Orientation

  • ORIENTATION
    GRADUATE STUDENTS
    AUGUST 13 - AUGUST 24, 2012
    PENN STATE COLLEGE OF MEDICINE 

      (for  complete schedule click HERE)

 

ANAT, PHS, LAM  and MD/PhD students:  please follow the orientation distributed by your programs.

If you have questions, please contact your program secretary.

 

 

First Year Graduate Core Curriculum

Most students entering graduate programs at Penn State Hershey and second-year ANAT students participate in all or part of the Core Curriculum. While your Program will let you know their specific course requirements, the complete Core Curriculum during Orientation and the Fall semester consists of the following:
 
Orientation:
  •  Introduction to Cell & Molecular Biology
Fall Semester:
  • BMS 501 - Regulation of Cellular and Systemic Energy Metabolism
  • BMS 502 - Cell and Systems Biology
  • BMS 503 - Flow of Cellular Information
 
The goal of these courses is to provide a foundation in topics that are fundamental for graduate studies in biomedical sciences. We recognize, however, that entering students differ in their areas of previous study and we offer several ways for you to prepare for these courses.
 
Course Syllabi for the Core courses (and program-specific courses) are posted on the Graduate Student Affairs website. The syllabi include course descriptions, schedules, and required textbooks.

Readings.  Below is a list of selected pre-readings. It is strongly recommend that you read these selections before you come for Orientation. Since the material is covered at a rapid pace in these courses, reading ahead during the summer is particularly important if your background is weak in the areas covered by the readings.

 

SELECTED READINGS FOR INDICATED COURSES
Introduction to Cell and Molecular Biology: see course outline
BMS 501 - Regulation of Cellular and Systemic Energy Metabolism
            Lehninger Principles of Biochemistry; 5th edition: Nelson and Cox eds. ISBN 0-7167-7108 or ISBN-13 978-0-716-77108
                        Essential: Chapters 1, 2, 6 & 13
                        Very helpful: Chapters 10 & 11
 
BMS 502 – Cell and Systems Biology
            Molecular Biology of the Cell; 5th edition:Alberts et al. ISBN 0-8153-4105-9
                        pp. 617-622; 695-704; 721-726; 771-776; 779-786; 815-817
 

Orientation Course:  Introduction to Cell & Molecular Biology

This short course is given during the two-week Orientation. The course covers prerequisite knowledge in molecular and cell biology and biochemistry that is necessary for students taking the Fall Core courses. The required textbooks for this course (which are also required for the Fall Core courses) are:
·        Molecular Biology of the Cell, Alberts et al., (Garland; 5th edition, 2008).
·        Lehninger Principles of Biochemistry, Nelson & Cox (Freeman, 5th edition, 2008).
The course outline below includes readings for each topic from these texts. Since the pace of this course is very rapid (the class meets two hours per day and there are additional orientation activities as well), students who took it last summer strongly suggested that the reading list be made available during the summer so incoming students could read the assignments prior to arriving.
Critical analysis of the primary literature is an essential skill for graduate study and is discussed in the first session of the introductory course. To illustrate this skill, we will use the paper,  "Attempt to fulfill Koch's postulates for pyloric campylobacter" by Marshall et al, Med J Aust 142: 436-9 (1985).  Please read this paper prior to the first session of the Introduction to Cell & Molecular Biology course.
Your grade in this introductory course is not reported on your transcript but the results of the exam are reported to your Program Director. Historically, there has been a strong correlation between a student's score in this course and their subsequent performance in the Core courses. Therefore, this introductory course provides a means for you and your Program to judge your preparation for the Core Curriculum.

    

Introduction to Biochemistry and Molecular Biology: Schedule & Topics, Fall 2012
 
#
Date
Time
Topic
Lecturer
Reading*
1
Aug 15
2 PM
Course Introduction Goals & overview of course.
How to read a scientific paper.
Verderame
MBC pp 1–11
Marshall et al, Med J Aust 142: 436-9 (1985)
2
Aug 15
3 PM
Water. pH, and chemical bonding in solution Structure of water, water interacts with itself and other compounds, pH and buffers. Methods: Precipitation of proteins & nucleic acids, pH titration and buffers, Henderson Hasselbach
Ropson
Lehninger chapter 2
MBC pp 51-54
3
Aug 16
2 PM
Thermodynamics, and Kinetics Basic Thermodynamics, chemical reactions, relationship between free energy and equilibrium, 1st and 2nd order kinetics, concept of transition state. Michaelis-Menten equation and assumptions, inhibition and the Lineweaver-Burk plot. Method: Statistics, how fitting can lie
Ropson
Lehninger chapter 1
MBC pp 75-87
4
Aug 16
3 PM
Amino acids Structure and function of amino acids, chemistry. The amide bond. Protein secondary and tertiary structure. Method: Chromatography
Ropson
Lehninger chapter 3
5
Aug 17
2:30 PM
Proteins Structure/function relationships. Homology. Mutation and drug activity. Paper: Mutations in HIV protease and drug resistance. Method: Blast searches
Ropson
Lehninger chapters 3-5
MBC 125-158
6
Aug 17
3:30 PM
Fold-It "Hands-on" protein structure
Ropson
 
7
Aug 20
2:30 PM
Carbohydrates and Lipids Basic carbohydrate structure. Complex carbohydrates. Lectins. Lipid types and structures. Membranes.
Ropson
Lehninger chapters 7 &10
MBC pp 55-60
8
Aug 20
3:30 PM
Nucleic Acids Structure of nucleic acids; organization & replication of DNA
Verderame
Lehninger chapter 8
MBC pp 195–201; 263–281
9
Aug 21
2 PM
Analysis of DNA Hybridization, restriction enzymes, electrophoresis, Southern & Northern blotting, DNA sequence analysis, PCR
Verderame
MBC pp 532–540; 544–553
10
Aug 21
3 PM
Transcription & Translation Transcription & regulation; genetic code & translation; protein targeting
Verderame
MBC pp 329–342; 366–388
11
Aug 22
1 PM
Cloning cDNA & genomic clones; clone selection
Verderame
Lehninger chapter 9
MBC pp 540–544
12
Aug 22
2 PM
Visualizing Cells & Components Cell fractionation, light & electron microscopy; in situ hybridization, immunocytochemistry
Verderame
MBC pp 510–512; 579–615
13
Aug 23
2 PM
Experimental systems In vivo vs in vitro systems; animal models; transgenics & knockouts
Verderame
MBC pp 501–510; 564–568
 
Aug 23
3 PM
Review
Ropson Verderame
 
 
Aug 24
9 -12
EXAM
 
 
*Required textbooks: MBC = Molecular Biology of the Cell, Alberts et al., (Garland; 5th edition, 2008). Lehninger Principles of Biochemistry, Nelson & Cox (Freeman, 5th edition, 2008).

 

 Orientation activities are mandatory for all incoming graduate students, unless you are notified of other program responsibilities.  Complete details can be found on the 2012 Orientation Schedule.  Orientation will begin on Monday, August 13 at 8:30 AM in Lecture Room C in the College of Medicine.