Methods in Life Sciencesfile.big.su.se/_html/utbildningar/schema/gamla/vt13/metoder_v13.pdf ·...

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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

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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


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


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


Tues 9/4 9.30-12.00: Lecture 4: Protein-protein interactions. Hong Sjölinder


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


mailto:[email protected]


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Thur 11/4 9.30-12.00: Lecture 6: Protein-nucleic acid interactions. Ylva Engström


Fri 12/4 9.30-12.00: Group Discussions: (Chapters 5-7) Lars Wieslander


Week 3 (week 16)

Mon 15/4 9.30-12.00: Lecture 7: Expression and crystallization of proteins. Pål Stenmark


Tues 16/4 9.30-12.00: Lecture 8: Mass spectrometry. Leopold Ilag


Wed 17/4 Morning: Experimental work/own studies


Thur 18/4 9.30-12.00: Introduction to case study. Lars Wieslander.


Fri 19/4 9.30-12.00: Group Discussions: (Chapters 8,9) Ulrich Theopold


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


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


Fri 26/4 9.30-12.00: Group Discussions: (Chapters 10,11) Lars Wieslander


Week 5 (week 18)

Mon 29/4 9.30-12.00: Lecture 12: Gene modifications in cells and animals. Marie Öhman


Tues 30/4 9.30-12.00: Lecture 13: Genetic analysis in yeast. Per Ljungdahl


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


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


Tues 7/5 9.30-12.00: Lecture 17: Epigenetics. Mattias Mannervik


Wed 8/5 9.30-12.00: Introduction to bioinformatic exercise. Gilad Silberberg


Thur 9/5 Kristi himmelfärds dag

Fri 10/5 Morning: Experimental work/own/studies


Week 7 (week 19)

Mon 13/5 9.30-12.00: Lecture 18: SNP analysis. Anna Kähler


Tues 14/5 9.30-12.00: Lecture 19: Microbial Genomics. Rolf Bernander


Wed 15/5 Morning: Experimental work/own/studies


Thur 16/5 9.30-12.00: Group presentations of Lab Work.


Fri 17/5 9.30-12.00: Follow-up to bioinformatics exercise. Gilad Silberberg


Week 8 (week 20)

Mon 20/5 9.30-12.00: Lecture 20: Medical Genomics, human model. Ulrich Theopold


Tues 21/5 9.30-12.00: Lecture 21: Glycobiology, talking surfaces. Ulrich Theopold


Wed 22/5 Morning: Experimental work/own studies

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Thur 23/5 9.30-12.00: Follow-up discussion to case study. Lars Wieslander.


Fri 24/5 Morning: 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.


Wed 29/5 9.30-12.00: Student Presentations of research articles.


Thur 30/5 9.30-12.00: Student Presentations of research articles.


Fri 31/5 Morning: Experimental work/own studies


Week 10 (week 22)

Mon 3/6 Morning: Experimental work/own studies


Tues 4/6 Morning: 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)

http://www.arabidopsis.org/

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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.

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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).

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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])





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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

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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?

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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?

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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?

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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?

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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.

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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?

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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.

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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?

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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?

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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

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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


The grade C is awarded if the student has achieved at least 75% of the maximum points


The grade D is awarded if the student has achieved at least 65% of the maximum points


The grade E is awarded if the student has achieved at least 60% of the maximum points


The grade Fx is awarded if the student has achieved at least 50% of the maximum points


The grade F is awarded if the student has achieved less than 50% of the maximum points


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?

- 28 -

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)

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