cell-Cell interactions
18,
7
693-708
222-229
2-24-17
Cell-Cell interactions and Cell Signaling, 20th day
7,
15
231-253,
582-590;
600-613
2-27-17
Cell-Cell interactions and signaling
7,
15
231-253,
582-590;
600-613
3-1-17
The Cytoskeleton.
9
309-338
Tentative Schedule
Date
Topic
Chapter
Pages
4,
5,
9
157-158,
195-197,
338-362
3-3-17
The Cytoskeleton and its roles in motility,
Channelopathies and Organelle Disorders Video
Lecture Due.
3-6-17
Review for Exam 2,
SimBio Modules Due, Multiple Choice 2 Due.
3-8-17
Genetics Introduction
10
366-377
3-10-17
Genomic Structure, techniques for studying the
genome, and the Gene
10
381-390
Week of
3-13-17
Spring Break
3-20-17
Exam 2 (Chapters 4,5,7,15, and 9)
3-22-17
Genomic Structure, techniques for studying the
genome, and the Gene
10
391-400
3-24-17
Transcription, Assignment of the Final Essay.
11
404-408
3-27-17
Transcription and Prokaryotic Transcription
11
408-416
3-29-17
Transcription and Transcript Modification, Discuss
Exam 2
11
417-429
3-31-17
RNAi and the Genetic Code
11
429-439
4-3-17
Translation, Part 1
11
439-453
4-5-17
Translation Part 2
11
439-453
4-7-17
The Endomembrane system
8
257-272,
275-286,
300-303
4-10-17
Review For Exam 3 - Video lecture on Future of
Genetic Medicine Due, Multiple Choice 3 Due.
4-12-17
Control of Gene Expression, Intro to the The Lac
Operon
12
455-459
4-14-17
Control of Gene Expression by The Lac Operon
12
455-459
4-17-17
Exam 3 (Chapter 8,10, 11)
4-19-17
The Histone Code and Eukaryotic Gene Regulation
12
460-504
4-21-17
The Histone Code and Eukaryotic Gene Regulation
(35)
12
460-504
4-24-17
The Histone Code and Eukaryotic Gene Regulation
Discuss Exam 3
12
460-504
10 400-403
Tentative Schedule
Date
Topic
4-26-17
Final Essay Due, Discuss Exam 3
4-28-17
Cell Cycle and Death, Review for Final, Video lecture
on Cancer Due, Multiple choice 4 due.
5-1-17
Study Day
Week of
5-1-17
Finals Week (Exam time TBA)
Chapter
Pages
14,
15,
16
540-543,
603-610,
621-625,
627-639