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 University
Chemistry Department
Chem 131B, Fall 2013
Class numbers: XXXXX
Instructors:
TBA
Office Location:
TBA
Telephone:
TBA
E-mail:
TBA
Office hours:
TBA
Class days/times:
Classroom:
W 14:30-17:20
F 13:30-17:20
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 Page
Copies of the course materials such as the green sheet, major assignment handouts, etc... may be
obtained by logging on to Canvas at http://www.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 Writing
Total writing will include a minimum of 3000 words:
In-class writing will include maintaining an
~1-2 pages per lab period (varies)
accurate and up-to-date Laboratory notebook
(200 words/lab period; ~2400 words)
Rough Draft of Scientific Journal Article
5-6 pages not counting references or figures
(Lab Report)
(~400 words per page; 2000-2400 words)
5-6 pages not counting references or figures
Final Draft of Scientific Journal Article
(~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 peerreviewed 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:
Telephone:
Email:
Classroom Protocol
Emily Chan
(408) 808-2044
emily.chan@sjsu.edu
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 Adding
Students 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 Policy
SJSU 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)
(GESLO 1,3; CLO(2)(4); PLO#5)
100 points
Laboratory Paper (scientific journal article style)
100 points
(GE writing requirement. GESLO 1, 3; CLO(3)(4)(5); PLO #5#10)
Assignments & Laboratory Participation
(GESLO 1,3; CLO(1)(2)(3); PLO #5#6#7)
100 points
Laboratory Notebook
(GE writing requirement; CLO(1)(2)(3)(4); PLO #7)
50 points
Lab Talk, Journal Article Presentation
(GESLO 1,3; CLO(4)(5); PLO#5#8)
50 points
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 Notebook
It 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 Reports
A 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 Presentations
Two 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/S072.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 Evacuations
If 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 coexpression 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.
B.
C.
D.
E.
F.
Title, Authors, Research Location, Journal Name, Year.
Introduction: Brief introduction/background of project. Goals of the project.
Overview of experimental design and key methods used.
Presentation of key results.
Critical analysis of methods used and results obtained.
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 17 of 22
Laboratory Report Rubric
Criteria
Introduction
Not Addressed
Novice
Intermediate
Proficient
Provides 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
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.
 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.
 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.
 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.




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.
 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
Hypotheses
Hypotheses have scientific
merit
Methods: Experimental Design
Experimental design is likely
to produce salient and
fruitful results (tests the
hypotheses posed).
 Inappropriate
 Poorly explained/indecipherable
Methods are:
Results: Data Presentation
Data 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
Chem 131B, Biochemistry Laboratory, Fall 2013
Page 18 of 22
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.
 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.
 Conclusions have little or no basis
in data provided.
 Connections between hypothesis,
data and conclusion are nonexisting, 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.
 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.
Results: Statistical Analysis
Statistical analysis is
appropriate for hypotheses
tested and appears correctly
performed and interpreted
with relevant values reported
and explained.
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.
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:
Chem 131B, Biochemistry Laboratory, Fall 2013
Page 19 of 22
Use of Primary Literature
Relevant and reasonably
complete discussion of how
this research project relates
to others' work in the field.
 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
 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.
Primary literature is defined
as:
 peer reviewed
 reports original data
 authors are the people who collected
the data
Writing Quality
Grammar, word usage and
organization facilitate the
reader's understanding of the
paper.
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 20 of 22
Not addressed
Journal Article Oral Presentation
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
• 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
• 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 on
handouts 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
• 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 future
avenues 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
• 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
Style/Delivery
Use of Visual Aids
Integration of
Knowledge
Ability to Answer
Questions
Chem 131B, Biochemistry Laboratory, Fall 2013
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Chem 131B, Biochemistry Laboratory, Fall 2013
Page 22 of 22