Chem 222 LabInstructor: Mona L. Hall, Ph.D. Office: Rm E204
Office Hours Tuesdays 10:30 to 11:30Thursdays 12:30 to 1:30*
*Office hour times were chosen when no lecture section of Chem 222 meets but I have 3 meeting conflicts on a Thursday. Therefore on Thurs. 10/7 and 10/28 and 12/2 an alternative office hour time will be posted on the lab conference.
Goals for the lab:
- Learn biochemical techniques
- Learn how to interpret results and think critically
- Understand what scientific questions can be answered with a particular technique.
- Develop skills to execute your own research plan.
- 3-ring binder with dividers to serve as lab notebook
- 2-pocket folder
- Laptop computer ( at least one per student pair recommended)
Guidelines for Success
1. Do not leave lab until you understand how to proceed with the data analyses and post-lab questions
2. Use the lab conference for updates, exchange of data and useful peer discourse
3. Keep you notebook up-to-date on a weekly basis
Assignments and Grading : Prelab assignments √ if turned in on time; √- if not submitted before lab
Post-lab assignments a. Concept Checks: 7 in total 55%
b. Lab Summaries: 25%
The Lab Notebook (evaluated by an open notebook assessment)10%
Effort (as reflected in Prelab Work, Presentation, Prompt work, etc)10%
Extra Credit: possible with submission of a Journal documenting any of the following:
1 . Personal Reflection: Add a commentary on the lab; indicate how the lab furthered your understanding of lecture material; give a student's perspective--mention what you liked about the lab and or offer suggestion that would improve learning experience.
2.One other entry is required from these other options:
a. Biochemistry in Context: how does the work conducted in lab relate to a real world application
b. Biochemistry in the News: Include the article and state how it relates to concepts learned in lecture or in lab
c. The Eureka Moment: State how material covered in another course ties in with Biochemistry or how you have a deeper understanding due to your biochemistry lectures or labs.
Late assignment Policy: Deductions are assessed for late assignments. Extenuating circumstances must be explained in person at least 24 hours before the due date; even then a penalty may be assessed. Assignments will be logged with a time-stamp when they're e-mailed to the Sakai's Lab Assignment site
Attendance: Passing the lab requires attendance of each lab and satisfactory completion of the above assignments. Every effort must be made to attend your lab section. Alternate lab times must be approved at least 1 week in advance. Attendance should then occur in the other 222 lab section. The 222 labs occur:
Thursday 1:30 to 5:00Friday 12:30 to 4:00
GENERAL NOTEBOOK GUIDELINES.
Dated entries journaling your lab work must in chronological order; this proves you have been working on your notebook each week as intended.
Clarity and neatness will be rewarded while notebooks requiring "detective work" will receive deductions. Any text copied from the lab manual should be in a black font; while your own entries must be made using a blue pen or blue font if typed.
Notebook Organization Your notebook is an organized record of all yourwork so for each week include:
- In a three-ring binder, begin with a Table of Contents and add tabbed dividers after each lab
- The pre-lab assignment that will serve as your Title, Purpose, and Introduction sections
- The procedure from the lab manual with added notes detailing observations, collected raw data procedural modifications and other specifics. Your added notes should appear on the left-hand page opposite of the provided procedure if handwritten; or embedded using a blue font if typed.
- A record of data analyses or calculations that translate raw data into data tables or plots.
- The post-lab assignment that serves as the Results and Discussion sections.
- Also include lab notes, hand-outs, concept checks and all data posted on the conference
Open Notebook Assessment:
Required Notebook content will be judged by an open notebook assessment at the end of the semester
(10% of your lab grade)
A well-organized notebook will allow you to complete the questions within a time limit
- the intent is to recall the information from a well organized notebook
- proper record keeping means you will not need to perform a calculation or consider the data or information for the first time
- the time limit of 45 minutes helps to assess the level of organization (since searching takes time).
- The assessment allows you, the author, to judge your own notebook ( if you can’t follow it, who can?)
If you can answer the question by locating the information your record-keeping skills were great!
If you can answer all the questions within the time limit your organizational skills were great!
- A sample assessment to give you guidance on how you are doing and show you what is expected will
be given after Fall Break. A peer will evaluate you notebook and feedback will be given during this trial instead of a grade since its purpose is to assist you with your notebook skills early on.
Format of the Open Notebook Assessment:
You will be directed to the relevant week’s lab and asked to recall information that is expected to be recorded in your notebook. Examples of the type of information you will have to recall will include:
- a recorded result and its interpretation
- features of a studied biochemical system
- an observation made during an experiment
- the details of a procedural step (final concentration of a dilution, instrument setting etc.)
- ability to report the importance of a procedural step ( to show understanding of a method)
- interpretation of a graph or figure generated during lab or in a post-lab assignment
- ability to quickly repeat a sample calculation ( showing the steps involved in an Excel spreadsheet)
- reporting class data posted on the lab conference (since it furthers the understanding of your own work)
Pre- lab assignments ( REQUIRED BUT NOT GRADED):
These assignments are preparation for the concepts, methods, or calculations needed to succeed in lab. Your effort will be rewarded ( without the necessity of a grade) since this preparative work benefits your understanding during the course of the lab. Download the preparative worksheet and the lab specific question each week from the lab conference, type your answers directly into the worksheet and submit it electronically before lab. The pre-lab work is never graded but can earn a √ - if not turned in electronically before lab. This submission will document your effort and allow you to arrive prepared for lab. Questions are welcomed and if you experience difficulties with the pre-lab work fill in the answers to the best of your ability. Bring a hard copy to lab and questions you identify will be answered during the lab's introductory lecture. The edited version can then be placed in a lab binder or E-notebook to serve as the lab’s Introduction section.
GRADED POST-LAB ASSIGNMENTS
These assignments require you to demonstrate an understanding of the lab you just completed and are generally due 1 week later (e-mail submissions or hard copy accepted). Graded work will be placed in a lab binder to serve as the Results and Discussion section. These assignments will involve one of the following two formats:
a. Concept Checks:
The goal of these lab-specific questions is to ensure that there is a good understanding of the employed techniques and the steps involved in the data analyses. The majority of the assignment should be completed during the lab period. This assignment must be submitted to the Sakai Assignment site via e-mail 1 week after the lab’s completion
b. Lab Summaries:
A standard format will be used and a worksheet will prompt you to include the necessary information. This typed summary must be submitted to the Sakai Assignment site via e-mail 1 week after the lab’s completion
Guidelines for Success in Lab: Execute on all five phases of the scientific process.
1. Complete preparative work in order to create a basis for inquiry
2. Establish experimental goals, pose questions and form hypotheses
3. Perform experiments to gather data
4. Analyze the data and assimilate information from other sources
5. Devise explanations and appreciate the relevance of your work
Guidelines For Data Analyses:
- Examine the quality of your data by using statistics
- Precision: standard deviation of replicate measurement
- Accuracy: % error if actual value is known
- Confidence intervals (C.I.) and/or hypothesis testing when appropriate
- For linear plots, interpret R2 values (values should be > 0.99 for good linearity)
- Show calculations and use units
a. During the calculations be sure units cancel
b. Check if answer is logical; if not check the math again
c When Excel is used a sample calculation is required below the spreadsheet
3. Report values using significant figures (computers and calculators won’t do this for you!)
Report standard deviation or confidence intervals using the same number of places to match
the mean ( example: 0.0109M +/- 0.0004)
4. Always interpret the meaning of your numerical values. Also, if comparing two values define the magnitude numerically (for example instead of simple stating one is less, state it is 10 times less)
Guidelines For all Figures:
Any Figure should be able to stand alone as a description of a chemical system and its behavior
1. Begin by giving your figure a descriptive title.
2. Add a legend that summarizes the key steps used to generate the data and highlights the key features.
Three types of Figures are useful in a scientific report:
- Include the labeled axes with units defined
- Scale the graph so that the data occupies most of the displayed graph area.
- Divide the axes into easy-to-understand units (i.e. 1/10th divisions if a value is reported to the 1/10th place)
- Display the equation of a line and the R2 value.
- Using the title and legend tell the reader as much as possible about the figure's meaning.
- Use data tables to summarize the key experimental data (include means with std.dev, report sign. figs )
- Include column headings with proper units
- If necessary add footnotes to properly describe a column’s contents ( a heading may not suffice)
- IMPORTANT NOTE: In your notebook you must include a sample calculation that shows how a final value was calculated. Excel hides the mathematics involved so a sample calculation serves to document the steps in your notebook as a record and ensures that units cancel.
- Structural Figures
- Use the SWISS-Pdb program to make a publication-quality drawing.
- Include an informative title.
- Label key features of the figure clearly or add arrows to highlight a feature.
- Rotate a figure to optimize the view.
- Structural comparisons must show the same scale and same orientation or be overlaid.
- Remove unnecessary features (reduce a protein to the backbone then add back key residues)
- Consider if a distance measurement and/or zoomed in region best depicts a highlighted fact
- Use the legend to tell the reader as much as possible about the figure's meaning.
Guidelines For the Discussion
- Be thorough (yet concise) when you interpret your data
- Yet be concise and summarize key conclusions
- To demonstrate your understanding, use knowledge learned from multiple sources including:
- your text
- The lab discussion and manual
- Related studies in journal articles
4. State if you verified any biochemical principles and support your statements.
5. Revisit the goals of the experiment, state if you accomplished them and support your statements.
6. Consider the sources of error and the impact of the error on the results
a. limitations of the procedure or instruments
b. human error ( be reasonable here as good technique is expected)
7. Decide on an interesting future direction for the lab experiment and explain what the proposed
experiment hopes to accomplish.
Lab Schedule and Due Date for Assignments
Wk/ Thurs. / Fri. / Laboratory / Post-Lab Assignment
Due dates on your lab day:
1 / Sept 9 / Sept 10 / Properties of Buffers and amino acids
Weak acid base Chemistry reviewed. / Concept Check
9/16 or 9/17
2 / Sept 16 / Sept 17 / Examining Protein structures via Swisspdb viewer
Crystallization of Lysozyme begins / Concept Check 9/23 or 9/24
3 / Sept 23 / Sept 24 / Examine Lysozyme Crystals
Introduction to Protein absorbance and fluorescence / Crystallization Summary
9/30 or 10/1
4 / Sept 30 / Oct 1 / Protein stability examined by flourescence
and circular dichroism / Concept Check
10/7 or 10/8
5 / Oct 7 / Oct 8 / Mass Spectrometry: characterizing a glycoprotein
Examining a glycosidase's carbohydrate substrate / Concept Check
10/14 or 10/15
6 / Oct 14 / Oct 15 / High Performance Liquid Chromatography
Peer Notebook Check conducted during lab / Concept Check
10/21 or 10/22
7 / Oct 21 / Oct 22 / Nature of Lipids revealed by Melting Transitions
Designing a purification strategy / No assignment
8 / Oct 28 / Oct 29 / Lysozyme purification / Exam recovery period
Lecture Exam on 10/26
9 / Nov 4 / Nov 5 / Enzyme Kinetics
SDS-PAGE performed / Concept Check
11/11 or 11/12
10 / Nov 11 / Nov 12 / Enzyme Assays
SDS-PAGE Gel analysis / Concept check
11/18 or 11/19
11 / Nov 18 / Nov 19 / A Binding Study using Isothermal Titration Calorimetry
Open Notebook assessment / ITC Summary
Exam recovery period
All due Sat 12/4
12 / Dec 2 / Dec 3 / ITC Review and
Presentation Topic Researched / Presentations given
In lab Thurs 12/9
or Fri 12/10
13 / Dec 9 / Dec 10 / Presentations : A Metabolic Disease and the Search for a Cure
A Look at the Biochemical Methods used to
Perform Leading Edge Research / In lab presentation
. E-Journals due for Extra Credit . / Dec 11
In order to pique your interest in Biochemistry and gain an appreciation for its importance in your field of study you will notice:
Biochemistry in Context questions that ask you to provide an application of the studied biochemical system in medicine, your field of study or your other interests.
A " Capstone" experience in the lab will be your presentation detailing a Metabolic Disease and the Search for a Cure: A Look at the Biochemical Methods used to Perform Leading Edge Research
An opportunity to submit an E-journal for extra credit at the end of the semester
Fill in your schedule and the rest of this sheet and bring this with you to your first lab.
NAME: ______CLASS YR ______MAJOR ______S / Time / Monday / Tuesday / Wednesday / Thursday / Friday
C / 8:30
H / 9:50
E / 11:10
D / 12:20
U / 1:30
L / 2:15
E / 4:00
Consider your past laboratory experiences and then decide what learning strategies allowed you to succeed in lab. Please give a list of approaches that worked in your first semester.
Examples: Collaborations with peers in a Lab Focus Group, Weekly use of office hours etc.
Is there any aspect of lab that you found challenging in past labs that you would like to improve upon this semester?