COMMUNITY CHRISTIAN COLLEGE 131B Spring... · Web viewChem 131B is a capstone course required for BS Chemistry, Biochemistry majors. Students in the course have taken at least these

Chem 131B is a capstone course required for BS Chemistry, Biochemistry majors. Students in the course have taken at least these courses: Chem 1A,1B – General Chemistry, Chem 112A,112B – Organic Chemistry, Chem 100W – Writing Workshop, Chemical Communications, Chem 130A-Biochemistry, Chem 131A – Biochemistry Lab.

Chem 131B is designed to be a research experience course. Students are part of a research team that is investigating an enzyme (protein) or binding protein that is currently part of an active research project of either the instructor of the course or another faculty member of the Chemistry department. Students are divided into teams of 3-4 students and spend the entire semester designing and performing research on the protein chosen/assigned to their group. The course is set up as a research group would be set up and includes presentations to keep the group updated on research progress and updated on other work in the field. During the semester, students write a rough draft of their research progress that is graded with feedback and a final research paper that includes work from the entire semester in the format of a scientific journal.

San José State UniversityChemistry Department Chem 131B, Fall 2013Class numbers: XXXXX

Instructors: TBA

Office Location: TBA

Telephone: TBA

E-mail: TBA

Office hours: TBA

Class days/times: W 14:30-17:20F 13:30-17:20

Classroom: DH609

GE/SJSU Studies Category: Some Area R learning outcomes are met by this course

Prerequisites: A letter grade of “C” or better in Chem 100W, 130A, 131A; NOTE: prerequisites will be checked

eCAMPUS Course PageCopies of the course materials such as the green sheet, major assignment handouts, etc... may be obtained by logging on to Canvas at http://ww w .sjsu.edu/at/ec/canvas/index.html . You are responsible for regularly checking the course page for updates. NOTE: In case website is not functioning properly, materials and announcements will be emailed directly to the students..

Course Description Chem 131B is the second semester of a two semester biochemistry laboratory course. Laboratory work associated with intermediate qualitative and quantitative techniques in modern biochemistry. This is a capstone course. A capstone experience requires students to integrate principles, theories, and methods learned in previous courses throughout the major. Students will be working on research projects that will allow analysis, synthesis, and evaluation of learned knowledge and will communicate the results of the projects effectively in a professional manner.

This course also contains content that overlaps with Area R learning objectives.

Student Learning Objectives

GE Area R (Earth and Environment) Goal

Students will cultivate knowledge of of the scientific study of the physical universe or its life forms. Students will understand and appreciate the interrelationship of science and human beings to each other.

SJSU Studies Area R Learning Outcomes addressed by Chem 131B

Upon successful completion of this course, students will be able to:

SLO 1: demonstrate an understanding of the methods and limits of a scientific investigation.

SLO 3: apply a scientific approach to answer questions about the earth and environment.

GE writing requirement: This course fulfills the GE writing requirement as follows:

Summary of Required WritingTotal writing will include a minimum of 3000 words:

In-class writing will include maintaining an accurate and up-to-date Laboratory notebook

~1-2 pages per lab period (varies)(200 words/lab period; ~2400 words)

Rough Draft of Scientific Journal Article(Lab Report)

5-6 pages not counting references or figures(~400 words per page; 2000-2400 words)

Final Draft of Scientific Journal Article5-6 pages not counting references or figures(~400 words per page; 2000-2400 words)

Total ~4400-4800 words

“A minimum aggregate GPA of 2.0 SJSU Studies (R, S, & V) shall be required of all students as a graduation requirement.” To see full text, review University Policy S11-3 at http://www.sjsu.edu/senate/docs/S11-3.pdf.

Course Content Learning Outcomes:

Upon successful completion of this course, students will be able to:

CLO(1) apply proper laboratory practices including safety, waste management, and record keeping.

CLO(2) use and understand modern biochemical techniques and instruments.

CLO(3) plan, design, and execute experiments based on biochemical literature.

CLO(4) interpret experimental results and draw reasonable conclusions.

CLO(5) communicate effectively through written and oral reports.

BS/BA CHEMISTRY PROGRAM LEARNING OUTCOMES ADDRESSED BY Chem 131B

PLO #5 - Demonstrate understanding of core concepts and to effectively solve problems in biochemistry.

PLO #6 - Answer questions regarding safe practices in the laboratory and chemical safety.

PLO #7 - Demonstrate safe laboratory skills (including proper handling of materials and chemical waste) for particular laboratory experiments.

PLO #9 - Effectively present a scientific paper orally, as per at an American Chemical Society symposium.

PLO #10 - Write a formal scientific laboratory report, using the format and style of an article in a peer-reviewed American Chemical Society journal

Required Text/Materials

Research laboratory notebook with duplicate pages; scientific calculator (equivalent to Ti30) capable of performing linear regression analysis.

Library Liaison

Liason: Emily Chan

Telephone: (408) 808-2044

Email: e [email protected]

Classroom Protocol

Students are expected to arrive on time and attend all classes. Students should be courteous to other students, instructors and guest instructors. Cell phones should be turned off during class time. NO FOOD OR DRINKS ALLOWED IN THE LABORATORY.

Dropping and AddingStudents are responsible for understanding the policies and procedures about add/drop, grade forgiveness, etc. Refer to the current semester’s Catalog Policies section at http://info.sjsu.edu/static/catalog/policies.html. Add/drop deadlines can be found on the current academic calendar web page located at http://www.sjsu.edu/academic_programs/calendars/academic_calendar/. The Late Drop Policy is available at http://www.sjsu.edu/aars/policies/latedrops/policy/. Students should be aware of the current deadlines and penalties for dropping classes.

Information about the latest changes and news is available at the Advising Hub at http://www.sjsu.edu/advising/.

Assignments and Grading PolicySJSU classes are designed such that in order to be successful, it is expected that students will spend a minimum of forty-five hours for each unit of credit (normally three hours per unit per week), including preparing for class, participating in course activities, completing assignments, and so on. More details about student workload can be found in University Policy S12-3 at http://www.sjsu.edu/senate/docs/S12-3.pdf.

The course will consist of the following:

1 Midterm Exam (Wed. March 20) 100 points(GESLO 1,3; CLO(2)(4); PLO#5)

Laboratory Paper (scientific journal article style) 100 points(GE writing requirement. GESLO 1, 3; CLO(3)(4)(5); PLO #5#10)

Assignments & Laboratory Participation 100 points(GESLO 1,3; CLO(1)(2)(3); PLO #5#6#7)

Laboratory Notebook 50 points(GE writing requirement; CLO(1)(2)(3)(4); PLO #7)

Lab Talk, Journal Article Presentation 50 points(GESLO 1,3; CLO(4)(5); PLO#5#8)

1 Final Exam (Thurs. May 16 @ 12:15 – 2:30pm) 100 points

The instructor evaluation is based on technique, performance, lab organization, lab work, comprehension of experiments, safety, attitude, proper use and disposal of chemicals, preparation prior to class, following directions, lab lecture involvement, etc.

Two exams will be given during the semester, a midterm and a final. The midterm will be given during one of the scheduled lab periods. The date is given on the attached schedule. The final will be given during the final exam period and is also noted on the schedule. Exams will cover theory, experimental protocol and data analysis. The content will be a combination of objective, calculations, short answer and short essay questions. Calculators (non-graphing, no memory) are permitted during exams and all exams are closed book.

Make-up midterms will NOT be given. The final exam must be taken to pass the class.

Letter grades for the course are A(+/-), B(+/-), C(+), No Credit. Letter grades will be based on a total percentage for the class as follows: 90s=A, 80s=B, 70s=C, etc., where appropriate “+” and “-” signs are added (as an example: 80-82=B-, 83-86=B, 87-89=B+). There is NO extra credit or extra assignments after the semester is over.

Laboratory NotebookIt is imperative that all experimental data are recorded in the laboratory notebook and that this information is kept up-to-date. Never depend on your memory to record such data; you will forget it if

it is not written down. Notebook entries should be clear and concise. Entries should be neat enough and annotated so that the experimental notes and data can be read and understood by others. Your notebook will be graded on these criteria.

The laboratory notebook does not have to look like a final report! Do NOT use scratch paper for experimental notes and data so that you can neatly transfer such into the notebook at a later time. It is quite acceptable to cross out information (with a single line) and rewrite it. Further, in professional settings, the notebook is the primary document verifying your intellectual property. Establishing good notebook habits now will prepare you for your career.

You will use the Laboratory Notebook with duplicate pages. The duplicate pages will be removed from the notebook and turned into the instructor at the end of each laboratory period.

Laboratory ReportsA report of all laboratory work will be required in the form of a scientific journal article. This is to be completed outside of the lab period. The required content and format will be explained in class. Although the experiments may be performed in groups, all interpretations must be your own.

Deadlines for submission of the first draft and final paper are noted on the class schedule. Failure to submit a report by a specified deadline will automatically lower the grade by 5% for each laboratory period it is late.

NOTE: Papers are due at the beginning of the laboratory period on the particular date (M 1:30; W 2:30). Reports submitted on the due date but later than the beginning of class are considered late. Details regarding the format of the paper will be available on Desire2Learn.

Oral PresentationsTwo oral presentations are required. One presentation is a “lab talk” covering background and progress on the laboratory project. The other presentation is a “journal article” presentation. The journal article must be approved by the instructor and the approved journal article must be uploaded into the “DROPBOX” in Desire2Learn at least one week in advance of the presentation. The selected article should be a recent primary article related to the laboratory project. The required content and format will be explained in class.

University Policies

Consent for Recording of Class and Public Sharing of Instructor Material

University Policy S12-7, http://www.sjsu.edu/senate/docs/S12-7.pdf, requires students to obtain instructor’s permission to record the course.

“Common courtesy and professional behavior dictate that you notify someone when you are recording him/her. You must obtain the instructor’s permission to make audio or video recordings in this class. Such permission allows the recordings to be used for your private, study purposes only. The recordings are the intellectual property of the instructor; you have not been given any rights to reproduce or distribute the material.”

“Course material developed by the instructor is the intellectual property of the instructor and cannot be shared publicly without his/her approval. You may not publicly share or upload instructor generated material for this course such as exam questions, lecture notes, or homework solutions without instructor consent.”

Academic Integrity

Your commitment as a student to learning is evidenced by your enrollment at San Jose State University. The University’s Academic Integrity policy, located at http://www.sjsu.edu/senate/S07-2.htm, requires you to be honest in all your academic course work. Faculty members are required to report all infractions to the office of Student Conduct and Ethical Development. The Student Conduct and Ethical Development website is available at http://www.sjsu.edu/studentconduct/.

Instances of academic dishonesty will not be tolerated. Cheating on exams or plagiarism (presenting the work of another as your own, or the use of another person’s ideas without giving proper credit) will result in a failing grade and sanctions by the University. For this class, all assignments are to be completed by the individual student unless otherwise specified. If you would like to include your assignment or any material you have submitted, or plan to submit for another class, please note that SJSU’s Academic Policy S07-2 requires approval of instructors.

Campus Policy in Compliance with the American Disabilities Act

“If you need course adaptations or accommodations because of a disability, or if you need to make special arrangements in case the building must be evacuated, please make an appointment with me as soon as possible, or see me during office hours. Presidential Directive 97-03 at http://www.sjsu.edu/president/docs/directives/PD_1997-03.pdf requires that students with disabilities requesting accommodations must register with the Accessible Education Center (AEC) at http://www.sjsu.edu/aec to establish a record of their disability.” [From the SJSU Accessible Syllabus template, updated Jan. 13, 2014]

Chemical Safety

Chem 120S is a required course for all Chemistry majors and minors and a prerequisite for all Chem 180/298 research.

Emergencies and EvacuationsIf you hear a continuously sounding alarm, or are told to evacuate by Emergency Coordinators (colored badge identification), walk quickly to the nearest stairway (end of each hall). Take your personal belongings, as you may not be allowed to immediately return. Follow instructions of Emergency Coordinators. Be quiet so you can hear. Once outside, move away from the building. Do not return to the building unless the Police or Emergency Coordinators announce that you may.

Laboratory Safety

You should read the safety section of the SJSU Catalog under the Chemistry Department. Note in particular: “Failure to comply with proper procedures and prescribed safety cautions shall subject the student to disciplinary action. 1) Any student who engages in unauthorized experimentation or who seriously disregards safety, thereby endangering self or others shall be withdrawn immediately from the class with a grade of F. 2) Any student who shows persistent disregard for safety may have his/her grade lowered, and may risk being withdrawn with a final grade of F.”

Student Technology Resources Computer labs for student use are available in the Academic Success Center located on the 1st floor of Clark Hall and on the 2nd floor of the Student Union. Additional computer labs may be available in your department/college. Computers are also available in the Martin Luther King Library.A wide variety of audio-visual equipment is available for student checkout from Media Services located in IRC 112. These items include digital and VHS camcorders, VHS and Beta video players, 16 mm, slide, overhead, DVD, CD, and audiotape players, sound systems, wireless microphones, projection screens and monitors.

Learning Assistance Resource Center The Learning Assistance Resource Center (LARC) is located in Room 600 in the Student Services Center. It is designed to assist students in the development of their full academic potential and to motivate them to become self-directed learners. The center provides support services, such as skills assessment, individual or group tutorials, subject advising, learning assistance, summer academic preparation and basic skills development. The LARC website is located at http:/www.sjsu.edu/larc/.

SJSU Writing Center/Plagiarism The SJSU Writing Center is located in Room 126 in Clark Hall. It is staffed by professional instructors and upper-division or graduate-level writing specialists from each of the seven SJSU colleges. Our writing specialists have met a rigorous GPA requirement, and they are well trained to assist all students at all levels within all disciplines to become better writers. The Writing Center website is located at http://www.sjsu.edu/writingcenter. See SJSU plagiarism policy, interactive tutorial and the relevant quiz (http://tutorials.sjlibrary.org/tutorial/plagiarism/index.htm). Note no editing of assignments by others.

Course Outline(schedule may deviate slightly as time dictates)

Important note: Many of the experiments in this lab will require you to work outside of the scheduled class period, so please plan ahead!

Important Dates

Midterm Wed. Oct. 16th

Rough Draft of Laboratory Paper Fri Oct 25th

Final Draft of Laboratory Paper Fri Dec 6th

Final Fri. Dec. 13th @ 12:15 - 14:30

Schedule for Laboratory Talks and Journal Article Presentations will be given out Fri. Sept. 30th

Course Overview and Introduction

Phase I - Transformation of Plasmids• Bacterial transformation of mosquito protease plasmid stocks

• Zymogen and modified mature forms

• Plasmid/Vector DNA isolation

• DNA sequencing and analysis

Phase II - DNA Cloning• Recombinant DNA technology

• Differences between expression vectors

• Tags vs native proteins

• Primer design

• Restriction enzymes and DNA ligase

• DNA gel electrophoresis

Phase III - Bacterial Protein Expression• Bacterial standard growth conditions

• Differences between commercially available bacterial competent cells

• Cell induction - IPTG

• Protein gel electrophoresis

• MW standards, MW and isoelectric point (pI) of mosquito proteases

• Soluble vs insoluble protein expression

Phase IV - Protein Purification• Soluble or insoluble protein purification

• His6-tagged affinity purification

• Buffers and solutions for Ni2+ columns

• Second or third-step ion exchange columns for further purification

Phase V - Auto-activation/Activity Assays of Mosquito Proteases• Auto-activation buffer conditions

• Enterokinase activation of modified mature forms (possible if auto-activation fails)

• Trypsin and other serine protease substrates

• Enzyme kinetics and inhibitor assays

• Michaelis-Menten and Lineweaver-Burke (or Double Reciprocal) plots

Appendix 1

Sample Exam Questions that address GELOs:

A. [GELO 1] (5 points) You amplify a P450 gene from E. coli using the polymerase chain reaction (PCR). You are expecting a PCR product of 1200 bp. When you analyze the PCR products on an agarose gel, you see three bands: 2000 bp, 1200 bp and 200 bp. What should you change about your PCR reaction the next time you run it to obtain your desired result?

B. [GELO 1] (5 points) You try amplifying another gene from E. coli again using the polymerase chain reaction (PCR). You are expecting a PCR product of 1800bp. When you analyze this PCR product on an agarose gel, you don’t see any bands. What should you change about your PCR reaction the next time you run it to obtain your desired result?

2. (24 points) Site-Directed Mutagenesis:

A. [GELO1] What is important in the design of mutagenic primers for a site-directed mutagenesis strategy?

B. [GELO1] Why is the product of the in vitro DNA replication reaction treated with restriction enzyme DpnI?

C. [GELO1] Why is it important to use “Pfu Turbo” DNA polymerase as compared to another thermostable DNA polymerase such as “Taq”?

D. [GELO1] When you transform the site-directed mutagenesis reaction treated with DpnI into competent cells, how will you know which colonies have the desired mutation?

3. [GELO3] In the middle of the semester, you decide that you want to work on a different project. You decide to clone the hemA gene from E. coli into an expression vector. The hemA gene codes for the enzyme that is the rate-limiting step for the production of heme, the prosthetic group in the BM3 P450 and the CamC P450 enzymes.

You do not need to make the HemA protein as a fusion protein with a tag for purification because you are not going to purify the protein. You are going to co-transfect your plasmid into the expression cells with either the BM3 P450 or the CamC P450 so that there will be plenty of heme groups for incorporation into the enzyme.

You are going to clone the hemA gene into the pET-15B vector (see attached vector map). You have the sequence of the hemA gene from the NCBI site and you have a print-out of a restriction site analysis of the hemA gene from Webcutter 2.0.

A. [GELO3] (8 points) Briefly describe two features of the pET-15B plasmid that are important for your project?

B. [GELO3] (4 points) The BM3 P450 and the CamC P450 are cloned into the pCal-n plasmid that has a gene for ampicillin resistance. You are going to clone the hemA into a plasmid that has a gene for kanamycin resistance. Why is it important that the two plasmids have different antibiotic resistance genes?

C. [GELO3] (6 points) What restriction sites will you incorporate into your forward and reverse primers in order to clone the hemA gene into the pET-15B plasmid?

D. [GELO3] (8 points) Design the primers you would use for the amplification of hemA. [TM = 81.5 + 0.41(%GC) – 675/N - % mismatch].

Enter the final primer sequences in the order form below. Underline and identify the restriction sites. Circle the start or stop codon. Show your work.

Primer Order Form:

Primer name Primer Sequence (5’→ 3’) TM

E. [GELO3] (4 points) Why is it important that the forward and reverse primers have similar TM values?

F. [GELO3] (4 points) What size PCR fragment do you expect to obtain using your primers to amplify the hisD gene?

G. [GELO3] How would the construction of this co-expression system be important to the study of heme-containing proteins?

H. [GELO1] What are some of the problems or difficulties might you encounter as you work on developing this co-expression system?

Oral Presentations that address GELO 1&3:

1. Lab presentation. Student will do oral presentation of 15-20 minutes on the research project including the following information:

A. Introduction: Brief introduction/background to the research project.

B. Short Term Goals: Research tasks student is trying to accomplish over ~ 3-4 week time period.

C. Long Term Goals: Overall purpose and importance of the project to the field.

D. Current Progress on Project: Methods and Results including discussion of problems encountered.

E. Next Steps: Plans for the coming 3-4 week time period.

2. Presentation of Journal Article. Student, with approval from instructor, will select a recent (within 5 years) primary journal article either related to the protein under study or a project that uses similar research techniques. Oral presentation will be 15-20 min. Student must be selective about methods/results to discuss. Presentation will include:

A. Title, Authors, Research Location, Journal Name, Year.B. Introduction: Brief introduction/background of project. Goals of the project.C. Overview of experimental design and key methods used. D. Presentation of key results.E. Critical analysis of methods used and results obtained.F. Summary of what key findings, importance of research and future directions.

GE Writing Requirements Assignments:

In Class Writing:

Keep an accurate Laboratory Notebook: Extremely important part of the scientific method. This is a critical skill for students that plan on working in the field or attending graduate school. See handout below “Guidelines for Laboratory Notebooks”.

“Guidelines for Laboratory Notebooks:

Your laboratory notebook is a COMPLETE record of ALL of your work done in the lab. It serves two functions:

1. It allows you to document your work so that you can write papers and reports accurately.2. It is a permanent lab record allowing others (years later) to know your specific techniques

and specific details about your experiments.

It is very important that your notebook contains precise, clear, detailed information about every experiment you do. Your notebook should “stand alone” and contain detailed information about every protocol you use. The date (both raw data and calculations, graphs, etc.) obtained from your experiments should be PERMANENTLY attached to your notebook.

1. Reserve the first two pages in your notebook for a table of contents so you (and others) can easily find information fast.2. Every page should be numbered.3. Each entry should be dated and have a title (so it can be entered in table of contents).4. The notebook should be recorded in ink.5. Make sure your entries are clear and legible.6. Each experiment should have a title, a brief explanation of why the experiment is being done, an EXACT explanation of how the experiment was done, any data collected, analysis of data, and some

kind of conclusion about the experiment turned out and possible suggestions for future experiments or changes to be made in the protocol for the next experiment.7. A record of how samples are being stored, and for long term samples, how the sample is labeled and its location.8. If you are working with someone else on a particular experiment, ALL of the details of protocol, data, etc, should be in BOTH notebooks.”

Outside of Class writing assignments:

Rough draft and final copy of laboratory report that includes all of the work on the research project during the semester. Report is written in the journal style of Journal of Biological Chemistry (JBC). Students must create an author account on JBC website and follow the instructions to authors on preparation of the paper. Below is a copy of the contents of the web page.

Instructions for Authors Click on headings in the Table of Contents to skip directly to that section:

Overview of submission and review process

Before preparing the manuscript

o Research suitable for submission

o Copyright and co-author consent

o JBC article types

o Publication charges

Preparing the manuscript text

o Text formatting

o Text organization

Order of sections

Title

Running title

Authors

Keywords

Capsule

Abstract

Introduction

Experimental procedures

Results

Discussion

References

Unpublished observations and personal communications

Abbreviations

Genetic nomenclature

Chemical and mathematical usage

Enzyme activity data

Protein and nucleic acid sequences

Genomic and proteomic studies

Database accession hyperlinks

Structural studies

Preparing tables & figures

Introduction

Tables

Figures

Policy on image manipulation

File formats

Color figures

Multipanel figures

Figure dimensions

Titles and legends

Letters, numbers and symbols

Graphs

Image resolution

Additional requirement for EPS files

Testing figure quality with Rapid Inspector

Allowable supplemental data

Preparing cover letter

Preparing manuscript PDF for submission

Resubmissions

Appendix 2:Rubrics Used for assessing Lab Reports and Journal Presentation

Chem 131B, Biochemistry Laboratory, Fall 2013 Page 18 of 23

Laboratory Report RubricCriteria Not Addressed Novice Intermediate ProficientIntroductionProvides rationale for why the question is important and/or interesting to the field of biochemistry

The importance of the question is not addressed.

How the question relates within the broader context of biochemistry is not addressed.

The writer provides a generic or vague rationale for the importance of the question.

The writer provides vague or generic references to the broader context of biochemistry

The writer provides one explanation of why others would find the topic interesting.

The writer provides some relevant context for the research question

The writer provides a clear sense of why this knowledge may be of interest to a broad audience.

The writer describes the current gaps in our understanding of this field and explains how this research will help fill those gaps.

Content knowledge is accurate, relevant, and provides appropriate background for reader including defining critical terms.

Background information is missing or contains major inaccuracies.

Background information is accurate but irrelevant or too disjointed to make relevance clear.

Primary literature references are absent or irrelevant.

Background omits information or contains inaccuracies which detract from major point of paper.

Background information is overly narrow or overly general (only partially relevant).

Primary literature references, if present are inadequately explained.

Background information may contain minor omissions or inaccuracies that do not detract from the major point of the paper.

Background information has the appropriate level of specificity to provide relevant context.

Primary literature references are relevant and adequately explained but too few.

Background information is information has the appropriate level of specificity to provide concise and useful context to aid the reader's understanding.

Primary literature references are relevant, adequately explained, and indicate a reasonable literature search.

HypothesesHypotheses have scientific merit

Hypotheses are trivial, obvious, incorrect or completely off-topic.

Hypotheses are plausible and appropriate though likely or clearly taken directly from course material.

Hypotheses indicate a level of understanding beyond the material directly provided to the student through course materials

Hypotheses are novel, insightful, or actually have the potential to contribute new knowledge to the field.

Methods: Experimental DesignExperimental design is likely to produce salient and fruitful results (tests the hypotheses posed).

Methods are:

Inappropriate Poorly explained/indecipherable

Appropriate Clearly explained Drawn directly from coursework Not modified where appropriate

Appropriate Clearly explained Modified from coursework in

appropriate places Or drawn directly from a novel source.

Appropriate Clearly explained A synthesis of multiple previous

approaches or an entirely new approach.

Results: Data PresentationData are comprehensive, accurate and relevant.

Data are summarized in a logical format. Table or graph types are appropriate. Data are properly labeled including units. Graph axes are appropriately labeled and scaled and captions are informative and complete.

Data are too incomplete or haphazard to provide a reasonable basis for testing the hypotheses

Labels or units are missing which prevent the reader from being able to derive any useful information from the graph.

Presentation of date is in an inappropriate format or graph type

At least one relevant dataset per hypothesis is provided but some necessary missing or inaccurate

contains some errors in or omissions or labels, scales, units, etc, but the reader is able to derive some relevant meaning from each figure.

is technically correct but inappropriate format prevents the reader from deriving meaning

data are mostly relevant, accurate and complete so reader can fully evaluate whether the hypotheses were supported or rejected with the data provided.

contains only minor mistakes that do not interfere with the reader's understanding of the figure's meaning.

the figure's meaning is clear without the reader referring to the text.

data are relevant, accurate and comprehensive.

reader can fully evaluate validity of writer's conclusions and assumptions

contains no mistakes uses a format or graph type which

highlights relationships between the data points or other relevant aspects of the data.

may be elegant, novel or otherwise

Chem 131B, Biochemistry Laboratory, Fall 2013 Page 19 of 23

Presentation of data: Captions are confusing or indecipherable.

captions are missing or inadequate Graph types or table formats are appropriate for data type.

includes captions that are at least somewhat useful.

allow unusual insight into data. has informative, concise, and

complete captions.

Results: Statistical Analysis

Statistical analysis is appropriate for hypotheses tested and appears correctly performed and interpreted with relevant values reported and explained.

statistical analysis is performed. Statistics are provided but are

inappropriate, inaccurate or incorrectly performed or interpreted so as to provide no value to the reader

Appropriate, accurate descriptive statistics only are provided.

Inferential statistics are provided but either incorrectly performed or interpreted or an inappropriate test was used.

Appropriate, correct inferential statistics are provided, but lack sufficient explanation.

Appropriate inferential (comparative) statistical analysis is properly performed and reasonably well explained.

Explanation of significant value may be limited or rote.

Statistical analysis is appropriate, correct and clearly explained.

includes a description of what constitutes a significant value and why that value was chosen as the threshold.

Discussion: Conclusion based on data selected

Conclusion is clearly and logically drawn from data provided. A logical chain of reasoning from hypothesis to data to conclusions is clearly and persuasively explained. Conflicting data, if present, are adequately addressed.

Conclusions have little or no basis in data provided.

Connections between hypothesis, data and conclusion are non-existing, limited, vague or otherwise insufficient to allow reasonable evaluation or their merit.

Conflicting data are not addressed.

Conclusions have some direct basis in the data, but may contain some gaps in logic or data or are overly broad.

Connections between hypothesis, data and conclusions are present but weak.

Conflicting or missing data are poorly addressed.

Conclusions are clearly and logically drawn from and bounded by the data provided with no gaps in logic.

A reasonable and clear chain of logic from hypothesis to data to conclusions is made.

Conclusions attempt to discuss or explain conflicting or missing data

Conclusions are completely justified by data.

Connections between hypothesis, data, and conclusions are comprehensive and persuasive.

Conclusions address and logically refute or explain conflicting data.

Synthesis of data in conclusion may generate new insights.

Discussion: Significance of research

Paper gives a clear indication of the significance of the research and its future directions.

Future directions and significance of this research:

are not addressed are vague, implausible (not possible with current technologies or methodologies), trivial or off-topic

are useful, but indicate incomplete knowledge of the field (suggest research that has already been done or is improbable with current methodologies)

suggest a fruitful line of research, but lack detail to indicate motivations for or implications of the future research.

are salient, plausible and insightful suggest work that would fill

knowledge gaps and move the field forward.

Chem 131B, Biochemistry Laboratory, Fall 2013 Page 20 of 23

Use of Primary Literature

Relevant and reasonably complete discussion of how this research project relates to others' work in the field.

Primary literature is defined as: peer reviewed reports original data authors are the people who collected

the data

Primary literature references are not included

Primary literature references are limited

References to the textbook, lab manual or websites may occur

Proper reference format is not consistently used

Primary literature references are more extensive but not completely adequate.

Literature cited is predominantly (>90%)

Primary literature references are used primarily to provide background information and context for conclusions.

Proper reference format is consistently used

Primary literature references indicate an extensive literature search was performed

Primary literature references frame the question in the introduction by indicating the gaps in current knowledge of the field.

Primary literature references are used in the discussion to make the connections between the writer's work and other research in the field clear.

Primary literature references are properly and accurately cited

Writing Quality

Grammar, word usage and organization facilitate the reader's understanding of the paper.

Grammar and spelling errors detract from the meaning of the paper.

Word usage is frequently confused or incorrect.

Subheadings are not used or poorly used.

Information is presented in a haphazard way.

Grammar and spelling mistakes do not hinder the meaning of the paper.

General work usage is appropriate, although use of technical language may have occasional mistakes.

Subheadings are used and aid the reader somewhat.

There is some evidence of an organizational strategy though it may have gaps or repetitions.

Grammar and spelling have few mistakes.

Word usage is accurate and aids the reader's understanding.

Distinct sections of the paper are delineated by informative subheadings.

A clear organizational strategy is present with a logical progression of ideas.

Correct grammar and spelling. Word usage facilitates reader's

understanding Informative subheadings

significantly and reader's understanding.

A clear organizational strategy is present with a logical progression of ideas. There is evidence of an active planning for presenting information; this paper is easier to read than most.

Adapted from: Timmerman, B.E., Johnson R.L. and Payne, J. 2007. Development of rubric for assessing students' science inquiry skills. National Association of Research in Science Teaching 2008 Annual Meeting New Orleans LA, April 15-18th.

Chem 131B, Biochemistry Laboratory, Fall 2013 Page 21 of 23

Journal Article Oral PresentationNot addressed Novice Intermediate Proficient

Clarity • Talk difficult to follow • Unclear language • Does not understand significance of paper • No handout or bibliography

• Talk a bit disorganized • Shows some effort to use proper language • Significance a bit unclear • Handout and bibliography are not well formatted

• Well thought out • Use of proper language • Significance clearly stated • Handout and bibliography provided for audience

• Well thought out • Use of proper language • Significance clearly stated • Previous work sets the stage for this study • Handout and bibliography provided for audience

Content • Does not understand research or work • Does not understand experimental approach • Does not understand conclusions or recognize implications for future work

• Research question a bit unclear • Description of experimental approach a bit confusing • Results and conclusions stated but not critically evaluated • No use of outside readings

• Identifies the research question or work •Has basic understanding of the experimental approach and significance • Critically evaluates results, methodology and/or conclusions • Well researched

• Identifies the research question or work • Has advanced understanding of the experimental approach and significance • Critically evaluates results, methodology and/or conclusions • Scientifically rigorous and well researched

Style/Delivery • Presentation poorly timed • Jumbled with no logical progression • Makes no eye contact and reads from notes • Hesitation and uncertainty are apparent

• Presentation poorly timed • Presentation jumping from different topics • Some hesitation and uncertainty are apparent • Makes little eye contact • Monotone and non-engaging delivery

• Spends too much time on introduction • Speaks well, but often back tracks • Makes good eye contact and looks at notes occasionally • Uses good vocabulary and tone

• Uses time wisely • Logical progression • Speaks with good pacing • Makes eye contact and does not read information • Uses engaging tone and vocabulary

Use of Visual Aids • Labeling is not clear • Too small to see • No logical placement • Mostly text and very few images • Figures are not explained • AV mishaps unresolved

• Labels and legends are a bit unclear• Size might be a bit too small • Too much detail • Blocks of text onhandouts or slides • Figures are explained well • AV mishaps resolved

• Excellent images but not always well placed • Size and labels are clear • Very little text • Figures and charts are explained well • AV mishaps resolved

• Well placed images • Charts summarize data and/or conclusions • Size and labels are clear • Very little text • Figures and images explained and described well

Integration of Knowledge

• Does not integrate the work or method into the broader context • Makes little effort to use data to support arguments • Misinterprets information Makes no connections between data, method, and conclusions • Lacks logic

• Does not integrate the work or method into the broader context • Supports argument or xplanation with few references • Makes some errors in interpretation and application of data or method • Makes few connections between data, method, and conclusions

• Supports arguments or explanation with references • Minimally integrates research findings to broader context • Has some understanding of the implications of data or method • Identifies some futureavenues of investigation

• Integrates research findings to broader context • Understands implication of data or method • Identifies future avenues of investigation • Supports arguments or explanation with references

Ability to Answer Questions

• Either makes no effort to respond to questions or does so poorly

• Does not anticipate audience questions • Makes an effort to address question • Can address some questions • Overlooks obvious questions • Often responds poorly to questions

• Does not anticipate audience questions • Understands the audience questions • Can integrate knowledge to answer the question • Thoroughly responds to most questions

• Anticipates audience questions • Understands audience questions • Can integrate knowledge to answer questions • Thoroughly responds to questions

Chem 131B, Biochemistry Laboratory, Fall 2013 Page 22 of 23

Chem 131B, Biochemistry Laboratory, Fall 2013 Page 23 of 23