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(New page: '''Chemistry L333: Advanced Biochemical Techniques Spring 2008 Syllabus''''''Bold text'''<br> Archer 631, Mondays 1-5pm and Fridays 1-5pm<br> <br> Professor: Dr. Melanie Berkmen <br> Ema...)
 
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'''Chemistry L333: Advanced Biochemical Techniques
 
Spring 2008 Syllabus''''''Bold text'''<br>
== '''Chemistry L333: Advanced Biochemical Techniques - Spring 2008'''< ==
 
== Headline text ==
br>
Archer 631, Mondays 1-5pm and Fridays 1-5pm<br>
Archer 631, Mondays 1-5pm and Fridays 1-5pm<br>


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<br>
<br>


Reading (prior to class) will be assigned from:<br>
'''Reading (prior to class) will be assigned from:<br>
 
'''
1. “FT”: Farrell & Taylor, Experiments in Biochemistry: A Hands On Approach, 2nd ed., 2006, Thomson Brooks/Cole.
1. “FT”: Farrell & Taylor, Experiments in Biochemistry: A Hands On Approach, 2nd ed., 2006, Thomson Brooks/Cole.
2. “SB”: Stryer, Berg, & Tymoczko, Biochemistry, 6th ed., 2007, WH  Freeman & Co..
2. “SB”: Stryer, Berg, & Tymoczko, Biochemistry, 6th ed., 2007, WH  Freeman & Co..
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<br>
<br>


Assignments:<br>
'''Assignments:<br>'''


Pre-lab quizzes (given at the beginning of class)
Pre-lab quizzes (given at the beginning of class)
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Final paper on independent research project
Final paper on independent research project


Tentative Grading:  
'''Tentative Grading: '''<br>
Lab reports 25%
Lab reports 25%
Post lab questions/problems 20%  
Post lab questions/problems 20%  
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Lab notebook 10%
Lab notebook 10%


Absences/Missed Assignments:
'''Absences/Missed Assignments:
'''<br>
Absences due to a health, family, or personal emergency can be made up.  In addition, if you know you will be absent due to a professional activity (such as attendance of a scientific conference or interview), please notify the professor as early as possible to schedule a make-up. All other absences cannot be made up, and will result in no-credit for the missed laboratory and the accompanying quizzes and assignments.  Late assignments will lose 4 percentage points for each day that they are late.
Absences due to a health, family, or personal emergency can be made up.  In addition, if you know you will be absent due to a professional activity (such as attendance of a scientific conference or interview), please notify the professor as early as possible to schedule a make-up. All other absences cannot be made up, and will result in no-credit for the missed laboratory and the accompanying quizzes and assignments.  Late assignments will lose 4 percentage points for each day that they are late.


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Three GOALS:
'''Three GOALS:
'''<br>
A. Acquire skills in basic modern biochemical techniques (1st half of semester):
A. Acquire skills in basic modern biochemical techniques (1st half of semester):
- Pipeting and preparation/sterilization of buffers
- Pipeting and preparation/sterilization of buffers
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C. You will start as my protégés and end as my colleagues.
C. You will start as my protégés and end as my colleagues.
TENTATIVE CALENDAR: Part I Basic Biochemical Techniques
Date
(Lab#) Pre-lab reading Lecture Topics
Laboratory Exercise Post–lab assignment
(Due 1 week after lab)
1/18 FRI Introduction, lab tour and safety
Notebooks & lab reports
How to search/cite literature
Biochemistry review & concept mapping
Math assessment (not for grade)
1/21 MON NO CLASS  –  Martin Luther King Holiday
1/25 FRI
Lab 1 FT p1-28 Data and measurements
Pipette tip packing and sterilization
Calibration and use of pipettes Problem Set
1/28 MON
Lab 2
FT p37-51 Acids, Bases, and Buffers
Calculating dilutions and solutions
Purified Water and sterilization
Making buffers Problem Set
2/1 FRI
Lab 3 SB p134-144
Handout Cloning and plasmids
Purification of Plasmid DNA
Preparation of an agarose gel
2/4 MON
Lab 4 FT p239-242 Agarose Gel Electrophoresis
Problem Set
2/8 FRI
Lab 5 Handout
SB p65-77 Enzyme purification & Pfu DNA Pol
Ni2+ affinity purif. Of His- Pfu DNA Pol
2/11 MON
Lab 6
FT p239-250
Weber & Osborn, JBC, 1969 Polyacrylamide gel electrophoresis
Discussion of Weber & Osborn, JBC, 1969
Graphing with Excel
SDS-PAGE of Pfu prep/Coomassie Lab report (on labs 5/6)
DUE 2/18/08
2/15 FRI
Lab 7
FT p63-73 Spectrophotometry & Beer’s Law
Bradford Assay & Calibration curves
Bradford Assay Lab report (on lab 7)
DUE 2/25/08
2/18 MON NO CLASS  –  President’s Day Holiday
2/22 FRI
Lab 8 FT p89, p94-95, p359-366 PCR, experimental design and controls
PCR to assay activity of purif. Pfu DNAP
2/25 MON
Lab 9 Agarose gel of PCR products Lab report (on labs 8/9)
DUE 3/3/08
TENTATIVE CALENDAR OF LABS: Part II Project Lab
Date
(Lab#) Pre-lab reading Lecture Topics
Laboratory Exercise Post–lab assignment
(Due 1 week after lab)
2/29 FRI
Lab 10 HANDOUT Journal Paper Explanation of project and project lab
Discussion of Berkmen et al, in prep. Choose mutations
3/3 MON
Lab 11 HANDOUT
Journal paper Principles of primer design
Design and order primers
3/7 FRI
Lab 12 FT p313-330 Prep plasmid vector
3/10 MON
Lab 13 HANDOUT PCR mutations
3/14 FRI
Lab 14 HANDOUT QIAQUICK PCR products
Run PCRs and plasmid on agarose gel
Guestimate DNA concentrations from gel Lab report
(on labs 10-14)
DUE 3/24/08
3/17 MON NO CLASS  –  SPRING BREAK (Troubleshoot PCRs?)
3/21 FRI NO CLASS  –  SPRING BREAK (Troubleshoot PCRs?)
3/24 MON
Lab 15 FT p295-302
p316-322
HANDOUT Restriction digests of PCR and plasmids
Qiaquick digests
3/28 FRI
Lab 16 HANDOUT Run digests on gel
Gel purify vector
3/31 MON
Lab 17 HANDOUT Discussion of ligation and transformation
Controls for both
Ligate vectors and PCRs
Transform
4/4 FRI
Lab 18 HANDOUT Analysis of Transformations
Colony PCR to check for inserts Lab report (labs 10-18)
DUE 4/7/08
4/7 MON
Lab 19 HANDOUT Run insert-check PCRs on gel
4/11 FRI
Lab 20 HANDOUT Plasmid prep – elute with water
Send for sequencing
4/14 MON
Lab 21 HANDOUT
BT p138 Analysis of sequences
Comparison of sequences: Clustal, Blast
Calculation of mutation rates
4/18 FRI
Lab 22 HANDOUT Bioinformatics –  viewing protein structures, navigating NCBI, etc. 
In class problem set
In-class concept mapping Problem Set
FINAL Paper
(on labs 10-22)
DUE 4/21/08
4/21 MON NO CLASS  –  Patriot’s Day

Revision as of 08:49, 25 June 2008

Chemistry L333: Advanced Biochemical Techniques - Spring 2008<

Headline text

br> Archer 631, Mondays 1-5pm and Fridays 1-5pm


Professor: Dr. Melanie Berkmen

Email: mberkmen@suffolk.edu

Phone: 617-973-5321

Office: Donahue 513 (but often found in lab Archer 631)

Office Hours: Tues. 12-1(D513), Thurs 3-4pm (A631), Friday 11-12 (A631) or by appointment. You are always welcome.


Reading (prior to class) will be assigned from:
1. “FT”: Farrell & Taylor, Experiments in Biochemistry: A Hands On Approach, 2nd ed., 2006, Thomson Brooks/Cole. 2. “SB”: Stryer, Berg, & Tymoczko, Biochemistry, 6th ed., 2007, WH Freeman & Co.. 3. Handouts. 4. Journal articles.

Assignments:

Pre-lab quizzes (given at the beginning of class) Lab notebook entries (required for all actual labs but not discussions/journal club) Post-lab problem sets ~5 Lab reports (required for labs 5/6, 7, 8/9, 10-14, 10-18) Final paper on independent research project

Tentative Grading:
Lab reports 25% Post lab questions/problems 20% Pre-lab quizzes 20% Final paper on independent research project 15% Laboratory technique, safety, participation, and courtesy 10% Lab notebook 10%

Absences/Missed Assignments:
Absences due to a health, family, or personal emergency can be made up. In addition, if you know you will be absent due to a professional activity (such as attendance of a scientific conference or interview), please notify the professor as early as possible to schedule a make-up. All other absences cannot be made up, and will result in no-credit for the missed laboratory and the accompanying quizzes and assignments. Late assignments will lose 4 percentage points for each day that they are late.

Please come to lab on time and prepared.


Three GOALS:
A. Acquire skills in basic modern biochemical techniques (1st half of semester): - Pipeting and preparation/sterilization of buffers - DNA/protein purification and electrophoresis - PCR and other biochemical assays

B. Understand the basic process of scientific discovery in the laboratory by development of an independent experimental research project (2nd half of semester) with special focus on experimental design and troubleshooting.

C. You will start as my protégés and end as my colleagues.