Name: ____________________________

BIOCHEMISTRY 551
Biochemical Methods
Laboratory Manual
Spring 2017

Instructors:

Prof. Vatsan Raman

Dr. Lynne Prost

Teaching Assistants:

Alejandra Canales Mark Klein

Tina Lynch Evan Glasgow

Qiao Li Yang Liu

Dylan Plaskon Sophia Sdao

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 Lab Manual v.20170104 Biochemistry 551

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 COURSE SCHEDULE AND DESCRIPTION

Course Description: Biochemistry 551 is an integrated lecture, lab and seminar course
that covers biochemistry-centered theory and techniques. The course is designed for
upper-level undergraduate students majoring in Biochemistry. Students learn how to
apply a broad range of biochemical, genetic, and physical techniques to modern
biochemical research. Students also learn how to analyze and interpret the primary
scientific literature, develop an understanding of the communication of data, and
extrapolate biochemical techniques to basic research.
Lectures introduce concepts and theory that are subsequently explored in detail in
experiments. The experiments are designed to provide hands-on experience with
instruments and techniques that are used in modern biochemical research. The
curriculum incorporates a small research project beginning with the PCR amplification
and cloning of the HCAII gene, which codes for human carbonic anhydrase II (HCAII).
As the semester progresses, students overexpress, purify and assay wild type and
mutant HCAII protein. Experiments focus on instrumental techniques including PCR,
spectrophotometry, gel electrophoresis, protein overexpression and purification, enzyme
assays and fluorescence spectroscopy.

Learning Objectives: By the end of Biochemistry 551, students should be able to:
1. Explain the theory of several fundamental biochemical techniques
2. Form hypotheses based on biochemical principles
3. Design and perform experiments to collect sound scientific data
4. Critically analyze ones own data as well as data from other sources
5. Communicate scientific findings in both oral and written form
6. Value the collaborative nature of biochemistry

Lab Sections:
301 - Monday: 12:20 4:00 pm T.A.s: Mark Klein and Tina Lynch
302 - Tuesday: 12:20 4:00 pm T.A.s: Qiao Li and Allie Canales
303 - Wednesday: 12:20 4:00 pm T.A.s: Sophie Sdao and Dylan Plaskon
305 - Thursday: 12:20 4:00 pm T.A.s: Evan Glasgow and Yang Liu

Room Locations:
Lectures will take place in room 1120 Biochemistry (the building at 420 Henry Mall).
Labs will take place in room 2118 Biochemistry.
During the first week of class, you will be assigned a seminar and a seminar room.

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Course Schedule:

Wed. Jan 18 Lecture 1: Class overview and description of HCAII

(Prof. Vatsan Raman, Dr. Lynne Prost)

Fri. Jan 20 Lecture 2: Protein structure and computational analysis (Prof.

Raman)

Mon. Jan 23 Seminar: How to give a scientific presentation (Dr. Prost)

Jan 23-26 Lab 1: Computational analysis of HCAII

- Analyze protein structure
- Each section selects 2 potential mutations

Wed. Jan 25 Lecture 3: PCR and Cloning 1 (Dr. Prost)

Fri. Jan 27 Lecture 4: PCR and Cloning 2 (Dr. Prost)

Mon. Jan 30 Seminar: Instructor Seminar

Jan 30-Feb 2 Lab 2: PCR amplification of the HCAII and pETblue2

- Check-in and pipet workshop
- PCR amplification of HCAII and pETblue2

Wed. Feb 1 Lecture 5: PCR and Cloning 3 (Dr. Prost)

Fri. Feb 3 Scientific writing (Dr. Prost)

Mon. Feb 6 Student seminar 1

Feb 6-9 Lab 3: Analysis of the PCR products

- Analysis and purification of PCR product
- DNA digest and purification

Wed. Feb 8 Lecture 6: Gel electrophoresis of biomolecules (Dr. Prost)

Fri. Feb 10 Pre-lab: Gibson assembly and transformation (2 TAs)

**ATTENDANCE STRONGLY RECOMMENDED**

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Mon. Feb 13 Student seminar 2

Feb 13-16 Lab 4: Gibson assembly reaction and transformation

- Gibson assembly reaction
- Transform the clones into E. coli DH5

Wed. Feb 15 Lecture 7: Overexpression of proteins (Prof. Raman)

Fri. Feb 17 Lecture 8: Overexpression systems (Prof. Raman)

Mon. Feb 20 Student seminar 3

Feb 20-23 Lab 5: Screening for pETblue2- HCAII clones

- Inoculate bacterial cultures prior to lab period
- Miniprep DNA
- Screen by restriction digest
- Transform clones into E. coli RB DE3

Wed. Feb 22 Exam Review

Fri. Feb 24 Exam 1 on lectures 2 - 8

Mon. Feb 27 Student seminar 4

Feb 27-Mar 2 Lab 6: Induction of His-tagged HCAII expression

- Induce cultures with IPTG
- Collect samples for analysis
- Measure cell growth
- Pellet culture for purification

Wed. Mar 1 Lecture 9: Emerging Biochemical Techniques 1: CRISPR/Cas

(Prof. Raman)

Fri. Mar 3 Lecture 10: Protein purification (Prof. Raman)

Mon. Mar 6 Student seminar 5

Mar 6-9 Lab 7: Purification of wild type and mutant HCAII

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 - Cell lysis, Ni Column

Wed. Mar 8 Lecture 11: UV/Vis and fluorescence spectroscopy (Dr. Prost)

Fri. Mar 10 Amino Acids/Hypothesis workshop (Dr. Prost)

Mon. Mar 13 Student seminar 6

Mar 13-16 Lab 8: Analysis of His-tagged HCAII expression and purification

- Pour SDS-PAGE gels
- Analysis of HCAII expression by electrophoresis
- Spectroscopic determination of concentration

Wed. Mar 15 Pre-lab: Intrinsic tryptophan fluorescence (2 TAs)

**ATTENDANCE REQUIRED**
Fri. Mar 17 NO CLASS

Mar 20-24 SPRING BREAK

Mon. Mar 27 Student seminar 7

Mar 27-30 Lab 9: Intrinsic tryptophan fluorescence

- Measure stability of wt and mutant protein

Wed. Mar 29 Lecture 12: Protein Folding (Prof. Raman)

Fri. Mar 31 Pre-lab: Enzymatic activity of HCAII (2 TAs)

**ATTENDANCE REQUIRED**

Mon. Apr 3 Student seminar 8

Apr 3-6 Lab 10: HCAII enzyme activity

- Measure enzymatic activity of wild type and mutant HCAII

Wed. Apr 5 Lecture 13: Enzyme Kinetics (Dr. Prost)

Fri. Apr 7 Pre-lab: FRET to detect ligand binding (2 TAs)

**ATTENDANCE REQUIRED**

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Mon. Apr 10 Student seminar 9

Apr 10-13 Labs 11/12: HCAII enzyme inhibitor assays and FRET
- Half the class will measure the ability of a small molecule
to inhibit HCAII enzymatic activity
- Half the class will use FRET to detect ligand binding to
wild type and mutant HCAII

Wed. Apr 12 Guidelines for Oral Report, Final Report, and Independent Lab
(Dr. Prost)

Fri. Apr 14 Lecture 14: Ligand Binding (Prof. Raman)

Mon. Apr 17 Student seminar 10

Apr 17-20 Labs 11/12: HCAII enzyme inhibitor assays and FRET
- Half the class will measure the ability of a small molecule
to inhibit HCAII enzymatic activity
- Half the class will use FRET to detect ligand binding to
wild type and mutant HCAII

Wed. Apr 19 Lecture 15: Emerging Biochemical Techniques 2: Microscopy (Dr.

Prost)

Fri. Apr 21 Exam Review

Mon. Apr 24 Student seminar 11 (if necessary)

Apr 24-27 Independent Lab

Wed. Apr 26 EXAM 2 on lectures 9 - 15

Fri. Apr 28 NO CLASS

Mon. May 1 NO CLASS

May 1-4 Group Oral Reports (Rooms TBD)

Wed. May 3 NO CLASS

Fri. May 5 NO CLASS

Mon. May 8 LAB REPORT DUE

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Point Breakdown Grades

Assignment Points per Total Points Grade

assignment Points
> 900 A
Exams (2) 150 300
850900 AB
Lab performance 100
800849 B
Pre-lab quizzes (10) 5 50
750799 BC
Mini lab reports (10) 10 100
700749 C
Final lab report 150
600699 D
Oral lab report 100
< 599 F
Literature seminar 150

Literature seminar 50
participation

Total 1000

NOTE: Students with disabilities who need accommodation are encouraged

to meet with the instructor as soon as possible.

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 LABORATORY ATTENDANCE POLICY

Attendance to lab each week is required.

If you must miss lab, please discuss with Dr. Prost as soon as possible. Absences for
activities such as interviews or school-sanctioned sporting events will be allowed;
however, you will have to coordinate with Dr. Prost to attend a makeup lab or otherwise
make up the work. In the case of an allowed absence, your mini lab report must be
turned in digitally by the start of your lab period.

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 GUIDELINES FOR ASSIGNMENTS

Lab Performance (100 pts)

Lab performance points will be awarded for general performance in the laboratory during
the semester. These will be based in part on the outcome of the experiments, and more
generally on preparedness, understanding of the material, timeliness, completion of pre-
labs, maintenance of a good lab notebook, and collaborative spirit. It is expected that
students contribute to a positive lab atmosphere and collaborate effectively with their lab
partner as well as other students in the lab, as appropriate. Points will be deducted from
the lab performance score for unexcused absences during the required pre-lab classes.

Pre-labs
Each lab description in the lab manual contains a list of pre-lab questions. Students are
expected to answer these questions in their lab notebooks BEFORE coming to lab.
When you enter the laboratory, the TAs will check that you have thoroughly answered
these questions. If you arrive to lab late, you will not get credit for that pre-lab.

Lab notebook checks

You must have a dedicated notebook for the lab any type is fine. If you use a regular
notebook (e.g. spiral-bound), you should number the pages. If you read the manual
before coming to lab, you will know what data you need to collect and what observations
you should record. The TAs will periodically check your notebook and give you points if
your notes are complete. Your notebook should contain the following for every lab
period:
Table of Contents: Reserve the first page of your notebook for a table of contents. Each
lab should have its own entry, including the date, name of the lab and the page number.
Date: You need to date every entry with the day, month, and year of the experiment.
Pre-lab: Before coming to lab you must read the lab manual and enter the following
information into your lab notebook:
1. Title of the experiment
2. Experiment summary and rationale - what will you be doing that day, and why?
3. Final product what are you supposed to have at the end of the lab period and
where will it be? The final product includes both data and physical product such
as an Eppendorf tube of DNA. (i.e. Final product for week 1: Four PCR reaction
tubes located in the PCR machine. These will be moved to the 20C freezer by
the TAs at the end of the reaction.)
4. Any pre-lab questions listed in the lab manual these will be located directly
before the procedure section of the lab. For some weeks, you will need to do
calculations or plan out parts of your experiment before coming to lab. These
calculations and/or plans should be included in your pre-lab section.

In-lab: During the lab period you will need to take note of what you are doing and the
data you collect. Examples include:
The order in which you loaded your gel samples.
Spectrophotometer readings and DNA concentrations.
If you measure cell growth, you would write down the time points and the O.D.
measurements at those time points.

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 Observations about your experiments; i.e., if something didnt work as expected.
Note anything unexpected that happens. For example, if you are supposed to
collect a 1 mL sample but you mistakenly collect a 0.5 mL sample, you should
note that.

Pre-lab Quizzes (10 x 5 pts)

For Labs 2-11, you will be asked to make a critical decision about the experimental
procedure before you come to lab. This will be assessed as an online quiz via
Learn@UW, due each Monday at noon. If you carefully study the lectures and lab
manual and work to understand the course material, you will be able to design your
experiment appropriately and correctly complete the quiz. Each quiz is worth 5 points.

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 MINI LAB REPORTS
Following labs 1 10, you will write a mini lab report to be turned in to your TAs at the
start of the next lab period. The purpose of these mini lab reports is for you to regularly
practice analyzing the results of your experiments and writing scientifically.

Each mini lab report is worth 10 points and is due at the beginning of the following lab
period. Late reports will not be accepted.

For reports 1 through 5: Every student must turn in his/her own work.

For reports 6 through 10: You will work with your lab partner. Each pair will turn in a
single report.

What to include in the reports

In the lab manual, following each weeks lab, there is a description of what should be
included in the mini lab report. You only need to write the sections that are listed for that
week. Some weeks you will write an Introduction and Methods, but no Results or
Discussion; other weeks, you will write Methods, Results and Discussion but not an
Introduction. Just be sure to pay attention to the directions for each week.

A general list of tips follows, but be sure to follow the specific instructions for each lab.
These general guidelines also apply to the Final Lab Report.

General guidelines for lab reports:

All lab reports should follow the general format for peer-reviewed research articles.
Since you are reading several peer-reviewed papers in your seminar sections, use
them as a template for your reports. During the first few weeks, we are doing
experiments that would generally not be published in articles, so this can be a little
tricky. We tried to write clearly in the instructions what we are looking for feel free
to email Dr. Prost and your TAs if you are unsure. In later weeks, it should be easier
to write your report as if it was a research article.
Part of the report grade will include writing style. We expect your reports to be well
written with correct spelling, punctuation and grammar. Use complete sentences and
paragraphs. Reports that are poorly written will lose points.
The reports must be typed. Some reports include page limits; be sure to adhere to
them.
Use the appropriate number of significant figures in your calculations.

Methods section:
You should use the past tense for this section because you are describing what you
did in the past.
Methods typically begin with a purpose statement to orient the reader to the goal of
the experiment. Look for these when you read peer-reviewed research articles. Aim
to write them formally; i.e. instead of saying The purpose of this lab was to amplify
the HCAII gene try In order to clone the HCAII gene, it was amplified via PCR.
Clearly explain how you did the experiment in enough detail that a person with a
scientific background (e.g. your TA) could repeat the experiment just by reading your
methods section.

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 You should always cite the lab manual, as it was a source you used to complete the
experiment. Try something like: All experiments were performed as described in
Biochemistry 551: Biochemical Methods, Fall 2016 by Prost. Briefly, and then
succinctly describe the experiments.
o Important note: Even if you cite the manual, the reader must still be able to
understand, in general terms, what experiments you conducted just by
reading your report.
Think about the difference between a protocol and a method. In general, it is NOT
appropriate to describe protocols in the methods section (i.e. how many L of Buffer
X you added to a miniprep).
If your experiment deviated from the lab manual (either on purpose or by accident),
your methods section should indicate what you did, not what the manual said to do.
One of the trickiest parts of writing Methods is knowing when it is appropriate to
report concentrations, amounts, or volumes of reactants. The general rule of thumb
is to always report concentrations, not volumes. One major exception to this is DNA
it is standard to report the total amount of DNA included in a reaction, in
nanograms or picomoles as appropriate. Another exception is enzymes, such as
restriction enzymes, which are typically reported as the total number of units per
reaction.

Equations:
When you use an equation to analyze data, it is important to include the equation in
the Methods section. Use your word processors Equation Generator function to
make an equation that is easy to read and understand.
Equations are not figures and generally do not need legends or titles. In cases where
you used a number of equations, you could combine them into a panel or box that
would have a title, but still would not need a legend.
A sample equation is shown below. Note that the equation is numbered via a bold
number to the right. You would then refer to this as Equation 1 in the text of the
Methods section.

1
r= (1)
" K DNSA
d
%" [AZ] free %
1+ $ '$1+ '
# [DNSA] &# K dAZ &

Results section:
The resultssection presents the results without interpretation using text, figures and
tables.
Results should be written in the past tense.
Start the Results section with a sentence to remind the reader of the overall goal
and/or hypothesis for the experiments you are describing something similar to the
purpose statement mentioned above for the Methods section.
The text should highlight the key results shown in the tables and figures. For
example, HCAII protein was induced to the highest level at 90 min. after IPTG
treatment (Fig. 2). Figure 2 will contain all of the results from the experiment, but
only the most important results are described in the text. The text also provides
information such as correlations, differences, trends, etc. that you want to highlight.
The results of controls should also be included in this section.

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 Report the results with as much information as possible about the relationship
between samples or conditions. For example, if you asked How much DNA in a
Gibson assembly reaction gave the most clones? The answer would not be The
lesser amount. Instead, the answer would be .04 picomoes of DNA resulted in
more clones than did .08 picomoes. Report the direction of difference (e.g. greater,
smaller, more, less) and the magnitude (e.g. % difference, -fold difference) whenever
possible.
Negative results should also be reported. DO NOT discard data unless you do the
appropriate statistical test to determine that it should be discarded (i.e. a Q-test, see
Appendix for more information on using statistics). Then in your report, you need to
state that the test was done and which data point was discarded.

Figures:
All data figures (e.g. graphs and gels) should be in the results section and each one
must have a title and a legend. The reader must be able to understand the figure
from the legend alone without reading the text of the results section. Therefore, the
legend must state what the experiment is, the treatment of the samples, the sample
size, and any information needed to interpret the results. However, the legend should
not include an interpretation of the figure; that belongs in the text of the Results
section. Legends should be placed below figures and it should include the figure or
table number and a descriptive title.
In figures of gels:
o The lanes should be labeled.
o The sizes of the markers should be labeled.
o Bands of interest should be indicated by an asterisk, arrow, or box.
For graphs, axes should be labeled and error bars should be included. If you fit a
curve to the data, the equation should be included on the graph.
Avoid the following:
Do not include a figure and then neglect to mention it in the text.
Do not present the same data in both a figure and a table.
Do not show raw data use summaries such as means and fold-differences.
Do not extensively discuss your conclusions in this section.
An example figure and legend can be seen below. Note the informative title and the
thorough legend.

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 2000 0 M

Normalized Fluorescence
0.5 M
1500 1 M
2 M
1000 3 M
(RFU) 4 M
500 4.5 M
5 M
0 6 M
300 320 340 360 7 M
8 M
Wavelength (nm)
9 M

Figure 1. Emission spectra pf HCAII T200A after short

incubation. HCAII T200A (0.2 uM) was incubated with urea at the
indicated concentrations ranging from 0 to 9 M for 1 hour 55
minutes. Tryptophans were excited at 280 nm and fluorescence
emission was measured from 300-370. One representative trial is
shown, the remaining two replicates yielded similar data.

Tables:
Like figures, all tables should be in the results section and each one must have a title
and a legend. The legend should be positioned above tables.
Note that tables and figures are assigned numbers separately: i.e. Table 1, Figure 1 ,
Figure 2, Table 2, etc.

Discussion section:
The discussion should interpret your results and explain how they led to a new
understanding of the question or hypothesis you were studying.
Like the Results, begin the Discussion section with a brief reminder to the reader of
the overall goal of the experiments you were describing. Also include a BRIEF
summary of the results you described in the Results section.
Do not include new results in the discussion section.
Use an active voice for this section.
The discussion section should address the following questions (you dont always have to
address all of them, and in some cases there might be something else you also want to
discuss):
1. What conclusions can you draw from your results?
2. Were your results expected? If not, how did they differ from your expectations,
and why? Similarly, how do your results compare to published data?
3. What were the limitations of this study? How could it be improved if you were to
try it again?
4. How do the results provide the answers to the questions or hypotheses you were
testing?

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 5. How do your results fit into the overall project you are working on in the lab?
6. Given what you found, what is the next logical step?

References
You must always include a references section at the end of the report to list any
references you cited, including the lab manual. Please use the following format:

Author(s). Year. Article title. Journal title. Volume: page numbers.

The lab manual can be cited as:

Prost, L.R. 2016. Biochemical Methods Laboratory Manual.

LATE POLICY FOR MINI LAB REPORTS

Late reports will not be accepted. If you have arranged to miss lab, you are still expected
to turn in a digital copy of your report before the start of lab.

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 FINAL LAB REPORT
At the end of the semester, you will work with your lab partner to write a final report that
describes all the work you did on the HCAII project. You will turn in one lab report per
pair.

By the time you write your final report, you should be well practiced in scientific writing
thanks to the weekly mini lab reports. (Youre welcome!) Pay close attention to the
feedback you receive from the TAs when they grade the mini reports. Incorporate their
comments into your writing when you are preparing the final lab report. It is acceptable
to copy parts of your mini lab reports into the final report, as long as the mini reports
themselves were acceptable.

The page limits will be strictly enforced (i.e. if your Introduction is three pages long, the
TAs will not read the third page and you will only be graded on pages 1-2). However,
you do not have to fill the number of pages listed. It is possible to write a great lab report
in fewer pages if you can be succinct. Use double-spaced 11 pt Helvetica font with 1-
inch page margins.

The general guidelines for this report are the same as for the mini lab reports. Again, the
report should follow the general format for peer-reviewed research articles. Specific
guidelines for each section are listed below. In addition to these guidelines, a detailed
grading rubric will be posted to Learn@UW. This rubric will describe exactly what the
TAs will look for when they are grading your report, so read it carefully!

Title page
The title page should include a title for your report, your name, your section, your group
number and the date.

Introduction (2 pages)
The introduction provides the context for your report by summarizing what is currently
known about your topic and stating the hypotheses or questions you are studying. The
introduction should briefly describe the rationale of the work and the approach you took.
Use the active voice. When presenting published information, use the present tense (i.e.
this is what we currently know). Introductions start out with a description of the general
background and then focus down to the specific problem you are studying.

Your introduction should address the following:

1. What is the protein you are working on and why is it interesting? Use 45
literature sources (at least 3 from the primary literature) for this section and be
sure to reference all your sources. Use figures as appropriate.
2. What is the hypothesis or question you are addressing with this project?
3. Give a general description of the experiments you used to address your
question/hypothesis.

Methods (8 pages)
In the methods section, you clearly explain how you did the study in enough detail that a
person with a scientific background (e.g. your TA) could repeat the experiment just by

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reading your methods section. Be sure to cite the lab manual. You should use the past
tense for this section because you are describing what you did in the past.

What to include in the Methods:

In lab 1 you practiced using PyMOL and selected some mutations that interested
you. None of this work has direct bearing on the rest of the experiments you did
this semester, so you do NOT need to discuss lab 1 in this report.
For the experiments that will be included, create a descriptive heading for each
(i.e. Enzymatic Activity of HCAII not Lab 10). In some cases, it may make
sense to combine the experiments from more than one week under a single
heading.
Labs 2-5 (Cloning) were conducted independently, so you have two sets of
experiments to describe. If only one partner was able to generate a successful
clone, you can describe their experiment and leave out the unsuccessful one. If
both partners were successful, you can choose one to describe. If both were
unsuccessful, describe what BOTH people did, explain that the cloning was
unsuccessful, and state where you obtained material to move forward.
Labs 6-8 (Protein purification) were conducted with your partner, so you can
describe what your pair did. You do NOT need to describe what the other pair at
your pod did. Be sure to make it clear whether you purified the mutant or wt
HCAII.
Labs 9-12 were conducted as a pod. Each group is therefore responsible for
describing the experiments for both the wt and mutant HCAII. Since you
designed much of these experiments on your own, you need to describe the
methods more extensively here than for the previous experiments.

Results (15 pages)

Follow all the guidelines for presenting results, tables and figures that were described for
the Mini Lab Reports. Remember that in this section you should present the results from
your experiments, without interpretation.

What to include in the Results:

Begin your Results section with a sentence or short paragraph to remind the
reader of the overall goal and/or hypothesis for the experiments you are
describing.
Divide the Results into subsections and, like with your Methods, create
informative headings for the results to be described therein.
DO NOT describe the cloning or protein expression in the Results. Those are
methods that allowed you to conduct the experiments of interest.
Starting with Lab 8 (protein purification gel), describe the results from each
experiment using text, figures and tables as appropriate.
It is okay to use text, figures and tables from your mini lab reports. However, it is
important that this final report read as one cohesive work, so you must add
transitions so the reader understands how the experiments are connected to
each other.

Discussion (8 pages)
Follow the guidelines already discussed for the Mini Lab Reports (be sure to review the
questions on pg. 14). It is again acceptable to copy text from the Mini Reports. However,
in the Discussion it is even more essential that the experiments are tied together to

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create a cohesive story. If you simply copy and paste the discussion sections from the
Mini Reports, you will not do well on your Final Report Discussion. You must think about
the semester as a whole, and integrate data from across multiple experiments (but again
focusing on labs 8-12).
Your discussion section should thoroughly answer the questions: what effect did
your mutation have on HCAII? How do you know? What did you learn about the
function of HCAII?
Include discussion of the biochemistry of the amino acid change, the structure
and stability of the protein, enzymatic function and ligand binding.
Connect your results to your hypothesis, as stated in your Introduction, and to the
broader scientific field.
Propose follow-up experiments.

References
Be sure to include references in the proper format for all works cited.

Acknowledgement & Contributions

Include the names of people you worked with to collect and analyze data, anyone who
read your report in any form, and anyone whose report you read. Describe the relative
contribution that each partner made to the writing and revision of this Final Lab Report.

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 ORAL LAB REPORT
At the end of the semester, you will work with your lab partner to create an oral
presentation that describes all the work you did on the HCAII project. You will present as
a pair to some of your classmates and one TA.

The report should be 15 minutes long. There will be an additional 15 minutes for the
audience to ask you questions.

There will be a lecture with details on how to prepare for the oral report, and a detailed
grading rubric will be posted to Learn@UW. Below you will find a general outline of what
to include to get you started.

What to include in the oral report

Start with an informative outline
Include background on why HCAII is interesting
Give a rationale for the entire project (question/hypothesis)
Mention that you cloned and expressed HCAII, but do not describe labs 1-8 in
detail
Focus on the results from labs 9-12
Include a thorough conclusion section:
o Concisely summarize your data
o Describe the effects of your mutation on HCAII
WHY do you think the mutation caused whatever phenotype you
observed?
o Suggest possible future directions

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 SAFETY IN THE LABORATORY

Lab Rules
1. Come to lab prepared! This will help you to anticipate potential hazards.
2. Arrive to lab on time. Some weeks the TAs will start the lab by discussing specific
safety issues. Also check the front board for important notes.
3. NEVER EAT, DRINK, CHEW GUM, OR SMOKE (gross) IN LAB.
4. Wear protective gear appropriate to the situation. Safety glasses are required at
all times, as are close-toed shoes. Long pants are strongly recommended. Wear
a lab coat and/or gloves if the situation requires it. If you are wearing gloves,
remember that pens, doorknobs, or anything that you touch may potentially be
contaminated with whatever might have been on the gloves.
5. Work in the designated areas; dispose of materials as indicated by your
instructors.
6. Bring to the lab bench only those notebooks and other items necessary for the
experiment; leave coats, backpacks, and other personal belongings in the hall
lockers.
7. Use sharp or breakable objects properly. Carry sharp objects (syringes with
needles, Pasteur pipettes, etc.) pointing down and away from you. Do not leave
pipette tips protruding from the lab bench into the aisle. When attaching a
pipetting device to a pipette, grasp the pipette close to the end to be inserted into
the pipetting device.
8. Potentially dangerous equipment (like gel electrophoresis power supplies) should
be pushed back on the lab bench to minimize the possibility of inadvertent
contact.
9. Wash your hands before leaving the laboratory.

Fire
1. Note where the showers, eyewashes and fire extinguishers are located in the
laboratory.
2. Fire exits:
a. Stairs outside lab
b. Hallway toward sky bridge to BSB building
c. Hallway toward 2139 and down stairs

3. Fire drill procedure:

a. Public-address system announces the emergency.

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 b. Listen for 551 staff announcements about turning off equipment as you
leave.
c. If there is time, obtain your coat and bag from your locker.
d. Down the stairs outside the lab.

4. Fire extinguisher use:

a. Break the plastic tab.

b. Pull the pin.
c. Aim the nozzle.
d. Squeeze the handle.

Note: you are never required to use a fire extinguisher if you feel in danger or
uncomfortable doing so.

Chemicals
1. Safety glasses must be worn in the lab at all times. You must bring your own pair
to class; they will not be provided. Contact lenses should be avoided, because
fumes and other materials can become lodged between the contact lens and the
eye, causing damage. If you must wear contacts, wear safety goggles over them.
2. Handle chemicals with care. Absolutely do not mouth-pipette.
3. Note the locations of showers, eyewashes, and fume hoods.
4. Tape color codes used in the lab:

Red = dangerous (strong acid or base, carcinogen, mutagen, or poison).

5. If a spill occurs:

a. Call a lab staff member.

b. Remove contaminated clothing immediately. Flush skin with water for at
least 5 min. Wash with mild soap and water. Seek medical advice.
c. Contain the spilled material; evacuate the area if necessary.

22
 LAB CHECK-IN, PRACTICES AND PROCEDURES
The lab sections will be composed of 10 14 pairs of students that we will refer to as a
group (there may be a few trios depending upon enrollment). Each group will be
assigned a number that will be used throughout the semester.

1. Each group will be assigned a set of drawers. Check to see that your drawer
contains the general-purpose glassware and other items for use during the
semester. You will be given a check-in list of all the items in your drawer.

NOTE:

If you are missing any of these items at the beginning of the semester, notify
your TA or the instructor.

Each student is responsible for keeping the contents of the drawer clean and
intact over the course of the semester. If you lose or break something, contact
the instructor or TAs.

Do not leave glassware from your drawer by the sink.

2. When you label glass wear, be sure to remove all marks when you are finished.
Sharpies may be used but be sure to rinse off all marks with ethanol. If you use
label tape, be sure to remove it

3. Clean test tubes (18x150 mm and 13x100 mm) can be obtained during any lab
period from one of the yellow trays. Used or dirty test tubes should be placed in
one of the dishpans located near the sinks. Please remove any tape, grease pencil
or Sharpie marks that have been put on the tubes and rinse them with tap water
before placing them in the dishpan. This ensures that the tubes will be properly
cleaned in the dishwashing machine.

4. Clean glass pipettes can be obtained from designated yellow bins placed on the
supplies bench for that period. Dirty pipettes must be placed (tips up) in a pipette
washing jar (long cylindrical container) adjacent to the sink or elsewhere as
indicated by the TA or instructor. Do not leave pipettes in the dishpans that are
meant for dirty test tubes.

5. Sterile micropipette tips: Each pair obtains one box of each size at the beginning of
lab 2 and labels them. If you empty a box during lab, fill the empty box from the
bag of tips at the tip-packing station left out for that purpose. Attach autoclave tape
and take it to a TA, who will take your filled, non-sterile box and give you a new
sterile box of tips. At the end of lab, put your labeled boxes on the designated cart
for use next week.

Please remember to keep your tip boxes closed to maintain sterility.

23
6. Dispose of used tips, and ONLY used tips, in the designated boxes. Tips can
poke through regular trash bags and so must be disposed of in cardboard boxes.
However, other lab waste, such as plastic tubes, gloves and paper towels should
go in the regular trash.

7. Broken glass, Pasteur pipettes, and other dangerous, sharp disposable material
should be placed in the cardboard glass disposal box located in the lab. Clean up
broken glassware with the broom and dustpan. Lab staff will obtain it for you.

8. You are responsible for cleaning your work area at the end of each lab period.
This includes all glassware, pipettes, waste paper, test tube racks, etc. It is
particularly important to return any special equipment that was used for a certain
experiment, according to instructions given by the TA. Please allow about 15-20
minutes at the end of each lab period to collect drawer contents, rinse glassware
being returned to us, etc.

9. Extraneous personal belongings (coats, backpacks, etc.) should not be placed on

lab bench space. There are lockers in the hallway outside of the lab entrance. Use
of these will be demonstrated during orientation. Please keep any items brought
into the lab pushed back under the bench; do not block the aisles.

10. Your samples to save for next week During weeks 2-5, there will be freezer boxes
in the front of lab for anything you need to save. The boxes are shared across
sections, so be sure you label your tubes so that you will be able to find them the
following week. During weeks 6-12, you and your lab partner will receive your own
freezer box for storing samples.

24
 HOW TO PREPARE FOR LAB EACH WEEK

Read the description of the lab in the lab manual.

Attend the prelab class (where applicable) or watch the prelab video on Learn@UW.
Slides will also be posted to Learn@UW each week.
Answer the prelab questions. Questions can be found in the lab manual at the
beginning of each lab, and should be answered in your lab notebook.
Complete the prelab quiz on Learn@UW.
Complete any required calculations, or any other planning that is possible before the
lab, as outlined in the lab manual. Note that some weeks this may require you to
coordinate with your lab partner and/or podmates before the lab.

25

26
LAB 1: Structural analysis of HCAII using PyMOL

27

28
LAB 1: Structural analysis of HCAII using PyMOL
OBJECTIVE
This week you will use the molecular graphics program PyMOL to learn how to explore
crystal structures downloaded from the Protein Data Bank (PDB). Then, you will
examine the structure of the HCAII (human carbonic anhydrase II) protein and determine
which mutations your section is most interested in analyzing. Due to time and financial
constraints, Dr. Prost will generate a total of six mutant clones based upon the requests
from the sections. Once the six mutants have been generated, you will be given one of
the mutant clones to express, purify, and analyze. Each pod will work on one mutation
so that each lab section analyzes all six.

NOTE: This lab requires you to bring a laptop that already has PyMOL installed. The full
version of PyMOL is available to UW students as a free download see Learn@UW for
the DoIT link to do so. It is important that you download the full version through DoIT, as
opposed to the Education Version, which is available for free to everyone but does not
include all the required functionality.

NOTE: The instructions for this lab were written for a Mac. However, PyMOL is virtually
identical on a PC, so we dont anticipate any problems.

NOTE: The times in parenthesis are approximate suggestions of how much time it
should take to complete the tasks. Ideally, this lab can be completed in about three
hours.

PRE-LAB
1) What will you be doing in lab and why?
2) What should you end up with at the end of the lab period?
3) Based on what you learned about HCAII during lecture, describe one amino acid you
would like to mutate, and to which residue you would change it. Why do you think this
mutation would be interesting?

29
PART 1: GETTING FAMILIAR WITH PROTEIN STRUCTURE (45 min)
Explore the PDB site (5 min)
Go to http://www.rcsb.org/pdb/
In the search box at the top of the page you can type the name of any protein
you like in the search box, or you can use the "PDB code", a code of four
alphanumeric characters that defines a structure. If you don't know what to type
try, for example, carbonic anhydrase.
You will get a list of results. Click on one of them and you will find its description
page, including the Primary Citation (the paper where the crystallography was
presented), the Molecular Description (the name of the protein and its
classification), possible ligands.
Under the picture you'll find the Experimental Details, which include the
resolution (<1.5 : very high; <2 high; <2.5 medium), space group (the
geometry of the crystal), R-value and R-free (quality control numbers; generally
these should be ~10% of the resolution or less).
The PDB code (e.g. 3IEO) is in the top-right corner.
Try a number of searches for proteins that you have studied. Note down the PDB
code to open them in PyMOL later.

Visualize proteins with PyMOL (15 min)

Open PyMOL.
Note the tool bar on top, the menus, and the command text box underneath them
(next to the "PyMOL>"). (See figure 1.1). Typing a command in the command
box can perform many of the functions.

Fig. 1.1. PyMOL displaying a protein in 'line' visualization. The sequence of the protein is
turned on (by pressing the S sequence button on the bottom right). Part of the
sequence is selected (highlighted both in the sequence and in the molecule). Actions
can be performed on the entire protein (3KOI) or on the selection ('sele').

30
 Type in the command fetch <pdb code> (e.g. fetch 3IEO). This will download
the structure from the PDB web site and the protein will appear in the main
portion of the screen.
Using the mouse:
o Clicking on the background and moving the mouse will rotate the
molecule around the X and Y axes (clicking at the edge of the screen will
rotate around Z axis).
o Clicking on the molecule will select residues (or chains, or atoms,
depending on the current mode).
o Right click will zoom in or out on the molecule (move mouse up and
down).
o The middle button can be either clicked or rolled.
o Clicking the middle button will allow you to move the structure sideways
(translation).
o Rolling the mouse wheel will slice away Z-planes (you'll see only a slice of
the protein), a good way to focus only on some details of the protein.
Objects: In the right panel you will see two or more objects: all, one or more <pdb
code> (i.e. 3IEO), and possibly some selections '(sele)'. You can click on these
buttons to display or hide molecules without deleting them (light grey buttons are
displayed, dark grey buttons are hidden).
Next to them there are five buttons: A, S, H, L, C
o A stands for action; you can zoom, center, rename, delete, and duplicate
objects from this menu
o S stands for show; here you can change the representation of the
molecules: e.g. line, cartoon, or stick.
o H stands for hide, it performs the same functions as S except that it hides
whatever selection you make.
o L stands for label
o C stands for color: here you change to a specific color, color by chain, by
secondary structure, or color by rainbow. Coloring by spectrum/rainbow
highlights visually the N- and C-termini of the protein. If you use color by
chain/rainbow each chain will have its own rainbow spectrum and it will
be easy to see where they start and end.
Selecting parts of the protein with commands:
o To select a chain type in the command box 'sele chain A'
o To select an amino acid name 'resn', type 'sele resn LEU'
o To select a residue by number ('resi') and chain, type 'sele chain A and
resi 74'
o You can also use the 'or' operator for complex logic: 'sele resi 74 or resn
LEU' will select residue number 74 and all the Leu in the protein
o Once you enter a selection, the corresponding residues become
highlighted and you can perform an action with the ASHLC buttons next
to '(sele)' in the object box

Play with the visualization modes (10 min)

Experiment with different proteins to familiarize yourself with PyMOL.
Load the structure, display it in both cartoon and line representations, and color
by chains to show the individual subunits.
Change the PyMOL background color to white (this will make things easier to
print): Click on the Display drop-down menu; click Background; choose White.

31
 Open the sequence display (the little square S button in the bottom-right corner,
near some controls that look like VCR control buttons, play, stop, etc.). The
sequence will show on the top.
Find a tryptophan in the protein, if there is one: check the sequence for a W, left
click on it to select it, and then in the right panel under the sele button use the A
button to zoom in on this atom. Use the S button to show the side chain in
"sticks". If there is no Trp, try Tyr (Y).
Use the middle button scroll to adjust the visible slab of the molecule (this takes
the stuff in the foreground and in the background away and let you focus on the
details)
Repeat for phenylalanine (F). Once zoomed in, lets display the whole structure
in lines, (use the show button); now try displaying in sphere representation.
Hide the sphere representation and display just the phenylalanine side chain in
sphere.
To help see the side chains beneath the spheres, go to settings in the above tool
bar, then transparency, then spheres, then 60%.
Hide spheres, then select any residue, zoom in, and only for this residue display
dots; this is a convenient way to see space filling models of single amino acids.
Zoom out of the structure, then display the whole molecule as surface; from the
S button. Another way to view this is show as mesh surface.

Practice following a fold with the structure of a TIM barrel (10 min):
Remove all the unneeded PDBs from the object box (A->delete object).
Download a TIM barrel, a very common enzyme fold. Fetch 1TRI (an engineered
monomeric triose isomerase).
The TIM barrel (so called because it was first identified in Triose IsoMerase) has
an / fold, with a central parallel -barrel (a -sheet that closes into itself) and -
helices on the outside.
Display by cartoon, color by rainbow, such as in Fig. 1.2, and follow the fold. You
will observe a series of inner -strands, loops, and -helices that repeat 8 times,
forming an inner -barrel surrounded by helices.

Fig. 1.2. Two views of the TIM barrel 1TRI. Note the alternating helices and sheets,
forming an inner parallel -barrel surrounded by helices.

Note that if you display the structure in sphere, you'll see that the center of the -
barrel is not empty.

32
 The active site is at the mouth of the -barrel.
Familiarize yourself with the fold.
Now delete 1TRI and fetch 2X2G. This protein has two molecules in the
asymmetric unit (in is not a biological dimer but it crystallizes as a pair).
Display the protein in cartoon.
Show the surface of the entire molecule (do not turn off the cartoon).
Set the surface transparent (menus Setting/Transparency/Surface/60%)
Now select the ligand: command 'sele resn 3PG'
Show the selection (the ligand) in spheres
Zoom into the ligand (Action Zoom next to '(sele)') and examine how the ligand
fits into the cavity of the active site.

PART 2: VISUALIZATION OF HUMAN CARBONIC ANHYDRASE II (30min)

Close and reopen PyMOL to start fresh.
Change the background to white.
Download 2VVA. This is a structure of HCAII with CO2 in the active site.

NOTE: the numbering of HCAII residues is not the logical 1260 consecutive
sequence that one would expect. Because a lot of work was done on HCAI,
which has an extra residue, HCAII is numbered with a gap at position 126:
Asn 124, Thr 125, Lys 127, Tyr 128...
Thr 125 and Lys 127 are consecutive in the sequence and connected to each
other (please verify that in PyMOL). The gap is a numbering convention for
convenience in discussion, so that the active site residues in HCAI and HCAII
have the same residue number.

Hide everything and show the protein in cartoon. Color it by spectrum/rainbow.

Show the sequence.
First select the catalytic atoms, the Zn2+ and the zinc-bound hydroxyl group. Type
the command: 'sele resn ZN or resi 2350'. That is, select the residue named ZN
or the residue number 2350, which happens to be the number of the water
molecule bound to the zinc. (The 'or' ensures that both are selected.)
Display them in sphere. You may want to rename the selection: press the A next
to the '(sele)', chose 'rename selection', call it 'Zn-OH,' or something else of your
choosing.

33
Fig. 1.3. A global and detailed view of HCAII from PDB 2ILI. Note how obnoxious the
color scheme is.

Clear the selection by clicking in a white area.

Find in the sequence the Zn-coordinating histidines (H): H94, H96 and H119 (you
could also select them with the following command 'sele resi 94+96+119'), and
display them in stick.
Rename the selection something like 'coorHis'.
Show the surface of the entire molecule (do not turn off the ribbon).
Set the surface transparent (menus Setting/Transparency/Surface/60%)
Now, play around with the color scheme. If you use the color as it is now, or as
shown in Fig 1.3, it is very difficult for the viewer to see what is important in the
figure. For your lab reports, you want to think about the story you want to tell with
this figure, and how to draw the viewers attention to the important parts.
Now, play around with the orientation of the model. You should be able to find an
orientation such that you can appreciate the location of the active site. There is a
clear cavity in the surface, and at the end of it there is the Zn-OH group.
Take two pictures from different angles (as in Figure 1.4) for your lab notebook.
o First, ray-trace the image for quality: type the command 'ray 1000,1000'
o Then save the file: File>Save Image As>PNG.
o Rotate, ray-trace and save a second view
Now select the polar residues of the active site: Tyr (Y) 7, Asn (N) 62 and 67, His
(H) 64, Gln (Q) 92, Glu (E) 106, and Thr (T) 199 and 200. First deselect
everything by clicking in a black area, then type the following command: 'sele resi
7+62+64+67+92+106+199+200'. Rename the selection 'polar' and display them
in sticks.

NOTE: His 64 is displayed in two conformations! This is because in the crystal

this side chain spends about 50% of the time toward the active site, and 50% in
the other orientation. The crystallographer was able to see electron density for
both conformations and fit a side chain in it. This is not unusual for high-
resolution structures.

34
 Now select the hydrophobic residues in the pocket: Ile (I) 91, Val (V) 121 and
143, Phe (F) 131, Leu (L) 141 and 198, and Trp (W) 209: type 'sele resi
91+121+131+141+143+198+209'.
Now select the CO2: 'sele resi 1264' and save the selection as 'CO2'. Display it in
spheres.
Now examine the structure and the residues that define the active site. Use
cartoon for the backbone of the whole structure. Hide the sticks for the
hydrophobic selection, and take a picture with just the polar selection for the lab
report. Then, without moving the protein, hide sticks for the polar, show sticks for
the hydrophobic residues and take another picture.
Save what you have gotten so far as a PyMOL session (File>Save Session).
Save the file as 2VVA.pse.

PART 3: SURFACE EXPOSURE OF KEY RESIDUES (30mins)

During lab 9, you will use the intrinsic fluorescence properties of tryptophan residues to
study the stability of wt and mutant HCAII. The assay relies on the change in
fluorescence properties of tryptophan depending on its environment. When a protein is
fully folded, most tryptophans are buried; this yields a characteristic spectrum. When a
protein is unfolded, all tryptophan residues become exposed, which alters the spectrum.
We will use this change in fluorescence upon unfolding to determine whether your
mutations affect the stability of HCAII. For now, you will generate some information on
the surface exposure of tryptophans. Make sure you save your figures so you can refer
back to them during lab 9.
Calculate surface exposure with an online tool
Download the 2VVA.pdb file from http://www.rcsb.org/pdb/
Go to http://curie.utmb.edu/getarea.html
Choose the pdb file you just downloaded. Leave the other fields at the default,
enter your email address, and hit Submit for Analysis.
You should now have a read-out for each residue in HCAII and a determination
for whether it is inside or outside on the protein. If you scroll to the bottom, you
will also get a count of the total number of surface vs. buried atoms.
Find each tryptophan residue (TRP) and note whether it is listed as in or out.
Visualize surface exposure in PyMOL
If you closed PyMOL, reopen and open your saved 2VVA.pse file.
Show all residues as spheres and color gray.
Select all TRP residues by typing select resn TRP and not name C+O+N+CA
Rename the selection trp.
Color the tryptophans yellow.
Look at the relative surface locations of each tryptophan. You may want to make
the protein transparent (by choosing Setting, Transparency, Spheres) to see
where they all are.
Make a list of each tryptophan with its residue number and whether you think
each is completely buried, minimally exposed, significantly exposed, fully
exposed.
Take pictures of the trp residues for use in lab 9. Also save this session as
2VVAtrp.pse

35
PART 4: DESIGNING MUTATIONS IN HCAII (1 hr 15mins)

Mutagenesis of HCAII active site (30 min)

Now it is time to mutate the protein!
Close PyMOL, reopen it, and load the first session you saved: 2VVA.pse
To make a mutation, go to the menu: Wizard>Mutagenesis (Fig. 1.4)

Fig. 1.4. The Mutagenesis

menu under Wizard.

Fig. 1.5. Select the mutated amino acid. Click on No

Mutation and pick an amino acid.

On the bottom of the side panel you will see the mutagenesis options. Click on
No Mutation and select the amino acid type you would like to mutate a side chain
to (Fig. 1.5).
Click on the side chain you would like to mutate, and the new amino acid type will
appear in grey on top of the old one (Fig. 1.6). You can change the conformation
of the new amino acid using the arrow buttons on the bottom-right corner.

36
 Fig 1.6. Making a Val-to-Ile mutation: select ILE as the mutated amino acid, then click
on the Val side chain. A gray ILE will appear on top. Red disks will show graphically if
the new side chain is clashing with other atoms. Use the arrow at the very bottom-right
of the PyMOL screen (displayed in the inset) to change conformation. When satisfied,
select 'Apply' in the Mutagenesis options.

You will see some red disks appearing. These are the clashes (atoms going into
other atoms). A few small disks mean mild clashes, which are likely to be
relieved by the protein (the backbone and the side chains will have some
flexibility that is not present in your rigid model). Big disks (and many of them)
means severe clashes.

NOTE: PyMOL has a problem mutating amino acids modeled in two conformations,
such as His64. The mutation tool will not work for this residue. You can still propose a
mutation here, but you wont be able to visualize it.

Take a picture of your mutation. Save the mutation as a separate PyMOL

session file (for example, mutation1.pse).

Reload the 2VVA.pse PyMOL session and work on the next mutation.

You should select three point mutations in the active site and explain the rationale
behind each mutation. You may, for example:
Change the proton-shuttling His64 to a different amino acid. As noted above, you
cant visualize mutations to this residue using the mutagenesis tool, but you
could still take a look at the residue and think about interesting mutations.
Change the polarity of the cavity (hydrophobic-to-polar mutations or vice versa),
while preserving the size
Change a smaller residue to a larger one in a way that can be accommodated by
the structure
Purposely create clashing mutations that will likely compromise the structure
Try to make a mutation that would increase HCAII catalytic activity
Make mutations that will interfere with the position of the CO2, or otherwise
change the shape of the active site

You may choose whatever mutations you want, but you must explain your
rationale in the mini lab report.

37
 Use figure 1.7 as a
reference for choosing
a mutation. Make sure
to comment on how
similar (or dissimilar)
are the structures of
the original residue
and the proposed
mutation (size/number
of atoms, polarity,
charge, etc.).

Fig. 1.7. Table of amino acid side chains. The circle

represents the C atom. The rest of the residue is not
represented, with the exception of the N atom of proline. The
amino acids are grouped by chemical characteristics. Note:
histidine can be either positively charged or neutral
depending on the pH and the structural context (its pKa is
around 6.0). When it coordinates the zinc atom it MUST be
neutral because it acts as a Lewis base by donating a lone
pair of electrons.

Effects of the mutations on DNSA binding (15 min)

Open a new PyMOL session.
Fetch PDB 1OKL, of HCAII complexed with dansylamide.
Select the ligand by name: 'sele resn MNS' and save the selection.
Consider the mutations you are proposing. Do you expect the binding of the
dansylamide to be affected? Are the mutations compatible, or will they clash or
generate a void? Be prepared to address these issues in your mini lab report.

38
Class presents the mutations and votes (30 min)
Find someone sitting near you and discuss the mutations you each made. Decide on
your favorite one (from your total of six) to present to the class. Also decide on your
second favorite in case someone else presents the same mutation.

Discuss your mutations with a partner. Between the two of you, choose one to
present to the class. Once youve decided, write it up on the board. If someone
else has already chosen your mutation, choose a different one.
Create a ppt slide to present your mutation and your rationale to the class. Be
sure to include a clear image of your mutation and where it is relative to the
active site. Address why you think this mutation is interesting and what effects
you expect to see on the enzyme.
Upload your ppt slide to the dropbox on Learn@UW.
We will move to a classroom with a projector to present and discuss the
proposed mutations.
A TA or volunteer will write the mutations on the board, along with a brief
summary of the rationale.
After every group has made a suggestion, the class will vote by a show of hands.
Dr. Prost will compile the mutations with the most votes. Ultimately, six of the
mutants will be made, expressed and analyzed in the lab.

39
MINI LAB REPORT 1

Refer to the general guidelines for Mini Lab Reports that start on pg. 12 of this manual.

Results Section
For each of the three mutations you made, address the following:
State the residue that you changed and what amino acid you changed it to (e.g.
V34K). Include a figure showing the change in the structure. Please make sure that
the PyMOL figures you use in the lab report have a white background this will
make them significantly easier to evaluate. Remember that figures need to have
informative titles and legends. Your legend should clearly state what is shown in
each color and what is depicted as sticks/spheres/etc.
Justify why you chose to change that amino acid and why you selected the mutant
residue that you did. Use your knowledge of the structure from the PyMOL session in
Lab 1 and the biochemical properties of the amino acids (Fig. 1.7 or any general
biochemistry textbook) to inform your answer.
Comment on clashes that appear with your mutated residues.
Study the effect of the mutations you picked on the ligand-binding structure. (The
ligand is dansylamide, DNSA). Do they seem compatible, or do the mutations create
clashes?

Discussion Section
What effect on HCAII function do you expect to observe for each of the three mutations?
Consider the following:
Different functionality of the new residue (is it a conservative or non-conservative
mutation?)
Effects on structure
Effects on enzymatic activity
Effects on ligand-binding
What is the next step? How would you test the function of the mutants?

40