This  syllabus  is  subject  to  change,  please  check  back  for  updates  (updated  01/03/18)  

 
Biochemistry   103b   -­   Advanced   Biochemistry:   Cellular   Information   Transfer  
Mechanisms  
 
Prof.  Tijana  Ivanovic,  office  Rosenstiel  450,  ivanovic@brandeis.edu  
Office  hours  by  appointment  on  Friday  (email  to  schedule  by  Thursday):  9-­10am  
Extra  office  hour  with  presenters  on  Friday  (email  to  schedule  a  week  ahead  of  time)  
 
TA:  Ingrid  Marko    
imarko@brandeis.edu  
Office  hours:  TBD  
 
Course  meeting  times:  M,  W  2-­3:20pm  (Block  K)  
Location:  TBD  
 
COURSE  OVERVIEW:  
 
The  course  will  focus  on  fundamental  principles  underlying  the  faithful  storage  of  genetic  information  
and  its  transfer  into  protein.  Through  in-­depth  analyses  of  primary  literature,  a  special  emphasis  will  
be   placed   on   understanding   experimental   approaches   and   critically   evaluating   conclusions   drawn  
from  experiments.  We  will  sample  historical  papers  describing  seminal  discoveries,  such  as  the  first  
evidence  for  DNA  as  the  genetic  material,  the  elucidation  of  DNA  structure,  and  the  discovery  of  DNA  
polymerase.  These  foundational  discoveries  have  shaped  much  of  biology  over  the  past  >65  years.  
We   will   further   explore   select   advanced   concepts   in   nucleic   acid-­enzyme   mechanisms   and   cutting-­
edge  approaches  used  in  discovering  them.  Topics  may  include:  DNA  recombination  and  replication;;  
transcription   (DNA   to   RNA);;   processing/maturation   of   precursor   RNA   transcripts;;   and   translation  
(RNA  to  protein).    
 
Prerequisites:   One   year   of   organic   chemistry   with   laboratory   and   BCHM   100a   or   equivalents.   BIOL  
14a  or  the  equivalent  is  recommended.  
 
COURSE  MATERIALS:  
 
Reading   materials   will   be   posted   on   LATTE   about   a   week   prior   to   their   assigned   date.   You   are  
encouraged  to  read  all  posted  materials  prior  to  the  lecture  where  they  are  discussed.  Each  week  you  
will   be   asked   to   read   an   assigned   paper   that   deals   with   the   topics   discussed   in   class.   You   are  
required  to  read  the  assigned  papers  in  depth  before  they  are  discussed  in  class.  The  recommended  
(not  required)  textbook  for  background  reading  is  Biochemistry  4th  edition  by  Voet  and  Voet.  
 
PROBLEM  SETS:  
 
Problem  sets  will  be  based  on  assigned  primary  literature  reading.  They  will  be  due  at  the  beginning  
of  the  class  when  a  given  paper  is  discussed.  
 
EXAMS:  
 
There  will  be  no  midterms.  There  will  be  a  final  exam.  The  final  exam  is  cumulative  and  will  cover  all  
topics  treated  throughout  the  course.  It  will  be  held  during  the  last  regular  class  period.  
 
DISCUSSIONS/PRESENTATIONS:  
  
You   are   strongly   encouraged   to   come   to   every   class   prepared.   This   will   help   you   participate   in  
lectures,  either  by  answering  questions  (posed  by  me  or  other  students),  or  by  asking  questions  that  
will   help   you   understand   concepts   being   covered.   I   welcome   confusions   from   students.   There   is   no  
stupid   question!   The   class   is   meant   to   challenge   you   to   push   the   limits   of   your   understanding   of   a  
range  of  concepts,  and  the  best  way  to  accomplish  that  is  if  we  all  actively  participate.    
 
I   will   present   the   first   couple   of   papers   and   lead   the   discussions   based   on   them.   After   that,   the  
students  will  take  up  the  role  of  presenters/discussion  leaders.  I  will  offer  an  additional  office  hour  (by  
appointment)  on  Fridays  prior  to  the  student  presentations  to  meet  with  student  presenters.  
 
ATTENDANCE:  
 
Attendance   is   required   and   class   participation   is   a   big   part   of   your   grade   (however,   if   you   are   sick,  
please  stay  home  and  get  better).  Even  if  you  know  that  you  will  miss  a  class,  you  are  still  responsible  
for  turning  in  your  problem  sets  in  a  timely  fashion  (in  this  context,  I  will  allow  electronic  submissions  
that  are  posted  by  the  deadline).  
 
EVALUATION:  
 
Final   grades   will   be   determined   by   your   performance   on   problem   sets   (25%),   presentations   (15%),  
attendance/in-­class  discussions  (35%),  and  the  final  exam  (25%).  
 
BACKGROUND  EXPECTATION:    
 
I   expect   that   everyone   will   have   familiarity   with   basic   chemical   structures   of   nucleotides   and   DNA,  
base   pairing   and   genetic   code.   I   further   expect   that   everyone   will   have   a   firm   knowledge   of   basic  
protein  biochemistry.  
 
Success  in  this  4  credit  hour  course  is  based  on  the  expectation  that  students  will  spend  a  minimum  
of   9  hours  of   study   time   per   week   in   preparation   for   class   (readings,   papers,   discussion   sections,  
preparation  for  exams,  etc.).      
 
 
POLICY  ON  ACADEMIC  HONESTY:  
 
Academic  integrity  is  central  to  the  mission  of  educational  excellence  at  Brandeis  University.  You  are  
expected   to   be   familiar   with   and   to   follow   the   University’s   policies   on   academic   integrity   (see  
http://www.brandeis.edu/studentaffairs/srcs/ai/).  I  will  refer  any  suspected  instances  of  dishonesty  to  
the   Office   of   Student   Development   and   Conduct.   Violations   of   university   policies   on   academic  
integrity   may   result   in   failure   in   the   course   and   could   end   in   suspension   from   the   university.   All  
homework   must   be   your   own   work,   except   when   assignments   specifically   authorize   a   collaborative  
effort.  
 
STUDENTS  WITH  DISABILITIES:  
 
If  you  are  a  student  with  a  documented  disability  on  record  at  Brandeis  University  and  wish  to  have  a  
reasonable  accommodation  made  for  you  in  this  class,  please  see  me  immediately.  Accommodations  
cannot  be  made  retroactively.  
 
COURSE  TOPICS  BY  WEEK:  
Note:  this  may  be  subject  to  change    
  
Week  1:  Introduction,  Basics  of  DNA  
Week  2:  Why  nature  chose  phosphates  
Week  3:  DNA  as  the  genetic  material  –  historical  perspective  
Week  4:  Discovery  of  DNA  polymerase  
Week  5:  DNA  replication    
Week  6:  Transcription,  Transcriptional  regulation  
Week  7:  RNA  splicing/processing  (Joerg  Braun)  
Week  8:  Translation  (Amy  Lee)  
Week  9:  Viral  mechanisms  (I)  
Week  10:  Viral  mechanisms  (II)  
Week  11:  DNA  repair,  Genome  editing  
Week  11:  DNA  repair,  Genome  Editing  
Week  12:  Review  
Week  13:  Final  exam