BIOL 4620 MOLECULAR BIOLOGY               SPRING 2012

Dr. Donna E. Crone

Office:    Sci Ctr 3C11
Office hours: see LMS for location/time

Phone: -3299

Anne Roberts

Office hours:  see LMS for location/time



Lewin’s Essential Genes (2nd ed)

printed or electronic version

Class meetings: 

Tues and Fri 10:00am -11:50am 

DCC 318

COURSE DESCRIPTION: Students will learn about organization of prokaryotic and eukaryotic genomes, the molecular tools and techniques for studying genomes, basic molecular processes in cells and organisms. The emphasis of this course will be on the control of gene expression from the transcription of chromosomal DNA to the translation of the gene transcript. The applications of sequenced genomes to basic scientific research, medical and forensic studies will be discussed.

At the end of the course a successful student will be able to:
Use proper scientific vocabulary to communicate information in molecular biology.
Demonstrate knowledge of structures, properties and biological significance of the major molecules in living organisms.
Demonstrate a thorough understanding of:

Compare and contrast major features of transcription, translation and replication in prokaryotic and eukaryotic organisms

ATTENDANCE:  Regular and prompt attendance is strongly encouraged.  When in class, students should refrain from any activity that is distracting to themselves and other students (including talking, checking email, doing homework for this class or any other class, playing computer games and other non-class related activities). 
LAPTOPS and CELLPHONES:  Laptops are not needed during class.  Cell phones should be on silent or vibrate.  If you are texting during class, you are not paying attention!  In the rare case of an urgent call, please leave the room quietly. 
Homework (20%).  A few multiple choice questions are assigned corresponding to almost every lecture as noted on syllabus.  These are done in RPI LMS and are due before the next class.  Late HW will be accepted but assessed a late penalty.
Exams 80%
Option 1: 4 in class exams – all grades counted toward final grade
Option 2: 3 highest scores on in-class exams plus score on final exam count toward final grade
In-class Exams  Four in-class exams will be given on the dates noted in the schedule.  Students should bring writing implement (pen or pencil) and RPI ID to exam.
Make-up exams will be scheduled for students with valid medical reasons or Dean’s excuse for missing the original exam.  An exam missed without an excuse will be counted as a zero and will be included among the three hour exams used to determine your grade.
Final exam .  Comprehensive final exam is optional.  Final exam can replace the lowest
Final grades are determined from the percent of total points accumulated.

BIOL 4620 grades

A     93-100%

A-     90-92%

B+     87-89%

B     83-86%

B-     80-82%

C+     77-79%

C     73-76%

C-     70-72%

D+     67-69%

D     60-66%

F     Below 60%

Students needing accommodations for exams (eg. extra time):  Please provide a copy of the letter to the instructor and, if appropriate, make appointment to discuss specific needs.  This should be done at least one week prior to the first exam (preferably earlier) so that accommodations can be arranged.  It is the student’s responsibility to confirm arrangements prior to each exam.
Grading appeals:  Students may request regrade of in-class exams.  Regrade requests are due one week after exams are returned to students.  Request should be written on a separate sheet of paper and include the following: 1) question number and 2) why student answer should be given consideration for additional credit.  Exams will only be considered for regrade if the exam is written in ink and there are no marks on the exam other than original answers and grader’s notes. 
Anyone found cheating on an exam will be given an F for that exam.  No books, notes, crib sheets or other written material can be used during an exam.  Looking at another student's paper is not permitted.  Anyone giving or receiving assistance during an exam will be considered cheating.  Any exams handed back to the instructor for regrading should have no additional marks on the exam.  Anyone altering an exam for the purpose of regrading will be given an F for the course grade.
Students who violate the spirit or letter of these rules are subject to penalties according to the principles outlined in the Rensselaer Handbook.

Tentative Schedule (any revisions to the schedule posted will be posted in webCT/ RPI LMS)



Text reference

HW due next class period

Jan 24

Genes are DNA

Ch 1


Jan 27

Genes codes for Proteins

Ch 2


Jan 31

Genomes 1

Ch 3 and 4


Feb 3

Genomes 2

Ch 4 and 5


Feb 7

Genomes 3

Ch 6

HW 5

Feb 10


Ch 1-6


Feb 14


Ch 7

HW 6

Feb 17

Bacterial transcription

Ch 11

HW 7

Feb 21

Bacterial Transcription regulation 1

Ch 12

HW 8

Feb 24

Chromosomes and chromatin

Ch 23 and 24

HW 9

Feb 28

Eukaryotic transcription

Ch 25

HW 10

Mar 2

Transcription regulators and chromatin remodeling:  End of material for exam 2

Ch 26

HW 11

Mar 6

Eukaryotic transcription regulation 2
Histone modification

Ch 26


Mar 9


Ch 7, 11,12, 23-25 and Ch 26(to p648)


Mar 12-16

No Class:  spring break



Mar 20

RNA processing 1

Ch 28

HW 12

Mar 23

RNA processing 2

Ch 29

HW 13

Mar 27

Translation 1

Ch 8, 9

HW 14

Mar 30

Translation 2

Ch 8, 9

HW 15

Apr 3


Ch 8,9, 26, 28-29


Apr 6

Regulatory RNA/ epigenetic regulation

Ch 13 and ch27

HW 16

Apr 10

Replication 1

Ch 15 -17


Apr 13

Replication 2

Ch 17 -18


Apr 17

No Class GM day

Apr 12


Apr 20



HW 19

Apr 24

Repair systems

Ch 20

HW 20

Apr 27


Ch 21

HW 21

May 1


Ch 15-20


May 4

Immune diversity

Ch 22

HW 22

May 10

Techniques in Molecular Biology

Ch 30

HW 23

May 13, 16-19

Final exam date and time determined by registrar