BIOL 4620 Molecular Biology                     Syllabus Spring 2014               4 credit hours

Meets Tues and Fri 10:00am -11:50am in DCC318
Prerequisites: BIOL2120 Intro to Cell and Molecular Biology; BIOL 2500 Genetics is strongly recommended

INSTRUCTOR: Dr. Donna E. Crone, Lecturer
Office location:  JROWL (Science Center) 3C11, Office phone number: 276-3299
Office hours:  Tues and Thurs 4:00 -5:00pm and by appointment

TA office location: CBIS 2113                         phone: 276-3471
TA office hours:  Mon 1:30-3:00pm

Office location: JROWL 3C15                     Office hrs: TBA

COURSE DESCRIPTION: This course will focus on the organization of prokaryotic and eukaryotic genomes and the molecular processes for storing, maintaining and expressing genomic information in cells and organisms. The emphasis of this course will be on the regulation and gene expression from the transcription of chromosomal DNA through the processing and translation of the gene transcript. The molecular tools and techniques for studying genomes and 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:
•    Structure, organization and packaging of typical eukaryotic, prokaryotic and viral genomes
•    Events involved in initiation, elongation, termination and processing of RNA and protein and the regulation of these events.
•    Functional RNA and its role in regulation of genome activity
•    Events involved in genome maintenance
•    Role of mutation, recombination and mobile genetic elements in generation of genome diversity and evolution
Compare and contrast major features of transcription, translation and replication in prokaryotic and eukaryotic organisms

COURSE TEXT:  (required)
Molecular Biology:  Principles of Genome Function N. Craig etal. Oxford University Press
2012 ISBN13: 9780199562053         Also available as e-book through Course Smart

ATTENDANCE Policy:  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.

GRADING Criteria/ Assessment

Homework (25%).  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 75%

Option 1: 4 in class exams – all grades counted toward final grade

Option 2: highest 3 of 4 scores on in-class exams plus score on final exam count toward final grade (i.e. drop lowest in-class exam score)

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.  Optional comprehensive final exam can replace the lowest in-class exam score

Final grades are determined from the percent of total available 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 (eg. extra time for exams):  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 a grade of zero (0) for that exam.  Cheating includes the use of books, notes, crib sheets or other written material (either in paper OR electronic form)  during an exam.  Electronic devices are PROHIBITED during exams.  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 re-grading should have no additional marks on the exam.  Anyone altering an exam for the purpose of re-grading will be given a zero (0) for that exam.  Any repeat occurrence of academic dishonesty will result in a grade of  F for the course grade.  Students who cheat in this course will be reported to ALAC.
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 RPI LMS)

Date 2014


Text reference

HW due next
class period

Jan 21

Introduction: flow of genomic info



Jan 24

Biological Molecules: nucleic acids



Jan 28

proteins and enzymes

ch2 and ch3


Jan 31




Feb 4



HW 5

Feb 7

Exam 1



Feb 11

Cell cycle

ch 5

HW 6

Feb 14

DNA replication 1

ch 6

HW 7

Feb 18

No class – Monday Schedule



Feb 21

DNA replication 2/ Segregation

ch 6 and 7

HW 8

Feb 25

Transcription 1

ch 8

HW 9

Feb 28

Transcription 2

ch 8

HW 10

Mar 4

finish and review


HW 11

Mar 7

Exam 2

ch 5 – 8 (to p331)


Mar 8-16

Spring Break- No classes



Mar 18

Transcription Regulation2/ RNA processing

Ch8 and 9

HW 12

Mar 21

RNA processing2

ch 9

HW 13

Mar 25


ch 10

HW 14

Mar 28

Translation 2

ch 10

HW 15

Apr 1

Post translational modification

ch 11


Apr 4

finish and review



Apr 8

Exam 3

ch 8-11


Apr 11

DNA damage response

ch 12


Apr 15

Repair/ recombination 1

ch 13


Apr 18

Repair/ recombination 2

ch 13

HW 19

Apr 22

Mobile DNA1

ch 14

HW 20

Apr 25

Mobile DNA2

ch 14

HW 21

Apr 29

Exam 4

ch 12-14


May 2

Intro to genomics

ch 15

HW 22

May 6

Molecular Bio toolkit

ch 16

HW 23

May 13-17

Final exam
date/time scheduled by registrar

comprehensive final
100 MC questions (2 hr limit)

©Donna E. Crone 2014