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Biology  3597A  –  Regulation  of  Gene  Expression  –  Fall  2017  


Lectures:     M  and  W  à  1:30-­2:30   Room:  KB-­K106  
   
Instructor:   Dr.  Jamie  Kramer   Office  hours:  M  and  W  à11  –  noon  
Office:     MSB  266    
Phone:                          X83740   Email  policies:  Checked  9:00  am  to  4:30  pm  most  days  
E-­mail:       jkramer6@uwo.ca   except  weekends.  Answered  within  24  hrs.  Emails  with  
questions  already  answered  in  the  syllabus  and  other  
course  materials  may  not  receive  immediate  replies.  
Students  must  use  their  Western  (@uwo.ca)  email  
addresses  when  contacting  their  instructors.  The  OWL  
forum  is  a  more  effective  way  to  address  broad  questions  
about  course  content.  
Tutorial:                  Tu  OR  Th  à  11:30-­12:30   Rooms:        Tu:  B&GS  0165              Th:  B&GS  0153  
TA:                                  Nicholas  Raun   Email:  nraun@uwo.c  
   
2  lecture  hours,  1  tutorial  hours,  0.5  course.   Prerequisites:  Biochemistry  2280A;;  Biology  2581A/B.  
Unless  you  have  either  the  requisites  for  this  course  or  written  special  
permission  from  your  Dean  to  enroll  in  it,  you  may  be  removed  from  this  
course  and  it  will  be  deleted  from  your  record.  This  decision  may  not  be  
appealed.  You  will  receive  no  adjustment  to  your  fees  in  the  event  that  you  
are  dropped  from  a  course  for  failing  to  have  the  necessary  prerequisites.  

COURSE  DESCRIPTION  
The  field  of  molecular  biology  is  rapidly  evolving  and  with  it  comes  a  greater  understanding  of  the  central  
dogma,  DNA  makes  RNA  makes  protein.  The  primary  aim  of  this  course  is  to  examine  the  regulatory  
mechanisms  that  control  the  production  of  RNA  from  DNA  (Transcription)  and  protein  from  RNA  
(Translation).  More  broadly,  this  course  looks  at  methods  of  gene  regulation  in  both  prokaryotic  and  
eukaryotic  systems.  
Topics  include  prokaryotic  and  eukaryotic  transcription,  RNA  splicing/processing/stability/localization,  
translation,  epigenetics  and  regulatory  RNA,  new  techniques  used  to  modulate  gene  expression.  
 
 
LEARNING  OUTCOMES  
By  the  end  of  this  course  student  will  be  able  to:  
1.   Discuss  the  processes  governing  gene  transcription  in  prokaryotic  and  eukaryotic  cells.    
2.   Describe  the  mechanisms  that  govern  chromatin  structure  and  explain  the  role  of  chromatin  in  
gene  regulation.  
3.   Discuss  the  topics  of  epigenetics  and  epigenomics.  
4.   Describe  the  processing  and  translation  of  RNA  and  explain  the  role  of  non-­coding  RNA  in  gene  
regulation.  
5.   Discuss  cutting  edge  methods  used  to  study  various  aspects  of  gene  regulation  covered  in  
lecture.  
6.   Read  primary  scientific  literature  at  sufficient  depth  to  provide  an  accurate  summary  and  
comment  on  the  overall  conclusion  and  importance  of  the  work.  
7.   Apply  concepts  and  knowledge  about  gene  regulation  and  scientific  methods  to  interpret  novel  
datasets.  
 
 
COURSE  MATERIAL  

1.   Textbook:  Fundamental  Molecular  Biology,  2nd  Edition  by  Lizabeth  A.  Allison.                                                      
ON  RESERVE  at  Taylor  Library.    Much  of  the  lecture  material  is  derived  from  this  text.  This  text  
will  be  very  useful  for  reinforcing  concepts  discussed  in  lecture.  Recommended  to  purchase.  

2.   Textbook:  Molecular  Biology  of  the  Gene,  7th  edition,  by  James  D.  Watson.                                                                
ON  RESERVE  at  Taylor  Library.  Some  subject  and  figures  covered  in  lecture  are  derived  from  
this  text  and  not  present  in  Allison.    

3.   Lecture  slides  available  on  OWL.    I  will  make  these  slides  available  usually  just  before  the  lecture  
time.  

4.   Other  reading  material  from  scientific  literature  will  be  suggested  for  selected  topics  that  are  not  
covered  in  text  books  

5.   Students  should  check  OWL  on  a  regular  basis  for  news  and  updates.  This  is  the  primary  method  
by  which  information  will  be  disseminated  to  all  students  in  the  class.  Students  are  responsible  for  
checking  OWL  on  a  regular  basis.  

EVALUATION  

The  overall  course  grade  will  be  calculated  as  follows:  


 
QUIZZES       20%  
ANNOTAIONS   15%  
MIDTERM  –  Oct  21.   25%  
FINAL  EXAM       40%  

 
METHODS:  
 
1.   Text  reading  prior  to  attending  class,  as  indicated  on  schedule  and  in  lecture.  
This  course  is  challenging  and  fast  paced.  To  be  successful,  you  must  attend  all  lectures  and  read  
the  assigned  material  BEFORE  and  after  each  lecture.  Do  not  fall  behind!    
 
2.   OWL  FORUM    
If  after  the  lecture  and  after  you  study,  you  do  not  understand  something,  please  consult  the  OWL  
forum,  where  your  question  might  already  have  been  addressed.  If  your  question  is  not  addressed  
in  the  forum,  then  post  your  own  question  there.  Students  should  feel  free  to  answer  questions  in  
the  forum  that  are  posted  by  your  classmates.  The  forum  will  also  be  monitored  by  the  instructors.  
 
3.   Tutorials      
The  goals  of  the  tutorials  will  be  to  review  lecture  material  and  learn  about  current  methods  in  
gene  regulation  research.  The  tutorial  will  start  with  a  quiz  and  a  review  of  the  previous  quiz.  This  
will  be  followed  by  a  20-­30  min  session  in  which  you  will  learn  about  an  important  method  in  gene  
regulation  research.    The  methods  discussed  will  be  directly  relevant  to  the  annotation  
assignments.  
a.   Quizzes  (20%):  9  quizzes  of  15  min.  (multiple  choice  or  short  answers)  at  the  beginning  of  
each  tutorial  –  lowest  1  dropped.  No  make-­up  quizzes.  The  purpose  of  the  quizzes  will  be  
to  review  lecture  material  from  the  previous  week.  
b.   Annotations  (15%):  3  in  total  –  see  schedule  for  due  dates.  Each  student  will  bring  an  
annotation  of  a  primary  research  paper,  which  will  be  posted  on  OWL  1-­2  weeks  prior  to  
the  deadline.    
 
4.   Mid-­term  and  Final  Exam  
a.   Both  with  cheat-­sheet  (one  side  of  an  8.5”  X  11”  page,  with  the  student’s  name,  to  be  handed  
along  with  the  exam).  
b.   Mid-­term  will  cover  lectures  1-­12.    Combined  multiple  choice  and  short  answer.  With  proper  
documentation,  the  grade  for  the  mid-­term  will  be  reported  to  the  final.  If  a  student  has  prior  
knowledge   of   a   conflict   with   the   scheduled   mid-­term   test,   they   must   inform   the   instructor  
prior  to  the  date  of  the  term  test.  There  will  be  NO  make-­up  mid-­term.  
c.   The  final  exam  will  be  scheduled  by  the  registrar  during  the  regular  exam  period.  It  will  be  
cumulative,  covering  material  from  the  entire  year.  It  will  combine  multiple  choice  and  short  
answer  and  will  contain  an  annotation  style  question  involving  a  novel  dataset.  
d.   Statement   on   the   Use   of   Electronic   Devices.   No   electronic   devices   (including   but   not  
limited   to   laptop   computers,   cell   phones,   iPods,   etc.)   will   be   allowed   during   examinations  
unless  expressly  authorized  by  the  instructor.  
 
ACCOMIDATION  AND  ACCESSIBILITY    
 
If  you  are  unable  to  meet  a  course  requirement  due  to  illness  or  other  serious  circumstances,  you  
must  provide  valid  medical  or  supporting  documentation  to  the  Academic  Counselling  Office  of  your  
home  faculty  as  soon  as  possible.  If  you  are  a  Science  student,  the  Academic  Counselling  Office  of  
the  Faculty  of  Science  is  located  in  WSC  140,  and  can  be  contacted  at  scibmsac@uwo.ca.  For  further  
information,  please  consult  the  university’s  medical  illness  policy  at:  
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_medical.pdf.  
 
If  you  miss  the  Final  Exam,  please  contact  your  faculty’s  Academic  Counselling  Office  as  soon  as  you  
are  able  to  do  so.  They  will  assess  your  eligibility  to  write  the  Special  Exam  (the  name  given  by  the  
university  to  a  makeup  Final  Exam).  You  may  also  be  eligible  to  write  the  Special  Exam  if  you  are  in  a  
“Multiple  Exam  Situation”.  See  http://www.registrar.uwo.ca/examinations/exam_schedule.html.  
 
ACADEMIC  POLICIES.    
 
The  website  for  Registrarial  Services  is  http://www.registrar.uwo.ca.  
 
In  accordance  with  policy,  http://www.uwo.ca/its/identity/activatenonstudent.html,  the  centrally  
administered  e-­mail  account  provided  to  students  will  be  considered  the  individual’s  official  university  
e-­mail  address.  It  is  the  responsibility  of  the  account  holder  to  ensure  that  e-­mail  received  from  the  
University  at  his/her  official  university  address  is  attended  to  in  a  timely  manner.  
 
Scholastic  offences  are  taken  seriously  and  students  are  directed  to  read  the  appropriate  policy,  
specifically,  the  definition  of  what  constitutes  a  Scholastic  Offence,  at  this  website:  
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/scholastic_discipline_undergrad.pdf  
 
 
Computer-­marked,  multiple-­choice  tests  and  exams  may  be  subject  to  submission  for  similarity  review  
by  software  that  will  check  for  unusual  coincidences  in  answer  patterns  that  may  indicate  cheating.  
 
We  may  use  iClickers  for  informal  assessment  in  class.  Students’  privacy  will  be  protected  with  
respect  to  data  gathered  from  the  responses,  that  the  data  gathered  using  the  devices  will  not  be  
used  for  research  purposes  without  their  consent,  and  that  they  cannot  be  used  by  anyone  but  the  
student.    
 
SUPPORT  SERVICES    
 
Please  contact  the  course  instructor  if  you  require  lecture  or  printed  material  in  an  alternate  format  or  
if  any  other  arrangements  can  make  this  course  more  accessible  to  you.  You  may  also  wish  to  contact  
Services  for  Students  with  Disabilities  (SSD)  at  661-­2111  ext.  82147  if  you  have  questions  regarding  
accommodation.  
 
The  policy  on  Accommodation  for  Students  with  Disabilities  can  be  found  here:  
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_disabilities.pdf  
 
The  policy  on  Accommodation  for  Religious  Holidays  can  be  found  here:  
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_religious.pdf  
 
Learning-­skills  counsellors  at  the  Student  Development  Centre  (  http://www.sdc.uwo.ca  )  are  ready  to  
help  you  improve  your  learning  skills.  They  offer  presentations  on  strategies  for  improving  time  
management,  multiple-­choice  exam  preparation/writing,  textbook  reading,  and  more.  Individual  
support  is  offered  throughout  the  Fall/Winter  terms  in  the  drop-­in  Learning  Help  Centre,  and  year-­
round  through  individual  counselling.  
 
Students  who  are  in  emotional/mental  distress  should  refer  to  Mental  Health@Western  (  
http://www.health.uwo.ca/mental_health  )  for  a  complete  list  of  options  about  how  to  obtain  help.  
 
 
   
Course  Schedule  (subject  to  change)  

Book   Tutorial    
Week   Lecture  Topic  
Chap.   Papers  on  owl  
Lec1:  Introduction:  The  Central  Dogma    
1   No  tutorial  
Lec2:  Genome  Organization  –  DNA  to   2,  3,  5  
Week  of  Sept  11    
RNA    
Lec3:  Transcription  in  Bacteria  1   10   Introduction  
2  
Lec4:  Transcription  in  Bacteria  2   METHODS:  RNA  
Week  of  Sept  18  
detection  
Lec5:  Transcription  in  Bacteria  3   10   Quiz  1  
3  
Lec6:  Transcription  in  Bacteria  4     METHOD:  Protein  
Week  of  Sept  25  
detection  
Lec9:  Transcription  in  Eukaryotes  1   11   Quiz  2  
4  
Lec10:  Transcription  in  Eukaryotes  2   METHOD:  RNA  and  
Week  of  Oct  2  
  protein  localization  
 
Annotation  1  due  Wed  Oct  4  in    
 
lecture  
5   STUDY  BREAK      
Week  of  Oct  9  
Lec11:  Transcription  in  Eukaryotes  3   11   Quiz  3  
6  
Lec12:  Transcription  in  Eukaryotes  4     METHOD:  Protein-­
Week  of  Oct  16  
DNA  interactions  
Oct  21   MID-­TERM  –  9:30-­12:30    AHB  1R40      
Lec13:  Epigenetics  and  chromatin  1   12   Review  midterm  
7  
Lec14:  Epigenetics  and  chromatin  2   METHOD:  Protein-­
Week  of  Oct  23  
  DNA  interactions    
Lec15:  Epigenetics  and  chromatin  3   12   Quiz  4  
Lec16:  Epigenetics  and  chromatin  4     METHOD:  Protein-­
8  
  DNA  interactions    
Week  of  Oct  30  
Annotation  2  due  Wed  Nov  1  in  
lecture  
Lec17:  RNA  1   13   Quiz  5  
                           9  
Lec18:  RNA  2     METHOD:  Protein-­
Week  of  Nov  6  
  RNA  interactions  
Lec19:  RNA  3   13   Quiz  6  
10  
Lec20:  RNA  4     METHOD:  Protein-­
Week  of  Nov  13  
  RNA  interactions  
Lec21:  Translation  1   14   Quiz  7  
11  
Lec22:  Translation  2   METHOD:  Protein-­
Week  of  Nov  20  
RNA  interactions  
12   Lec21/22  –  to  be  determined     No  tutorial  
Week  of  Nov  27    
Lec23:  Translation  3   14   Quiz  8  
Lec24:  Translation  4     Exam  Review  
13  
 
Week  of  Dec  4  
Annotation  3  due  Wed  Nov  22  in  
lecture  

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