bio 285- syllabus.pdf

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Cell and Molecular Biology Bio285 Spring 2013 Lecture: MWF 11:15am12:05pm Morrill I North N375 Instructor Dr. Laura Francis Department of Biology Office: ISB241D Email: [email protected] Office phone: 5452599 Office Hours: Monday: 12pm Wednesday: 23pm Thursday: noon1pm If those times do not work, feel free to make an appointment. Textbook: Your textbook is your resource guide. I do not design the course around any particular textbook so any good cell and/or molecular biology textbook should serve you just fine in this course. Here are a few options: Essential Cell Biology 3 rd edition; Alberts et al; ISBN: 978-0815341291 Molecular Cell Biology 7 th edition; Lodish et al; ISBN: 978-1429234139 Molecular Biology of the Cell 5 th edition; Alberts et al; ISBN: 978-0815341055 Other classroom resource: i>clicker2 (clicker) required Websites you might need for this class: Course Learning Management website: https://moodle.umass.edu/ For students with disabilities: http://www.umass.edu/disability/students.html Course Description Course designed for sophomores in Biology, Biochemistry, or Microbiology. Building upon concepts learned in Biology 100 (now Bio151), consideration is given to structure and function. The course is equally divided between aspects of molecular and cellular biology.

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Page 1: Bio 285- Syllabus.pdf

Cell  and  Molecular  Biology  Bio285  Spring  2013  

Lecture:  MWF  11:15am-­‐12:05pm  Morrill  I  North  N375  

   Instructor  Dr.  Laura  Francis    Department  of  Biology    Office:  ISB241D    Email:  [email protected]    Office  phone:  545-­‐2599    Office  Hours:    Monday:  1-­‐2pm  Wednesday:  2-­‐3pm  Thursday:  noon-­‐1pm  If  those  times  do  not  work,  feel  free  to  make  an  appointment.      Textbook:    Your  textbook  is  your  resource  guide.    I  do  not  design  the  course  around  any  particular  textbook  so  any  good  cell  and/or  molecular  biology  textbook  should  serve  you  just  fine  in  this  course.        Here  are  a  few  options:  Essential  Cell  Biology  3rd  edition;  Alberts  et  al;  ISBN:  978-0815341291    Molecular  Cell  Biology  7th  edition;  Lodish  et  al;  ISBN:  978-1429234139    Molecular  Biology  of  the  Cell  5th  edition;  Alberts  et  al;  ISBN:  978-0815341055    Other  classroom  resource:  i>clicker2  (clicker)  required    Websites  you  might  need  for  this  class:    Course  Learning  Management  website:  https://moodle.umass.edu/    For  students  with  disabilities:  http://www.umass.edu/disability/students.html    Course  Description  Course  designed  for  sophomores  in  Biology,  Biochemistry,  or  Microbiology.  Building  upon  concepts  learned  in  Biology  100  (now  Bio151),  consideration  is  given  to  structure  and  function.  The  course  is  equally  divided  between  aspects  of  molecular  and  cellular  biology.  

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 Course  Design  I  like  to  think  about  molecular  biology  in  some  sort  of  “real  world”  context  and  so  we  will  use  a  disease/treatment-­‐based  (i.e.  human  health  and  disease)  model  to  investigate  concepts  in  how  cells  function  at  the  molecular  level.    Emphasis  will  be  on  conceptual  understanding  of  the  topics,  as  well  as  developing  critical-­‐thinking  and  problem-­‐solving  skills.        Learning  Topics  (subject  to  change)  1.  Proteins    

Subtopics:    a.  Amino  acids  and  their  chemistry  b.  Protein  folding  c.  Protein  trafficking  d.  Enzyme  function  

Selected  disease  topics:  Prion  disease  (protein  mis-­‐folding)    2.  Cancer  Biology  

Subtopics:    a.  Signal  Transduction  (Selected  disease/drug  topics:  Chronic  Myolegenous  Leukemia/Gleevec;  Breast  cancer/Herceptin)  

  b.  Control  of  Cell  Cycle  c.  DNA  mutations/DNA  damage  repair  and  response  (Selected  disease/drug  topics:  Xeroderma  Pigmentosum)  

  d.  DNA  replication  (Selected  disease/drug  topics:  Werner  Syndrome)     e.  Mitotic  Spindle  Assembly  (Selected  disease/drug  topics:  Taxol)    

3.  Control  of  Gene  expression  Subtopics:  

a. Transcriptional  control  b. Translational  control  c. RNA  interference  d. Epigenetic  silencing  

 Examinations  Three  1-­‐hour  examinations  will  be  held  in  the  evening  at  7pm.  Rooms  for  the  exams  will  be  announced  in  class  the  week  before,  and  there  will  be  alternate  exam  times  that  day  for  students  with  a  conflict,  signup  sheets  will  be  available  in  class  the  week  before  the  exam.    You  can  find  exam  dates  below  under  Course  Schedule.    Make-­‐up  Exam  Policy:  Students  with  a  valid  excuse  for  missing  an  exam  must  present  these  to  Dr.  Francis  before  the  exam.    If  the  excuse  is  valid  and  verified,  the  student  may  take  a  make-­‐up  exam.    Students  may  do  this  only  once  in  a  semester.  An  exam  missed  without  a  valid  excuse  will  be  recorded  as  a  zero.  A  schedule  conflict  is  not  a  valid  reason  for  missing  an  exam.  The  day  of  the  exam  there  will  be  earlier  exams  during  the  day  for  students  with  a  conflict  for  the  evening  exam.  Sign  ups  for  

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early  exams  will  be  available  in  class  the  week  before  the  exam.  A  make-­‐up  final  exam  will  be  available  to  students  with  valid  and  verifiable  excuses.    The  three  exams  during  the  semester  are  not  cumulative  –  you  will  be  assessed  on  the  material  covered  since  the  previous  exam.    The  final  exam  is  cumulative.        Final  Exam  Grade  Substitution:  If  you  have  a  higher  percentage  on  your  final  exam  than  your  lowest  exam  grade,  I  will  replace  your  lowest  exam  grade  with  your  final  exam  grade.    For  example,  if  you  receive  a  40/50  (80%)  on  the  1st  exam,  a  45/50  (90%)  on  the  next  two  exams  and  then  a  90/100  (90%)  on  your  final,  I  will  change  the  first  exam  grade  to  a  45/50  (90%).    Quizzes  There  will  be  nine  (9)  quizzes  each  worth  10  points.    Two  quizzes  will  be  dropped  at  the  end  of  the  semester.    You  may  make  up  a  quiz  with  a  valid  excuse  (illness,  family  emergency,  etc)  but  the  quiz  make-­‐up  should  be  scheduled  with  me  ASAP  and  make-­‐up  quizzes  will  not  be  offered  more  than  a  week  after  the  actual  quiz.    You  may  only  make  up  two  quizzes  in  a  semester.    A  note  about  Quiz  and  Exam  assessments:    In  this  course,  students  generally  find  quizzes  easier  than  exams.    My  goal  for  quiz  assessments  is  to  test  knowledge  of  concepts,  whereas  on  exams  there  may  also  be  questions  focused  more  on  critical  thinking  and  problem  solving.    These  types  of  questions  ask  you  to  take  the  knowledge  that  you’ve  learned  in  the  course  and  solve  a  different  or  new  problem  with  that  conceptual  knowledge.        i>clicker2  (Audience  Response  System)  i>clicker2  is  an  in-­‐class  communication  system  that  uses  wireless  transmitters  to  allow  students  to  send  answers  to  questions  posed  by  the  instructor  during  class.  Responses  from  all  students  are  recorded,  tallied  and  used  as  the  basis  of  discussions  of  problem  solving.  We  will  use  this  system  almost  every  class  period  and  you  are  required  to  participate  to  earn  a  significant  fraction  of  your  course  participation  points.  Please  make  sure  to  bring  your  transmitter  to  EVERY  class.  When  a  question  is  posed,  you  are  encouraged  to  discuss  the  answers  with  your  classmates  before  sending  a  response.  The  responses  for  all  the  students  will  be  compiled  and  displayed  for  class  discussion.  After  each  question,  we  will  discuss  the  results  as  a  class.    The  iclicker  participation  grade  is  based  on  participation,  not  correctly  answering  the  question.    Some  clicker  questions  are  designed  as  assessment  of  knowledge,  but  some  clicker  questions  are  designed  to  generate  discussion  and  may  not  have  one  formally  correct  answer.    These  types  of  questions  are  designed  to  mimic  the  conversation  that  you  might  have  during  scientific  inquiry  (i.e.  as  a  scientist),  rather  than  being  designed  to  mimic  exam  or  quiz-­‐type  questions.    Grading  (Grades  will  be  posted  in  Moodle)  

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 The  TA  and  I  aim  to  grade  as  fairly  and  objectively  as  possible.    We  will  use  the  same  criteria  and  standards  for  all  students  in  the  course.    When  assigning  final  letter  grades  I  do  not  “take  into  account  improvement”  or  weigh  your  “good”  exams  more  heavily  than  your  “bad”  exams.    However,  there  may  be  one  opportunity  to  make  up  for  a  poor  exam  performance  by  substituting  your  final  exam  grade  for  your  lowest  regular  exam  grade  (see  Exam  section).    I  do  not  offer  “extra  credit”  and  I  do  not  “round  up”  final  grade  percentages  (i.e.  if  an  “A-­‐“  is  a  90-­‐92.99%  and  you  receive  a  92.78%,  you  will  receive  an  “A-­‐“  in  the  course).    Moreover,  I  will  not  change  your  grade  if  you  are  very  close  to  the  next  letter  grade,  even  if  you  need  that  grade  to  graduate  or  move  on  to  the  next  course.    The  only  exception  to  this  rule  is  a  change  of  grade  due  to  clerical  error.  If  you  find  a  clerical  error  in  grading,  please  let  me  know  as  soon  as  possible  (preferably  before  grades  are  finalized).    I  will  base  your  grades  on  your  performance  in  this  class,  which  I  expect  to  be  the  result  of  your  honest  efforts.    1)  Exams:  150  pts              Three  exams  worth  50  points  each.  

 2)  Final  Exam:  100  pts    

 3)  Quizzes:  70  pts    

There  will  be  quizzes  in-­‐class  Fridays  at  the  end  of  class  in  any  week  in  which  there  is  no  exam.  Check  schedule  for  more  details.  There  will  be  9  quizzes  worth  10  points  each;  the  2  lowest  quiz  scores  will  be  dropped.  

 4)  i>clicker2  participation:  30  pts  

Answers  to  clicker  questions  will  not  be  graded,  full  points  will  be  given  provided  80%  of  clicker  questions  are  answered.    

You  can  earn  a  maximum  of  350  points  in  the  course      Grades  will  be  assigned  as  follows  unless  the  final  grade  median  is  less  than  75%,  in  which  case  the  letter  grade  ranges  will  be  adjusted  so  that  the  class  average  is  in  the  middle  of  the  “C”  range  of  grades.    To  calculate  your  percentage  grade,  add  up  the  points  you’ve  accumulated  and  divide  by  the  total  possible  points.    A  =  93-­‐100%     B-­‐  =  80-­‐82.99%   D+  =  67-­‐69.99%  A-­‐  =  90-­‐92.99%   C+  =  77-­‐79.99%   D  =  60-­‐66.99%  B+  =  97-­‐89.99%   C  =  73-­‐76.99%   F  =  0-­‐59.99%  B  =  83-­‐86.99%   C-­‐  =  70-­‐72.99%    Course  Schedule    Bio285  Spring  2013  Exam  Schedule  All  exams  are  at  7pm  except  for  the  final  exam  

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 Exam  1:  Wednesday,  Feb  13  Exam  2:  Wednesday,  Mar  13  Exam  3:  Wednesday,  Apr  10  Final  Exam  is  TBA  during  finals  week  **Note  that  the  Final  Exam  is  cumulative  (meaning  it  will  contain  subject  matter  from  previous  exams)    Bio285  Spring  2013  Quiz  schedule    Friday,  Jan  25:  No  Quiz  (First  week  of  classes)  Friday,  Feb  1:  Quiz  1  Friday,  Feb  8:  Quiz  2  Friday,  Feb15:  No  Quiz  (Exam  week)  Friday,  Feb  22:  Quiz  3  Friday,  Mar  1:  Quiz  4  Friday,  Mar  8:  Quiz  5  Friday,  Mar  15:  No  Quiz  (Exam  week)  Friday,  Mar  22:  No  Quiz  (Spring  Break)  Friday,  Mar  29:  Quiz  6  Friday,  Apr  5:  Quiz  7  Friday,  Apr  12:  No  Quiz  (Exam  week)  Friday,  Apr  19:  Quiz  8  Friday,  Apr  26:  Quiz  9    Academic  Honesty  http://www.umass.edu/dean_students/codeofconduct/acadhonesty/  I.  STATEMENT  OF  POLICY  Since  the  integrity  of  the  academic  enterprise  of  any  institution  of  higher  education  requires  honesty  in  scholarship  and  research,  academic  honesty  is  required  of  all  students  at  the  University  of  Massachusetts  Amherst.  Academic  dishonesty  is  prohibited  in  all  programs  of  the  University.  Academic  dishonesty  includes  but  is  not  limited  to:  cheating,  fabrication,  plagiarism,  and  facilitating  dishonesty.  [See  Appendix  B  for  detailed  examples  of  behavior  that  constitutes  academic  dishonesty.]  Appropriate  sanctions  may  be  imposed  on  any  student  who  has  committed  an  act  of  academic  dishonesty.  Instructors  should  take  reasonable  steps  to  address  academic  misconduct.  [See  Appendix  C  for  some  suggested  ways  to  deal  with  issues  of  academic  integrity.]  Any  person  who  has  reason  to  believe  that  a  student  has  committed  academic  dishonesty  should  bring  such  information  to  the  attention  of  the  appropriate  course  instructor  as  soon  as  possible.  Instances  of  academic  dishonesty  not  related  to  a  specific  course  should  be  brought  to  the  attention  of  the  appropriate  department  Head  or  Chair.  The  procedures  outlined  below  are  intended  to  provide  an  efficient  and  orderly  process  by  which  action  may  be  taken  if  it  appears  that  academic  dishonesty  has  occurred  and  by  which  students  may  appeal  such  actions.  Since  students  are  expected  to  be  familiar  with  this  policy  and  the  commonly  

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accepted  standards  of  academic  integrity,  ignorance  of  such  standards  is  not  normally  sufficient  evidence  of  lack  of  intent.