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Methods and Concepts in Molecular Life Sciences
Contents
Course Plan 2
Course Schedule 5
Experimental work 11
Contact people for experimental work 12
Schedule for experimental work presentations 13
Group Discussion questions 14
Information about written examination 23
Grading criteria 24
Course Evaluation 26
Directions to lab visits 28
Lab compendiums Back of the folder
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Kursplan
för kurs på grundnivå Metoder och koncept inom molekylär livsvetenskaper 15 Högskolepoäng
Methods and Concepts in Molecular Life Sciences 15 ECTS credits
Kurskod: BL4015
Gäller från: VT 2013 Fastställd: 2012-01-16
Ändrad: 2012-10-08
Institution: Institutionen för biologisk grundutbildning
Huvudområde: Biologi
Fördjupning: G2F - Grundnivå, har minst 60 hp kurs/er på grundnivå som förkunskapskrav
Beslut Denna kursplan är fastställd av Naturvetenskapliga fakultetsnämnden vid Stockholms universitet
2012-01-16 och reviderad 2012-10-08..
Förkunskapskrav och andra villkor för tillträde till kursen För tillträde till kursen krävs kunskaper motsvarande Grundläggande kemi - Oorganisk, Fysikalisk,
Organisk och Biokemi GN 30 hp (KZ2001), inklusive 7,5 hp i biokemi, samt Cell- och
molekylärbiologi 30 hp (BL3007).
Kursens uppläggning
Provkod Benämning Högskolepoäng
4015 Metoder och koncept inom molekylära livsvetenskaper 15
4C15 Teori 7
4D15 Fallstudie 2 4B15 Laborationer 6
Kursens innehåll a) Kursen behandlar metoder och experimentella verktyg som används inom molekylär cellbiologi och
genomforskning för att undersöka struktur och funktion hos eukaryota och prokaryota organismer.
Metodernas teoretiska grunder och deras tillämpningar i konkreta forskningssammanhang presenteras.
Kursens teoretiska del behandlar följande: rekombinant DNA, analys av genexpression, "high-
throughput"-metoder, strukturella analyser, modellsystem, genetiska analyser, biokemiska analyser
samt genomsekvensering,metagenomik, molekylärekologi, mikromatriser, proteomik, bioinformatik
och annotering av genom.
b) Kursen består av följande moment:
1. Teori (Theory) 7 hp
2. Fallstudie (Case Study) 2hp
3. Laborationer (Laboratory exercises) 6 hp
- 3 -
Förväntade studieresultat Efter att ha genomgått kursen förväntas studenten:
* kunna redovisa fördjupade kunskaper om moderna metoder för att studera struktur och funktion hos
biomolekyler och makromolekylära komplex
* kunna beskriva teorin för de metoder som ligger till grund för funktionell genomforskning
* kunna visa praktisk färdighet i relevant metodologi samt i experimentell planering och kritisk
resultatanalys
* kunna visa insikt i hur metoderna tillämpas inom forskning och i samhället
Undervisning Undervisningen består föreläsningar, seminarier/ gruppdiskussioner, laborationer samt studiebesök.
Deltagande i seminarier, gruppdiskussioner samt laborationer och därmed integrerad
gruppundervisning är obligatoriskt. Om särskilda skäl föreligger kan examinator efter samråd med
vederbörande lärare medge den studerande befrielse från skyldigheten att delta i vissa obligatoriska
moment.
Kunskapskontroll och examination a. Kursen examineras på följande vis: kunskapskontroll av moment 1 sker genom skriftligt prov.
Om undervisningen sker på engelska kan även examination komma att genomföras på engelska.
b. Betygssättning sker enligt sjugradig målrelaterad betygsskala:
A = Utmärkt
B = Mycket bra
C = Bra
D = Tillfredsställande
E = Tillräckligt
Fx = Otillräckligt
F = Helt Otillräckligt
c. Kursens betygskriterier delas ut vid kursstart.
d. För godkänt krävs lägst betygsgraden E, godkänt moment 2, samt deltagande i övrig obligatorisk
undervisning.
e. Studerande som underkänts i ordinarie prov har rätt att genomgå ytterligare prov så länge kursen
ges. Antalet provtillfällen är inte begränsat. Med prov jämställs också andra obligatoriska kursdelar.
Studerande som godkänts på prov får inte genomgå förnyat prov för högre betyg. Studerande som
underkänts på prov två gånger har rätt att begära att annan examinator utses vid nästkommande prov.
Framställan härom ska göras till institutionsstyrelsen. Kursen har minst två examinationstillfällen per
läsår de år då undervisning ges. Mellanliggande år ges minst ett examinationstillfälle.
f. Vid betyget Fx ges möjlighet att komplettera upp till betyget E. Examinator beslutar om vilka
kompletteringsuppgifter som ska utföras och vilka kriterier som ska gälla för att bli godkänd på
kompletteringen. Kompletteringen ska äga rum före nästa examinationstillfälle.
Övergångsbestämmelser Studerande kan begära att examination genomförs enligt denna kursplan även efter det att den upphört
att gälla, dock högst tre gånger under en tvåårsperiod efter det att undervisning på kursen upphört.
Framställan härom ska göras till institutionsstyrelsen. Bestämmelsen gäller även vid revidering av
kursplanen.
Övrigt
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Kursen ingår i kandidatprogrammet i molekylärbiologi men kan även läsas som fristående kurs.
Kurslitteratur Kurslitteratur beslutas av institutionsstyrelsen och redovisas därefter i bilaga till kursplanen.
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Methods and Concepts in Molecular Life Sciences, 15/3 –10/6 2013
Lectures will be in Frescati Backe 105 (including group discussions and presentation of
experimental work). Experimental work will be in labs as specified later.
Textbook: Principles and Techniques of Biochemistry and Molecular Biology (seventh
edition), ed. by Keith Wilson and John Walker, Cambridge University Press.
Organizers: Lars Wieslander ([email protected]), Jamie Morrison
([email protected]), Ulrich Theopold ([email protected]), Lisbeth
Jonsson ([email protected]), Roger Karlsson ([email protected]).
Schedule
Week 1 (week 13)
Mon 25/3 9.00-09.45: Introduction (Jamie Morrison).
9.45-12.00: Lecture 1: Methodological approaches in the analysis of biological
processes. Jamie Morrison
Afternoon: Experimental work/own studies
Tues 26/3 9.30-12.00: Lecture 2: Genome Analysis. Uli Theopold
Afternoon: Experimental work/own studies
Wed 27/3 9.30-12.00: Presentation of papers for discussion group in week 9.
Study visit. (Jamie Morrison) SciLifeLab. Next generation DNA sequencing.
13.00-16.00: Joakim Lundeberg, Patrik Ståhl
Thur 28/3 9.30-12.00: Group Discussions: (Chapters 2-4) Jamie Morrison
Afternoon: Experimental work/own studies
Fri 29/3 Långfredagen
Week 14 – EASTER BREAK
Week 2 (week 15)
Mon 8/4 9.30-12.00: Lecture 3: Nucleic acids, properties, hybridization and its
applications. Lars Wieslander
Afternoon: Experimental work/own studies
Tues 9/4 9.30-12.00: Lecture 4: Protein-protein interactions. Hong Sjölinder
Afternoon: Experimental work/own studies
Wed 10/4 9.30-12.00: Lecture 5: Cell fractionation, protein purification and analysis of
their components. Neus Visa and Ann-Kristin Östlund Farrants
Afternoon: Experimental work/own studies
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Thur 11/4 9.30-12.00: Lecture 6: Protein-nucleic acid interactions. Ylva Engström
Afternoon: Experimental work/own studies
Fri 12/4 9.30-12.00: Group Discussions: (Chapters 5-7) Lars Wieslander
Afternoon: Experimental work/own studies
Week 3 (week 16)
Mon 15/4 9.30-12.00: Lecture 7: Expression and crystallization of proteins. Pål Stenmark
Afternoon: Experimental work/own studies
Tues 16/4 9.30-12.00: Lecture 8: Mass spectrometry. Leopold Ilag
Afternoon: Experimental work/own studies
Wed 17/4 Morning: Experimental work/own studies
Afternoon: Experimental work/own studies
Thur 18/4 9.30-12.00: Introduction to case study. Lars Wieslander.
Afternoon: Experimental work/own studies
Fri 19/4 9.30-12.00: Group Discussions: (Chapters 8,9) Ulrich Theopold
Afternoon: Experimental work/own studies
Week 4 (week 17)
Mon 22/4 9.30-12.00: Lecture 9: Microscopy. Roger Karlsson
13.00-17.00: Demonstration of microscopy. Petra Björk and Stina Höglund
Tue 23/4 9.30-12.00: Lecture 10: Immunomethods. Jamie Morrison
Afternoon: Experimental work/own studies
Wed 24/4 Morning: Experimental work/own studies.
Afternoon: Experimental work/own studies.
Thur 25/4 9.30-12.00: Lecture 11: In vitro mutagenesis. Lars Wieslander
Afternoon: Experimental work/own studies.
Fri 26/4 9.30-12.00: Group Discussions: (Chapters 10,11) Lars Wieslander
Afternoon: Experimental work/own studies
Week 5 (week 18)
Mon 29/4 9.30-12.00: Lecture 12: Gene modifications in cells and animals. Marie Öhman
Afternoon: Experimental work/own studies.
Tues 30/4 9.30-12.00: Lecture 13: Genetic analysis in yeast. Per Ljungdahl
Afternoon: Experimental work/own studies
Wed 1/5 Första maj
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Thur 2/5 9.30-12.00: Lecture 14: Flies as a model system. Ylva Engström
Afternoon: Experimental work/own studies.
Fri 3/5 9.30-12.00 Lecture 15: Plant Genetics. Katharina Pawlowski.
13.30-16.00 Study visit. (Ulrich Theopold) Thomas Burglin’s lab – C. Elegans
as a model system.
Week 6 (week 18)
Mon 6/5 9.30-12.00: Lecture 16: Eukaryotic Transcriptome. Marie Öhman
Afternoon: Experimental work/own studies
Tues 7/5 9.30-12.00: Lecture 17: Epigenetics. Mattias Mannervik
Afternoon: Experimental work/own studies
Wed 8/5 9.30-12.00: Introduction to bioinformatic exercise. Gilad Silberberg
Afternoon: Experimental work/own studies
Thur 9/5 Kristi himmelfärds dag
Fri 10/5 Morning: Experimental work/own/studies
Afternoon: Experimental work/own studies
Week 7 (week 19)
Mon 13/5 9.30-12.00: Lecture 18: SNP analysis. Anna Kähler
Afternoon: Experimental work/own studies.
Tues 14/5 9.30-12.00: Lecture 19: Microbial Genomics. Rolf Bernander
Afternoon: Experimental work/own studies
Wed 15/5 Morning: Experimental work/own/studies
Afternoon: Experimental work/own studies
Thur 16/5 9.30-12.00: Group presentations of Lab Work.
Afternoon: Experimental work/own studies
Fri 17/5 9.30-12.00: Follow-up to bioinformatics exercise. Gilad Silberberg
Afternoon: Experimental work/own studies
Week 8 (week 20)
Mon 20/5 9.30-12.00: Lecture 20: Medical Genomics, human model. Ulrich Theopold
Afternoon: Experimental work/own studies.
Tues 21/5 9.30-12.00: Lecture 21: Glycobiology, talking surfaces. Ulrich Theopold
Afternoon: Experimental work/own studies
Wed 22/5 Morning: Experimental work/own studies
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Afternoon: Experimental work/own studies
Thur 23/5 9.30-12.00: Follow-up discussion to case study. Lars Wieslander.
Afternoon: Experimental work/own studies
Fri 24/5 Morning: Experimental work/own studies
Afternoon: Experimental work/own studies
Week 9 (week 21)
Mon 27/5 9.30-12.00: Student Presentations of research articles.
13.00-16.00: Student presentation of research articles.
Tues 28/5 9.30-12.00: Student Presentations of research articles.
13.00-16.00: Student presentation of research articles.
Wed 29/5 9.30-12.00: Student Presentations of research articles.
13.00-16.00: Student presentation of research articles.
Thur 30/5 9.30-12.00: Student Presentations of research articles.
13.00-16.00: Student presentation of research articles.
Fri 31/5 Morning: Experimental work/own studies
Afternoon: Experimental work/own studies
Week 10 (week 22)
Mon 3/6 Morning: Experimental work/own studies
Afternoon: Experimental work/own studies.
Tues 4/6 Morning: Experimental work/own studies
Afternoon: Experimental work/own studies
Wed 5/6 9.00-12.00: Examination (End of course)
Own studies
Time is reserved for individual studies of the textbook, for preparing for experimental work
and for preparing for the lab report and the presentation of the experimental work.
Group discussions
All students should read the following chapters in the textbook. The chapters will be
discussed during the four group discussions as indicated. During each group discussion, a
teacher will be present.
Group discussion 1
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2. Cell culture techniques
3. Centrifugation
4. Microscopy
Group discussion 2
5. Molecular biology
6. Recombinant DNA
7. Immunological techniques
Group discussion 3
8. Protein structure, purification, characterization and functional analysis
9. Mass spectrometric techniques
Group discussion 4
10. Electrophoretic techniques
11. Chromatographic techniques
Experimental work
The students will be divided into three groups. Each group will participate in one of the three
wet-labs as detailed below. Each experiment will have its own time requirements and each
group will follow that particular time requirement. This means that each group will have a
somewhat different schedule that is dictated by the experimental work. At all times when the
experimental work allows, the students have time for their own studies (reading the text book,
preparation of lab. report and presentation of the experimental work). Each group will present
their work for the other students (10 May).
Lab. report
Students must hand in a written report of their experimental work. The report should be
written in English. It should present the purpose of the experimental work, the principal
behind the methods used, the results, and a discussion in which the results are evaluated from
a methodological point of view.
The three experiments are:
1. Analysis of gene expression in Saccharomyces cerevisiae
Methods: Transformation of yeast cells, galactose induction, extraction of proteins and
Western blot analysis, extraction of RNA and Northern blot analysis, fluorescence
microscopy.
2. Analysis of stress responses by qPCR in barley plants
Methods: primer design, gDNA isolation, genotyping mutants, RNA isolation, cDNA
synthesis, RT-PCR, navigating TAIR web site (www.arabidopsis.org)
- 10 -
3. RNA interference – knockdown of nuclear Williams syndrome transcription factor
(WSTF)
Methods: Growing human/murine cells, transfection of mouse cells, light- and
fluorescence microscopy, Western blot analysis.
Study visits
There will be two study visits during the course at the times and places indicated in the
schedule. It is important that all students show up at the correct time.
1. SciLifelabs. Title: Next generation DNA sequencing. Joakim Lundeberg and Patrik
Ståhl.
2. Thomas Burglin lab: C. elegans as a model system.
Case Study
A Case Study will take place on Thursday 18 April (9.30-12.00), with follow-up discussions
planned for Thursday 23 May (9.30-12.00). Students will be given a question on Thursday 18
April, to work on by themselves before the final written examination (Monday 10 June 9.00-
12.00). Students have up until and including Monday 10 June to hand-in their answer sheet to
Jamie Morrison. A student failing to hand in their answer sheet before the deadline will forfeit
the 2hp allocated for this part of the course.
- 11 -
Methods and Concepts in Life Sciences VT-13
Experimental Work
The course contains three separate experiments. The students will be divided into three
groups. Each group will perform only one of the experiments, but should be familiar with the
principles exemplified in all four experiments. Each experiment has a contact person who will
be in charge of the experimental work.
Each experiment will follow its own pace. This means that each group of students will have a
different schedule for the experimental work. These scheduled will be evident from the
planning of each experiment. When there is no experimental work, time can be used for
individual studies.
Each student has to write a laboratory report that will be checked and accepted by the contact
person responsible for each experiment. Every group also has to give a presentation (short
written summary handed out before the presentation and a short seminar) of their
experimental work for the other students (Thursday 10 May). The accepted written report and
the presentation are both compulsory parts of the course (see grading criteria).
- 12 -
Methods and Concepts in Molecular Life Sciences, 2012
Contact persons: Experimental work
1. Analysis of gene expression in Saccharomyces cerevisiae
Contact persons: Fredrik Lackman ([email protected])
Lars Wieslander ([email protected])
2. Analysis of stress responses by qPCR in barley plants
Contact persons: Sara Mehrabi ([email protected])
Mattias Persson ([email protected])
Lisbeth Jonsson ([email protected])
3. RNA interference – knockdown of nuclear Williams syndrome transcription factor (WSTF)
Contact persons: Naveen Kumar ([email protected])
Antonio Martins ([email protected])
Anna Idh ([email protected])
Roger Karlsson ([email protected])
- 13 -
Schedule for presentations of experimental work, Thursday 16/5 2013 at 9.30 (FB105)
Each group gives one presentation. The presentation can be given by one person in the group,
or together by several persons.
Each presentation shall describe the background for the experimental work, the individual
experiments, the results obtained by the group and a discussion of the results from a
methodological point of view. Emphasis should be on extracting the information that each
experiment gave and a discussion of theoretical and practical limitations.
Each group is given 30 minutes, including discussion and questions involving the whole
course.
9.30–10.00 Group 1
10.10-10.40 Group 2
11.00-11.30 Group 3
- 14 -
Group discussion 1
Chapter 2: Cell Culture Techniques
General questions:
1. What are the differences between classI, II and III hoods? What type would you
purchase if you are to set a lab studying gene regulation in (1) Escherichia coli or (2)
human cells?
2. Why are CO2 incubators used for human cells but not for E.Coli?
3. What can you do to avoid contamination of microorganisms in a CO2 incubator?
Animal cell culture:
1. What are the most common infections?
2. How do you detect it?
3. What can you do about it?
4. What are the main differences between primary cells and immortalized cells? What
are the advantages or disadvantages with one or the other?
5. Why do you have to subculture the cells? How do you subculture cells that adhere to
the surface?
6. Why is it important to know the cell density before subculturing and how do you
determine cell density?
7. How can you determine whether the cells are dead or alive?
8. How can anima cells be stored? At what growth stage should you rake the cells for
storage?
9. What happens if you let the cells taken for storage to directly warm to 37oC?
Bacterial cultures:
1. What are the most common infections?
2. How do you detect it?
- 15 -
3. What can you do about it?
4. Define an autotroph vs heterotroph?
5. A common lab strain is E.coli strain C-600. Some of its genotypes are F-, McrA-, thr-
1, leuB6, thi-1, lacY1, glnV44. Using a synthetic medium, containing phosphate
buffer, sodium citrate, salts and glucose, what do you have to add?
Chapter 3. Centrifugation
1. What parameters affect the sedimentation of a particle during centrifugation?
2. You do not have to calculate the centrifugal field, the angular velocity or the relative
centrifugal field, but you must be able to handle the nomograph on Fig. 3.1.
3. How many rpm are required in a microcentrifuge (for eppendorf tubes) with a rotor
having a radial distance of 50mm to get 10,000 x g and in a preparative ultracentrifuge
with a rotor radial distance of 140mm to get 600,000 x g?
4. What are the advantages/disadvantages with fixed-angle rotors compared to swinging
buckets rotors?
5. Why is it important to keep a record-book of time and speed for use of rotors?
6. Describe the differences between differential centrifugation, zone velocity/gradient
centrifugation and isopycnic centrifugation and give an example of how you can
determine where you would use them.
7. Why are membranes so difficult to isolate? Give an example of how you can
determine the purity of your membrane fraction.
8. What is meant by affinity purification and give an example of one and its uses.
9. What type of experiments needs an analytical ultracentrifuge?
- 16 -
Chapter 4. Microscopy
1. Light microscope and electron microscope are two fundamentally different types of
microscope. What are the main differences between them regarding basic components,
resolution and applications?
2. What is the resolution range for the light microscope?
3. Why does the use of UV light increase the resolution of the light microscope?
4. What is a microtome? What is it used for?
5. What are the main components of an epifluorescent microscope?
6. What is a fluorophore?
7. What are the excitation and emission wavelengths of a fluorophore?
8. What is FISH?
9. What is a quantum dot?
10. Compare an epifluorescent microscope with a laser scanning confocal microscope.
Indicate similarities and differences.
11. Is it possible to visualize an endogenous protein in living cells? How?
12. What is the fundamental difference between the transmission and the scanning
electron microscope?
13. How can you stain the sample for electron microscopy?
14. What is a “cell sorter” or FACS?
15. What is FRET? What type of information does it provide?
16. What is atomic force microscopy?
- 17 -
Group Discussion 2
Chapter 5: Molecular Biology
1. What is the melting temperature or Tm of a DNA molecule? What kind of information
does the Tm provide?
2. What is SNP?
3. Describe the main steps of a classical DNA extraction protocol?
4. How can DNA degradation be prevented?
5. Which methods do you know for RNA extraction? Describe the main steps of each
extraction protocol.
6. Why is ethidium bromide useful as a DNA stain?
7. What dos the term “in silico” research mean?
8. There are several enzymatic reactions that can be used to label DNA probes. Describe
them briefly.
9. What are the main features of Taq polymerase?
10. Explain the principle of quantitative PCR. What is a TaqMan assay?
11. What is pyrosequencing? In what way does it differ from the classical Sanger
sequencing?
Chapter 6: Recombinant DNA
1. Describe the main steps involved with the construction of a cDNA library?
2. What is the principle of subtractive hybridization? What is it used for?
3. Which are the essential components/sequences that a plasmid should contain to be
useful as a cloning vector?
4. There are different types of vectors used for DNA cloning. Which ones? Describe
their main feature.
5. What are BAC and YACs?
- 18 -
6. What does transfection mean? Which methods can be used to transfect a plasmid into
a eukaryotic cell?
7. What is the purpose of colony hybridization? Describe the main steps of the process.
8. How would you construct a synthetic DNA fragment carrying a defined mutation
using PCR?
9. What is GST? What is it used for?
10. What is a ribonuclease protection assay?
11. What is a reporter gene? What is it used for? Give an example.
12. Which methods can be used to detect DNA polymorphisms?
13. What dos the term “positional cloning” mean?
Chapter 7: Immunological techniques
1. What is a polyclonal antibody?
2. Why is it often necessary to use adjuvants for antibody production?
3. Describe the main steps involved in the production of a monoclonal antibody?
4. Explain the principle of immunoaffinity chromatography?
5. How can an antibody be eluted from an affinity column?
6. What do the terms “direct Immunohistochemistry” and “indirect
Immunohistochemistry” refer to?
7. Which enzymes are commonly used as markers to visualize immunochemical
reactions?
8. What kind of markers are used for immuno-electron microscopy?
9. Discuss the terms “affinity” and “avidity” of an antibody.
- 19 -
Group Discussion 3
Chapter 8: Protein structure, purification, characterization and functional analysis
1. What kinds of forces stabilize the tertiary structure of a protein?
2. What types of post-translational modifications of proteins are there?
3. When you study a protein, it is often possible to get away with less than 100% purified
protein. Give some examples.
4. How do you determine the concentration of proteins?
5. Why does extraction buffers usually contain:
a. anti-oxidants such as Dithiothreitol (DTT)
b. protease inhibitors
6. Why is it difficult to extract membrane proteins?
7. Give some examples of cell disruption methods and discuss which method you would
use for mammalian cells and yeast cells respectively.
8. How can you monitor the success of a fractionation procedure?
9. Define the following terms:
a. fold purification
b. yield
10. During protein purification, the cell extract initially contains insoluble material and
nucleic acids. How do you get rid of these?
11. Protein fractionation relies on four properties that differ between different proteins.
Which properties?
12. Discuss how you can simplify purification of a protein in the case where you have the
cDNA encoding the protein and you express the protein in for example bacteria?
13. How can you determine the relative molecular mass of a protein?
14. How do you determine the primary structure of a protein?
- 20 -
15. How do you determine the tertiary structure of a protein?
16. How do you decide where disulphide bonds are in a protein?
17. How can you use lectins to detect glycoprotein?
18. What is 2–D PAGE and how many different proteins can you detect by this method?
19. Describe how you can detect that two specific proteins interact with each other?
Chapter 9: Mass spectrometric techniques
1. What principal components make up a mass spectrometer?
2. What is measured in a mass spectrometer?
3. What are the advantages of electrospray ionization and matrix-assisted laser
desorption/ionization?
4. Describe the principle of TOF.
5. Give examples of the kinds of data that can be obtained by mass spectrometry.
6. Describe the steps in identification of individual protein components in an isolated
protein complex.
- 21 -
Group Discussion 4
Chapter 10: Electrophoretic techniques
1. What do we mean with electrophoresis?
2. Why is it usually not possible to increase the voltage to very high levels during
agarose electrophoresis?
3. Why does separation tend to be less good if the voltage is too low in electrophoresis?
4. Describe what support media are used for protein and nucleic acid electrophoresis.
5. Why is SDS in SDS-PAGE electrophoresis of proteins?
6. How do you obtain the relative molecular mass of a protein by SDS-PAGE?
7. What is the basis for separation of proteins in isoelectric focusing gels?
8. How are proteins detected after SDS-PAGE?
9. Make sure you know how Western blots work.
10. What type of electrophoresis would you use for separating extremely long DNA
molecules?
11. What do you have to think of when separating RNA by electrophoresis?
Chapter11: Chromotographic techniques
1. What is the principal for column chromatography?
2. When selecting stationary and mobile phases for chromatography, you can select
different principles for obtaining distribution coefficients. What principles are there?
3. Describe the principles for:
a. gel filtration chromatography
b. affinity chromatography
4. Why does HPLC give fast results and high resolution?
5. What is FPLC?
- 22 -
6. Reverse-phase liquid chromatography is a type of partition chromatography. Why is it
called reverse-phase liquid chromatography?
7. In thin layer chromatography, what is mean by the retardation factor?
- 23 -
Methods and Concepts in Life Sciences
Information about the written examination
The questions of the written examination will consist of a number of questions that require
multi-choice and short-answers. Each of these questions will give between 1 and 3 points.
The types of short-answer questions will be as follows:
1. Explain why a mixture of proteins can be used for immunization when a monoclonal
antibody is made against a specific protein.
2. Why are proteins heated in solution containing SDS before SDS-PAGE?
3. Describe how DNA and RNA are treated before agarose electrophoresis.
4. Which kind of genetic polymorphism is large-scale genotyping based on?
5. How are 3D images obtained with confocal microscopy?
The types of multi-choice questions will be as follows:
1. Which of the following types of vector would be most suitable for introducing DNA into a
human cell?
a. Plasmid
b. Bacteriophage
c. Cosmid
d. Adenovirus
2. E.Coli cells take up plasmid DNA in laboratory experiments by which of the following
methods?
a. Conjugation
b. Electrophoresis
c. Transduction
d. Transformation
- 24 -
Grading criteria, Methods and Concepts in Molecular Life Sciences
The grading is based on:
1. The result from the written examination.
2. The result from the case study.
3. That you pass the experimental work, including presentation.
This means that in order to pass the course, you have to fulfill the criteria for pass for the
experimental work (see below) and you have to have at least 60% of the maximum points in
the written examination.
It is highly recommended that you attend the lectures, group discussions and site visits since
these are important parts of the course and since questions in the written examination will
partly cover these parts of the course.
Grading criteria for the written examination and case study (seven-point grading scale)
The grade A is awarded if the student has achieved at least 95% of the maximum points
available in the written examination.
The grade B is awarded if the student has achieved at least 85% of the maximum points
available in the written examination.
The grade C is awarded if the student has achieved at least 75% of the maximum points
available in the written examination.
The grade D is awarded if the student has achieved at least 65% of the maximum points
available in the written examination.
The grade E is awarded if the student has achieved at least 60% of the maximum points
available in the written examination.
The grade Fx is awarded if the student has achieved at least 50% of the maximum points
available in the written examination.
The grade F is awarded if the student has achieved less than 50% of the maximum points
available in the written examination.
Grading criteria for the experimental work (two-point grading scale): Pass or Not Pass
In order to pass the experimental work that are part of the course, you must in a group of 4-8
carry out and subsequently individually present the experimental work. The presentation is to
be in the form of a short seminar and in the form of a written report. The report shall be in
English and is to have the following structure, unless otherwise specified.
Title
Introduction
Describe briefly and clearly the aim of the exercise and describe the theoretical background.
Materials and Methods
Summarize what you have done (without simply reproducing large parts of the lab
instructions). Specify clearly any deviations from the lab instructions. Feel free to supplement
the text with figures and flow diagrams.
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Results
Raw data is to be presented in tables such that it is easy to gain an overview. Each table is to
have a title and it is to be clear what the rows and columns of the table represent. Large
quantities of raw data may be presented as an appendix. Calculations are to be presented such
that each step is clear and such that the calculation is easy to follow for the person assessing
the report. The results of the calculations are to be clearly presented. Any graphs included
must be attractively drawn and the axes labeled with the correct units.
Discussion
Summarize and interpret the results that have been presented in the preceding section.
Conclusions must be clearly expressed and well supported. Answer any questions that the lab
instructions pose. If the results deviate from the expected, the reasons for this must be
discussed and possible sources of error must be described.
References
References are to be given if they lie outside of the lab instructions or the compulsory course
literature.
General Information
It is preferred that the report is written on computer. If this is not the case, it must be written
with tidy and easy-to-read handwriting. Write the report as running text with complete
sentences and make every effort to use a clear, correct and objective language. Avoid using
informal language and laboratory jargon. Check the spelling carefully! Follow the rules laid
down for nomenclature (the scientific names of organisms) and other scientific terminology
(such as the names of genes and proteins).
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Course evaluation for VT-2012 Methods and Concepts in Molecular Life Sciences
course.
Questions 1-10, please answer with 1, 2, 3, 4 or 5, where 1 means: no, 2 means: not really, 3
means: to some extent, 4 means: to a large extent and 5 means: definitely yes.
1. Was the goal for this course clear at the start of the course?
2. Was the goal with the course reached?
3. Did you get sufficient information about the schedule, localities, etc.?
4. Did the textbook cover the content of the course?
5. Were the study visits useful parts of the course?
6. Were the group discussions useful parts of the course?
7. Did the examination correspond to the content of the course?
8. Did you have a constructive dialogue with the teachers?
9. Did you have a constructive dialogue with the course assistants?
10. Was the experimental part of the course useful?
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Please write short comments for the following questions.
1. Were there any parts of the course that you find difficult to understand?
2. Which parts of the course did you find particularly interesting?
3. Any other comments?
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Directions to SciLifeLab, Stockholm
Directions to Thomas Burglin’s Lab
Dept. of Biosciences and Nutrition
Karolinska Institutet
Hälsovägen 7,
6th
Floor of Novum Building (Rooms 6A and 6D)