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NORTH CAROLINA AGRICULTURAL AND TECHNICALSTATE UNIVERSITY

Course Syllabus

Course InformationCourse Number & Section Biology 642 Section 001 (CRN 17632)Course Title Designer Proteins and Society

Term Fall 2012Location 224 Barnes HallDays & Times Tuesday & Thursday 12:30pm - 1:45pmWebsite http://blackboard.ncat.edu

Professor Contact InformationProfessor Dr. Justin ShafferEmail Address jfshaffe@ncat.eduOffice Phone 724-301-2712Office Location G10 Barnes HallOffice Hours Tuesday 10:00am 12:00pm

Thursday 2:00pm 4:00pm

Course Description and GoalsProteins can be so much more than what you find in a burger or a nutritional supplement! Didyou know that scientists and engineers can design and produce custom proteins to meetspecific functional and technical needs? Whether they are for medical, pharmaceutical,industrial, agricultural, or environmental settings, recombinant proteins are used in a variety ofways to benefit society. This course provides an introduction to the fascinating and diverse fieldof recombinant proteins. Once we cover the basics of how recombinant proteins are made,

youll learn how to use recombinant DNA technology to design protein expression vectors. Next,youll learn how various expression systems (bacterial, insect, and animal cells) and purificationschemes (chromatography, centrifugation, dialysis, etc) are used to produce and purifyrecombinant proteins. Youll also have the opportunity to perform a realistic laboratory researchproject to express, purify, and functionally assess a recombinant protein. Throughout the coursewell discuss the many ways that recombinant proteins are used in modern day medicine,industry, and agriculture, and will discuss their societal and ethical impacts.Specifically, at the end of this course, you will be able to

Define and explain key fundamental terms and concepts of protein biochemistry

Apply molecular biology methods and recombinant DNA technology to createrecombinant protein expression vectors

Design an expression and purification scheme for a recombinant protein based on theproteins biochemical properties

Develop a design proposal to clone, express, purify, and assess a recombinant protein

Explain how recombinant proteins are used in medical, pharmaceutical, industrial,environmental, and agricultural applications and why they are so important to society

Explain and evaluate the ethical implications surrounding recombinant DNA technologyand the use of recombinant proteins

Design, execute, and troubleshoot laboratory experiments and methods relating torecombinant protein expression and purification

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More specific learning objectives and goals are presented for each unit as described in thecourse schedule below, and will also be provided at the beginning of each day of class.

PrerequisitesMolecular biology (BIOL 401). If you do not meet the prerequisites please contact me.

Required Textbooks and MaterialsThere are no required textbooks for this course. You might want to consult your biology,molecular biology, or biochemistry textbooks from time to time to help brush up on somematerial. Reading materials will be posted on Blackboard for you to read and print out.

Course Requirements and EvaluationActive Learning:You might be used to taking courses in which the professor simply lectures theentire class period. This course is going to be very different, as it is going to be an activeclassroom. By active I mean that you will be required to interact with myself and your fellowstudents to learn the material presented in this course. We will be using activities such as smallgroup work, case studies, and class discussions to actively engage in the learning process. Inorder to have an active classroom, attendance is extremely important. By attending class and

working through these active learning exercises you will develop critical thinking and problemsolving skills that are essential to performing well in this course and others.

Recombinant Protein of the Day: Recombinant proteins are essential to medicine, industry,agriculture, and the environment. To highlight the importance of recombinant proteins in oursociety, each day of class will feature a Recombinant Protein of the Day. During these short, 5minute presentations, we will learn about the function of the recombinant protein, how it is usedby society, and how it is produced. I will give the first handful of presentations, but then you as aclass will be responsible for presenting the remainder. The goal is not to learn everythingpossible about the specific recombinant protein, but rather to be exposed to the many, manyways that recombinant proteins positively affect our society! See the handout for more details.

Design Project:The overall goal of this course is that you will be able to design and map out aprocedure to clone, express, purify, and functionally assess a recombinant protein. This projectwill be in the form of a written proposal. The proposal will include the following sections: 1)background on the biological importance of the protein you want to produce; 2) design of thecloning process (choice of vector, primer design, choice of restriction enzymes, etc); 3) choiceof the expression system; 4) design of a purification scheme (type of chromatography, etc); and5) design of experiments to assess the function of the protein. All sections will require

justifications as to why you designed the process the way you did. Throughout the semester,there will be checkpoints where you will have to turn in parts of the project to keep you on track.The final project will be due at the end of the semester. Further instructions and guidelines forthe project will be given out in class.

Laboratory Project:During the last few weeks of this course you will have the chance to takepart in a realistic research project where you will express, purify, and functionally assess arecombinant protein, dihydrofolate reductase (DHFR), an important enzyme involved in thesynthesis of nucleic acid precursors. We will be using the Bio-rad Biotechnology ExplorerProtein Expression and Purification series of modules that will give you the opportunity to growE. colibacteria to express DHFR, to purify DHFR using affinity chromatography, and to assessthe enzymatic activity of DHFR using a spectrophotometric assay. Assessments of the labportion of the class will include pre-lab assignments, in-class worksheets, and a written labreport. Further instructions and guidelines will be given out in class.

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Guest Speakers and Field Trip:In this course you will be exposed to a variety of techniques andprinciples that are used in the biotechnology sector. To give you more insight into this type ofindustry, we will be having a guest speaker in class from a local biotechnology company toshare their experiences in working with recombinant proteins in industry. We will also be takinga field trip to a local biotechnology company to see the production of recombinant proteins on alarge scale. Further details will be announced in class.

Evaluation: There will be multiple grading opportunities in this course, giving you many chancesto do well. A summary of the various grading opportunities is given below.

Pre-Test: The pre-test will cover basic DNA and protein concepts that you need to know to dowell in this course. The pre-test is worth 50 points, or 5% of your course grade.

Recombinant Protein of the Day: You are required to give a 5 minute presentation describingthe recombinant protein of your choice. The due date is variable, as you will sign up for aspecific date to present. This presentation is worth 50 points, or 5% of your course grade.

Quizzes: Throughout the semester, we will have brief, unannouncedin-class quizzes that will

assess your knowledge of the course material. If you miss a quiz, you will not be able tomake it up. Quizzes are worth 50 points, or 5% of your course grade.

Homework Assignments: There will be four homework assignments that will help you stay upto date on the course material. Homework assignments will be due at the beginning of classon the day they are due. Homework due dates are listed in the detailed course schedulebelow. Homework assignments are worth 100 points, or 10% of your course grade.

Exams: There will be two take-home exams in this course, with each worth 10% of yourcourse grade. The first exam will be due on September 25 th and will cover material from Units1 and 2. The second exam will be due on October 23 rd and will cover material from Unit 3.

Laboratory Project: There will be several components of the lab project, including pre-labassignments, in-class worksheets, and a final written report (due December 5th at 5pm). All ofthese activities will add up to 250 points, or 25% of your course grade. More details about thelaboratory project will be handed out in class.

Design Project: There will be several due dates throughout the semester where you will haveto turn in updates on your design project. The project will culminate in oral presentations heldduring the final exam period (Friday December 7 from 1 3pm). All of the components of thedesign project will add up to 300 points, or 30% of your course grade. More details about thedesign project will be handed out in class.

The breakdown for course points is as follows:

Pre-Test 5% 50 pointsProtein of the Day 5% 50 points (see handout for details)Quizzes 5% 50 pointsHomework 10% 100 points (4 at 25 points each)Exams 20% 200 points (2 at 100 points each)Laboratory Project 25% 250 points (see handout for details)Design Project 30% 300 points (see handout for details)Total 100% 1000 points

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Based on the above point structure, you can calculate your grade at any time during thesemester (ask for help if you need it), and you should calculate your grade regularly to keeptrack of how you are doing in the course. The number of points will be converted to letter gradesbased on the following:

895 1000 points A

795 894 points B695 794 points C595 694 points DLess than 595 points F

Course PoliciesCourtesy to Fellow Students:We are going to have a positive learning environment in this class,so courtesy to your fellow students (and to me!) is imperative. Do you want to be distractedwhile trying to learn? Probably not, so please treat your classmates as you want to be treated.This includes putting your cell phones on silent before class starts, not using cell phones duringclass, limiting side conversations and comings and goings during class, not reading newspapersor doing the crossword puzzles, and other possible distractions.

Attendance:Attendance is vital to succeeding in this course. Participation in the active learningactivities during class will help you develop your critical thinking and problem solving skills whichwill help you on the exams in this course and in other courses. Finally, attendance is required byNorth Carolina A&T State University, and failure to attend class regularly will result in areduction of your grade and possible failure of the course.

Academic Integrity:Enrollment in this class means that you agree to abide by the expectationsof North Carolina A&T State University regarding academic integrity. For specific information,refer to your Student Handbook. Also, refer to the most current Undergraduate Bulletin for theacademic dishonesty policy. The Universitys Academic Honor Code will be strictly enforced.Your responsibilities in the area of honor include, but are not limited to, avoidance of cheating,

plagiarism and improper or illegal use of technology. Your assignments are expected to be yourown work. If you have questions, please ask. Integrityis an important characteristic that shouldbe exemplified in the lives of all North Carolina A & T State University students. Dishonesty willnot be tolerated in any form in this class. Any student caught cheating on an examination or anyother class assignment will be given a grade of zero for that examination or class activity andreported to University officials for further disciplinary actions. Plagiarism (i.e. citing informationwritten by another person without referencing the persons work) will also lead to a grade of zerofor the assignment. Changing a few words in material taken from a book or the internet withoutreferencing the author of the material is still plagiarism.

Late Work:No late work will be accepted. All assignments are due at the beginning of class onthe day that they are due. Please plan accordingly to make sure your homeworks and other

assignments are turned in on time.

Make-up Work: If you have an official university excuse for missing an exam (death in thefamily, sickness, university activity), then a make-up exam will be possible. Please see meahead of time if you know you will miss an exam due date. Quizzes cannot be made up.

Field Trips:We will be going on a field trip in this course. See the university policy on field tripsand class travel. More details will be announced in class.

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Course ScheduleThe following is the schedule for the course. The course is broken up into four units, with thefirst three units being classroom-based, and the last unit being a hands-on laboratory project.Due dates for homework (HW), exams, design project (DP), and pre-lab (Pre) assignments arelisted when appropriate. See design project and laboratory project hand-outs for more details onthese assignments. The schedule is subject to change.

Unit 1: Introduction to Recombinant Proteins

BIG QUESTION: What is a recombinant protein?At the end of this unit you will be able to

Evaluate the use of recombinant DNA technology to make recombinant proteins

Outline the major steps in the design and production of a recombinant protein

Use online tools and databases to research and create recombinant proteins

Thursday August 16 Course introduction and overviewTuesday August 21 Insulin: the first recombinant drugThursday August 23 How to make a recombinant protein

Tuesday August 28 Online tools for protein design Pre-test due

Unit 2: Recombinant DNA Technology

BIG QUESTION: How do you use recombinant DNA technology to make proteins?At the end of this unit you will be able to

Outline the steps necessary to prepare a functional expression vector

Identify and describe the essential features of cloning and expression vectors

Design PCR primers to clone a gene of interest

Explain how restriction enzymes are used to clone genes

Explain how to screen for positive recombinant clones

Thursday August 30 Overview and RNA and cDNA preparationTuesday September 4 Polymerase chain reaction & primer design HW 1Thursday September 6 Plasmids and Expression vectorsTuesday September 11 DNA manipulation (restriction enzymes & ligation) DP 1Thursday September 13 Transformation and screening of recombinantsTuesday September 18 Verification of vector contents & DNA sequencing HW 2

Unit 3: Recombinant Protein Expression and Purification

BIG QUESTION: How do you produce and purify a recombinant protein?At the end of this unit you will be able to

Compare and contrast recombinant protein expression systems

Describe protein purification methods and technologies

Evaluate purification methods for a given protein given its properties

Describe methods used to assess protein purity

Explain how to quantify and assess recombinant protein activity/function

Thursday September 20 Expression systemsTuesday September 25 Cell culture growth, induction, and expression Exam 1Thursday September 27 Crude purification methods

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Tuesday October 2 Chromatography I HW 3Thursday October 4 Chromatography IITuesday October 9 Fall Break no classThursday October 11 Assessment of protein purity and yield DP 2Tuesday October 16 Assessment of protein functionThursday October 18 Scale-up of protein production schemes HW 4

Tuesday October 23 Guest lecture X-ray crystallography Exam 2

Unit 4: Laboratory Project

BIG QUESTION: How do you express, purify, and functionally assess DHFR?At the end of this unit you will be able to

Grow, induce, and handle E.colibacteria using sterile techniques

Express and purify DHFR from E.coliusing affinity chromatography

Assess the purity and function of DHFR using SDS-PAGE and enzymatic assays

Collect and analyze data in a realistic research project

Thursday October 25 Introduction to project & basic lab techniques Pre 1

Tuesday October 30 Lyse cells Pre 2Thursday November 1 Crude purification of DHFR Pre 3Tuesday November 6 Affinity purification of DHFR Pre 4Thursday November 8 Desalting and SDS-PAGE DP 3, Pre 5Tuesday November 13 Concentration measurement of DHFR Pre 6Thursday November 15 Enzymatic assay of DHFR activity Pre 7Tuesday November 20 Data analysisThursday November 22 Thanksgiving break no classTuesday November 27 Guest speakerThursday November 29 Course summary and evaluations DP 4

Final lab report due December 5 at 5pm

Final exam period: Friday December 7 from 1 3pm DP 5

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