Revised July 2007 NORTH CAROLINA STATE UNIVERSITY GRADUATE COURSE ACTION FORM

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DEPARTMENT/PROGRAM

COURSE PREFIx/NuMBER

PREVIOUS PREFIx/NuMBER

COURSE TITLE

ABBREVIATED TITLE

SCHEDULING Fall 0 Every Year [8J

COURSE OFFERED

CREDIT HOURS ~

Biotechnology Program

CH/BIT 572

PROTEOMICS

PROTEOMICS

Spring ~ Summer 0 AIL Year Odd 0 AIL Year Even 0 Other 0

By DISTANCE EDUCATION ONLY 0 ON CAMPUS ONLY ~

BOTH ON CAMPUS AND BY DISTANCE EDUCATION 0 GRADING ABCDF ~ StU 0

CONTACT HOURS: Lecture/Seminar J Laboratory/Studio Q Researchllndependent Study _

REPEAT FOR CREDIT: YES _ _No]:;

INSTRUCTOR NAME: David Muddiman

TITLE: Professor

GRADUATE FACULTY STATUS: Associate 0 Full ~

ANTICIPATED ENROLLMENT Per semester 1ll. Multiple sections Yes 0 PREREQUISITE(S) BIT 410 OR BIT 510 OR BCH 454

COREQUISITE(S)

PRE/COREQUISITE FOR

RESTRICTIVE STATEMENT

REQUIRED CURRiCULA/MINOR

No ~ Max. per Section 1ll.

TYPE OF PROPOSAL

New Course 0 Drop Course 0 Course Revision r8J Dual-Level Course 0

REVISION Content ~ Prefix/Number 0 Title 0 Abbreviated Title 0 Credit Hours 0 Contact Hours 0 Grading Method 0 Pre-Corequisites 0 Restrictive Statement 0 Description 0 Scheduling 0

PROPOSED EFFECTIVE DATE Fall 2010 ApPROVED EFFECTIVE DATE

CATALOG DESCRIPTION IN CONCISE FORM MEANINGFUL TO STUDENT (INCLUDING RESTRICTIVE STATEMENT; LIMIT TO TOTAL OF 80 WORDS): Introduction and history of the field of proteomics followed by the principles and applications of proteomics technology to understand protein expression and protein post-translational modifications. Laboratory sessions include growing yeast with stable-isotope labeled amino acids , protein purification, Western blots, protein identification and quantification, and protein bioinformatic analysis. This is a half-semester course .

DOCUMENTATION REQUIRED Please number all document pages

Course Justification r8J Proposed Revision(s) with

r8JJustification

Enrollment for Last 5 Years r8J

ConSUltation with other Departments r8J

Student Learning Outcomes r8J

Evaluation Methods and Weighting I2l

Explanation of Differences for Dual­0level Courses

Resource Statement I2l

Topical Outl ine and Time Devoted [XJ

ST BY: The course syllabus has been developed and is in irements of the Provost 's website.

C Date

C¢1 lege Dean(s) Date

A PPROVED:

Dean of the Graduate School Date

INSTRUCTIONS

Provide the following information . If add itional table rows are needed place cursor at location, select Table, Insert, Rows Above or Rows Below. Please limit your submission to 4 pages using 1 O-point font.

I. Course Justification (Explain the need for the course and its place in the curriculum in terms of the educational needs and interests of the

students for whom the course is intended):

Proteomics is the study of proteomes and a proteome is the proteins expressed by a genome at a specific point in time which changes based on such stimuli as environment and disease. Proteins are the key components in a cell which cause function and dysfunction and understanding protein expression and how they are post-translat ionally modified is critical to living systems. In this course, students gain hands-on experiments on how to express proteins in cell culture, purify them, prepare them for analysis by liquid separations coupled to high performance mass spectrometry, and carry out protein identification using sophisticated bioinformatics tools This course was created due to the demand from graduate students and faculty asking that their students be trained in this highly contemporary field of proteomics.

II. Proposed Revisions with J ustification (Briefly list the changes and the justification for each): We propose adding one additional credit to this course. One of the great benefits of this course is that it incorporates reading of primary literature Uourna l articles) in the field . Given the complexity of the topic, the amount of time allotted in lecture is not sufficient to both cover the lecture material and thoroughly discuss the primary literature. Students have requested additional time in class to go over and discuss the articles in a "journal club" format We would like to add one additional hour of lecture to the course in order to accomplish this . This will give students the opportunity to critically discuss the papers.

Additionally, students spend significant time outside of the laboratory doing bioinformatics (computer lab). Therefore, the laboratory component of this course may be considered "non-contained" .

For both of these reasons (ie. an additional 1 hour of lecture added to the half semester course, and the cons ideration that the laboratory extends outside of the regular period), adding an additional credit to the course is justified.

III. Enrollment for Last Five Years (Enter data -look up at R&R website for either existing course number or special topics number as applicable. If

not offered , indicate n/a. If previously offered as special topic, indicate deSignation after number enrolled [e.g. 17 - XX 592B]) :

Academic Year Fall SjJring Summer 2009 BIT 595 J/K - 12 students 2010 CH/BIT 572

IV. Consultation with Other Departments (List all departments and individuals contacted , and any statements of objection, non-objection, or support. Inclusion of the entire document/communication is not necessary . Consultation is needed whenever there is a possibility of content duplication or when establishment or dropping would affect other programs .

The consultation below was for the original course action. Since this course is not required in any other majo r, we don't believe that the change in credit numbers requires a new consultation. Both the BIT program and the chemistry department are in agreement regarding the change.

Department Contact Name I Statement Biochemistry James Knopp Several faculty in our department have reviewed your proposed

course and are supportive of your course action. Thank you for the o!2!2ortunitt to review it. [received 4/3/09]

V. Student Learning Outcomes. The goal of this course is for students to gain an understanding of how proteomics can be used to study gene expression at the protein level. Students will receive hands-on experience with culturing yeast, preparing the sample for analysis, separation science, mass spectrometry, bioinformatics, and Western blots.

Upon completion of the course, stUdent will be able to: 1. Design proteomic experiments to address a specific hypothesis 2. Generate data and understand the outcome of proteomic experiments.

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3. Read and dissect contemporary proteomic literature. 4. Use bioin formatic software for protein identification and quantification . 5. Discuss the advantages and disadvantages of different separation science and mass spectrometry strategies for the

analysis of proteins. 6. Be able to validate protein identifications using Western Blots .

VI. Student Evaluation Methods (List types of evaluation [tests, exam, papers, homework, etc.] and % weighting nonmally anticipated):

Weekly Exams 25% Journal Article Presentation 10% Laboratory Report Progress Report 10% Final Laboratory Report 25% Final Exam 25% Laboratory Notebook 5%

VII. Explanation of Differences for Dual-Level Cou rse (Explain differences in content, expectations, and outcomes for graduate level version of

dual-level course and indicate evaluation above) :

This is a graduate-level course, only.

VIII. Resource Statement (New courses only. Indicate the resource requirements of this course and the source (s) of those resources.)

No new resources will be needed. The Biotechnology Program pays for supplies/reagentslTA for the course, and the Chemistry Department is providing the faculty-member (instructor) salary.

IX. Topical Outline of Course and Time Devoted to Each Topic (Definition should be adequate to allow understanding of the course content.

Indicate time measure used, e.g. weeks, 50 min. lectures, 75 min. lectures, etc. ):

Lecture Dates (Bolded Dates are Weekly Exam Dates) January 8, 15, 22, 29 February 5, 12, 19, 26

WEEK 1 Lecture Introduction to Course

From Genomics to Proteomics - Chapter 1

WEEK2 Lab Culture, Harvest and Prepare Sl lAC Yeast

Protein Quantification - Chapter 4 Relative and Absolute Stable Isotope labeling

Journal Disc. Mini -Exam 1: Nature, 2008 , 455, 1251 .

Lecture Genetics Primer/Review Characteristics of Amino Acids , Peptides, and Proteins Yeast: Statistics, Proteome, ORFs

WEEK3 Lab Total Protein Digestion

Journal Disc. Mini-Exam 2: Biotechniques, 2007 , 43,5,563.

Lecture MAlDI-TOF and Peptide Mass Fingerprinting

WEEK4 Lab 1 D Gel Fractionation, In-Gel Protein Digestion

Journal Disc. Mini-Exam 3: Nature Reviews, 2004, 5, 699.

Lecture NanolC l TQ-FT and Protein Identification, Pre-lab 4 Sign up f or 1 hour time slot for Tuesday 's lab 2/3/09.

WEEK5 Lab linear Quadrupole Ion Trap Fourier Transform MS/MS for

Global Proteomics Identification Meet in Dabney 28 during time slot.

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Journal Disc.

Lecture

WEEK6 Lab

February 17, 2010

Journal Disc.

Lecture

WEEK 7 Lab

Lecture

WEEK8 Lab Lecture

March 18, 2010

Mini-Exam 4: Molecular & Cellular Proteomics , 2005 , 4 , 1265.

Analysis of Protein Sequences - Chapter 5 10 and 20 PAGE, Western Blots Relative Quantification Including Label-Free Proteomics

10 gels and Western Blots

Laboratory Progress Report Due Date

Mini-Exam 5: Journal of Proteome Research, 2004, 3, 644.

Mass Spectrometry and Absolute Protein Quantification Sign up for 1 hour t im e slot for Tuesday's lab 2/17/09.

Triple Quadrupole MS/MS for Absolute Protein Quantification Meet in Dabney 28 during time slot.

Protein Modifications - Chapter 8 Phosphorylation, Glycosylation

Final Examination Expected Experimental Results Presented and Discussion

Final Laboratory Report Due Date

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